Beyond Intra-Base-Pair Hydrogen Bonds in DNA Structures: A Comprehensive Analysis
Jürgen Sühnel 1), Klaus Lindauer 1)
Institut für Molekulare Biotechnologie, Postfach 100813, D-07708 Jena /
Germany
1) E-Mail: jsuehnel@imb-jena.de; klaus@imb-jena.de
Table II
Non-intra-base-pair hydrogen bonds in DNA structures
Base-pairs are vaguely defined as nucleotides located more or less
in one plane and connected by at least one hydrogen bond.
This definition includes planes of three or four nucleotides occurring
in triplex or quadruplex structures.
Hydrogen bonds within base-pairs defined in this way are intra-basepair H-bonds.
All other H-bonds are non-intra-base-pair H-bonds.
Non-intra-base-pair H-bonds may occur
between different base-pairs
or
between a not base-paired nucleotide and a basepair
or
between two nucleotides both not belonging to base-pairs.
The set of DNA structures given below was scanned for non-intra-base-pair H-bonds
using the program HBexplore.
HBexplore identifies hydrogen bonds according to geometrical criteria.
The criteria used are:
dHA < 2.5 A
dDA < 3.9 A
aDHA > 90 deg
aHAA1(2) > 90 deg
aDAA1(2) > 90 deg
Here A and D stand for the acceptor an donor atoms of the H-bond.
A1(2) are the bonded neighbors of A and a and d indicate angle
and distance.
For each non-intra-base-pair H-bond identified the following information
is given:
EXAMPLE 1dn6 YES
EXAMPLE
EXAMPLE donor acceptor dDA H-bond type
EXAMPLE at rt rn at rt rn
EXAMPLE 1****** 15 N1 G A 9 O4 T B 2 2.7655 b-b
EXAMPLE
EXAMPLE donor acceptor dDA dHA aDHA aHAA1 aHAA2 aDAA1 aDAA2
EXAMPLE at rt rn at rt rn
EXAMPLE 15 N1 G A 9 O4 T B 2 2.7655 2.113 120.4 100.9 108.2 + 93.7 110.3
EXAMPLE
EXAMPLE H-BOND TYPE: G - T, interstrand, three-center, one-H donor
EXAMPLE MOTIF: 14 N1 G A 9 N3 C B 1 3.0920 b-b
EXAMPLE 15 N1 G A 9 O4 T B 2 2.7655 b-b
EXAMPLE MOTIF TYPE: Db3nbA(3ibA)
The H-bonds are labeled using the HBexplore identification number.
H-BOND TYPE describes properties of the non-intra-basepair H-bonds alone.
MOTIF is given if a donor atom forms more than one H-bond.
MOTIF TYPE describes the complete H-bond motif of one donor with all H-bonded acceptors
including possibly intra-basepair H-bonds.
It takes into account different acceptor atoms H-bonded to one and the same donor,
but it does not take into account different donors connected to one and the same acceptor.
The terminology for the MOTIF TYPE is:
i - intra-basepair H-bond
n - non-intra-basepair H-bond
p - nucleic acid-protein H-bond
2 - two-center (standard, can be omitted)
3 - three-center
b - base
s - sidechain (amino acid)
B - nucleic acid or protein backbone
Examples:
DbibA - two-center intra-basepair H-bond between one donor and one acceptor
DbnBA - two-center non-intra-basepair H-bond betweem one donor base atom and one
acceptor backbone atom
DbpsA - two-center nucleic acid-protein H-bond between one donor and one acceptor
DbnbA(ibA) - one intra-basepair and one non-intra-basepair two-center H-bond between
one donor and two acceptors (requires two-H donor)
DbnbA(nBA) - two non-intra-basepair H-bonds between one donor and two acceptors
Db3nbA(3ibA) - three-center H-bond system where one bond is a non-intra-basepair and the other
one is an intra-basepair H-bond between one donor and two acceptors
(requires two-H donor)
Db3nbA(3nbA) - three-center H-bond system where both bonds are non-intra-basepair H-bonds
between one donor and two acceptors
DbnBA(3iBA)(3ibA) - two-H donor forms one two-center non-intra-basepair H-bond with one hydrogen and
a three-center intra-basepair H-bond with the other hydrogen
Db3nbA(3iBA)(psA) - two-H donor forms one three-center non-intra-basepair H-bond and one three-center
intra-basepair H-bond with one H-atom and an nucleic acid-protein H-bond with the
other hydrogen
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
STRUCTURE NON-INTRA-BASEPAIR SEQUENCE
(PDB CODE) H-BONDS (YES/NO)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
A-DNA:
######
115d NO GGXAXACC / GGXAXACC
137d NO GCGGGCCCGC / GCGGGCCCGC
160d NO CCCGGCCGGG / CCCGGCCGGG
172d NO GAAGCTTC / GAAGCTTC / GAAGCTTC/ GAAGCTTC
197d NO GTACGTAC / GTACGTAC
1ana NO CCGG / CCGG
1d91 NO GGGGTCCC / GGGGTCCC
1d92 NO GGGGCTCC / GGGGCTCC
----------------------------------------------------------------------------------------------------------------------
1dn6 YES GGATGGGAG / CTCCCATCC
1****** 15 N1 G A 9 O4 T B 2 2.7655 b-b
15 N1 G A 9 O4 T B 2 2.7655 2.113 120.4 100.9 108.2 + 93.7 110.3
H-BOND TYPE: G - T, interstrand, three-center, one-H donor
MOTIF: 14 N1 G A 9 N3 C B 1 3.0920 b-b
15 N1 G A 9 O4 T B 2 2.7655 b-b
MOTIF TYPE: Db3nbA(3ibA)
----------------------------------------------------------------------------------------------------------------------
218d NO CGTGAATTCXCG / CGTGAATTCXCG
221d NO ACCGGCCGGT / ACCGGCCGGT
2ana NO GGGGCCCC / GGGGCCCC
---------------------------------------------------------------------------------------------------------------------
2d47 YES CCCCCGCGGGGG / CCCCCGCGGGGG
2****** 3 N4 C A 3 O6 G B 11 2.9681 b-b
3 N4 C A 3 O6 G B 11 2.9681 2.307(1) 122.0 102.4 108.5 + 102.0 115.9
H-BOND TYPE: C - G, interstrand, three-center, two-H donor
MOTIF: 2 N4 C A 3 O6 G B 10 2.9678 b-b
3 N4 C A 3 O6 G B 11 2.9681 b-b
MOTIF TYPE: Db3nbA(3ibA)
COMMENTS: This is one of the rare cases of a C - G interstrand H-bond.
----------------------------------------------------------------------------------------------------------------------
3ana NO GGGATCCC / GGGATCCC
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
B-DNA:
######
111d NO CGCAAATTGGCG / CGCAAATTGGCG
112d NO CGCGAATTAGCG / CGCGAATTAGCG
113d NO CGCGAATTTGCG / CGCGAATTTGCG
114d NO CGCXAATTAGCG / CGCXAATTAGCG
119d NO CGTAGATCTACG / CGTAGATCTACG
122d NO CCAGGCXTGG / CCAGGCXTGG
123d NO CCAGGCXTGG / CCAGGCXTGG
126d NO CATGGCCATG / CATGGCCATG
150d NO CGCGAATTXGCG / CGCGAATTXGCG
153d NO CGAGAATTCXCG / CGAGAATTCXCG
158d NO CCAAGCTTGG / CCAAGCTTGG
167d NO CCATTAATGG / CCATTAATGG
---------------------------------------------------------------------------------------------------------------------
178d YES CGCAAATTXGCG / CGCAAATTXGCG
3****** 5 N6 A A 5 O4 T B 19 2.7425 b-b
5 N6 A A 5 O4 T B 19 2.7425 2.447(2) 96.0 105.0 110.9 + 124.9 132.0
H-BOND TYPE: A - T, interstrand, three-center, two-H donor
MOTIF: 6 N6 A A 5 O4 T B 19 2.7425 b-b
7 N6 A A 5 O4 T B 20 2.7081 b-b
MOTIF TYPE: Db3nbA(3ibA)
----------------------------------------------------------------------------------------------------------------------
194d NO CGCGTTAACGCG / CGCGTTAACGCG
196d NO CTCTCGAGAG / CTCTCGAGAG
1bdnA NO CGCAAAAATGCG / CGCATTTTTGCG (two structures in one PDB file)
----------------------------------------------------------------------------------------------------------------------
1bdnC YES CGCAAAAATGCG / CGCATTTTTGCG (two structures in one PDB file)
4****** 7 N6 A C 6 O4 T D 6 2.8095 b-b
7 N6 A C 6 O4 T D 6 2.810 2.455(2) 99.8 118.3 110.6 136.3 130.9
H-BOND TYPE: A - T, interstrand, three-center, two-H donor
MOTIF: 7 N6 A C 6 O4 T D 6 2.8095 b-b
8 N6 A C 6 O4 T D 7 2.4826 b-b
MOTIF TYPE: Db3nbA(3ibA)
----------------------------------------------------------------------------------------------------------------------
1bna NO CGCGAATTCGCG / CGCGAATTCGCG
1cgc NO CCGGCGCCGG / CCGGCGCCGG
1d23 NO CGATCGATCG / CGATCGATCG
1d27 NO CGCXAATTTGCG / CGCXAATTTGCG
1d28 NO CGTGAATTCACG / CGTGAATTCACG
1d29 NO CGTGAATTCACG / CGTGAATTCACG
1d49 NO CGATTAATCG / CGATTAATCG
1d56 NO CGATATATCG / CGATATATCG
1d57 NO CGATATATCG / CGATATATCG
1d60 NO CCAACXTTGG / CCAACXTTGG
1d65 NO CGCAAATTTGCG / CGCAAATTTGCG
1d75 NO CGCGAATTXGCG / CGCGAATTXGCG
1d77 NO CGCXAATTCGCG / CGCXAATTCGCG
1d80 NO CGCGAATTGGCG / CGCGAATTGGCG
1d81 NO CGCAAATTXGCG / CGCAAATTXGCG
-----------------------------------------------------------------------------------------------------------------------
1d89 YES CGCGAAAAAACG / CGTTTTTTCGCG
CGCGAAAAAACG / CGTTTTTTCGCG
CGCGAAAAAACG / CGTTTTTTCGCG
5****** 15 N6 A A 10 O6 G B 14 2.7774 b-b
15 N6 A A 10 O6 G B 14 2.7774 2.499(2) 95.1 105.6 104.0 + 121.0 124.7
H-BOND TYPE: A - G, interstrand, three-center, two-H donor
MOTIF: 15 N6 A A 10 O6 G B 14 2.7774 b-b
16 N6 A A 10 O4 T B 15 3.1486 b-b
MOTIF TYPE: Db3nbA(3ibA)
6****** 44 N6 A C107 O4 T D117 2.9314 b-b
44 N6 A C107 O4 T D117 2.9314 2.490(2) 105.8 107.2 105.0 + 125.0 124.1
H-BOND TYPE: A - T, interstrand, three-center, two-H donor
MOTIF: 44 N6 A C107 O4 T D117 2.9314 b-b
45 N6 A C107 O4 T D118 2.8968 b-b
MOTIF TYPE: Db3nbA(3ibA)
7****** 78 N6 A E209 O4 T F215 2.9410 b-b
78 N6 A E209 O4 T F215 2.9410 2.499(2) 105.9 102.7 110.5 + 119.0 129.8
H-BOND TYPE: A - T interstrand, three-center, two-H donor
MOTIF: 78 N6 A E209 O4 T F215 2.9410 b-b
79 N6 A E209 O4 T F216 2.9278 b-b
MOTIF TYPE: Db3nbA(3ibA)
8****** 80 N6 A E210 O6 G F214 2.6745 b-b
80 N6 A E210 O6 G F214 2.6745 2.425(2) 92.9 115.8 109.6 + 131.4 131.4
H-BOND TYPE: A - G, interstrand, three-center, two-H donor
MOTIF: 80 N6 A E210 O6 G F214 2.6745 b-b
81 N6 A E210 O4 T F215 3.2010 b-b
MOTIF TYPE: Db3nbA(3ibA)
-----------------------------------------------------------------------------------------------------------------------
1d97 NO GXGXGX / GXGXGX
1d98 NO CGCAAAAAAGCG / CGCTTTTTTGCG (Nelson, Klug paper !!!! Nature 1987, 330, 221-226)
------------------------------------------------------------------------------------------------------------------------
1d99 YES CGCAAATTCGCG / CGCAAATTCGCG
9****** 14 N2 G A 10 O2 C A 11 3.0539 b-b
14 N2 G A 10 O2 C A 11 3.0539 2.459(1) 117.1 108.6 113.1 + 102.4 116.6
H-BOND TYPE: G - C, intrastrand, two-center, two-H donor
MOTIF: 13 N1 G A 10 N3 C B 15 2.7699 b-b
14 N2 G A 10 O2 C A 11 3.0539 b-b
15 N2 G A 10 O2 C B 15 2.6801 b-b
MOTIF TYPE: DbnbA(3ibA)(3ibA)
COMMENTS: One H of the amine group forms two base-pair H-bonds,
the other H forms one non-intra-basepair H-bond.
------------------------------------------------------------------------------------------------------------------------
1da3 NO CGATCGXTCG / CGATCGXTCG
------------------------------------------------------------------------------------------------------------------------
1dn9 YES CGCATATATGCG / CGCATATATGCG
10***** 20 N4 C B 3 O4 T A 9 2.9083 b-b
20 N4 C B 3 O4 T A 9 2.9083 2.449(1) 106.9 117.3 112.1 + 135.3 130.9
H-BOND TYPE: C - T, interstrand, three-center, two-H donor
MOTIF: 20 N4 C B 3 O4 T A 9 2.9083 b-b
21 N4 C B 3 O6 G A 10 2.7916 b-b
MOTIF TYPE: Db3nbA(3ibA)
11***** 11 N2 G A 10 O2 C A 11 2.8379 b-b
11 N2 G A 10 O2 C A 11 2.8379 2.322(1) 110.5 104.8 102.6 + 101.3 109.9
H-BOND TYPE: G - C, intrastrand, two-center, two-H donor
MOTIF: 11 N2 G A 10 O2 C A 11 2.8379 b-b
12 N2 G A 10 O2 C B 3 2.6560 b-b
MOTIF TYPE: DbnbA(ibA)
COMMENTS: One H of the amine group forms one base-pair H-bond,
the other H forms one non-intra-basepair H-bond
------------------------------------------------------------------------------------------------------------------------
1dnm YES CGCAAGCTGGCG / CGCAAGCTGGCG
12***** 6 N6 A A 4 O4 T B 20 2.8948 b-b
6 N6 A A 4 O4 T B 20 2.8948 2.349(2) 112.9 96.2 101.5 + 95.0 109.4
H-BOND TYPE: A - T, interstrand, two-center, two-H donor
MOTIF: 6 N6 A A 4 O4 T B 20 2.8948 b-b
7 N6 A A 4 O6 G B 21 2.6764 b-b
MOTIF TYPE: DbnbA(ibA)
13***** 23 N4 C B 15 O6 G A 9 2.8152 b-b
23 N4 C B 15 O6 G A 9 2.8152 2.132(1) 123.2 123.7 125.1 + 138.9 142.2
H-BOND TYPE: C - G, interstrand, three-center, two-H donor
MOTIF: 23 N4 C B 15 O6 G A 9 2.8152 b-b
24 N4 C B 15 O6 G A 10 2.9058 b-b
MOTIF TYPE: Db3nbA(3ibA)
COMMENTS: This is one of the rare cases of a C - G interstrand H-bond.
It occurs between the C of a G-C pair and the G of a G-A pair
------------------------------------------------------------------------------------------------------------------------
1ndnA YES CGCGAAAACGCG / CGCGTT / TTCGCG (two structures in one PDB file)
14***** 23 N2 G B 16 N3 G A 10 2.9531 b-b
23 N2 G B 16 N3 G A 10 2.953 2.409(2) 113.0 100.9 90.4 119.2 82.0
H-BOND TYPE: G - G, interstrand, three-center, two-H donor
MOTIF: 22 N2 G B 16 O2 C A 9 2.9806 b-b
23 N2 G B 16 N3 G A 10 2.9531 b-b
MOTIF TYPE: Db3nbA(3ibA)
------------------------------------------------------------------------------------------------------------------------
1ndnT YES CGCGAAAACGCG / CGCGTT / TTCGCG (two structures in one PDB file)
15***** 26 N3 T V 19 N1 A T 7 2.6342 b-b
26 N3 T V 19 N1 A T 7 2.634 2.217 102.9 87.2 110.3 107.9 103.6
H-BOND TYPE: T - A, interstrand, three-center, two-H donor
MOTIF: 25 N3 T V 19 N1 A T 6 2.9221 b-b
26 N3 T V 19 N1 A T 7 2.6342 b-b
MOTIF TYPE: Db3nbA(3ibA)
------------------------------------------------------------------------------------------------------------------------
2bna NO CGCGAATTCGCG / CGCGAATTCGCG
2d25 NO CCAGGCXTGG / CCAGGCXTGG
3bna NO CGCGAATTCGCG / CGCGAATTCGCG
------------------------------------------------------------------------------------------------------------------------
4bna YES CGCGAATTCGCG / CGCGAATTCGCG
16***** 15 N2 G A 10 O2 C A 11 3.1394 b-b
15 N2 G A 10 O2 C A 11 3.1394 2.458(1) 124.3 97.4 108.9 + 91.5 110.7
H-BOND TYPE: G - C, intrastrand, two-center, two-H donor
MOTIF: 15 N2 G A 10 O2 C A 11 3.1394 b-b
16 N2 G A 10 O2 C B 3 2.7757 b-b
MOTIF TYPE: DbnbA(ibA)
-----------------------------------------------------------------------------------------------------------------------
4dnb NO CGCGAXTTCGCG / CGCGAXTTCGCG
7bna NO CGCGAATTCGCG / CGCGAATTCGCG
9bna NO CGCGAATTCGCG / CGCGAATTCGCG
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Z-DNA:
######
131d NO CGCGCG / CGCGCG
133d NO CGCGXG / CGCGXG
145d_AB NO XGGGXG / XGCCXG (two structures in one PDB file)
145d_CD NO XGCCXG / XGGGXG (two structures in one PDB file)
180d NO CGCACG / CGTGCG
181d NO CACGCG / CGCGTG
1d24 NO CGCXCG / CGCXCG
1d39 NO CGCGCG / CGCXCG
1d40 NO XGUAXG / XGUAXG
1d41 NO XGUAXG / XGUAXG
1d48 NO CGCGCG / CGCGCG
1d53 NO CG / CG / CGCG / CGCG
1d76 NO CGUXCG / CGUXCG
1da1 NO XGCGCG / XGCGCG
1da2 NO CGCGXG / CGCGXG
1dcg NO CGCGCG / CGCGCG
1dn4 NO XGXGXG / XGXGXG
1dn5 NO XGXGXG / XGXGXG
1dn8 NO TG / TG
1dnf NO CGCGUG / CGCGUG
1zna NO CGCG / CGCG
223d NO CGCGXG / CGCGXG
2dcg NO CGCGCG / CGCGCG
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Other DNA:
#########
190d NO CCCC / CCCC / CCCC / CCCC / CCCC / CCCC / CCCC / CCCC
191d NO CCCT / CCCT / CCCT / CCCT
192d NO CCGCGG / CCGCGG
1d16 NO CGCGCGTTTTCGCGCG
-------------------------------------------------------------------------------------------------------------------
1d31 YES CGCAGAATTCGCG / CGCAGAATTCGCG
17***** 39 N1 G B 26 O1P C B 25 2.5711 b-B
39 N1 G B 26 O1P C B 25 2.571 2.072 108.1 149.1 161.1 127.6 149.2
H-BOND TYPE: G - C, intrastrand, two-center, one-H donor
MOTIF TYPE: DbnBA
-------------------------------------------------------------------------------------------------------------------
1d59 NO GGGGTTTTGG / GGGGTTTTGG / GGGGTTTTGG / GGGGTTTTGG (tetraplex)
-------------------------------------------------------------------------------------------------------------------
200d YES TAACCC / TAACCC
18***** 5 N4 C A 4 O1P A A 3 2.7537 b-B
5 N4 C A 4 O1P A A 3 2.754 1.817(2) 152.7 152.0 148.2 143.6 147.7
H-BOND TYPE: C - A, intrastrand, two-center, two-H donor
MOTIF: 5 N4 C A 4 O1P A A 3 2.7537 b-B
6 N4 C A 4 O2 C B 14 2.5998 b-b
MOTIF TYPE: DbnBA(ibA)
19***** 15 N4 C B 14 O2P A B 13 2.5444 b-B
15 N4 C B 14 O2P A B 13 2.544 1.552(2) 166.1 137.2 116.0 139.4 120.2
H-BOND TYPE: C - A, intrastrand, two-center, two-H donor
MOTIF: 14 N4 C B 14 O2 C A 4 2.8180 b-b
15 N4 C B 14 O2P A B 13 2.5444 b-B
MOTIF TYPE: DbnBA(ibA)
-------------------------------------------------------------------------------------------------------------------
208d NO GCGAATTCG / GCGAATTCG
241d NO CCCAAT / CCCAAT
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
DRUG-DNA:
#########
101d NO CGCGAATTXGCG / CGCGAATTXGCG
102d NO CGCAAATTTGCG / CGCAAATTTGCG
109d NO CGCGAATTCGCG / CGCGAATTCGCG
---------------------------------------------------------------------------------------------------------------------
121d YES CGCAAATTTGCG / CGCAAATTTGCG
20***** 5 N6 A A 4 O4 T B 20 3.0525 b-b
5 N6 A A 4 O4 T B 20 3.0525 2.498(2) 114.1 108.9 108.3 + 123.2 125.8
H-BOND TYPE: A - T, interstrand, three-center, two-H donor
MOTIF: 5 N6 A A 4 O4 T B 20 3.0525 b-b
6 N6 A A 4 O4 T B 21 2.9019 b-b
MOTIF TYPE: Db3nbA(3ibA)
21***** 7 N6 A A 5 O4 T B 19 2.8954 b-b
7 N6 A A 5 O4 T B 19 2.8954 2.342(2) 113.4 124.2 120.5 + 142.0 137.8
H-BOND TYPE: A - T, interstrand, three-center, two-H donor
MOTIF: 7 N6 A A 5 O4 T B 19 2.8954 b-b
8 N6 A A 5 O4 T B 20 2.8715 b-b
MOTIF TYPE: Db3nbA(3ibA)
----------------------------------------------------------------------------------------------------------------------
127d NO CGCGAATTCGCG / CGCGAATTCGCG
128d NO CGCXAATTCGCG / CGCXAATTCGCG
129d NO CGCGAATTCGCG / CGCGAATTCGCG
130d NO CGCXAATTCGCG / CGCXAATTCGCG
144d NO CGCXAATTCGCG / CGCXAATTCGCG
154d NO XGCG / XGCG
166d NO CGCGAATTCGCG / CGCGAATTCGCG
182d NO TGATCA / TGATCA
195d NO CGCGTTAACGCG / CGCGTTAACGCG
198d NO CGATCG / CGATCG / CGATCG / CGATCG
1d21 NO XGTXXG / XGTXXG
1d22 NO XGTXXG / XGTXXG
1d30 NO CGCGAATTCCCG / CGCGAATTCCCG
1d32 NO CGCG / CGCG
----------------------------------------------------------------------------------------------------------------------
1d43 YES CGCGAATTCGCG / CGCGAATTCGCG
22***** 15 N2 G A 10 O2 C A 11 3.1846 b-b
15 N2 G A 10 O2 C A 11 3.1846 2.469(1) 127.4 104.8 115.7 + 99.6 117.8
H-BOND TYPE: G - C, intrastrand, two-center, two-H donor
MOTIF: 15 N2 G A 10 O2 C A 11 3.1846 b-b
16 N2 G A 10 O2 C B 15 2.7238 b-b
MOTIF TYPE: DbnbA(ibA)
----------------------------------------------------------------------------------------------------------------------
1d44 YES CGCGAATTCGCG / CGCGAATTCGCG
23***** 13 N2 G A 10 O2 C A 11 3.1585 b-b
13 N2 G A 10 O2 C A 11 3.1585 2.447(1) 126.9 102.7 113.1 + 98.5 116.4
H-BOND TYPE: G - C, intrastrand, two-center, two-H donor
MOTIF: 14 N2 G A 10 O2 C A 11 3.1585 b-b
15 N2 G A 10 O2 C B 15 2.8490 b-b
MOTIF TYPE: DbnbA(ibA)
----------------------------------------------------------------------------------------------------------------------
1d45 NO CGCGAATTCGCG / CGCGAATTCGCG
---------------------------------------------------------------------------------------------------------------------
1d46 YES CGCGAATTCGCG / CGCGAATTCGCG
24***** 7 N6 A A 5 O4 T B 19 2.9397 b-b
7 N6 A A 5 O4 T B 19 2.9397 2.381(2) 113.9 111.3 122.9 + 127.1 141.1
H-BOND TYPE: A - T, interstrand, three-center, two-H donor
MOTIF: 7 N6 A A 5 O4 T B 19 2.9397 b-b
8 N6 A A 5 O4 T B 20 3.2941 b-b
MOTIF TYPE: Db3nbA(3ibA)
----------------------------------------------------------------------------------------------------------------------
1d63 NO CGCAAATTTGCG / CGCAAATTTGCG
1d64 NO CGCGAATTCGCG / CGCGAATTCGCG
1d86 NO CGCGAATTCGCG / CGCGAATTCGCG
1dne1 NO CGCGATATCGCG / CGCGATATCGCG
1dnh NO CGCGAATTCGCG / CGCGAATTCGCG
1gpg NO CCXCTXXTCTCC / GGAGACCAGAGG / CCXCTXXTCTCC / GGAGACCAGAGG
1lex NO CGCGAATTCGCG / CGCGAATTCGCG
1ley NO CGCGAATTCGCG / CGCGAATTCGCG
1prp NO CGCGAATTCGCG / CGCGAATTCGCG
209d NO GAAGCTTC / GAAGCTTC
224d NO TGATCA / TGATCA
227d NO CGCGAATTCGCG / CGCGAATTCGCG
---------------------------------------------------------------------------------------------------------------------
264d YES CGCAAATTTGCG / CGCAAATTTGCG
25***** 13 N2 G A 10 O2 C A 11 3.0526 b-b
13 N2 G A 10 O2 C A 11 3.0526 2.481(1) 115.3 104.2 111.0 + 97.8 113.4
H-BOND TYPE: G - C, intrastrand, two-center, two-H donor
MOTIF: 13 N2 G A 10 O2 C A 11 3.0526 b-b
14 N2 G A 10 O2 C B 15 2.6006 b-b
MOTIF TYPE: DbnbA(ibA)
----------------------------------------------------------------------------------------------------------------------
2d55 NO GAAGCTTC / GAAGCTTC
2dbe NO CGCGAATTCGCG / CGCGAATTCGCG
2des NO CGTACG / CGTACG
----------------------------------------------------------------------------------------------------------------------
2dnd YES CGCAAATTTGCG / CGCAAATTTGCG
26***** 6 N6 A A 5 O4 T B 7 2.7074 b-b
6 N6 A A 5 O4 T B 7 2.7074 2.148(2) 113.0 121.6 121.7 + 140.6 140.3
H-BOND TYPE: A - T, interstrand, three-center, two-H donor
MOTIF: 6 N6 A A 5 O4 T B 7 2.7074 b-b
7 N6 A A 5 O4 T B 8 2.8949 b-b
MOTIF TYPE: Db3nbA(3ibA)
----------------------------------------------------------------------------------------------------------------------
5bna NO CGCGAATTCGCG / CGCGAATTCGCG
6bna NO CGCGAATTCGCG / CGCGAATTCGCG
8bna NO CGCGAATTCGCG / CGCGAATTCGCG
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
PROTEIN-DNA:
############
1apl NO ACATGTAACATTTACACGC / TGCGTGTAAATGAATTACATG
1brn NO CGAC / CGAC
----------------------------------------------------------------------------------------------------------------------
cd
YES GTCACACTTTTCGGCGAAAAGTGTGACATAT / GTCACACTTTTCGGCGAAAAGTGTGACATAT
27***** 452 N6 A D 21 O4 T D 10 2.9910 b-b
452 N6 A D 21 O4 T D 10 2.991 2.441(2) 113.5 116.7 119.6 132.6 137.5
H-BOND TYPE: A - T, interstrand, three-center, two-H donor
MOTIF: 452 N6 A D 21 O4 T D 10 2.9910 b-b
453 N6 A D 21 O4 T D 11 2.7856 b-b
MOTIF TYPE: Db3nbA(3ibA)
28***** 457 N2 G D 23 O2 T D 10 2.6710 b-b
457 N2 G D 23 O2 T D 10 2.671 2.468(1) 90.3 110.3 100.8 93.3 93.2
H-BOND TYPE: G - T, interstrand, two-center, two-H donor
MOTIF: 456 N2 G D 23 O2 C D 9 2.7367 b-b
457 N2 G D 23 O2 T D 10 2.6710 b-b
MOTIF TYPE: DbnbA(ibA)
----------------------------------------------------------------------------------------------------------------------
1cma NO TTAGACGTCT / AGACGTCTA
----------------------------------------------------------------------------------------------------------------------
1d66 YES CCGGAGGACAGTCCTCCGG / CCGGAGGACTGTCCTCCGG
29***** 49 N2 G E 30 O4* T E 31 2.9561 b-B
49 N2 G E 30 O4* T E 31 2.956 2.199(1) 130.5 97.9 137.4 91.8 151.3
H-BOND TYPE: G - T, intrastrand, two-center, two-H donor
MOTIF: 48 N2 G E 30 O2 C D 9 2.7774 b-b
49 N2 G E 30 O4* T E 31 2.9561 b-B
MOTIF TYPE: DbnBA(ibA)
----------------------------------------------------------------------------------------------------------------------
1dct YES ACCAGCAGGXCACCAGTG / TCACTGGTGGXCTGCTGG / ACCAGCAGGXCACCAGTG / ACCAGCAGGXCACCAGTG
30***** 35 N2 G M 9 O4* A F 12 3.1569 b-B
35 N2 G M 9 O4* A F 12 3.157 2.348(2) 136.4 112.5 128.7 102.9 129.9
H-BOND TYPE: G - A, interstrand, two-center. two-H donor
MOTIF TYPE: DbnBA
COMMENTS: Only one H of N2 is involved in an H-bond. Other atoms of G M 9 form H-bonds with
an amino acid.
31***** 33 N2 G N 9 O4* A G 12 3.2031 b-B
33 N2 G N 9 O4* A G 12 3.203 2.396(2) 136.3 112.3 128.0 102.8 129.3
H-BOND TYPE: G - A, interstrand, two-center, two-H donor
MOTIF TYPE: DbnBA
COMMENTS: Only one H of N2 is involved in an H-bond. Other atoms of G N 9 form H-bonds with
an amino acid.
---------------------------------------------------------------------------------------------------------------------
1dnk NO GGTATAC / GGTATACC
1glu NO CCAGAACATCGATGTTCTG / CCAGAACATCGATGTTCTG
---------------------------------------------------------------------------------------------------------------------
1hcr YES TGTTTTTGATAAGA / TCTTATCAAAAAC
32***** 57 N2 G B 3 O4 T B 2 2.7222 b-b
57 N2 G B 3 O4 T B 2 2.722 1.959(1) 130.2 99.6 127.9 115.3 143.5
H-BOND TYPE: G - T, intrastrand, two-center, two-H donor
MOTIF: 57 N2 G B 3 O4 T B 2 2.7222 b-b
58 N2 G B 3 O2 C C 29 2.5676 b-b
MOTIF TYPE: DbnbA(ibA)
COMMENTS: T2 is last nucleotide in strand B
33***** 84 N6 A C 26 O4 T B 5 2.8834 b-b
84 N6 A C 26 O4 T B 5 2.883 2.404(1) 108.1 108.6 120.9 90.7 108.4
H-BOND TYPE: A - T, interstrand, two-center, two-H donor
MOTIF: 84 N6 A C 26 O4 T B 5 2.8834 b-b
85 N6 A C 26 O4 T B 6 2.7098 b-b
MOTIF TYPE: DbnbA(ibA)
---------------------------------------------------------------------------------------------------------------------
1hdd NO TTTTGCCATGTAATTACCTAA / ATTAGGTAATTACATGGCAAA
1hut NO GGTTGGTGTGGTTGG (single-stranded quadruplex)
---------------------------------------------------------------------------------------------------------------------
1kln YES GCCTCGCGGCGGCGCCGCGAGGC (single stranded double helix with missing nucleotides 1, 15-18)
34***** 553 N2 G B 2 O4* C B 3 3.0779 b-B
553 N2 G B 2 O4* C B 3 3.078 2.405(1) 123.4 111.6 133.1 101.4 148.3
H-BOND TYPE: G - C, intrastrand, two-center, two-H donor
MOTIF: 553 N2 G B 2 O4* C B 3 3.0779 b-B
554 N2 G B 2 O2 C B 29 3.4722 b-b
MOTIF TYPE: DbnBA(ibA)
---------------------------------------------------------------------------------------------------------------------
1lli YES AATACCACTGGCGGTGATAT / TATATCACCGCCAGTGGTAT
35***** 228 N6 A D 1 O4 T E 20 3.0092 b-b
228 N6 A D 1 O4 T E 20 3.009 2.345(2) 122.4 99.6 102.9 97.5 108.8
H-BOND TYPE: A - T, interstrand, two-center, two-H donor
MOTIF TYPE: DbnbA
COMMENTS: Only one H of N6 is involved in a H-bond. However A1 is last single nucleotide in
strand D.
---------------------------------------------------------------------------------------------------------------------
1lmb YES AATACCACTGGCGGTGATAT / TATATCACCGCCAGTGGTAT
36***** 1 N6 A 1 1 O4 T 2 40 3.0777 b-b
1 N6 A 1 1 O4 T 2 40 3.078 2.481(2) 117.3 95.0 99.0 93.4 105.8
H-BOND TYPE: A - T, interstrand, two-center, two-H donor
MOTIF TYPE: DbnbA
COMMENTS: Only one H of N6 is involved in a H-bond. However, A1 is last single nucleotide in
strand 1.
---------------------------------------------------------------------------------------------------------------------
1mdy YES TCAACAGCTGTTGA / TCAACAGCTGTTGA / TCAACAGCTGTTGA / TCAACAGCTGTTGA
37***** 285 N4 C E 5 O4 T F 9 2.7753 b-b
285 N4 C E 5 O4 T F 9 2.775 2.241(1) 111.5 126.2 125.7 145.7 141.8
H-BOND TYPE: C - T, interstrand, three-center, two-H donor
MOTIF: 284 N4 C E 5 OE1 GLU A118 3.1039 b-s
285 N4 C E 5 O4 T F 9 2.7753 b-b
286 N4 C E 5 O6 G F 10 3.3227 b-b
MOTIF TYPE: Db3nbA(3ibA)(psA)
COMMENTS: Interesting motif: One H of N4 forms a three-center H-bond with T F 9 and G F 10,
the other H forms a two-center H-bond with GLU A 118.
38***** 307 N4 C F 5 O4 T E 9 2.7083 b-b
307 N4 C F 5 O4 T E 9 2.708 2.223(1) 107.8 125.5 125.2 146.1 142.1
H-BOND TYPE: C - T, interstrand, three-center, two-H donor
MOTIF: 306 N4 C F 5 OE1 GLU B118 2.9687 b-s
307 N4 C F 5 O4 T E 9 2.7083 b-b
308 N4 C F 5 O6 G E 10 3.2557 b-b
MOTIF TYPE: Db3nbA(3ibA)(psA)
COMMENTS: Interesting motif: like above.
39***** 328 N4 C G 5 O4 T H 9 2.8043 b-b
328 N4 C G 5 O4 T H 9 2.804 2.340(1) 106.8 121.2 122.3 141.2 139.3
H-BOND TYPE: C - T, interstrand, three-center, two-H donor
MOTIF: 328 N4 C G 5 O4 T H 9 2.8043 b-b
329 N4 C G 5 O6 G H 10 3.3032 b-b
MOTIF TYPE: Db3nbA(3ibA)
COMMENTS: Iteresting motif: like above, the H-bond to GLU C 118 is not identified because
the H...A distance is slightly above the limit of 2.5 A
40***** 345 N4 C H 5 O4 T G 9 2.7816 b-b
345 N4 C H 5 O4 T G 9 2.782 2.315(1) 106.9 120.2 121.9 140.3 139.4
H-BOND TYPE: C - T, interstrand, three-center, two-H donor
MOTIF: 345 N4 C H 5 O4 T G 9 2.7816 b-b
346 N4 C H 5 O6 G G 10 3.2528 b-b
MOTIF TYPE: Db3nbA(3ibA)
COMMENTS: Interesting motif: like above, the H-bond to GLU D 118 is not identified because
the H...A distance is slightly above the limit of 2.5 A.
--------------------------------------------------------------------------------------------------------------------
1oct NO TGTATGCAAATAAGG / ACCTTATTTGCATAC
1par NO TATAGTAGAGTGCTTCTATCAT / AATGATAGAAGCACTCTACTAT
--------------------------------------------------------------------------------------------------------------------
1per YES AAGTACAGTTTTTCTTGTAT / TATACAAGAAAAACTGTACT
41***** 37 N6 A B 12 O4 T A 9 2.8232 b-b
37 N6 A B 12 O4 T A 9 2.823 2.393(2) 104.6 107.4 107.4 126.7 126.8
H-BOND TYPE: A - T, interstrand, three-center, two-H donor
MOTIF: 37 N6 A B 12 O4 T A 9 2.8232 b-b
38 N6 A B 12 O4 T A 10 2.6969 b-b
MOTIF TYPE: Db3nbA(3ibA)
--------------------------------------------------------------------------------------------------------------------
1pdn NO AACGTCACGGTTGAC / TTGTCAACCGTGACG
1pvi NO TGACCAGCTGGTC / TGACCAGCTGGTC
1pyi NO TCGGCAATTGCCGA / TCGGCAATTGCCGA
1rpe NO GACAAACAAGATACATTGTAT / TATACAATGTATCTTGTTT
--------------------------------------------------------------------------------------------------------------------
1rva YES AAAGATATCTT / AAAGATATCTT
42***** 624 N6 A C 7 O4 T C 6 3.0492 b-b
624 N6 A C 7 O4 T C 6 3.049 2.277(1) 132.2 114.4 111.5 115.9 120.5
H-BOND TYPE: A - T, intrastrand, two-center, two-H donor
MOTIF: 624 N6 A C 7 O4 T C 6 3.0492 b-b
625 N6 A C 7 O4 T D 6 2.9498 b-b
MOTIF TYPE: DbnbA(ibA)
43***** 641 N6 A D 7 O4 T D 6 2.9757 b-b
641 N6 A D 7 O4 T D 6 2.976 2.263(1) 126.4 115.5 109.9 117.9 120.5
H-BOND TYPE: A - T, intrastrand, two-center, two-H donor
MOTIF: 640 N6 A D 7 O4 T C 6 3.0138 b-b
641 N6 A D 7 O4 T D 6 2.9757 b-b
MOTIF TYPE: DbnbA(ibA)
---------------------------------------------------------------------------------------------------------------------
1rvb YES AAAGATATCTT / AAAGATATCTT
44***** 597 N6 A D 7 O4 T D 6 2.9506 b-b
597 N6 A D 7 O4 T D 6 2.951 2.151(1) 134.8 118.6 112.9 120.7 122.3
H-BOND TYPE: A - T intrastrand, two-center, two-H donor
MOTIF: 596 N6 A D 7 O4 T C 6 3.0284 b-b
597 N6 A D 7 O4 T D 6 2.9506 b-b
MOTIF TYPE: DbnbA(ibA)
45***** 579 N6 A C 7 O4 T C 6 3.0036 b-b
579 N6 A C 7 O4 T C 6 3.004 2.173(1) 138.4 121.7 118.1 120.9 124.5
H-BOND TYPE: A - T intrastrand, two-center, two-H donor
MOTIF: 579 N6 A C 7 O4 T C 6 3.0036 b-b
596 N6 A D 7 O4 T C 6 3.0284 b-b
MOTIF TYPE: DbnbA(ibA)
--------------------------------------------------------------------------------------------------------------------
1rvc YES AAAGAT / ATCTT / AAAGAT / ATCTT
46***** 601 N6 A D 7 O4 T C 6 3.1279 b-b
601 N6 A D 7 O4 T C 6 3.128 2.274(1) 141.5 104.4 103.7 113.1 115.2
H-BOND TYPE: A - T, intrastrand, two-center, two-H donor
MOTIF: 601 N6 A D 7 O4 T C 6 3.1279 b-b
602 N6 A D 7 O4 T E 6 3.1704 b-b
MOTIF TYPE: DbnbA(ibA)
COMMENTS: The second H-bond like for 1rva and rvb is slightly longer than tolerated by the
geometrical criteria.
---------------------------------------------------------------------------------------------------------------------
1tro NO TGTACTAGTTAACTAGTAC / TGTACTAGTTAACTAGTAC / TGTACTAGTTAACTAGTAC
TGTACTAGTTAACTAGTAC
--------------------------------------------------------------------------------------------------------------------
1ysa YES TTCCTATGACTCATCCAGTT / AAACTGGATGAGTCATAGGA
47***** 25 N4 C B 24 N7 A B 23 3.1813 b-b
25 N4 C B 24 N7 A B 23 3.181 2.208(2) 161.3 87.9 164.6 87.3 159.9
H-BOND TYPE: C - A, intrastrand, two-center, two-H donor
MOTIF: 24 N4 C B 24 O6 G A 18 2.6330 b-b
25 N4 C B 24 N7 A B 23 3.1813 b-b
MOTIF TYPE: DbnbA(ibA)
48***** 46 N2 G B 38 O4* G B 39 3.0860 b-B
46 N2 G B 38 O4* G B 39 3.086 2.473(1) 118.6 136.5 118.5 120.3 133.4
H-BOND TYPE: G - G, intrastrand, two-center, two-H donor
MOTIF: 45 N2 G B 38 O2 C A 4 3.0978 b-b
46 N2 G B 38 O4* G B 39 3.0860 b-B
MOTIF TYPE: DbnBA(ibA)
---------------------------------------------------------------------------------------------------------------------
1ytb YES GTATATAAAACGGGTGGCGTTTTATATAC / GTATATAAAACGGGTGGCGTTTTATATAC
49***** 437 N6 A C 3 O4 T C 2 2.8788 b-b
437 N6 A C 3 O4 T C 2 2.879 2.098(1) 132.6 117.2 112.5 119.2 122.4
H-BOND TYPE: A - T, intrastrand, two-center, two-H donor
MOTIF: 437 N6 A C 3 O4 T C 2 2.8788 b-b
438 N6 A C 3 O4 T C 27 3.0593 b-b
MOTIF TYPE: DbnBA(ibA)
50***** 456 N1 G C 16 O3* G C 13 3.1937 b-B
456 N1 G C 16 O3* G C 13 3.194 2.217 162.4 92.3 146.2 97.6 140.7
H-BOND TYPE: G - G, intrastrand, three-center, one-H donor
MOTIF: 456 N1 G C 16 O3* G C 13 3.1937 b-B
457 N1 G C 16 O2P G C 14 3.0688 b-B
Db3nBA(3nBA) (!!!! see below)
51***** 457 N1 G C 16 O2P G C 14 3.0688 b-B
457 N1 G C 16 O2P G C 14 3.069 2.313 130.7 91.8 113.4 106.1 127.3
H-BOND TYPE: G - G, intrastrand, three-center, one-H donor
MOTIF: 456 N1 G C 16 O3* G C 13 3.1937 b-B
457 N1 G C 16 O2P G C 14 3.0688 b-B
MOTIF TYPE: Db3nBA(3nBA) (!!! see below)
COMMENTS: This bond and the previous bond are the only three-center bonds (?),
where both are of the non-inter-basepair type. This means that they belong the
same motif.
52***** 458 N2 G C 16 O2P G C 14 2.7920 b-B
458 N2 G C 16 O2P G C 14 2.792 1.980(2) 135.6 126.1 116.8 136.1 131.3
H-BOND TYPE: G - G, intrastrand, two-center, two-H donor
MOTIF TYPE: DbnBA
COMMENTS: The three last bonds are intrastrand within a loop (no neighbours).
The last two non-intra-basepair H-bonds are formed between two different donors
and one and the same acceptor.
53***** 480 N6 A D 3 O4 T D 2 2.8148 b-b
480 N6 A D 3 O4 T D 2 2.815 2.096(1) 126.4 117.5 110.6 120.4 122.3
H-BOND TYPE: A - T, intrastrand, two-center, two-H donor
MOTIF: 480 N6 A D 3 O4 T D 2 2.8148 b-b
515 N6 A D 28 O4 T D 2 2.9571 b-b
MOTIF TYPE: DbnbA(ibA)
54***** 497 N1 G D 16 O3* G D 13 3.2429 b-B
497 N1 G D 16 O3* G D 13 3.243 2.315 152.1 85.1 152.5 93.5 144.3
H-BOND TYPE: G - G, intrastrand, two-center, one-H donor
MOTIF: 497 N1 G D 16 O3* G D 13 3.2429 b-B
498 N1 G D 16 O2P G D 14 2.8957 b-B
MOTIF TYPE: Db3nBA(3nBA) (!!!! see below)
55***** 498 N1 G D 16 O2P G D 14 2.8957 b-B
498 N1 G D 16 O2P G D 14 2.896 2.059 138.8 96.6 118.9 109.9 131.5
H-BOND TYPE: G - G, intrastrand, two-center, one-H donor
MOTIF: 497 N1 G D 16 O3* G D 13 3.2429 b-B
498 N1 G D 16 O2P G D 14 2.8957 b-B
MOTIF TYPE: Db3nBA(3nBA) (!!!! see above)
56***** 499 N2 G D 16 O2P G D 14 2.7476 b-B
499 N2 G D 16 O2P G D 14 2.748 1.872(2) 143.1 143.8 128.2 147.4 139.5
H-BOND TYPE: G - G, intrastrand, two-center, two-H donor
MOTIF: 498 N1 G D 16 O2P G D 14 2.8957 b-B
499 N2 G D 16 O2P G D 14 2.7476 b-B
MOTIF TYPE: DbnBA
COMMENTS: Strand D shows the same characteristics like C described above.
---------------------------------------------------------------------------------------------------------------------
1zaa NO AGCGTGGGCGT / TACGCCCACGC
2bpf NO CGGCGCC / GGGCGCCG
---------------------------------------------------------------------------------------------------------------------
2bpg YES CGGCGCC / GGGCGCCG / CGGCGCC / GGGCGCCG / CGGCGCC / GGGCGCCG
57***** 626 N4 C C 9 O6 G D 2 2.6083 b-b
626 N4 C C 9 O6 G D 2 2.608 2.050(1) 112.4 110.2 111.6 128.4 132.6
H-BOND TYPE: C - G, interstrand, two-center, two-H donor
MOTIF: 626 N4 C C 9 O6 G D 2 2.6083 b-b
627 N4 C C 9 O6 G D 3 2.3479 b-b
MOTIF TYPE: DbnbA(ibA)
COMMENTS: This is one of the rare cases of a C - G interstrand H-bond.
---------------------------------------------------------------------------------------------------------------------
2dnj NO GCGATCGC / GCGATC
2drp NO CTAATAAGGATAACGTCCG / TCGGACGTTATCCTTATTA
---------------------------------------------------------------------------------------------------------------------
2or1 YES AAGTACAAACTTTCTTGTAT / TATACAAGAAAGTTTGTACT
58***** 1 N6 A A 1 O4 T B 20 2.9727 b-b
1 N6 A A 1 O4 T B 20 2.973 2.223(2) 129.9 139.0 127.8 150.2 142.9
H-BOND TYPE: A - T, interstrand, two-center, two-H donor
MOTIF TYPE: DbnbA
COMMENTS: First nucleotide in a strand.
59***** 16 N3 T A 13 N1 A B 10 3.1322 b-b
16 N3 T A 13 N1 A B 10 3.132 2.347 133.8 132.2 77.8 144.2 77.3
H-BOND TYPE: T - A, interstrand, two-center, one-H donor
MOTIF TYPE: DbnbA
COMMENTS: Not an end nucleotide.
----------------------------------------------------------------------------------------------------------------------
2rve NO CGAGCTCG / CGAGCTCG / CGAGCTCG / CGAGCTCG
----------------------------------------------------------------------------------------------------------------------
3cro YES AAGTACAAACTTTCTTGTAT / TATACAAGAAAGTTTGTACT
60***** 1 N6 A A 1 O4 T B 20 2.4299 b-b
1 N6 A A 1 O4 T B 20 2.430 2.024(2) 101.1 102.5 95.8 125.9 118.6
H-BOND TYPE: A - T, interstrand, two-center, two-H donor
MOTIF TYPE: DbnbA
COMMENTS: A1 is a single nucleotide at the end of a strand.
----------------------------------------------------------------------------------------------------------------------
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
DNA-NMR:
175d NO GCGAATGAGC / GCGAATGAGC
---------------------------------------------------------------------------------------------------------------------
107d YES CCTTTTC / GAAAAGG
61***** 12 N6 A B 11 O4 T A 3 3.1007 b-b
12 N4 C A 10 O6 G B 11 2.927 1.974(1) 156.3 139.1 167.2 134.4 162.1
H-BOND TYPE: A - T, interstrand, three-center, two-H donor
MOTIF: 12 N6 A B 11 O4 T A 3 3.1007 b-b
13 N6 A B 11 O4 T A 4 3.1151 b-b
MOTIF TYPE: Db3nbA(3ibA)
---------------------------------------------------------------------------------------------------------------------
108d YES CGCTAGCG / CGCTAGCG
62***** 1 N4 C A 1 O6 G A 2 3.0728 b-b
1 N4 C A 1 O6 G A 2 3.073 2.351(1) 127.5 110.6 100.4 112.0 95.
H-BOND TYPE: C - G, intrastrand, three-center, two-H donor
MOTIF: 1 N4 C A 1 O6 G A 2 3.0728 b-b
2 N4 C A 1 O6 G B 8 2.8355 b-b
MOTIF TYPE: Db3nbA(3ibA)
--------------------------------------------------------------------------------------------------------------------
146d NO TCGCGA / TCGCGA
--------------------------------------------------------------------------------------------------------------------
185d YES GACGTC / GACGTC
63***** 14 N3 T C 15 O6 G D 17 2.7661 b-b
14 N3 T C 15 O6 G D 17 2.766 2.021 128.6 125.6 130.8 141.1 146.5
H-BOND TYPE: T - G, interstrand, three-center, one-H donor
MOTIF: 14 N3 T C 15 O6 G D 17 2.7661 b-b
15 N3 T C 15 N1 A D 18 2.6398 b-b
MOTIF TYPE: Db3nbA(3ibA)
-------------------------------------------------------------------------------------------------------------------
193d NO ACACGTGT / ACACGTGT
199d NO XCACGTCXT / ACGACGTGC
202d NO GACATGTC / GACATGTC
1gat NO AGATAAACGTTTATCT (duplex)
1gau NO AGATAAACGTTTATCT (duplex)
1mse NO CCTAACTGACACACAT / ATGTGTGTCAGTTAGG
1msf NO CCTAACTGACACACAT / ATGTGTGTCAGTTAGG
-------------------------------------------------------------------------------------------------------------------
103d YES GTGGAATGGAAC / GTGGAATGGAAC
64***** 30 N6 A B 22 O2 T A 2 2.8928 b-b
30 N6 A B 22 O2 T A 2 2.893 2.341(2) 113.3 115.8 124.0 103.7 120.8
H-BOND TYPE: A - T, interstrand, three-center, two-H donor
MOTIF: 30 N6 A B 22 O2 T A 2 2.8928 b-b
31 N6 A B 22 O4* G A 3 3.0124 b-B
MOTIF TYPE: Db3nbA(3iBA)
COMMENTS: The intra-basepair H-bond is a little bit unusual (backbone).
This is due to the fact that the planes of the bases B22 and A3
are twisted. Nevertheless, we consider them as a basepair.
In addition to the H-bond mentioned there are further intra-basepair
H-bonds between B22 and A3.
65**** 5 N2 G A 4 O2P A B 22 2.8234 b-B
5 N2 G A 4 O2P A B 22 2.823 1.833(1) 166.0 152.8 151.5 150.7 154.9
H-BOND TYPE: G - A, interstrand, two-center, two-H donor
MOTIF TYPE: DbnBA
66***** 6 N6 A A 5 O2 T B 19 2.9653 b-b
6 N6 A A 5 O2 T B 19 2.965 2.338(2) 119.2 112.4 122.8 100.8 118.9
H-BOND TYPE: A - T, interstrand, three-center, two-H donor
MOTIF: 6 N6 A A 5 O2 T B 19 2.9653 b-b
7 N6 A A 5 O4* G B 20 3.0139 b-B
8 N6 A A 5 N3 G B 20 2.8697 b-b
MOTIF TYPE: Db3nbA(3iBA)(ibA)
COMMENTS: The second H not involved in the three-center bond forms another H-bond.
67***** 29 N2 G B 21 O2P A A 5 2.8039 b-B
29 N2 G B 21 O2P A A 5 2.804 1.811(1) 166.9 152.5 156.3 150.1 159.5
H-BOND TYPE: G - A, interstrand, three-center, two-H donor
29 N2 G B 21 O2P A A 5 2.8039 b-B
MOTIF TYPE: DbnBA
68***** 23 N6 A B 17 O2 T A 7 2.9721 b-b
23 N6 A B 17 O2 T A 7 2.972 2.341(2) 119.6 112.3 122.8 100.8 118.9
H-BOND TYPE: A - T, interstrand, three-center, two-H donor
MOTIF: 23 N6 A B 17 O2 T A 7 2.9721 b-b
24 N6 A B 17 O4* G A 8 3.0166 b-B
25 N6 A B 17 N3 G A 8 2.8698 b-b
MOTIF TYPE: Db3nbA(3iBA)(ibA)
COMMENTS: Same motif as above.
69***** 13 N6 A A 10 O2 T B 14 2.8980 b-b
13 N6 A A 10 O2 T B 14 2.898 2.337(2) 114.0 115.8 124.3 103.7 121.1
H-BOND TYPE: A - T, interstrand, three-center, two-H donor
MOTIF: 13 N6 A A 10 O2 T B 14 2.8980 b-b
14 N6 A A 10 O4* G B 15 3.0165 b-B
15 N6 A A 10 N3 G B 15 2.8790 b-b
MOTIF TYPE: Db3nbA(3iBA)(ibA)
COMMENTS: Same motif as above.
70**** 22 N2 G B 16 O2P A A 10 2.8205 b-B
22 N2 G B 16 O2P A A 10 2.820 1.828(1) 166.6 153.4 152.8 151.0 155.9
H-BOND TYPE: G - A, interstrand, two-center, two-H donor
MOTIF TYPE: DbnBA
71***** 12 N2 G A 9 O2P A B 17 2.8029 b-B
12 N2 G A 9 O2P A B 17 2.803 1.808(1) 167.5 152.8 157.6 150.1 160.5
H-BOND TYPE: G - A, interstrand, two-center, two-H donor
MOTIF TYPE: DbnBA
------------------------------------------------------------------------------------------------------------------
105d NO TCC / TCC / TCC / TCC (quadruplex)
106d NO XCT / XCT / XCT / XCT (quadruplex)
134d NO TCCTCCTTTTTTAGGAGGATTTTTTGGTGGT (triplex)
136d NO TCCTCCTTTTTAGGAGGATTTTTTGGTGG (triplex)
139d NO TTGGGGT / TTGGGGT / TTGGGGT / TTGGGGT(quadruplex)
-----------------------------------------------------------------------------------------------------------------
143d YES AGGGTTAGGGTTAGGGTTAGGG (quadruplex)
72***** 8 N6 A 7 O2 T 18 2.4236 b-b
8 N6 A 7 O2 T 18 2.424 1.425(1) 168.5 109.8 119.9 110.8 118.3
H-BOND TYPE: A - T, intrastrand, two-center, two-H donor
MOTIF: 8 N6 A 7 O2 T 18 2.4236 b-b
9 N6 A 7 O4* A 19 2.8890 b-B
MOTIF TYPE: DbnbA(nBA)
73***** 9 N6 A 7 O4* A 19 2.8890 b-B
9 N6 A 7 O4* A 19 2.889 1.920(2) 159.9 129.8 116.4 125.9 122.2
H-BOND TYPE: A - A, intrastrand, two-center, two-H donor
MOTIF: 8 N6 A 7 O2 T 18 2.4236 b-b
9 N6 A 7 O4* A 19 2.8890 b-B
MOTIF TYPE: DbnBA(nbA)
COMMENTS: The two non-intra-basepair bonds belong to the same motif. A two-H donor forms with
his two different hydrogens two two-center non-intra-base-pair H-bonds.
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149d NO CCTATTCGAATAGGCTTGTCC (triplex)
156d NO GGGGTTTTGGGG / GGGGTTTTGGGG (quadruplex)
177d NO GAACAGGTTTTTCCTGTTCTTTTTXTTTTXX (triplex)
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179d YES TCGA / TCGA
74***** 1 N3 T A 1 O4* C B 6 2.8491 b-B
1 N3 T A 1 O4* C B 6 2.849 1.843 173.6 127.1 100.4 128.3 101.3
H-BOND TYPE: T - C, interstrand, two-center, one-H donor
MOTIF TYPE: DbnBA
75***** 6 N3 T B 5 O4* C A 2 2.8416 b-B
6 N3 T B 5 O4* C A 2 2.842 1.855 164.7 117.8 108.2 122.9 106.8
H-BOND TYPE: T - C, interstrand, two-center, one-H donor
MOTIF TYPE: DbnBA
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186d YES TTGGGGTTGGGGTTGGGGTTGGGG (quadruplex)
76***** 1 N3 T 2 O4 T 14 2.9324 b-b
1 N3 T 2 O4 T 14 2.932 2.232 125.2 133.3 108.9 146.9 119.4
H-BOND TYPE: T - T, intrastrand, three-center, one-H donor
MOTIF: 1 N3 T 2 O4 T 14 2.9324 b-b
2 N3 T 2 O6 G 15 2.8788 b-b
MOTIF TYPE: Db3nbA(3ibA)
77***** 8 N2 G 5 O3* G 6 2.9379 b-B
8 N2 G 5 O3* G 6 2.938 2.368(1) 114.7 93.1 112.6 105.6 113.3
H-BOND TYPE: G - G, intrastrand, two-center, two-H donor
MOTIF: 8 N2 G 5 O3* G 6 2.9379 b-B
9 N2 G 5 N7 G 10 2.8982 b-b
MOTIF TYPE: DbnBA(ibA)
78***** 10 N2 G 6 O4* T 7 2.7799 b-B
10 N2 G 6 O4* T 7 2.780 1.826(1) 156.2 137.9 110.8 131.1 115.6
H-BOND TYPE: G - T, intrastrand, two-center, two-H donor
MOTIF TYPE: DbnBA
79***** 12 N2 G 9 O1P T 8 2.6473 b-B
12 N2 G 9 O1P T 8 2.647 1.686(1) 157.5 129.6 142.6 121.3 135.9
H-BOND TYPE: G - T, intrastrand, three-center, two-H donor
MOTIF: 12 N2 G 9 O1P T 8 2.6473 b-B
13 N2 G 9 O6 G 10 2.7695 b-b
14 N2 G 9 O6 G 24 2.7000 b-b
MOTIF TYPE: Db3nBA(3nbA)(ibA)
COMMENTS: Two non-intra-basepair H-bonds are involved in a three-center bond.
80***** 13 N2 G 9 O6 G 10 2.7695 b-b
13 N2 G 9 O6 G 10 2.769 2.467(1) 96.5 100.0 92.5 115.4 113.0
H-BOND TYPE: G - G intrastrand, three-center, two-H donor
MOTIF: 12 N2 G 9 O1P T 8 2.6473 b-B
13 N2 G 9 O6 G 10 2.7695 b-b
14 N2 G 9 O6 G 24 2.7000 b-b
MOTIF TYPE: Db3nbA(3nBA)(ibA)
COMMENTS: Two non-intra-basepair H-bonds are involved in a three-center bond.
81***** 11 N1 G 9 O6 G 23 2.8318 b-b
11 N1 G 9 O6 G 23 2.832 2.496 98.8 99.7 98.7 118.4 110.9
H-BOND TYPE: G - G intrastrand, two-center, one-H donor
MOTIF TYPE: DbnbA
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1d18 NO CATGCATG / CATGCATG
1d19 NO GTACGTAC / GTACGTAC
1d20 NO TCTATCACCG / CGGTGATAGA
1d70 NO GTATAATG / CATTATAC
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1da4 YES CTCTAGTGCTCAC / GTGAGCACTAGAG
82***** 12 N6 A A 12 O6 G B 14 2.8693 b-b
12 N6 A A 12 O6 G B 14 2.869 2.427(2) 105.6 105.9 106.7 121.6 126.4
H-BOND TYPE: A - G, interstrand, three-center, two-H donor
MOTIF: 12 N6 A A 12 O6 G B 14 2.8693 b-b
13 N6 A A 12 O4 T B 15 2.9245 b-b
MOTIF TYPE: Db3nbA(3ibA)
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201d NO GGGGTTTTGGGGTTTTGGGGTTTTGGGG (quadruplex)
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