The Base Pair Directory
| GC base pairs with two standard hydrogen bonds |
| base | potential H-bond donor/acceptor sites |
guanine G  |
G(1da3) N3... C2 N2-H... |
G(dd3) N1-H... C2 N2-H... |
G(2da3) O6... C6 N1-H... |
G(aa4) O6... C6 C5 N7... |
cytosine C  |
C(aa3) N3... C2 O2... |
C(da3) N4-H... C4 N3... |
| base pair H-bond motif | structure images |
G(1da3)...C(da3)
GC N3-amino, N3-amino N3...H-N4 C2 C4 N2-H N3
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C(da3)...C(da3)
GC reverse Watson Crick N1-H...O2 C2 C2 N2-H...N3 |
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G(2da3/dd3)...C(da3/aa3) GC Watson-Crick O6...H-N4 C6 C4 N1-H...N3 C2 C2 N2-H...O2 |
| GC base pairs with 3 heavy-atom H-bond donor/acceptor site |
| base pair H-bond motif | structure images |
G(dd3)...C(O2), N1-N3 cis GC, N1-carbonyl, N2-carbonyl, N1-N3 cis N1-H... C2 O2 N2-H...
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G(dd3)...C(O2), N1-N3 trans GC, N1-carbonyl, N2-carbonyl, N1-N3 trans N1-H... C2 O2 N2-H...
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G(aa4)...C(N4-H1/H2), N7-N3 cis GC, N7-amino, carbonyl-amino`, N7-N3 cis N7...H1 C5 | C6 N4 O6...H2
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G(aa4)...C(N4-H1/H2), N7-N3 trans GG, amino-carbonyl, amino-N7, N7-N3 trans N7...H1 C5 | C6 N4 O6...H2
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