The Base Pair Directory  

GA 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..


 
 

adenine A

A(da3)

N6-H...
C6
N1...

A(da4)

N6-H...
C6
C5
N7...


 
 

GA base pairs with 4 heavy-atom H-bond donor/acceptor sites
base pair H-bond motif structure images

G(1da3)...A(da3)

GA N3-amino, amino-N1
  

N3...H-N6
C2     C2
N2-H...N1
  • Tinoco compilation: 
    • yes (AG base pairs, G.A N3-amino, amino-N1) 
  • Westhof compilation: 
    • no 
  • Jeffrey/Saenger compilation: 
    • no 
PDF | VRML

G(1da3)...A(da4)

GA N7-amino, amino-N3
  

N3...H-N6
C2     C6
       C5
N2-H...N7
  • Tinoco compilation: 
    • yes (AG base pairs, G.A N7-amino, amino-N3) 
  • Westhof compilation: 
    • no 
  • Jeffrey/Saenger compilation: 
    • no 
PDF | VRML

G(2da3)...A(da3)

GA N1-N1 carbonyl-amino
  

N1-H...N1
C6     C6
O6...H-N6
  • Tinoco compilation: 
    • yes (AG base pairs, G.A N1-N1, carbonyl-amino) 
  • Westhof compilation: 
  • Jeffrey/Saenger compilation: 
    • no 
PDF | VRML

G(2da3)...A(da4)

GA N1-N7, carbonyl-amino
  

N1-H...N7
C6     C5
       C6
O6...H-N6
  • Tinoco compilation: 
    • yes (AG base pairs, G.A N1-N7, carbonyl-amino) 
  • Westhof compilation: 
  • Jeffrey/Saenger compilation: 
    • no 
PDF | VRML


 
 

GA base pairs with 3 heavy-atom H-bond donor/acceptor sites
base pair H-bond motif structure images

A(N6-H1/H2)...G(aa4)

AG amino-N7, amino-O6, N7-cis
  

N7...H
C5   N6
C6   |
O6...H
  • Tinoco compilation: 
    • no 
  • Westhof compilation: 
  • Jeffrey/Saenger compilation: 
    • no 
PDF | VRML

A(N6-H1/H2)...G(aa4)

AG amino-N7, amino-O6, N7-trans
  

N3...H-N6
C2     C2
N2-H...N1
  • Tinoco compilation: 
    • no 
  • Westhof compilation: 
  • Jeffrey/Saenger compilation: 
    • no 
PDF | VRML