The Base Pair Directory

AC base pairs with two standard hydrogen bonds
base  potential H-bond donor/acceptor sites


 
 

adenine A

A(da3)

N6-H...
C6
N1...

A(da4)

N6-H...
C6
C5
N7...
cytosine C
C(aa3)
N3...
C2
O2...
C(da3)
N4-H...
C4
N3...
Base pairs with 4 heavy-atom H-bond donor/acceptor sites
base pair H-bond motif structure images

A(da3)...C(da3)

AC reverse wobble
 

N1...H-N4
C6     C4
N6-H...N3

  • Tinoco compilation: 
    • yes (AC reverse wobble) 
  • Westhof compilation: 
  • Jeffrey/Saenger compilation: 
    • yes (AC4) 
PDF | VRML

A(da4)...C(da3)

AC reverse Hoogsteen
 

N7...H-N4
C5     C4
C6      |
N6-H...N3

  • Tinoco compilation: 
    • yes (AC reverse Hoogsteen) 
  • Westhof compilation: 
  • Jeffrey/Saenger compilation: 
    • yes (AC2) 
PDF | VRML
Base pairs with 3 heavy-atom H-bond donor/acceptor sites
base pair H-bond motif structure images

A(N6-H1/H2)...C(aa3)

AC N6-N3 N6-carbonyl
 

H...N3
N6  C2
H...O2

  • Tinoco compilation: 
    • no 
  • Westhof compilation: 
    • no 
  • Jeffrey/Saenger compilation: 
    • no 
PDF | VRML

A(da4)...C(da3)

AC reverse Hoogsteen
 

N7...H-N4
C5     C4
C6      |
N6-H...N3

  • Tinoco compilation: 
    • no 
  • Westhof compilation: 
    • no 
  • Jeffrey/Saenger compilation: 
    • no 
PDF | VRML