TABLE 4.
Direct hydrogen bonds between BPV-1 E2 and its DNA target
| Residue identity | Secondary structure location | Identity of most contacted bases | Protein subunit and % of residue occurrence | Hydrogen-bond number |
|---|---|---|---|---|
| Asn336 | α1-helix | A(−6) | A.100 - B.100 | 2 |
| C(−5) | ||||
| Gln337 | α1-helix | G(−7) | A.98 - B.98 | 2 |
| Lys339 | α1-helix | G(+4) | A.96 - B.91 | 2 |
| G(−5) | ||||
| Cys340 | α1-helix | A(−6) | A.91 - B.94 | 2 |
| Arg342 | α1-helix | C(+3) | A.100 - B.100 | 2 |
| G(+4) | ||||
| Arg344 | α1-helix | C(−8) | A.100 - B.100 | 2 |
| G(−7) | ||||
| Tyr359 | β2-β3 loop | C(+3) | A.100 - B.100 | 2 |
| Arg370 | β2-β3 loop | C(+3) | A.100 - B.100 | 2 |
| G(+4) |
Residues making a direct hydrogen bond in the MD simulation with an occurrence ≥50% of trajectory time.