TABLE 5.
Residues of the protein-protein interfaces in gD-receptor complexes
| Amino acid position | HSV-1 gD (solved structure)a |
B virus gD (model)b,e |
Remarks | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Residue | No. of H bondsc | No. of hydrophobic contacts | No. of clashesd | Residue | No. of H bondsc | No. of hydrophobic contacts | No. of clashesd | ||
| 7 | A | 1 | 2 | 0 | R | NA | NA | 5 | Too many clashes in the model suggest that the residues will disrupt the complex |
| 11 | M | 0 | 10 | 0 | R | NA | NA | 5 | Too many clashes in the model suggest that the residues will disrupt the complex |
| 12 | A | 1 | 0 | 0 | V | 1 | 0 | 0 | |
| 14 | P | 1 | 11 | 0 | P | 0 | 9 | 0 | A hydrogen bond is lost |
| 15 | N | 2 | 1 | 0 | G | 0 | 0 | 0 | Hydrogen bonding interactions are lost |
| 24 | V | 0 | 3 | 0 | P | 0 | 0 | 0 | Protein-protein packing is disrupted |
| 26 | D | 2 | 1 | 0 | E | 1 | 3 | 1 | Hydrogen bonding interactions are lost |
| 27 | Q | 2 | 1 | 0 | Q | 1 | 0 | 1 | A hydrogen bond is lost |
| 28 | L | 0 | 4 | 0 | K | 0 | 4 | 1 | |
| 29 | W | 2 | 2 | 0 | Y | 3 | 1 | 0 | |
| 31 | P | 0 | 2 | 0 | P | 0 | 2 | 0 | |
a
Downloaded from the Protein Data Bank (PDB entry 1JMA).
b
Based on the complex of HSV-1 gD and HVEM.
c
Residues of the interfaces were identified using lists of intersubunit hydrogen bonds and van der Waals contacts as described earlier (59, 60).
d
An atom-atom “clash” was registered if the distance between two nonbonded atoms was less than 2 Å.
e
NA, not applicable (too many clashes in this region).