TABLE 1.
Solvent accessibility of cysteine residues in T7 gp5/trx
The relative surface accessibility for all cysteines of gp5/trx complex was calculated using the program Naccess (32). Naccess calculates the solvent-accessible surface that is defined by rolling a probe with the size of a water molecule around a Van der Waals surface of a protein from a PDB file. The values represent the surface accessibility of each cysteine based on the crystal structure of T7 gp5/trx (PDB code 1T8E) (18). “Side chain” refers to the fraction of amino acid side chain that is exposed to the solvent, “Main chain” refers to the fraction of main chain (not including the side chain) that is exposed to the solvent, and “All atoms” refers to the entire surface area of the amino acid that is exposed to the solvent.
| Residue no. | All atoms | Side chain | Main chain |
|---|---|---|---|
| % | % | % | |
| Cys-20 | 0 | 0 | 0 |
| Cys-88 | 0.4 | 0.2 | 1 |
| Cys-275 | 43.7 | 50 | 27.2 |
| Cys-313 | 24.2 | 25.6 | 20.4 |
| Cys-451 | 0.5 | 0.6 | 0 |
| Cys-483 | 0 | 0 | 0 |
| Cys-622 | 0.4 | 0.6 | 0 |
| Cys-660 | 0 | 0 | 0 |
| Cys-688 | 2.1 | 0.7 | 5.6 |
| Cys-703 | 1.5 | 0 | 5.5 |
| Cys-32a | 0.1 | 0 | 0.4 |
| Cys-35a | 2.6 | 0.3 | 8.8 |
a Cysteine in redox-active site of trx in complex with T7 gp5.