Surface Diver uses the hydrophobicity scale introduced by Rose et al.:
| residue | hydrophobicity |
| ALA | 0.74 |
| GLY | 0.72 |
| VAL | 0.86 |
| LEU | 0.85 |
| ILE | 0.88 |
| PRO | 0.64 |
| PHE | 0.88 |
| TYR | 0.76 |
| TRP | 0.85 |
| SER | 0.66 |
| THR | 0.70 |
| ASN | 0.63 |
| GLN | 0.62 |
| CYS | 0.91 |
| MET | 0.85 |
| ASP | 0.62 |
| GLU | 0.62 |
| HIS | 0.78 |
| LYS | 0.52 |
| ARG | 0.64 |
To map hydrophobicity onto the surface of a molecule, using the above table, each atom of a certain residue is assigned a similar hydrophobicity index, which is equal to the hydrophobicity of the residue that contains this atom.
Hydrophobicity at a particular point of the surface of the molecule is computed as:
where HBa,aa is the hydrophobicity index of a given atom (residue) and ga is a Gaussian function centered on atom a