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