Hydrophobicity is computed initially on a by-residue basis: that is, initially all atoms in each residue are assigned a score representing the hydrophobicity value for that residue type, taken from a standard table of free energies of transfer from water to organic solvent (Fauchere, J.L. & Pliska, V. (1983), Eur. J. Med. Chem.-Chem. Ther. 18, 369.) Positive is hydrophobic, negative is hydrophilic.

After this, the hydrophobicity value for each atom is smoothed out in space by replacing it with a weighted average of the values of its exposed neighboring atoms within a sphere of radius 9.0Å. Thus, different atoms in the same residue are assigned different values after smoothing. Buried atoms get zero values.