Here is how to select and color surface exposed residues that are hydrophobic.
Use measure sasa to define an “area” attribute of residues, then assign residue hydrophobicities from a file with the defattr command, and then use a single select command to intersect these two attributes.
In the defattr example files I already happened to include a file kdHydrophobicity.txt to assign Kyte-Doolittle hydrophobity, as well as for several other hydrophobicity scales. Just download whichever one(s) you want.
The commands could be something like:
open 6g2j measure sasa protein defattr ~/Desktop/kdHydrophobicity.txt select ::area>25 & ::kdHydrophobicity>0.0 surface protein enclose protein color sel magenta
… which looks like this …
… in pretty good agreement with MLP coloring, e.g.
mlp surfaces #1.3
In the select command you may want to experiment with the surface-area and hydrophobicity cutoffs, as well as which hydrophobicity scale you use. I didn’t try a lot of values for surface-area cutoff, but here is with all residues with values >25 colored red, reasonable at least as a first approximation:
Elaine Meng, September 7, 2020