Open Pymol and load up your protein of choice. Download color_h.py which is a script from the University of Osaka that colours the residues according to Eisenberg's scale of hydrophobicity. Load this into Pymol by File->Run->PATH/TO/color_h.py. Then in Pymol run the following commands:
show surface
color_h
# color_h # ------- # PyMOL command to color protein molecules according to the Eisenberg hydrophobicity scale # # Source: http://us.expasy.org/tools/pscale/Hphob.Eisenberg.html # Amino acid scale: Normalized consensus hydrophobicity scale # Author(s): Eisenberg D., Schwarz E., Komarony M., Wall R. # Reference: J. Mol. Biol. 179:125-142 (1984) # https://protein-sol.manchester.ac.uk/ # https://www.nature.com/articles/s41598-018-36950-8 # Amino acid scale values: # # Ile: 1.38 [0.996,0.062,0.062] # Phe: 1.19 [0.996,0.109,0.109] # Val: 1.08 [0.992,0.156,0.156] # Leu: 1.06 [0.992,0.207,0.207] # Trp: 0.81 [0.992,0.254,0.254] # Met: 0.64 [0.988,0.301,0.301] # Ala: 0.62 [0.988,0.348,0.348] # Gly: 0.48 [0.984,0.394,0.394] # Cys: 0.29 [0.984,0.445,0.445] # Tyr: 0.26 [0.984,0.492,0.492] # Pro: 0.12 [0.980,0.539,0.539] # Thr: -0.05 [0.980,0.586,0.586] # Ser: -0.18 [0.980,0.637,0.637] # His: -0.4 [0.977,0.684,0.684] # Glu: -0.74 [0.977,0.730,0.730] # Asn: -0.78 [0.973,0.777,0.777] # Gln: -0.85 [0.973,0.824,0.824] # Asp: -0.9 [0.973,0.875,0.875] # Lys: -1.5 [0.899,0.922,0.922] # Arg: -2.53 [0.899,0.969,0.969] # # load https://shaker.umh.es/computing/hydrophobic.pdb # extract ligand, organic # show surface # File->Run->PATH/TO/color_h.py # color_h # ramp_new prox, ligand, [1.38, 1.19, 1.08, 1.06, 0.81, 0.64, 0.62, 0.48, 0.29, 0.26, 0.12, -0.05, -0.18, -0.4, -0.74, -0.78, -0.85, -0.9, -1.5, -2.53], [[0.996,0.062,0.062], [0.996,0.109,0.109], [0.992,0.156,0.156], [0.992,0.207,0.207], [0.992,0.254,0.254], [0.988,0.301,0.301], [0.988,0.348,0.348], [0.984,0.394,0.394], [0.984,0.445,0.445], [0.984,0.492,0.492], [0.980,0.539,0.539], [0.980,0.586,0.586], [0.980,0.637,0.637], [0.977,0.684,0.684], [0.977,0.730,0.730], [0.973,0.777,0.777], [0.973,0.824,0.824], [0.973,0.875,0.875], [0.899,0.922,0.922], [0.899,0.969,0.969]] # # Usage: # color_h (selection) # from pymol import cmd def color_h(selection='all'): s = str(selection) print s cmd.set_color('color_ile',[0.996,0.062,0.062]) cmd.set_color('color_phe',[0.996,0.109,0.109]) cmd.set_color('color_val',[0.992,0.156,0.156]) cmd.set_color('color_leu',[0.992,0.207,0.207]) cmd.set_color('color_trp',[0.992,0.254,0.254]) cmd.set_color('color_met',[0.988,0.301,0.301]) cmd.set_color('color_ala',[0.988,0.348,0.348]) cmd.set_color('color_gly',[0.984,0.394,0.394]) cmd.set_color('color_cys',[0.984,0.445,0.445]) cmd.set_color('color_tyr',[0.984,0.492,0.492]) cmd.set_color('color_pro',[0.980,0.539,0.539]) cmd.set_color('color_thr',[0.980,0.586,0.586]) cmd.set_color('color_ser',[0.980,0.637,0.637]) cmd.set_color('color_his',[0.977,0.684,0.684]) cmd.set_color('color_glu',[0.977,0.730,0.730]) cmd.set_color('color_asn',[0.973,0.777,0.777]) cmd.set_color('color_gln',[0.973,0.824,0.824]) cmd.set_color('color_asp',[0.973,0.875,0.875]) cmd.set_color('color_lys',[0.899,0.922,0.922]) cmd.set_color('color_arg',[0.899,0.969,0.969]) cmd.color("color_ile","("+s+" and resn ile)") cmd.color("color_phe","("+s+" and resn phe)") cmd.color("color_val","("+s+" and resn val)") cmd.color("color_leu","("+s+" and resn leu)") cmd.color("color_trp","("+s+" and resn trp)") cmd.color("color_met","("+s+" and resn met)") cmd.color("color_ala","("+s+" and resn ala)") cmd.color("color_gly","("+s+" and resn gly)") cmd.color("color_cys","("+s+" and resn cys)") cmd.color("color_tyr","("+s+" and resn tyr)") cmd.color("color_pro","("+s+" and resn pro)") cmd.color("color_thr","("+s+" and resn thr)") cmd.color("color_ser","("+s+" and resn ser)") cmd.color("color_his","("+s+" and resn his)") cmd.color("color_glu","("+s+" and resn glu)") cmd.color("color_asn","("+s+" and resn asn)") cmd.color("color_gln","("+s+" and resn gln)") cmd.color("color_asp","("+s+" and resn asp)") cmd.color("color_lys","("+s+" and resn lys)") cmd.color("color_arg","("+s+" and resn arg)") cmd.extend('color_h',color_h) def color_h2(selection='all'): s = str(selection) print s cmd.set_color("color_ile2",[0.938,1,0.938]) cmd.set_color("color_phe2",[0.891,1,0.891]) cmd.set_color("color_val2",[0.844,1,0.844]) cmd.set_color("color_leu2",[0.793,1,0.793]) cmd.set_color("color_trp2",[0.746,1,0.746]) cmd.set_color("color_met2",[0.699,1,0.699]) cmd.set_color("color_ala2",[0.652,1,0.652]) cmd.set_color("color_gly2",[0.606,1,0.606]) cmd.set_color("color_cys2",[0.555,1,0.555]) cmd.set_color("color_tyr2",[0.508,1,0.508]) cmd.set_color("color_pro2",[0.461,1,0.461]) cmd.set_color("color_thr2",[0.414,1,0.414]) cmd.set_color("color_ser2",[0.363,1,0.363]) cmd.set_color("color_his2",[0.316,1,0.316]) cmd.set_color("color_glu2",[0.27,1,0.27]) cmd.set_color("color_asn2",[0.223,1,0.223]) cmd.set_color("color_gln2",[0.176,1,0.176]) cmd.set_color("color_asp2",[0.125,1,0.125]) cmd.set_color("color_lys2",[0.078,1,0.078]) cmd.set_color("color_arg2",[0.031,1,0.031]) cmd.color("color_ile2","("+s+" and resn ile)") cmd.color("color_phe2","("+s+" and resn phe)") cmd.color("color_val2","("+s+" and resn val)") cmd.color("color_leu2","("+s+" and resn leu)") cmd.color("color_trp2","("+s+" and resn trp)") cmd.color("color_met2","("+s+" and resn met)") cmd.color("color_ala2","("+s+" and resn ala)") cmd.color("color_gly2","("+s+" and resn gly)") cmd.color("color_cys2","("+s+" and resn cys)") cmd.color("color_tyr2","("+s+" and resn tyr)") cmd.color("color_pro2","("+s+" and resn pro)") cmd.color("color_thr2","("+s+" and resn thr)") cmd.color("color_ser2","("+s+" and resn ser)") cmd.color("color_his2","("+s+" and resn his)") cmd.color("color_glu2","("+s+" and resn glu)") cmd.color("color_asn2","("+s+" and resn asn)") cmd.color("color_gln2","("+s+" and resn gln)") cmd.color("color_asp2","("+s+" and resn asp)") cmd.color("color_lys2","("+s+" and resn lys)") cmd.color("color_arg2","("+s+" and resn arg)") cmd.extend('color_h2',color_h2)