Hi Mattias, CCP4mg will list contact areas in the form of the attached file. This is evaluating the buried area (ie difference is solvent accessible area with and without the ligand bound).
It ought to be possible to run a script if you have a significant number of structures - contact me for help there. Liz On Tuesday 27 February 2007 18:43, mathias wrote: > Dear all, > > Can anyone of you guys recommend free software, or any open access > internet server, to calculate VDW interactions of small molecules > binding to protein. The only information I need is an output file > which lists all amino acids of the target protein which make VDW > interactions with the binding small molecule. > Thank you very much for your help and recommendations, > > Mathias
Residue contact area for:/home/lizp/ccp4mg_tutorial/1df7.pdb :: All peptide Full selection command: amino_acid Solvent Accessible area by residue ---------------------------------- A/5(ILE) 8.89 A/6(TRP) 5.08 A/7(ALA) 0.61 A/20(ILE) 22.14 A/25(PRO) 10.42 A/27(ASP) 12.92 A/28(GLN) 67.26 A/29(ALA) 12.42 A/30(HIS) 0.73 A/31(PHE) 45.34 A/32(ARG) 28.13 A/46(THR) 3.44 A/49(SER) 15.28 A/50(LEU) 20.84 A/51(PRO) 19.36 A/53(LYS) 5.19 A/54(VAL) 24.08 A/57(LEU) 13.83 A/58(PRO) 1.87 A/60(ARG) 5.47 A/94(ILE) 6.73 A/111(GLU) 0.13 A/113(THR) 1.07 //500(NDP) 22.55 //502(GOL) 13.01 Solvent Accessible area by atom ------------------------------- A/5(ILE)/C 0.15 A/5(ILE)/O 2.49 A/5(ILE)/CG1 5.57 A/5(ILE)/CD1 0.69 A/6(TRP)/CA 1.89 A/6(TRP)/C 2.64 A/6(TRP)/O 0.56 A/7(ALA)/N 0.18 A/7(ALA)/CB 0.43 A/20(ILE)/CG1 0.73 A/20(ILE)/CD1 21.40 A/25(PRO)/CA 0.03 A/25(PRO)/O 5.61 A/25(PRO)/CB 4.78 A/27(ASP)/OD1 4.42 A/27(ASP)/OD2 8.50 A/28(GLN)/CA 0.40 A/28(GLN)/C 1.30 A/28(GLN)/O 4.55 A/28(GLN)/CB 6.98 A/28(GLN)/CG 8.79 A/28(GLN)/CD 4.61 A/28(GLN)/OE1 26.03 A/28(GLN)/NE2 14.61 A/29(ALA)/N 0.91 A/29(ALA)/CA 5.76 A/29(ALA)/CB 5.75 A/30(HIS)/CD2 0.73 A/31(PHE)/CA 0.00 A/31(PHE)/CB 5.01 A/31(PHE)/CG 2.65 A/31(PHE)/CD1 10.20 A/31(PHE)/CD2 10.49 A/31(PHE)/CE1 5.70 A/31(PHE)/CE2 7.06 A/31(PHE)/CZ 4.23 A/32(ARG)/CB 5.64 A/32(ARG)/CG 0.34 A/32(ARG)/CD 14.03 A/32(ARG)/NH1 8.12 A/46(THR)/CG2 3.44 A/49(SER)/O 6.04 A/49(SER)/CB 0.40 A/49(SER)/OG 8.84 A/50(LEU)/CA 0.29 A/50(LEU)/CD2 20.55 A/51(PRO)/CG 7.12 A/51(PRO)/CD 12.24 A/53(LYS)/NZ 5.19 A/54(VAL)/CG1 14.02 A/54(VAL)/CG2 10.06 A/57(LEU)/CD1 0.44 A/57(LEU)/CD2 13.39 A/58(PRO)/CG 1.31 A/58(PRO)/CD 0.56 A/60(ARG)/NH1 1.44 A/60(ARG)/NH2 4.03 A/94(ILE)/O 3.57 A/94(ILE)/CD1 3.16 A/111(GLU)/O 0.13 A/113(THR)/OG1 1.07 //500(NDP)/NO2*1.04 //500(NDP)/NC7 0.02 //500(NDP)/NO7 8.52 //500(NDP)/NC4 8.04 //500(NDP)/NC5 4.12 //500(NDP)/NC6 0.81 //502(GOL)/C1 4.27 //502(GOL)/O2 8.73 Total solvent accessible area: 366.79Angstoem*2
