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Re: [ccp4bb] software to calculate VDW interactions between small molecule and protein |
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- Protein crystallographyMain steps:- Protein purification- Crystallisation Special:- Programs for crystallography- X-ray detectors Basic tutorials:- Chemistry- Protein - Peptide - Amino Acids Xtal community:- CCP4BB |
CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: software to calculate VDW interactions between small molecule and protein From: lizp {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2007-02-28 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 CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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