# Configuration file for minimal Superstar functionality. # # The only probes that are used are # N-H as a universal hydrogen bond donor and # O=C as a universal hydrogen bond acceptor. # # The mapping of scatter plots to aminoacids are done # explicitly. This makes it very simple to apply the # scatter plots to the protein structures. # # The format of the file is # # group.n = group_name # group_name.istr = filename # group_name.type = donor/acceptor # group_name.0 = pdb_atom0,scatter_plot_atom0 # group_name... = ..... # group_name.i = pdb_atomi,scatter_plot_atomi # # The mappings must start at 0 and run to the # maximum number of mappings. # # The first pdb_atom specifier must include a # residue specifier followed by a '.'. # This ties the atoms to a particular residue. # For the peptide groups '*' can be used to indicate # any residue (although really this should be # any residue except proline). # # The .istr property describes the name of the .istr # file that contains the scatter plot for that group. # This will be symmetry expanded and the hetero atoms # within vdw radius of any of the fitting atoms will # be added to the plot. # # The .type property describes whether these atoms are # donors or acceptors. In fact the type can be an # arbitrary string and serves to group the different # types together within molecules in the generation # process. # # The radii for the different element types are # specified at the end of the file. # # radius.n = r # # Where n is the atomic number of the element and # r is its radius. # # The setting rmsd.warning indicates the threshold # for printing out the rmsd of the fragment fitting. # This is just information that may indicate poor # geometry of a particular group. # # The setting rmsd.fail indicates the threshold above # which a fitting is deemed to have failed. In this # case no points will be added to the scatter plot. # This may happen for peptides due to a chain break, # or due to very poor geometry of other groups. It is # used to identify the mislabelling of ARG guanidino # groups (see below). They will generate a rmsd after # fitting of ~0.7A if the NH1 and NH2 atoms are # mislabelled. There is an alternate definition that # will match in these cases. # # Mike Hartshorn, Marcel Verdonk # Copyright (C) Astex Technology Ltd., 2004 group.0 = peptide_NH peptide_NH.istr = data/superstar/pdb0284_1_03.istr.properties peptide_NH.type = donor peptide_NH.0 = *.O,5 peptide_NH.1 = N+,4 peptide_NH.2 = C,3 group.1 = peptide_CO peptide_CO.istr = data/superstar/pdb0284_1_11.istr.properties peptide_CO.type = acceptor peptide_CO.0 = *.N,4 peptide_CO.1 = C-,3 peptide_CO.2 = O-,5 group.2 = ASP_carboxylate_NH #ASP_carboxylate_NH.istr = data/superstar/pdb0273_03.istr.properties ASP_carboxylate_NH.istr = data/superstar/csd0273_03.istr.properties ASP_carboxylate_NH.type = donor ASP_carboxylate_NH.0 = ASP.CG,2 ASP_carboxylate_NH.1 = OD1,3 ASP_carboxylate_NH.2 = OD2,4 group.3 = GLU_carboxylate_NH #GLU_carboxylate_NH.istr = data/superstar/pdb0273_03.istr.properties GLU_carboxylate_NH.istr = data/superstar/csd0273_03.istr.properties GLU_carboxylate_NH.type = donor GLU_carboxylate_NH.0 = GLU.CD,2 GLU_carboxylate_NH.1 = OE1,3 GLU_carboxylate_NH.2 = OE2,4 group.4 = TER_carboxylate_NH #TER_carboxylate_NH.istr = data/superstar/pdb0273_03.istr.properties TER_carboxylate_NH.istr = data/superstar/csd0273_03.istr.properties TER_carboxylate_NH.type = donor TER_carboxylate_NH.0 = *.OXT,3 TER_carboxylate_NH.1 = O,4 TER_carboxylate_NH.2 = C,2 group.5 = ASN_carbamoyl_NH #ASN_carbamoyl_NH.istr = data/superstar/pdb0272_03.istr.properties ASN_carbamoyl_NH.istr = data/superstar/csd0272_03.istr.properties ASN_carbamoyl_NH.type = donor ASN_carbamoyl_NH.0 = ASN.CG,2 ASN_carbamoyl_NH.1 = OD1,3 ASN_carbamoyl_NH.2 = ND2,4 group.6 = GLN_carbamoyl_NH #GLN_carbamoyl_NH.istr = data/superstar/pdb0272_03.istr.properties GLN_carbamoyl_NH.istr = data/superstar/csd0272_03.istr.properties GLN_carbamoyl_NH.type = donor GLN_carbamoyl_NH.0 = GLN.CD,2 GLN_carbamoyl_NH.1 = OE1,3 GLN_carbamoyl_NH.2 = NE2,4 group.7 = ASN_carbamoyl_CO #ASN_carbamoyl_CO.istr = data/superstar/pdb0272_11.istr.properties ASN_carbamoyl_CO.istr = data/superstar/csd0272_11.istr.properties ASN_carbamoyl_CO.type = acceptor ASN_carbamoyl_CO.0 = ASN.CG,2 ASN_carbamoyl_CO.1 = OD1,3 ASN_carbamoyl_CO.2 = ND2,4 group.8 = GLN_carbamoyl_CO #GLN_carbamoyl_CO.istr = data/superstar/pdb0272_11.istr.properties GLN_carbamoyl_CO.istr = data/superstar/csd0272_11.istr.properties GLN_carbamoyl_CO.type = acceptor GLN_carbamoyl_CO.0 = GLN.CD,2 GLN_carbamoyl_CO.1 = OE1,3 GLN_carbamoyl_CO.2 = NE2,4 # The usual convention for ARG gaunidino groups # is that CD is cis to NH1. # # Sometimes this is not the case in the structure # and you find that CD is cis to NH2 instead # # ARG_guanidino_COa describes the usual case. If # they are the other way round the RMSD will be # about 0.7 which will fail the RMSD test. # In this case the rule ARG_guanidino_COb should # match instead. group.9 = ARG_guanidino_COa ARG_guanidino_COa.istr = data/superstar/pdb0275_1_11.istr.properties ARG_guanidino_COa.type = acceptor ARG_guanidino_COa.0 = ARG.CD,1 ARG_guanidino_COa.1 = NE,2 ARG_guanidino_COa.2 = CZ,3 ARG_guanidino_COa.3 = NH2,4 ARG_guanidino_COa.4 = NH1,5 # Alternative stereoisomerism for ARG guanidino group.10 = ARG_guanidino_COb ARG_guanidino_COb.istr = data/superstar/pdb0275_1_11.istr.properties ARG_guanidino_COb.type = acceptor ARG_guanidino_COb.0 = ARG.CD,1 ARG_guanidino_COb.1 = NE,2 ARG_guanidino_COb.2 = CZ,3 ARG_guanidino_COb.3 = NH2,5 ARG_guanidino_COb.4 = NH1,4 group.11 = SER_hydroxyl_NH SER_hydroxyl_NH.istr = data/superstar/pdb0276_03.istr.properties SER_hydroxyl_NH.type = donor SER_hydroxyl_NH.scale = 1.5 SER_hydroxyl_NH.0 = SER.CA,1 SER_hydroxyl_NH.1 = CB,2 SER_hydroxyl_NH.2 = OG,3 group.12 = SER_hydroxyl_CO SER_hydroxyl_CO.istr = data/superstar/pdb0276_11.istr.properties SER_hydroxyl_CO.type = acceptor SER_hydroxyl_CO.scale = 3.0 SER_hydroxyl_CO.0 = SER.CA,1 SER_hydroxyl_CO.1 = CB,2 SER_hydroxyl_CO.2 = OG,3 group.13 = THR_hydroxyl_NH THR_hydroxyl_NH.istr = data/superstar/pdb0276_03.istr.properties THR_hydroxyl_NH.type = donor THR_hydroxyl_NH.scale = 1.5 THR_hydroxyl_NH.0 = THR.CA,1 THR_hydroxyl_NH.1 = CB,2 THR_hydroxyl_NH.2 = OG1,3 group.14 = THR_hydroxyl_CO THR_hydroxyl_CO.istr = data/superstar/pdb0276_11.istr.properties THR_hydroxyl_CO.type = acceptor THR_hydroxyl_CO.scale = 3.0 THR_hydroxyl_CO.0 = THR.CA,1 THR_hydroxyl_CO.1 = CB,2 THR_hydroxyl_CO.2 = OG1,3 group.15 = TYR_hydroxyl_NH TYR_hydroxyl_NH.istr = data/superstar/pdb0304_03.istr.properties TYR_hydroxyl_NH.type = donor TYR_hydroxyl_NH.scale = 2.0 TYR_hydroxyl_NH.0 = TYR.CE1,1 TYR_hydroxyl_NH.1 = CE2,2 TYR_hydroxyl_NH.2 = CZ,3 TYR_hydroxyl_NH.3 = OH,4 group.16 = TYR_hydroxyl_CO TYR_hydroxyl_CO.istr = data/superstar/pdb0304_11.istr.properties TYR_hydroxyl_CO.type = acceptor TYR_hydroxyl_CO.scale = 2.0 TYR_hydroxyl_CO.0 = TYR.CE1,1 TYR_hydroxyl_CO.1 = CE2,2 TYR_hydroxyl_CO.2 = CZ,3 TYR_hydroxyl_CO.3 = OH,4 group.17 = TRP_hydroxyl_CO TRP_hydroxyl_CO.istr = data/superstar/pdb0305_11.istr.properties TRP_hydroxyl_CO.type = acceptor TRP_hydroxyl_CO.0 = TRP.CD1,1 TRP_hydroxyl_CO.1 = CE2,2 TRP_hydroxyl_CO.2 = NE1,3 group.18 = LYS_amino_CO LYS_amino_CO.istr = data/superstar/pdb0270_11.istr.properties LYS_amino_CO.type = acceptor LYS_amino_CO.0 = LYS.CD,1 LYS_amino_CO.1 = CE,2 LYS_amino_CO.2 = NZ,3 # not much data group.19 = MET_thioether_NH MET_thioether_NH.istr = data/superstar/pdb0308_03.istr.properties MET_thioether_NH.type = donor MET_thioether_NH.0 = MET.CG,1 MET_thioether_NH.1 = CE,2 MET_thioether_NH.2 = SD,3 group.20 = HIS_telen_CO HIS_telen_CO.istr = data/superstar/pdb0307_11.istr.properties HIS_telen_CO.type = acceptor HIS_telen_CO.0 = HIS.CD2,1 HIS_telen_CO.1 = CE1,2 HIS_telen_CO.2 = NE2,3 group.21 = HIS_pron_CO HIS_pron_CO.istr = data/superstar/pdb0306_11.istr.properties HIS_pron_CO.type = acceptor HIS_pron_CO.0 = HIS.CG,1 HIS_pron_CO.1 = CE1,2 HIS_pron_CO.2 = ND1,3 group.22 = HIS_telen_NH HIS_telen_NH.istr = data/superstar/pdb0307_03.istr.properties HIS_telen_NH.type = donor HIS_telen_NH.0 = HIS.CD2,1 HIS_telen_NH.1 = CE1,2 HIS_telen_NH.2 = NE2,3 group.23 = HIS_pron_NH HIS_pron_NH.istr = data/superstar/pdb0306_03.istr.properties HIS_pron_NH.type = donor HIS_pron_NH.0 = HIS.CG,1 HIS_pron_NH.1 = CE1,2 HIS_pron_NH.2 = ND1,3 # lipophilic interactions # # aliphatic # # methyl C.3 interactions group.224 = ALA_CB_C ALA_CB_C.istr = data/superstar/pdb0280_19.istr.properties ALA_CB_C.type = lipo_ali ALA_CB_C.0 = ALA.CB,3 ALA_CB_C.1 = CA,2 ALA_CB_C.2 = C,1 group.225 = VAL_CG1_C VAL_CG1_C.istr = data/superstar/pdb0280_19.istr.properties VAL_CG1_C.type = lipo_ali VAL_CG1_C.0 = VAL.CG1,3 VAL_CG1_C.1 = CB,2 VAL_CG1_C.2 = CA,1 group.226 = VAL_CG2_C VAL_CG2_C.istr = data/superstar/pdb0280_19.istr.properties VAL_CG2_C.type = lipo_ali VAL_CG2_C.0 = VAL.CG2,3 VAL_CG2_C.1 = CB,2 VAL_CG2_C.2 = CA,1 group.227 = ILE_CD1_C ILE_CD1_C.istr = data/superstar/pdb0280_19.istr.properties ILE_CD1_C.type = lipo_ali ILE_CD1_C.0 = ILE.CD1,3 ILE_CD1_C.1 = CG1,2 ILE_CD1_C.2 = CB,1 group.228 = ILE_CG2_C ILE_CG2_C.istr = data/superstar/pdb0280_19.istr.properties ILE_CG2_C.type = lipo_ali ILE_CG2_C.0 = ILE.CG2,3 ILE_CG2_C.1 = CB,2 ILE_CG2_C.2 = CA,1 # CD is actually CD1 in pdb files group.229 = LEU_CD1_C LEU_CD1_C.istr = data/superstar/pdb0280_19.istr.properties LEU_CD1_C.type = lipo_ali LEU_CD1_C.0 = LEU.CD1,3 LEU_CD1_C.1 = CG,2 LEU_CD1_C.2 = CD2,1 group.230 = LEU_CD2_C LEU_CD2_C.istr = data/superstar/pdb0280_19.istr.properties LEU_CD2_C.type = lipo_ali LEU_CD2_C.0 = LEU.CD2,3 LEU_CD2_C.1 = CG,2 LEU_CD2_C.2 = CD1,1 group.231 = THR_CG2_C THR_CG2_C.istr = data/superstar/pdb0280_19.istr.properties THR_CG2_C.type = lipo_ali THR_CG2_C.0 = THR.CG2,3 THR_CG2_C.1 = CB,2 THR_CG2_C.2 = CA,1 # methylene C.3 interactions group.231 = ILE_CG1_C ILE_CG1_C.istr = data/superstar/pdb0302_19.istr.properties ILE_CG1_C.type = lipo_ali ILE_CG1_C.0 = ILE.CG1,3 ILE_CG1_C.1 = CD1,2 ILE_CG1_C.2 = CB,1 group.232 = LEU_CB_C LEU_CB_C.istr = data/superstar/pdb0302_19.istr.properties LEU_CB_C.type = lipo_ali LEU_CB_C.0 = LEU.CB,3 LEU_CB_C.1 = CG,2 LEU_CB_C.2 = CA,1 group.233 = PHE_CB_C PHE_CB_C.istr = data/superstar/pdb0302_19.istr.properties PHE_CB_C.type = lipo_ali PHE_CB_C.0 = PHE.CB,3 PHE_CB_C.1 = CG,2 PHE_CB_C.2 = CA,1 group.234 = PRO_CB_C PRO_CB_C.istr = data/superstar/pdb0302_19.istr.properties PRO_CB_C.type = lipo_ali PRO_CB_C.0 = PRO.CB,3 PRO_CB_C.1 = CG,2 PRO_CB_C.2 = CA,1 group.235 = PRO_CG_C PRO_CG_C.istr = data/superstar/pdb0302_19.istr.properties PRO_CG_C.type = lipo_ali PRO_CG_C.0 = PRO.CG,3 PRO_CG_C.1 = CD,2 PRO_CG_C.2 = CB,1 group.236 = PRO_CD_C PRO_CD_C.istr = data/superstar/pdb0302_19.istr.properties PRO_CD_C.type = lipo_ali PRO_CD_C.0 = PRO.CD,3 PRO_CD_C.1 = N,2 PRO_CD_C.2 = CG,1 group.237 = MET_CB_C MET_CB_C.istr = data/superstar/pdb0302_19.istr.properties MET_CB_C.type = lipo_ali MET_CB_C.0 = MET.CB,3 MET_CB_C.1 = CG,2 MET_CB_C.2 = CA,1 # is this right for met cg? what about the sulphur? group.238 = MET_CG_C MET_CG_C.istr = data/superstar/pdb0302_19.istr.properties MET_CG_C.type = lipo_ali MET_CG_C.0 = MET.CG,3 MET_CG_C.1 = SD,2 MET_CG_C.2 = CB,1 group.239 = TRP_CB_C TRP_CB_C.istr = data/superstar/pdb0302_19.istr.properties TRP_CB_C.type = lipo_ali TRP_CB_C.0 = TRP.CB,3 TRP_CB_C.1 = CG,2 TRP_CB_C.2 = CA,1 group.240 = CYS_CB_C CYS_CB_C.istr = data/superstar/pdb0302_19.istr.properties CYS_CB_C.type = lipo_ali CYS_CB_C.0 = CYS.CB,3 CYS_CB_C.1 = SG,2 CYS_CB_C.2 = CA,1 group.241 = SER_CB_C SER_CB_C.istr = data/superstar/pdb0302_19.istr.properties SER_CB_C.type = lipo_ali SER_CB_C.0 = SER.CB,3 SER_CB_C.1 = OG,2 SER_CB_C.2 = CA,1 group.242 = ASN_CB_C ASN_CB_C.istr = data/superstar/pdb0302_19.istr.properties ASN_CB_C.type = lipo_ali ASN_CB_C.0 = ASN.CB,3 ASN_CB_C.1 = CG,2 ASN_CB_C.2 = CA,1 group.243 = GLN_CB_C GLN_CB_C.istr = data/superstar/pdb0302_19.istr.properties GLN_CB_C.type = lipo_ali GLN_CB_C.0 = GLN.CB,3 GLN_CB_C.1 = CG,2 GLN_CB_C.2 = CA,1 group.244 = GLN_CG_C GLN_CG_C.istr = data/superstar/pdb0302_19.istr.properties GLN_CG_C.type = lipo_ali GLN_CG_C.0 = GLN.CG,3 GLN_CG_C.1 = CD,2 GLN_CG_C.2 = CB,1 group.245 = TYR_CB_C TYR_CB_C.istr = data/superstar/pdb0302_19.istr.properties TYR_CB_C.type = lipo_ali TYR_CB_C.0 = TYR.CB,3 TYR_CB_C.1 = CG,2 TYR_CB_C.2 = CA,1 group.246 = HIS_CB_C HIS_CB_C.istr = data/superstar/pdb0302_19.istr.properties HIS_CB_C.type = lipo_ali HIS_CB_C.0 = HIS.CB,3 HIS_CB_C.1 = CG,2 HIS_CB_C.2 = CA,1 group.247 = ASP_CB_C ASP_CB_C.istr = data/superstar/pdb0302_19.istr.properties ASP_CB_C.type = lipo_ali ASP_CB_C.0 = ASP.CB,3 ASP_CB_C.1 = CG,2 ASP_CB_C.2 = CA,1 group.248 = GLU_CB_C GLU_CB_C.istr = data/superstar/pdb0302_19.istr.properties GLU_CB_C.type = lipo_ali GLU_CB_C.0 = GLU.CB,3 GLU_CB_C.1 = CG,2 GLU_CB_C.2 = CA,1 group.249 = GLU_CG_C GLU_CG_C.istr = data/superstar/pdb0302_19.istr.properties GLU_CG_C.type = lipo_ali GLU_CG_C.0 = GLU.CG,3 GLU_CG_C.1 = CD,2 GLU_CG_C.2 = CB,1 group.250 = LYS_CB_C LYS_CB_C.istr = data/superstar/pdb0302_19.istr.properties LYS_CB_C.type = lipo_ali LYS_CB_C.0 = LYS.CB,3 LYS_CB_C.1 = CG,2 LYS_CB_C.2 = CA,1 group.251 = ARG_CB_C ARG_CB_C.istr = data/superstar/pdb0302_19.istr.properties ARG_CB_C.type = lipo_ali ARG_CB_C.0 = ARG.CB,3 ARG_CB_C.1 = CG,2 ARG_CB_C.2 = CA,1 group.252 = LYS_CG_C LYS_CG_C.istr = data/superstar/pdb0302_19.istr.properties LYS_CG_C.type = lipo_ali LYS_CG_C.0 = LYS.CG,3 LYS_CG_C.1 = CD,2 LYS_CG_C.2 = CB,1 group.253 = ARG_CG_C ARG_CG_C.istr = data/superstar/pdb0302_19.istr.properties ARG_CG_C.type = lipo_ali ARG_CG_C.0 = ARG.CG,3 ARG_CG_C.1 = CD,2 ARG_CG_C.2 = CB,1 group.254 = LYS_CD_C LYS_CD_C.istr = data/superstar/pdb0302_19.istr.properties LYS_CD_C.type = lipo_ali LYS_CD_C.0 = LYS.CD,3 LYS_CD_C.1 = CE,2 LYS_CD_C.2 = CG,1 group.255 = ARG_CD_C ARG_CD_C.istr = data/superstar/pdb0302_19.istr.properties ARG_CD_C.type = lipo_ali ARG_CD_C.0 = ARG.CD,3 ARG_CD_C.1 = NE,2 ARG_CD_C.2 = CG,1 group.256 = GLY_CA_C GLY_CA_C.istr = data/superstar/pdb0302_19.istr.properties GLY_CA_C.type = lipo_ali GLY_CA_C.0 = GLY.CA,3 GLY_CA_C.1 = N,2 GLY_CA_C.2 = C,1 # tertiary CH # CA rule. will fail for glycine currently # but this has its own rule in the previous # section of methylene carbons group.257 = ANY_CA_C ANY_CA_C.istr = data/superstar/pdb0294_19.istr.properties ANY_CA_C.type = lipo_ali ANY_CA_C.0 = *.CA,4 ANY_CA_C.1 = N,1 ANY_CA_C.2 = C,2 ANY_CA_C.3 = CB,3 # this seems to be the correct orientation for VAL # Schulz and Schirmer has it the other way around... group.258 = VAL_CB_C VAL_CB_C.istr = data/superstar/pdb0294_19.istr.properties VAL_CB_C.type = lipo_ali VAL_CB_C.0 = VAL.CB,4 VAL_CB_C.1 = CA,1 VAL_CB_C.2 = CG2,2 VAL_CB_C.3 = CG1,3 group.259 = ILE_CB_C ILE_CB_C.istr = data/superstar/pdb0294_19.istr.properties ILE_CB_C.type = lipo_ali ILE_CB_C.0 = ILE.CB,4 ILE_CB_C.1 = CA,1 ILE_CB_C.2 = CG1,2 ILE_CB_C.3 = CG2,3 group.260 = LEU_CG_C LEU_CG_C.istr = data/superstar/pdb0294_19.istr.properties LEU_CG_C.type = lipo_ali LEU_CG_C.0 = LEU.CG,4 LEU_CG_C.1 = CB,1 LEU_CG_C.2 = CD2,2 LEU_CG_C.3 = CD1,3 group.261 = THR_CB_C THR_CB_C.istr = data/superstar/pdb0294_19.istr.properties THR_CB_C.type = lipo_ali THR_CB_C.0 = THR.CB,4 THR_CB_C.1 = CA,1 THR_CB_C.2 = OG1,3 THR_CB_C.3 = CG2,2 # sulphur group.261 = MET_SD_C MET_SD_C.istr = data/superstar/pdb0308_19.istr.properties MET_SD_C.type = lipo_ali MET_SD_C.0 = MET.SD,3 MET_SD_C.1 = CG,1 MET_SD_C.2 = CE,2 # # Start of marcels definitions for the remainder of # the aliphatic interaction maps # group.200 = ARG_guanidino_Ca ARG_guanidino_Ca.istr = data/superstar/pdb0275_1_19.istr.properties ARG_guanidino_Ca.type = lipo_ali ARG_guanidino_Ca.0 = ARG.CD,1 ARG_guanidino_Ca.1 = NE,2 ARG_guanidino_Ca.2 = CZ,3 ARG_guanidino_Ca.3 = NH2,4 ARG_guanidino_Ca.4 = NH1,5 group.201 = ARG_guanidino_Cb ARG_guanidino_Cb.istr = data/superstar/pdb0275_1_19.istr.properties ARG_guanidino_Cb.type = lipo_ali ARG_guanidino_Cb.0 = ARG.CD,1 ARG_guanidino_Cb.1 = NE,2 ARG_guanidino_Cb.2 = CZ,3 ARG_guanidino_Cb.3 = NH2,5 ARG_guanidino_Cb.4 = NH1,4 group.202 = HIS_telen_C HIS_telen_C.istr = data/superstar/pdb0307_19.istr.properties HIS_telen_C.type = lipo_ali HIS_telen_C.0 = HIS.CD2,1 HIS_telen_C.1 = CE1,2 HIS_telen_C.2 = NE2,3 group.203 = HIS_pron_C HIS_pron_C.istr = data/superstar/pdb0306_19.istr.properties HIS_pron_C.type = lipo_ali HIS_pron_C.0 = HIS.CG,1 HIS_pron_C.1 = CE1,2 HIS_pron_C.2 = ND1,3 group.204 = HIS_telec_C HIS_telec_C.istr = data/superstar/pdb0310_19.istr.properties HIS_telec_C.type = lipo_ali HIS_telec_C.0 = HIS.CE1,3 HIS_telec_C.1 = ND1,1 HIS_telec_C.2 = NE2,2 group.205 = HIS_proc_C HIS_proc_C.istr = data/superstar/pdb0310_19.istr.properties HIS_proc_C.type = lipo_ali HIS_proc_C.0 = HIS.CD2,3 HIS_proc_C.1 = CG,1 HIS_proc_C.2 = NE2,2 group.206 = HIS_CG_C HIS_CG_C.istr = data/superstar/pdb0293_19.istr.properties HIS_CG_C.type = lipo_ali HIS_CG_C.0 = HIS.CG,4 HIS_CG_C.1 = ND1,1 HIS_CG_C.2 = CD2,2 HIS_CG_C.3 = CB,3 group.207 = TYR_phe_C TYR_phe_C.istr = data/superstar/pdb0290_19.istr.properties TYR_phe_C.type = lipo_ali TYR_phe_C.0 = TYR.CB,1 TYR_phe_C.1 = CG,5 TYR_phe_C.2 = CD1,6 TYR_phe_C.3 = CE1,7 TYR_phe_C.4 = CZ,2 TYR_phe_C.5 = CE2,3 TYR_phe_C.6 = CD2,4 group.208 = PHE_phe_C PHE_phe_C.istr = data/superstar/pdb0290_19.istr.properties PHE_phe_C.type = lipo_ali PHE_phe_C.0 = PHE.CB,1 PHE_phe_C.1 = CG,5 PHE_phe_C.2 = CD1,6 PHE_phe_C.3 = CE1,7 PHE_phe_C.4 = CZ,2 PHE_phe_C.5 = CE2,3 PHE_phe_C.6 = CD2,4 group.209 = TRP_phe_C TRP_phe_C.istr = data/superstar/pdb0290_19.istr.properties TRP_phe_C.type = lipo_ali TRP_phe_C.0 = TRP.CG,1 TRP_phe_C.1 = CD2,5 TRP_phe_C.2 = CE2,6 TRP_phe_C.3 = CZ2,7 TRP_phe_C.4 = CH2,2 TRP_phe_C.5 = CZ3,3 TRP_phe_C.6 = CE3,4 group.210 = TRP_CG_C TRP_CG_C.istr = data/superstar/pdb0293_19.istr.properties TRP_CG_C.type = lipo_ali TRP_CG_C.0 = TRP.CG,4 TRP_CG_C.1 = CD1,1 TRP_CG_C.2 = CD2,2 TRP_CG_C.3 = CB,3 group.211 = TRP_CD1_C TRP_CD1_C.istr = data/superstar/pdb0310_19.istr.properties TRP_CD1_C.type = lipo_ali TRP_CD1_C.0 = TRP.CD1,3 TRP_CD1_C.1 = CG,1 TRP_CD1_C.2 = NE1,2 group.212 = TRP_NE1_C TRP_NE1_C.istr = data/superstar/pdb0305_19.istr.properties TRP_NE1_C.type = lipo_ali TRP_NE1_C.0 = TRP.NE1,3 TRP_NE1_C.1 = CD1,1 TRP_NE1_C.2 = CE2,2 # carboxyl and carbomoyl lipophilic definitions #group.213 = peptide_C peptide_C.istr = data/superstar/pdb0284_1_19.istr.properties peptide_C.type = lipo_ali peptide_C.0 = *.O,5 peptide_C.1 = N+,4 peptide_C.2 = C,3 #group.214 = ASN_carbamoyl_C ASN_carbamoyl_C.istr = data/superstar/csd0272_19.istr.properties ASN_carbamoyl_C.type = lipo_ali ASN_carbamoyl_C.0 = ASN.CG,2 ASN_carbamoyl_C.1 = OD1,3 ASN_carbamoyl_C.2 = ND2,4 #group.215 = GLN_carbamoyl_C GLN_carbamoyl_C.istr = data/superstar/csd0272_19.istr.properties GLN_carbamoyl_C.type = lipo_ali GLN_carbamoyl_C.0 = GLN.CD,2 GLN_carbamoyl_C.1 = OE1,3 GLN_carbamoyl_C.2 = NE2,4 # VDW radii used for screening contact distances # Hydrogen radius.1 = 1.20 # Carbon radius.6 = 1.70 # Nitrogen radius.7 = 1.55 # Oxygen radius.8 = 1.52 # Phosphorous (not used in proteins) radius.15 = 1.80 # Sulphur radius.16 = 1.80 # Radius offset for checking proximity to central groups radius.offset = 0.5 # Maximum penetration distance for non-central group atoms radius.dtol = 0.4 # Level at which we warn about fitting RMSD rmsd.warning = 0.2 # Level at which we say fit has failed rmsd.fail = 0.5 # aromatic lipophile settings # not currently used as they are very similar to # aliphatic lipophile maps # aromatic # methyl C.3 interactions # ##group.24 = ALA_CB_c #ALA_CB_c.istr = data/superstar/pdb0280_20.istr.properties #ALA_CB_c.type = lipo_aro #ALA_CB_c.0 = ALA.CB,3 #ALA_CB_c.1 = CA,2 #ALA_CB_c.2 = C,1 # ##group.25 = VAL_CG1_c #VAL_CG1_c.istr = data/superstar/pdb0280_20.istr.properties #VAL_CG1_c.type = lipo_aro #VAL_CG1_c.0 = VAL.CG1,3 #VAL_CG1_c.1 = CB,2 #VAL_CG1_c.2 = CA,1 # ##group.26 = VAL_CG2_c #VAL_CG2_c.istr = data/superstar/pdb0280_20.istr.properties #VAL_CG2_c.type = lipo_aro #VAL_CG2_c.0 = VAL.CG2,3 #VAL_CG2_c.1 = CB,2 #VAL_CG2_c.2 = CA,1 # ##group.27 = ILE_CD1_c #ILE_CD1_c.istr = data/superstar/pdb0280_20.istr.properties #ILE_CD1_c.type = lipo_aro #ILE_CD1_c.0 = ILE.CD1,3 #ILE_CD1_c.1 = CG1,2 #ILE_CD1_c.2 = CB,1 # ##group.28 = ILE_CG2_c #ILE_CG2_c.istr = data/superstar/pdb0280_20.istr.properties #ILE_CG2_c.type = lipo_aro #ILE_CG2_c.0 = ILE.CG2,3 #ILE_CG2_c.1 = CB,2 #ILE_CG2_c.2 = CA,1 # ## CD is actually CD1 in pdb files # ##group.29 = LEU_CD1_c #LEU_CD1_c.istr = data/superstar/pdb0280_20.istr.properties #LEU_CD1_c.type = lipo_aro #LEU_CD1_c.0 = LEU.CD1,3 #LEU_CD1_c.1 = CG,2 #LEU_CD1_c.2 = CD2,1 # ##group.30 = LEU_CD2_c #LEU_CD2_c.istr = data/superstar/pdb0280_20.istr.properties #LEU_CD2_c.type = lipo_aro #LEU_CD2_c.0 = LEU.CD2,3 #LEU_CD2_c.1 = CG,2 #LEU_CD2_c.2 = CD1,1 # ##group.31 = THR_CG2_c #THR_CG2_c.istr = data/superstar/pdb0280_20.istr.properties #THR_CG2_c.type = lipo_aro #THR_CG2_c.0 = THR.CG2,3 #THR_CG2_c.1 = CB,2 #THR_CG2_c.2 = CA,1 # ## methylene C.3 interactions # ##group.31 = ILE_CG1_c #ILE_CG1_c.istr = data/superstar/pdb0302_20.istr.properties #ILE_CG1_c.type = lipo_aro #ILE_CG1_c.0 = ILE.CG1,3 #ILE_CG1_c.1 = CD1,2 #ILE_CG1_c.2 = CB,1 # ##group.32 = LEU_CB_c #LEU_CB_c.istr = data/superstar/pdb0302_20.istr.properties #LEU_CB_c.type = lipo_aro #LEU_CB_c.0 = LEU.CB,3 #LEU_CB_c.1 = CG,2 #LEU_CB_c.2 = CA,1 # ##group.33 = PHE_CB_c #PHE_CB_c.istr = data/superstar/pdb0302_20.istr.properties #PHE_CB_c.type = lipo_aro #PHE_CB_c.0 = PHE.CB,3 #PHE_CB_c.1 = CG,2 #PHE_CB_c.2 = CA,1 # ##group.34 = PRO_CB_c #PRO_CB_c.istr = data/superstar/pdb0302_20.istr.properties #PRO_CB_c.type = lipo_aro #PRO_CB_c.0 = PRO.CB,3 #PRO_CB_c.1 = CG,2 #PRO_CB_c.2 = CA,1 # ##group.35 = PRO_CG_c #PRO_CG_c.istr = data/superstar/pdb0302_20.istr.properties #PRO_CG_c.type = lipo_aro #PRO_CG_c.0 = PRO.CG,3 #PRO_CG_c.1 = CD,2 #PRO_CG_c.2 = CB,1 # ##group.36 = PRO_CD_c #PRO_CD_c.istr = data/superstar/pdb0302_20.istr.properties #PRO_CD_c.type = lipo_aro #PRO_CD_c.0 = PRO.CD,3 #PRO_CD_c.1 = N,2 #PRO_CD_c.2 = CG,1 # ##group.37 = MET_CB_c #MET_CB_c.istr = data/superstar/pdb0302_20.istr.properties #MET_CB_c.type = lipo_aro #MET_CB_c.0 = MET.CB,3 #MET_CB_c.1 = CG,2 #MET_CB_c.2 = CA,1 # ## is this right for met cg? what about the sulphur? # ##group.38 = MET_CG_c #MET_CG_c.istr = data/superstar/pdb0302_20.istr.properties #MET_CG_c.type = lipo_aro #MET_CG_c.0 = MET.CG,3 #MET_CG_c.1 = SD,2 #MET_CG_c.2 = CB,1 # ##group.39 = TRP_CB_c #TRP_CB_c.istr = data/superstar/pdb0302_20.istr.properties #TRP_CB_c.type = lipo_aro #TRP_CB_c.0 = TRP.CB,3 #TRP_CB_c.1 = CG,2 #TRP_CB_c.2 = CA,1 # ##group.40 = CYS_CB_c #CYS_CB_c.istr = data/superstar/pdb0302_20.istr.properties #CYS_CB_c.type = lipo_aro #CYS_CB_c.0 = CYS.CB,3 #CYS_CB_c.1 = SG,2 #CYS_CB_c.2 = CA,1 # ##group.41 = SER_CB_c #SER_CB_c.istr = data/superstar/pdb0302_20.istr.properties #SER_CB_c.type = lipo_aro #SER_CB_c.0 = SER.CB,3 #SER_CB_c.1 = OG,2 #SER_CB_c.2 = CA,1 # ##group.42 = ASN_CB_c #ASN_CB_c.istr = data/superstar/pdb0302_20.istr.properties #ASN_CB_c.type = lipo_aro #ASN_CB_c.0 = ASN.CB,3 #ASN_CB_c.1 = CG,2 #ASN_CB_c.2 = CA,1 # ##group.43 = GLN_CB_c #GLN_CB_c.istr = data/superstar/pdb0302_20.istr.properties #GLN_CB_c.type = lipo_aro #GLN_CB_c.0 = GLN.CB,3 #GLN_CB_c.1 = CG,2 #GLN_CB_c.2 = CA,1 # ##group.44 = GLN_CG_c #GLN_CG_c.istr = data/superstar/pdb0302_20.istr.properties #GLN_CG_c.type = lipo_aro #GLN_CG_c.0 = GLN.CG,3 #GLN_CG_c.1 = CD,2 #GLN_CG_c.2 = CB,1 # ##group.45 = TYR_CB_c #TYR_CB_c.istr = data/superstar/pdb0302_20.istr.properties #TYR_CB_c.type = lipo_aro #TYR_CB_c.0 = TYR.CB,3 #TYR_CB_c.1 = CG,2 #TYR_CB_c.2 = CA,1 # ##group.46 = HIS_CB_c #HIS_CB_c.istr = data/superstar/pdb0302_20.istr.properties #HIS_CB_c.type = lipo_aro #HIS_CB_c.0 = HIS.CB,3 #HIS_CB_c.1 = CG,2 #HIS_CB_c.2 = CA,1 # ##group.47 = ASP_CB_c #ASP_CB_c.istr = data/superstar/pdb0302_20.istr.properties #ASP_CB_c.type = lipo_aro #ASP_CB_c.0 = ASP.CB,3 #ASP_CB_c.1 = CG,2 #ASP_CB_c.2 = CA,1 # ##group.48 = GLU_CB_c #GLU_CB_c.istr = data/superstar/pdb0302_20.istr.properties #GLU_CB_c.type = lipo_aro #GLU_CB_c.0 = GLU.CB,3 #GLU_CB_c.1 = CG,2 #GLU_CB_c.2 = CA,1 # ##group.49 = GLU_CG_c #GLU_CG_c.istr = data/superstar/pdb0302_20.istr.properties #GLU_CG_c.type = lipo_aro #GLU_CG_c.0 = GLU.CG,3 #GLU_CG_c.1 = CD,2 #GLU_CG_c.2 = CB,1 # ##group.50 = LYS_CB_c #LYS_CB_c.istr = data/superstar/pdb0302_20.istr.properties #LYS_CB_c.type = lipo_aro #LYS_CB_c.0 = LYS.CB,3 #LYS_CB_c.1 = CG,2 #LYS_CB_c.2 = CA,1 # ##group.51 = ARG_CB_c #ARG_CB_c.istr = data/superstar/pdb0302_20.istr.properties #ARG_CB_c.type = lipo_aro #ARG_CB_c.0 = ARG.CB,3 #ARG_CB_c.1 = CG,2 #ARG_CB_c.2 = CA,1 # ##group.52 = LYS_CG_c #LYS_CG_c.istr = data/superstar/pdb0302_20.istr.properties #LYS_CG_c.type = lipo_aro #LYS_CG_c.0 = LYS.CG,3 #LYS_CG_c.1 = CD,2 #LYS_CG_c.2 = CB,1 # ##group.53 = ARG_CG_c #ARG_CG_c.istr = data/superstar/pdb0302_20.istr.properties #ARG_CG_c.type = lipo_aro #ARG_CG_c.0 = ARG.CG,3 #ARG_CG_c.1 = CD,2 #ARG_CG_c.2 = CB,1 # ##group.54 = LYS_CD_c #LYS_CD_c.istr = data/superstar/pdb0302_20.istr.properties #LYS_CD_c.type = lipo_aro #LYS_CD_c.0 = LYS.CD,3 #LYS_CD_c.1 = CE,2 #LYS_CD_c.2 = CG,1 # ##group.55 = ARG_CD_c #ARG_CD_c.istr = data/superstar/pdb0302_20.istr.properties #ARG_CD_c.type = lipo_aro #ARG_CD_c.0 = ARG.CD,3 #ARG_CD_c.1 = NE,2 #ARG_CD_c.2 = CG,1 # ##group.56 = GLY_CA_c #GLY_CA_c.istr = data/superstar/pdb0302_20.istr.properties #GLY_CA_c.type = lipo_aro #GLY_CA_c.0 = GLY.CA,3 #GLY_CA_c.1 = N,2 #GLY_CA_c.2 = C,1 # ## tertiary CH # ## CA rule. will fail for glycine currently ## but this has its own rule in the previous ## section of methylene carbons # ##group.57 = ANY_CA_c #ANY_CA_c.istr = data/superstar/pdb0294_20.istr.properties #ANY_CA_c.type = lipo_aro #ANY_CA_c.0 = *.CA,4 #ANY_CA_c.1 = N,1 #ANY_CA_c.2 = C,3 #ANY_CA_c.3 = CB,2 # ## this seems to be the correct orientation for VAL ## Schulz and Schirmer has it the other way around... ##group.58 = VAL_CB_c #VAL_CB_c.istr = data/superstar/pdb0294_20.istr.properties #VAL_CB_c.type = lipo_aro #VAL_CB_c.0 = VAL.CB,4 #VAL_CB_c.1 = CA,1 #VAL_CB_c.2 = CG2,3 #VAL_CB_c.3 = CG1,2 # ##group.59 = ILE_CB_c #ILE_CB_c.istr = data/superstar/pdb0294_20.istr.properties #ILE_CB_c.type = lipo_aro #ILE_CB_c.0 = ILE.CB,4 #ILE_CB_c.1 = CA,1 #ILE_CB_c.2 = CG1,3 #ILE_CB_c.3 = CG2,2 # ##group.60 = LEU_CG_c #LEU_CG_c.istr = data/superstar/pdb0294_20.istr.properties #LEU_CG_c.type = lipo_aro #LEU_CG_c.0 = LEU.CG,4 #LEU_CG_c.1 = CB,1 #LEU_CG_c.2 = CD2,3 #LEU_CG_c.3 = CD1,2 # ##group.61 = THR_CB_c #THR_CB_c.istr = data/superstar/pdb0294_20.istr.properties #THR_CB_c.type = lipo_aro #THR_CB_c.0 = THR.CB,4 #THR_CB_c.1 = CA,1 #THR_CB_c.2 = OG1,2 #THR_CB_c.3 = CG2,3 # ## sulphur # ##group.61 = MET_SD_c #MET_SD_c.istr = data/superstar/pdb0308_20.istr.properties #MET_SD_c.type = lipo_aro #MET_SD_c.0 = MET.SD,3 #MET_SD_c.1 = CG,1 #MET_SD_c.2 = CE,2 # ## ## Start of marcels definitions for the remainder of ## the aliphatic interaction maps ## # ##group.100 = ARG_guanidino_Ca #ARG_guanidino_Ca.istr = data/superstar/pdb0275_1_20.istr.properties #ARG_guanidino_Ca.type = lipo_aro #ARG_guanidino_Ca.0 = ARG.CD,1 #ARG_guanidino_Ca.1 = NE,2 #ARG_guanidino_Ca.2 = CZ,3 #ARG_guanidino_Ca.3 = NH2,4 #ARG_guanidino_Ca.4 = NH1,5 # ##group.101 = ARG_guanidino_Cb #ARG_guanidino_Cb.istr = data/superstar/pdb0275_1_20.istr.properties #ARG_guanidino_Cb.type = lipo_aro #ARG_guanidino_Cb.0 = ARG.CD,1 #ARG_guanidino_Cb.1 = NE,2 #ARG_guanidino_Cb.2 = CZ,3 #ARG_guanidino_Cb.3 = NH2,5 #ARG_guanidino_Cb.4 = NH1,4 # ##group.102 = HIS_telen_c #HIS_telen_c.istr = data/superstar/pdb0307_20.istr.properties #HIS_telen_c.type = lipo_aro #HIS_telen_c.0 = HIS.CD2,1 #HIS_telen_c.1 = CE1,2 #HIS_telen_c.2 = NE2,3 # ##group.103 = HIS_pron_c #HIS_pron_c.istr = data/superstar/pdb0306_20.istr.properties #HIS_pron_c.type = lipo_aro #HIS_pron_c.0 = HIS.CG,1 #HIS_pron_c.1 = CE1,2 #HIS_pron_c.2 = ND1,3 # ##group.104 = HIS_telec_c #HIS_telec_c.istr = data/superstar/pdb0310_20.istr.properties #HIS_telec_c.type = lipo_aro #HIS_telec_c.0 = HIS.CE1,3 #HIS_telec_c.1 = ND1,1 #HIS_telec_c.2 = NE2,2 # ##group.105 = HIS_proc_c #HIS_proc_c.istr = data/superstar/pdb0310_20.istr.properties #HIS_proc_c.type = lipo_aro #HIS_proc_c.0 = HIS.CD2,3 #HIS_proc_c.1 = CG,1 #HIS_proc_c.2 = NE2,2 # ##group.106 = HIS_CG_c #HIS_CG_c.istr = data/superstar/pdb0293_20.istr.properties #HIS_CG_c.type = lipo_aro #HIS_CG_c.0 = HIS.CG,4 #HIS_CG_c.1 = ND1,1 #HIS_CG_c.2 = CD2,2 #HIS_CG_c.3 = CB,3 # ##group.107 = TYR_phe_c #TYR_phe_c.istr = data/superstar/pdb0290_20.istr.properties #TYR_phe_c.type = lipo_aro #TYR_phe_c.0 = TYR.CB,1 #TYR_phe_c.1 = CG,5 #TYR_phe_c.2 = CD1,6 #TYR_phe_c.3 = CE1,7 #TYR_phe_c.4 = CZ,2 #TYR_phe_c.5 = CE2,3 #TYR_phe_c.6 = CD2,4 # ##group.108 = PHE_phe_c #PHE_phe_c.istr = data/superstar/pdb0290_20.istr.properties #PHE_phe_c.type = lipo_aro #PHE_phe_c.0 = PHE.CB,1 #PHE_phe_c.1 = CG,5 #PHE_phe_c.2 = CD1,6 #PHE_phe_c.3 = CE1,7 #PHE_phe_c.4 = CZ,2 #PHE_phe_c.5 = CE2,3 #PHE_phe_c.6 = CD2,4 # ##group.109 = TRP_phe_c #TRP_phe_c.istr = data/superstar/pdb0290_20.istr.properties #TRP_phe_c.type = lipo_aro #TRP_phe_c.0 = TRP.CG,1 #TRP_phe_c.1 = CD2,5 #TRP_phe_c.2 = CE2,6 #TRP_phe_c.3 = CZ2,7 #TRP_phe_c.4 = CH2,2 #TRP_phe_c.5 = CZ3,3 #TRP_phe_c.6 = CE3,4 # ###group.110 = TRP_CG_c #TRP_CG_c.istr = data/superstar/pdb0293_20.istr.properties #TRP_CG_c.type = lipo_aro #TRP_CG_c.0 = TRP.CG,4 #TRP_CG_c.1 = CD1,1 #TRP_CG_c.2 = CD2,2 #TRP_CG_c.3 = CB,3 # ##group.111 = TRP_CD1_c #TRP_CD1_c.istr = data/superstar/pdb0310_20.istr.properties #TRP_CD1_c.type = lipo_aro #TRP_CD1_c.0 = TRP.CD1,3 #TRP_CD1_c.1 = CG,1 #TRP_CD1_c.2 = NE1,2 # ##group.112 = TRP_NE1_c #TRP_NE1_c.istr = data/superstar/pdb0305_20.istr.properties #TRP_NE1_c.type = lipo_aro #TRP_NE1_c.0 = TRP.NE1,3 #TRP_NE1_c.1 = CD1,1 #TRP_NE1_c.2 = CE2,2 #