Contacts of the helix formed by residues 1194 - 1220 (chain A) in PDB entry 5YS0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU1194 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1157A PRO* 5.2 6.3 - - + -
1158A TYR* 3.6 31.9 - - + +
1192A SER* 2.9 13.0 + - - +
1193A MET* 1.3 81.9 - - + +
1195A LYS* 1.3 52.9 + - - +
1196A GLY 3.3 1.3 - - - -
1197A THR* 2.7 62.1 + - + +
1198A ILE* 3.1 20.0 + - + +
1301A ERG 4.8 10.1 - - + -
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Residues in contact with LYS1195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188A TRP* 3.4 42.9 - - + +
1192A SER* 3.0 21.2 + - - +
1193A MET 3.1 2.1 - - - +
1194A LEU* 1.3 75.1 - - - +
1196A GLY* 1.3 59.0 + - - +
1198A ILE 3.4 0.7 + - - -
1199A GLU* 2.8 51.3 + - + +
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Residues in contact with GLY1196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193A MET 4.7 2.4 + - - -
1194A LEU 3.3 0.8 - - - -
1195A LYS* 1.3 77.5 - - - +
1197A THR* 1.3 61.0 + - - +
1199A GLU* 4.0 11.8 - - - +
1200A LYS* 3.7 17.5 + - - +
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Residues in contact with THR1197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1194A LEU* 2.7 41.3 + - + +
1196A GLY* 1.3 71.4 - - - +
1198A ILE* 1.3 56.9 + - + +
1200A LYS* 3.4 5.4 + - - +
1201A GLY* 2.6 33.4 + - - -
1301A ERG 3.9 28.3 - - + -
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Residues in contact with ILE1198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157A PRO 3.8 15.7 - - - +
1158A TYR* 4.2 7.4 - - + -
1162A PHE* 3.6 51.4 - - + -
1186A VAL* 4.6 2.2 - - + -
1188A TRP* 3.5 28.5 - - + -
1194A LEU* 3.1 20.8 + - + +
1195A LYS 3.7 5.8 - - - +
1197A THR* 1.3 80.6 - - + +
1199A GLU* 1.3 54.2 + - - +
1201A GLY* 2.8 2.1 + - - +
1202A SER* 2.7 43.3 + - - +
1301A ERG 4.6 21.3 - - + -
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Residues in contact with GLU1199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1185A ASN* 5.2 0.9 - - - -
1186A VAL* 3.8 30.6 + - + +
1188A TRP* 3.0 30.1 + - + +
1195A LYS* 2.8 50.9 + - + +
1196A GLY* 4.1 8.5 - - - -
1198A ILE* 1.3 74.7 - - - +
1200A LYS* 1.3 58.6 + - - +
1202A SER* 3.4 1.4 + - - -
1203A ILE* 3.1 36.6 + - + +
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Residues in contact with LYS1200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1196A GLY 3.7 14.9 + - - +
1197A THR* 3.4 5.0 + - - +
1198A ILE 3.3 0.2 - - - -
1199A GLU* 1.3 75.8 - - - +
1201A GLY* 1.3 65.3 + - - +
1203A ILE* 4.0 12.6 - - + +
1204A ASP* 3.1 53.4 + - - +
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Residues in contact with GLY1201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197A THR 2.6 21.7 + - - -
1198A ILE 2.8 5.2 + - - -
1200A LYS* 1.3 73.0 - - - +
1202A SER* 1.3 63.0 + - - -
1204A ASP* 3.4 3.4 + - - +
1205A GLY* 3.2 18.7 + - - -
1301A ERG 4.1 35.1 - - - +
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Residues in contact with SER1202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1164A VAL* 3.2 38.5 - - - +
1184A THR* 4.8 1.1 - - - -
1186A VAL* 3.3 15.8 - - - +
1198A ILE* 2.7 24.1 + - - +
1199A GLU 3.6 7.0 - - - -
1201A GLY* 1.3 72.1 - - - +
1203A ILE* 1.3 67.9 + - - +
1205A GLY* 4.2 0.2 - - - -
1206A GLN* 3.0 28.9 + - - +
1301A ERG 4.4 16.9 - - - +
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Residues in contact with ILE1203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061A THR 3.9 25.6 - - - +
1063A ILE* 3.8 22.0 - - + +
1184A THR* 3.6 21.3 - - - +
1185A ASN* 5.0 3.6 - - - +
1186A VAL* 5.2 1.1 - - + -
1199A GLU* 3.1 35.1 + - + +
1200A LYS* 4.4 12.3 - - + +
1202A SER* 1.3 82.1 - - - +
1204A ASP* 1.3 64.9 + - - +
1206A GLN* 3.7 1.0 - - - +
1207A ARG* 2.9 47.5 + - - +
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Residues in contact with ASP1204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1200A LYS* 3.1 47.4 + - - +
1201A GLY* 3.9 4.7 - - - +
1202A SER 3.2 0.2 - - - -
1203A ILE* 1.3 79.3 - - - +
1205A GLY* 1.3 62.1 + - - +
1207A ARG* 3.0 45.2 + - - +
1208A SER* 3.2 7.8 + - - -
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Residues in contact with GLY1205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1201A GLY 3.2 9.7 + - - -
1204A ASP* 1.3 76.4 - - - +
1206A GLN* 1.3 54.1 + - - +
1208A SER* 2.7 12.5 + - - -
1209A SER* 2.6 34.8 + - - -
1301A ERG 3.9 25.5 - - - -
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Residues in contact with GLN1206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063A ILE* 3.6 11.9 - - + -
1164A VAL* 5.9 2.2 - - + -
1166A THR* 3.3 26.1 + - - +
1168A PHE* 4.4 7.1 - - - -
1182A VAL* 3.9 5.4 - - - +
1184A THR* 3.4 24.0 - - + -
1202A SER 3.0 20.9 + - - +
1203A ILE 3.7 2.5 - - - +
1205A GLY* 1.3 73.7 - - - +
1207A ARG* 1.3 57.9 + - - +
1209A SER* 4.1 9.2 + - - -
1210A THR* 2.3 54.5 + - - +
1301A ERG 3.3 34.2 + - + +
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Residues in contact with ARG1207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063A ILE* 3.4 30.0 + - + +
1064A ASP* 4.7 7.3 - - - +
1203A ILE* 2.9 28.4 + - - +
1204A ASP* 3.0 38.8 + - - +
1206A GLN* 1.3 76.3 - - - +
1208A SER* 1.3 61.7 - - - +
1210A THR* 3.6 2.6 + - - -
1211A LYS* 3.2 20.8 + - - +
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Residues in contact with SER1208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1204A ASP 3.2 6.1 + - - -
1205A GLY* 2.7 19.3 + - - -
1207A ARG* 1.3 72.8 - - - +
1209A SER* 1.3 59.9 + - - -
1211A LYS* 2.9 24.1 + - - +
1212A GLN* 3.0 26.3 + - - +
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Residues in contact with SER1209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095A GLN* 2.7 44.5 + - - +
1117A LYS* 5.7 0.2 - - - -
1205A GLY 2.6 18.4 + - - -
1206A GLN* 3.6 8.2 + - - -
1208A SER* 1.3 73.0 - - - +
1210A THR* 1.3 57.1 + - - +
1212A GLN* 3.3 4.9 + - - -
1213A LEU* 3.0 20.5 + - - +
1301A ERG 3.6 37.3 + - - +
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Residues in contact with THR1210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063A ILE* 4.3 2.6 - - - +
1064A ASP* 3.9 18.8 - - - +
1067A ILE* 4.2 4.7 - - + -
1168A PHE* 4.8 2.2 - - + -
1180A MET* 4.1 13.5 - - + -
1182A VAL* 3.7 31.4 - - + +
1206A GLN* 2.3 47.3 + - - +
1207A ARG 3.9 4.3 - - - -
1209A SER* 1.3 73.8 + - - +
1211A LYS* 1.3 62.1 + - - +
1213A LEU* 4.3 7.2 - - + -
1214A VAL* 3.0 29.0 + - + +
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Residues in contact with LYS1211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064A ASP* 5.3 2.0 + - - +
1207A ARG 3.2 13.5 + - - +
1208A SER* 2.9 13.9 + - - +
1210A THR* 1.3 76.8 - - - +
1212A GLN* 1.3 60.8 + - + +
1214A VAL* 3.5 10.3 - - + +
1215A ASP* 2.4 67.8 + - - +
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Residues in contact with GLN1212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094A ASN* 3.1 32.0 + - - +
1095A GLN* 3.6 33.1 - - + +
1096A ASN* 4.8 4.2 + - - +
1208A SER* 3.0 32.9 + - - +
1209A SER* 4.0 1.0 - - - -
1211A LYS* 1.3 79.2 - - + +
1213A LEU* 1.3 54.7 + - - +
1215A ASP* 4.0 6.7 - - + +
1216A ASP* 2.7 47.4 + - - +
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Residues in contact with LEU1213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080A LEU* 4.1 23.6 - - + -
1081A TYR* 6.1 0.2 - - - +
1088A ILE* 4.6 6.7 - - + -
1091A ILE* 3.6 36.2 - - + +
1095A GLN* 4.1 6.0 + - - +
1168A PHE* 5.0 12.1 - - + -
1170A TYR* 4.6 8.3 - - - +
1180A MET* 3.6 33.7 - - + -
1209A SER* 3.0 17.7 + - - +
1210A THR* 3.4 6.7 + - - +
1211A LYS 3.3 0.2 - - - -
1212A GLN* 1.3 77.9 - - - +
1214A VAL* 1.3 60.6 + - + +
1216A ASP* 4.1 1.0 - - - +
1217A LEU* 2.7 37.0 + - + +
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Residues in contact with VAL1214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067A ILE* 3.7 43.7 - - + -
1069A ILE* 4.6 5.8 - - + -
1180A MET* 3.8 31.2 - - + -
1210A THR* 3.0 20.3 + - + +
1211A LYS* 3.5 12.1 - - + +
1213A LEU* 1.3 74.2 - - + +
1215A ASP* 1.3 68.5 - - - +
1217A LEU* 4.0 7.0 - - - -
1218A LYS* 3.2 32.9 + - + +
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Residues in contact with ASP1215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1211A LYS* 2.4 51.5 + - - +
1212A GLN* 3.4 8.6 - - + +
1214A VAL* 1.3 81.3 - - - +
1216A ASP* 1.3 65.7 + - - +
1218A LYS* 4.4 2.8 - - - +
1219A LYS* 3.8 24.1 + - - +
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Residues in contact with ASP1216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091A ILE* 3.5 32.5 - - + +
1094A ASN* 2.9 41.2 + - - +
1212A GLN* 2.7 28.7 + - - +
1213A LEU* 4.1 2.4 - - - +
1215A ASP* 1.3 78.2 - - - +
1217A LEU* 1.3 66.1 + - - +
1218A LYS 3.3 0.3 + - - -
1219A LYS* 3.4 15.9 + - + +
1220A ILE* 3.0 25.9 - - + +
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Residues in contact with LEU1217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069A ILE* 4.4 34.8 - - + +
1071A VAL* 5.5 4.3 - - - +
1076A VAL* 4.6 10.3 - - + -
1079A LEU* 4.5 24.0 - - + +
1080A LEU* 3.5 48.0 - - + -
1091A ILE* 5.7 4.3 - - + -
1180A MET* 4.7 5.2 - - - -
1213A LEU* 2.7 33.0 + - + +
1214A VAL* 4.0 7.0 - - - +
1215A ASP 3.4 0.2 - - - -
1216A ASP* 1.3 75.2 - - - +
1218A LYS* 1.3 63.5 + - - +
1220A ILE* 3.7 16.9 + - + +
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Residues in contact with LYS1218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067A ILE* 4.1 14.5 - - - +
1068A ASN* 3.0 29.4 + - - +
1069A ILE* 3.7 20.2 - - + -
1070A PRO* 3.8 23.3 - - + +
1071A VAL* 6.1 2.4 - - - +
1214A VAL* 3.2 20.4 + - + +
1215A ASP* 4.4 3.6 - - - +
1216A ASP 3.2 0.2 - - - -
1217A LEU* 1.3 75.2 - - - +
1219A LYS* 1.3 67.8 + - - +
1220A ILE 2.8 12.8 - - - +
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Residues in contact with LYS1219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1215A ASP* 3.8 19.1 + - - +
1216A ASP* 3.4 17.2 + - + +
1217A LEU 3.4 0.2 - - - -
1218A LYS* 1.3 77.1 - - - +
1220A ILE* 1.3 68.4 + - + +
1223B ASN* 5.5 4.8 + - - -
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Residues in contact with ILE1220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1071A VAL* 5.6 5.2 - - - +
1079A LEU* 4.7 26.7 - - + -
1087A TYR* 5.0 18.2 - - + -
1091A ILE* 5.4 7.0 - - + -
1216A ASP* 3.0 32.5 - - + +
1217A LEU* 3.7 11.1 + - + +
1218A LYS 2.8 21.2 + - - +
1219A LYS* 1.3 80.3 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il