Contacts of the helix formed by residues 1187 - 1208 (chain A) in PDB entry 1VDV
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 ASN1187 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A ARG 3.4 8.7 - - - +
577A LEU 2.7 31.8 + - - +
1044A THR* 4.2 2.6 - - - +
1045A LYS* 4.5 7.2 - - - +
1048A GLN* 3.0 25.0 + - - +
1185A SER* 3.0 6.1 + - - -
1186A LEU* 1.3 83.7 - - - +
1188A PRO* 1.3 67.4 - - - +
1189A ALA* 3.0 13.0 + - - +
1190A ILE* 3.0 34.9 + - + +
1191A ASP* 3.0 22.0 + - - -
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Residues in contact with PRO1188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 4.3 2.0 - - - -
560A PHE* 3.5 45.5 - - + -
574A GLY 3.2 28.9 - - - +
575A ARG 3.6 4.3 - - - +
576A PRO* 3.9 9.0 - - + -
1185A SER* 3.0 11.6 - - - +
1187A ASN* 1.3 83.2 - - - +
1189A ALA* 1.3 56.5 + - - +
1191A ASP* 4.4 0.2 - - + -
1192A ILE* 2.9 35.3 + - - +
1243A LEU* 3.8 15.3 - - + -
5017A GOL 3.7 7.9 - - - +
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Residues in contact with ALA1189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A HIS* 3.3 50.8 - - + +
195A LEU* 3.7 13.5 - - + +
576A PRO* 3.6 14.6 - - + +
577A LEU 4.6 1.1 - - - +
1187A ASN* 3.0 9.7 + - - +
1188A PRO* 1.3 80.3 - - - +
1190A ILE* 1.3 65.6 + - + +
1192A ILE* 4.0 2.4 - - - +
1193A GLY* 3.1 19.1 + - - -
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Residues in contact with ILE1190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A HIS* 5.3 4.0 - - + +
112A GLN* 5.5 3.4 + - + -
577A LEU 4.2 2.2 - - - +
578A PRO* 4.9 0.4 - - + -
579A HIS* 4.2 34.8 - - + +
1039A GLY 6.1 0.2 - - - +
1040A GLN 3.1 27.8 - - - +
1041A GLY* 4.5 10.3 - - - +
1044A THR* 5.0 5.6 - - + -
1045A LYS* 3.8 20.4 - - + +
1187A ASN* 3.0 33.7 + - + +
1189A ALA* 1.3 78.6 - - + +
1191A ASP* 1.3 57.2 + - - +
1193A GLY* 3.1 3.3 + - - -
1194A GLN* 2.9 32.2 + - + +
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Residues in contact with ASP1191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045A LYS* 2.7 31.1 + - - -
1182A VAL* 4.3 11.7 - - + +
1185A SER* 2.6 34.9 + - - +
1186A LEU 4.0 4.3 + - - -
1187A ASN 3.0 14.4 + - - +
1188A PRO* 4.1 2.5 - - + +
1190A ILE* 1.3 73.2 - - - +
1192A ILE* 1.3 61.7 + - - +
1194A GLN* 3.1 7.0 + - - +
1195A VAL* 2.9 32.8 + - - +
1243A LEU* 4.6 8.3 - - + -
1256A SER* 6.0 0.5 - - - -
1257A LYS 5.2 2.6 - - - +
1259A VAL* 3.3 22.3 - - + +
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Residues in contact with ILE1192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ARG* 4.3 0.7 - - - +
195A LEU* 3.9 20.9 - - + -
558A GLN* 3.7 37.2 - - + -
559A LEU 4.6 2.7 - - - +
560A PHE* 4.3 13.2 - - + -
1188A PRO 2.9 21.9 + - - +
1189A ALA 4.0 2.5 - - - +
1191A ASP* 1.3 75.3 - - - +
1193A GLY* 1.3 58.6 + - - +
1195A VAL* 3.1 8.3 + - - +
1196A GLU* 2.8 52.0 + - + +
1241A VAL* 4.3 13.7 - - + +
1243A LEU* 4.0 26.2 - - + -
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Residues in contact with GLY1193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A HIS* 6.1 1.3 - - - -
112A GLN* 3.2 26.1 + - - -
151A THR 4.2 2.1 - - - +
155A PRO* 6.2 2.0 - - - -
1189A ALA 3.1 15.1 + - - -
1190A ILE* 3.4 5.4 - - - -
1191A ASP 3.1 0.2 - - - -
1192A ILE* 1.3 78.8 - - - +
1194A GLN* 1.3 54.4 + - - +
1196A GLU* 4.0 9.0 - - - +
1197A GLY* 2.8 25.5 + - - -
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Residues in contact with GLN1194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLN* 3.2 28.1 + - - -
912A ARG* 3.2 9.2 + - - +
1040A GLN* 3.5 20.6 + - - +
1045A LYS* 5.5 0.4 - - - +
1190A ILE* 2.9 25.5 + - + +
1191A ASP 3.1 8.0 + - - +
1193A GLY* 1.3 73.4 - - - +
1195A VAL* 1.3 60.2 + - - +
1198A ALA* 2.9 34.0 + - - +
1259A VAL* 3.8 32.5 - - + +
1260A GLY* 3.6 10.0 - - - -
1263A PRO* 4.5 0.8 - - - +
3003A MTE 2.7 38.5 + - - +
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Residues in contact with VAL1195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1178A ILE* 4.0 28.7 - - + -
1180A MET* 4.0 26.7 - - + -
1191A ASP 2.9 20.1 + - - +
1192A ILE* 3.1 11.4 + - - +
1194A GLN* 1.3 76.9 - - - +
1196A GLU* 1.3 58.7 + - - +
1199A PHE* 3.0 31.4 + - - +
1241A VAL* 3.9 20.0 - - + -
1243A LEU* 4.6 8.3 - - + -
1259A VAL* 4.0 11.0 - - + -
1263A PRO* 3.9 18.0 - - + +
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Residues in contact with GLU1196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A THR 3.8 12.6 - - - +
152A GLY* 4.8 1.1 - - - -
154A ARG* 2.8 56.7 + - - +
155A PRO* 3.8 10.0 - - - +
558A GLN* 4.6 1.9 - - - +
1178A ILE* 5.8 0.2 - - - -
1192A ILE* 2.8 31.9 + - - +
1193A GLY* 4.0 4.3 - - - +
1195A VAL* 1.3 71.6 - - - +
1197A GLY* 1.3 62.6 + - - +
1199A PHE* 3.7 5.1 - - - +
1200A VAL* 3.1 29.6 + - - +
1239A PHE* 4.3 19.5 - - + +
1241A VAL* 3.8 27.4 - - + +
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Residues in contact with GLY1197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ARG 4.7 1.4 - - - +
150A CYS 3.0 27.5 - - - +
151A THR 3.8 7.9 + - - -
152A GLY 4.1 1.8 - - - -
912A ARG* 4.0 7.9 - - - -
1193A GLY 2.8 17.8 + - - -
1194A GLN 4.0 0.4 - - - -
1196A GLU* 1.3 74.4 - - - +
1198A ALA* 1.3 60.2 + - - +
1200A VAL* 3.3 4.0 + - - +
1201A GLN* 3.1 25.6 + - - +
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Residues in contact with ALA1198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912A ARG* 3.5 30.5 - - - +
1194A GLN 2.9 19.1 + - - +
1197A GLY* 1.3 75.7 - - - +
1199A PHE* 1.3 63.3 + - - +
1201A GLN* 3.2 2.6 + - - +
1202A GLY 3.0 18.7 + - - -
1260A GLY 3.9 5.2 - - - +
1263A PRO* 3.8 9.0 - - + -
1264A LEU* 3.4 35.7 - - + +
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Residues in contact with PHE1199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1158A ALA* 4.5 1.3 - - + -
1160A SER* 3.9 5.6 - - - -
1176A THR* 3.5 38.1 - - + -
1178A ILE* 3.7 20.9 - - + -
1195A VAL* 3.0 19.9 + - + +
1196A GLU* 3.7 4.3 - - - +
1197A GLY 3.3 0.2 - - - -
1198A ALA* 1.3 77.4 - - - +
1200A VAL* 1.3 61.7 + - + +
1202A GLY* 3.3 1.9 + - - -
1203A LEU* 2.9 42.2 + - + +
1236A PRO* 4.4 4.9 - - + -
1239A PHE* 3.7 21.3 - + - -
1263A PRO* 4.1 9.6 + - + +
1264A LEU 4.5 1.6 - - - -
1266A LEU* 3.2 28.5 - - + -
1267A GLY* 3.6 19.3 - - - -
1269A SER* 3.8 4.9 - - - -
1270A VAL* 4.0 11.9 - - + -
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Residues in contact with VAL1200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A CYS 5.8 1.1 - - - +
149A ARG 6.2 0.2 - - - +
152A GLY* 3.5 31.0 - - - +
153A TYR* 4.8 5.4 - - + -
1196A GLU 3.1 18.3 + - - +
1197A GLY 3.8 3.8 - - - +
1199A PHE* 1.3 84.3 - - + +
1201A GLN* 1.3 60.4 + - + +
1203A LEU* 3.2 13.8 + - + +
1204A GLY 2.9 22.7 + - - -
1230A PRO* 3.3 32.4 - - + +
1235A ILE* 4.2 15.9 - - + -
1236A PRO* 5.5 0.2 - - + -
1239A PHE* 4.5 6.7 - - + -
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Residues in contact with GLN1201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ARG* 3.4 52.4 - - - +
739A GLN* 3.1 14.8 + - - +
798A PHE* 3.4 28.5 - - - -
911A PHE* 3.8 14.0 - - - -
912A ARG* 2.8 45.3 + - - +
1197A GLY 3.1 14.0 + - - +
1198A ALA 3.2 6.7 + - - +
1200A VAL* 1.3 76.7 - - + +
1202A GLY* 1.3 58.5 + - - +
1204A GLY* 3.2 1.1 + - - +
1205A LEU* 2.9 23.2 + - - +
1230A PRO* 5.4 0.2 - - - -
1264A LEU* 4.0 9.2 - - + -
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Residues in contact with GLY1202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1198A ALA 3.0 10.3 + - - -
1199A PHE 3.7 0.7 - - - -
1201A GLN* 1.3 73.2 - - - +
1203A LEU* 1.3 65.8 + - - +
1205A LEU* 3.1 3.9 + - - +
1206A PHE* 2.9 37.9 + - - -
1264A LEU* 3.5 36.7 - - - +
1267A GLY* 4.2 1.6 - - - -
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Residues in contact with LEU1203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1173A ASN* 3.8 22.9 - - - +
1199A PHE* 2.9 28.9 + - + +
1200A VAL* 3.2 20.4 - - + +
1202A GLY* 1.3 74.9 - - - +
1204A GLY* 1.3 61.3 + - - +
1206A PHE* 5.0 0.9 - - - -
1207A THR* 2.6 41.3 + - + +
1208A LEU* 6.4 1.1 - - + -
1230A PRO* 5.2 5.4 - - + -
1234A SER* 3.8 12.6 - - - +
1235A ILE* 4.7 2.5 - - - -
1236A PRO* 4.3 9.9 - - + -
1267A GLY* 4.0 8.6 - - - +
1270A VAL* 3.3 46.7 - - + -
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Residues in contact with GLY1204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1200A VAL 2.9 10.7 + - - -
1201A GLN 3.2 1.1 + - - -
1202A GLY 3.1 0.6 - - - -
1203A LEU* 1.3 74.9 - - - +
1205A LEU* 1.3 64.0 + - - +
1208A LEU* 3.0 12.2 + - - -
1209A GLU* 2.9 49.5 + - - -
1230A PRO* 3.6 16.3 - - - +
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Residues in contact with LEU1205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A ILE* 4.4 10.5 - - + -
737A GLY 3.9 9.3 - - - +
738A GLY 3.6 21.9 - - - +
739A GLN* 3.5 30.3 - - + +
839A ARG* 3.6 34.8 - - - +
917A PRO* 4.4 9.6 - - + -
1201A GLN 2.9 8.7 + - - +
1202A GLY* 3.1 8.0 + - - +
1204A GLY* 1.3 75.8 - - - +
1206A PHE* 1.3 88.2 + - + +
1209A GLU* 4.0 7.2 - - - +
1264A LEU* 4.5 3.4 - - + -
1298A SER* 3.5 3.5 + - - -
1299A PRO* 3.2 21.3 - - - +
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Residues in contact with PHE1206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A ILE* 3.6 23.1 - - + -
917A PRO* 4.3 6.5 - - + -
921A PHE* 3.9 22.9 - + + -
1202A GLY* 2.9 29.9 + - - +
1203A LEU 4.4 0.2 - - - +
1205A LEU* 1.3 95.0 - - + +
1207A THR* 1.3 59.4 + - + +
1264A LEU* 5.0 0.7 - - + -
1265A PHE* 3.8 31.2 - + - -
1267A GLY 3.7 3.8 - - - +
1268A ALA* 3.5 34.8 - - + -
1271A PHE* 3.3 23.8 - - + -
1298A SER* 3.4 17.0 - - - -
1299A PRO* 3.2 4.0 - - - +
1300A ALA 2.7 26.3 + - - -
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Residues in contact with THR1207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1171A HIS* 4.5 14.1 - - - -
1173A ASN* 5.7 0.3 + - - -
1203A LEU* 2.6 31.6 + - + +
1204A GLY 3.4 0.2 + - - -
1205A LEU 3.7 0.2 + - - -
1206A PHE* 1.3 90.7 - - + +
1208A LEU* 1.3 77.6 + - - +
1270A VAL* 4.0 15.7 - - + -
1271A PHE* 4.4 6.3 - - - +
1274A ILE* 3.8 24.2 - - + -
1299A PRO* 4.2 4.7 - - - -
1300A ALA* 3.3 23.6 - - + +
1301A THR* 3.7 8.7 - - - -
1302A PRO* 4.6 1.0 - - - +
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Residues in contact with LEU1208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A SER* 3.6 30.2 - - - +
426A ARG* 4.0 18.8 - - + -
1171A HIS* 5.0 11.4 - - + -
1203A LEU* 6.5 0.7 - - + -
1204A GLY* 3.0 10.3 + - - +
1207A THR* 1.3 97.2 + - - +
1209A GLU* 1.3 64.8 + - - +
1210A GLU* 3.6 3.1 + - - +
1228A LYS* 3.5 25.7 + - + +
1229A ILE 4.1 0.2 - - - +
1230A PRO* 4.1 19.1 - - + -
1234A SER* 3.7 27.1 - - - +
1299A PRO* 4.2 1.2 - - - +
1301A THR* 4.3 12.3 - - - +
1302A PRO* 5.2 2.2 - - + -
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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