Contacts of the helix formed by residues 1173 - 1197 (chain A) in PDB entry 2RNY
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 ARG1173 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1172A SER* 1.3 75.1 + - - +
1174A VAL* 1.3 66.9 + - - +
1175A TYR 3.0 1.6 - - - -
1176A LYS* 2.9 56.0 + - - +
1177A PHE* 3.4 38.0 + - + -
13B GLY 5.5 5.4 + - - -
14B GLY* 5.5 7.8 - - - -
21B VAL* 3.7 32.2 + - + +
22B LEU* 3.5 15.3 - - + +
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Residues in contact with VAL1174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1110A PRO* 4.5 7.4 - - + -
1111A PHE* 3.4 35.7 - - + -
1164A ALA* 3.6 9.9 - - + -
1168A ASN* 3.0 41.3 - - - +
1173A ARG* 1.3 75.5 - - - +
1175A TYR* 1.3 55.7 + - - +
1177A PHE* 2.4 44.3 + - + -
1178A CYS* 2.6 13.7 + - - -
20B ALY 3.9 13.0 - - + +
21B VAL 5.5 0.2 - - - +
22B LEU* 3.9 13.0 - - + -
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Residues in contact with TYR1175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1164A ALA 4.8 3.5 + - - -
1165A TRP* 4.4 11.3 + + - -
1170A LYS* 2.9 70.4 + - + +
1172A SER* 3.3 20.2 + - - +
1173A ARG 3.0 0.2 - - - -
1174A VAL* 1.3 77.5 - - - +
1176A LYS* 1.3 68.3 + - + +
1178A CYS* 3.3 11.2 - - - -
1179A SER* 3.1 36.3 + - - -
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Residues in contact with LYS1176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107A GLU* 2.9 16.4 - - - +
1172A SER 4.3 7.0 - - - +
1173A ARG* 3.1 59.5 - - - +
1174A VAL 2.7 3.4 + - - -
1175A TYR* 1.3 82.6 - - + +
1177A PHE* 1.3 71.5 + - + +
1179A SER* 3.4 6.2 + - - -
1180A LYS* 3.3 13.5 + - - +
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Residues in contact with PHE1177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106A PRO* 3.1 34.1 - - + -
1107A GLU* 3.2 36.3 - - + +
1110A PRO* 4.0 11.9 - - + -
1173A ARG* 3.4 41.3 - - + -
1174A VAL* 2.4 35.8 + - + +
1176A LYS* 1.3 82.0 - - + +
1178A CYS* 1.3 59.2 + - - +
1180A LYS 3.6 0.2 + - - -
1181A LEU* 2.9 28.8 + - - +
21B VAL* 3.5 27.1 - - + -
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Residues in contact with CYS1178 (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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1111A PHE* 4.5 4.5 - - + -
1161A PHE* 3.6 14.9 - - + +
1164A ALA* 3.5 26.7 - - + -
1165A TRP* 3.1 37.7 - - + +
1174A VAL* 2.6 46.0 + - - +
1175A TYR* 3.3 12.3 - - - -
1177A PHE* 1.3 72.7 - - - +
1179A SER* 1.3 63.6 + - - +
1181A LEU* 3.3 6.4 + - - +
1182A ALA* 2.9 27.2 + - - +
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Residues in contact with SER1179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1165A TRP* 4.1 12.6 - - - +
1175A TYR* 3.1 31.2 + - - -
1176A LYS* 3.4 8.3 - - - -
1177A PHE 3.3 0.2 - - - -
1178A CYS* 1.3 78.2 - - - +
1180A LYS* 1.3 58.2 + - - +
1182A ALA* 3.5 2.9 + - - +
1183A GLU* 3.0 25.6 + - - +
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Residues in contact with LYS1180 (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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1104A GLN* 2.7 40.8 - - + +
1107A GLU* 3.0 38.1 - - - +
1176A LYS 3.3 3.2 + - - +
1178A CYS 3.2 0.4 - - - -
1179A SER* 1.3 77.1 - - - +
1181A LEU* 1.3 60.8 + - - +
1183A GLU* 2.5 41.4 + - + -
1184A VAL* 2.7 48.1 + - - +
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Residues in contact with LEU1181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101A LEU* 2.9 18.0 - - + +
1104A GLN* 3.6 14.6 - - + -
1107A GLU* 3.1 33.9 - - + +
1108A SER* 3.3 25.4 - - - +
1111A PHE* 3.2 26.9 - - + -
1135A LEU* 4.2 1.1 - - + -
1160A MET* 3.8 10.8 - - + -
1161A PHE* 3.1 18.4 - - + -
1177A PHE 2.9 20.2 + - - +
1178A CYS 3.3 3.6 + - - +
1180A LYS* 1.3 77.5 - - - +
1182A ALA* 1.3 57.6 + - - +
1184A VAL* 3.9 0.4 - - - -
1185A PHE* 2.8 29.8 + - - +
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Residues in contact with ALA1182 (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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1158A TRP* 3.5 12.5 - - + -
1161A PHE* 3.4 33.2 - - + -
1165A TRP* 3.5 27.1 - - + -
1178A CYS 2.9 12.7 + - - +
1179A SER 3.9 1.8 - - - +
1181A LEU* 1.3 76.7 - - - +
1183A GLU* 1.3 55.5 + - - +
1186A GLU* 2.8 35.3 + - - +
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Residues in contact with GLU1183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179A SER* 3.0 16.5 + - - +
1180A LYS* 2.5 35.8 + - + +
1182A ALA* 1.3 68.3 - - - +
1184A VAL* 1.3 71.0 + - - +
1186A GLU* 2.9 29.8 + - - +
1187A GLN* 2.9 25.7 + - + +
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Residues in contact with VAL1184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100A ALA* 4.2 21.5 - - + +
1101A LEU* 3.5 18.6 - - + -
1103A ARG* 6.0 1.1 - - - -
1104A GLN* 3.9 9.6 - - + +
1180A LYS* 2.7 55.3 + - + +
1181A LEU* 3.9 0.2 - - - -
1183A GLU* 1.3 74.3 - - - +
1185A PHE* 1.3 51.5 - - - +
1187A GLN* 2.7 11.1 + - + +
1188A GLU* 2.6 45.6 + - - +
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Residues in contact with PHE1185 (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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1097A THR* 2.8 37.7 - - - -
1101A LEU* 3.2 25.9 - - + +
1153A TYR* 3.1 16.8 - + - -
1154A VAL* 3.6 5.2 - - + -
1157A VAL* 3.3 20.0 - - + -
1158A TRP* 3.0 36.6 - + - -
1161A PHE* 3.7 6.7 - + + -
1181A LEU 2.8 22.3 + - - +
1182A ALA 4.1 0.2 - - - +
1184A VAL* 1.3 77.5 - - - +
1186A GLU* 1.3 54.7 + - - +
1188A GLU* 3.8 4.0 - - - -
1189A ILE* 2.5 70.7 + - + +
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Residues in contact with GLU1186 (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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1158A TRP* 3.5 22.1 - - + -
1182A ALA 2.8 23.3 + - - +
1183A GLU* 2.9 26.0 + - - +
1185A PHE* 1.3 72.7 - - - +
1187A GLN* 1.3 61.5 + - + +
1189A ILE* 3.6 17.4 - - - +
1190A ASP* 3.6 18.7 + - - +
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Residues in contact with GLN1187 (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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1183A GLU* 2.9 14.6 + - + +
1184A VAL* 2.7 14.7 + - + +
1186A GLU* 1.3 84.1 + - + +
1188A GLU* 1.3 69.3 + - - +
1190A ASP* 4.2 10.4 + - - +
1191A PRO* 3.6 15.1 - - - +
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Residues in contact with GLU1188 (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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1096A PRO 4.6 3.6 - - - +
1097A THR* 3.2 40.6 - - - +
1100A ALA* 3.2 36.4 - - + +
1184A VAL* 2.6 38.6 + - - +
1185A PHE* 3.5 2.9 - - - +
1187A GLN* 1.3 91.7 - - - +
1189A ILE* 1.3 57.4 + - - +
1190A ASP 3.0 5.2 - - - -
1191A PRO* 3.1 19.2 - - - +
1192A VAL* 3.3 6.4 - - - +
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Residues in contact with ILE1189 (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 LEU* 4.1 4.7 - - + -
1097A THR* 3.8 1.1 - - + +
1154A VAL* 3.3 22.0 - - + -
1158A TRP* 4.7 4.5 - - + +
1185A PHE* 2.5 62.8 + - + +
1186A GLU* 3.6 17.7 - - - +
1188A GLU* 1.3 70.6 - - - +
1190A ASP* 1.3 58.6 + - - +
1192A VAL* 3.3 28.7 - - + -
1193A MET* 2.6 51.9 + - + +
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Residues in contact with ASP1190 (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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1186A GLU 3.6 17.7 + - - +
1187A GLN* 4.2 11.6 + - - +
1189A ILE* 1.3 77.4 - - - +
1191A PRO* 1.3 72.5 - - + +
1192A VAL 2.9 4.8 + - - -
1193A MET* 4.4 1.5 - - - +
1194A GLN* 3.0 35.3 + - - +
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Residues in contact with PRO1191 (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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1093A ALA* 4.9 1.5 - - - +
1187A GLN* 3.6 13.5 - - - +
1188A GLU* 3.1 14.8 - - - +
1190A ASP* 1.3 97.9 - - + +
1192A VAL* 1.3 56.5 + - + +
1194A GLN* 3.2 30.6 - - - +
1195A SER* 3.2 17.5 + - - -
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Residues in contact with VAL1192 (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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1093A ALA* 3.0 39.3 - - + +
1094A LEU* 3.2 17.0 - - + -
1097A THR* 3.0 20.9 - - + -
1150A PRO* 4.6 0.9 - - + -
1188A GLU 3.3 3.8 - - - +
1189A ILE* 3.3 16.8 - - + +
1190A ASP 2.9 1.0 - - - -
1191A PRO* 1.3 77.0 - - + +
1193A MET* 1.3 53.3 + - - +
1194A GLN 2.6 9.5 + - - -
1195A SER 2.7 1.7 + - - -
1196A LEU* 2.6 65.6 + - + +
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Residues in contact with MET1193 (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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1150A PRO* 3.5 23.8 - - + -
1151A TRP* 3.4 63.5 - - + +
1154A VAL* 3.8 13.9 - - + -
1189A ILE* 2.6 44.8 + - + +
1190A ASP* 4.4 2.0 - - - +
1192A VAL* 1.3 73.3 - - - +
1194A GLN* 1.3 56.3 + - - +
1197A GLY* 3.0 29.8 + - - +
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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
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1190A ASP* 3.0 26.3 + - - +
1191A PRO* 3.2 24.6 - - - +
1192A VAL 2.6 5.7 + - - -
1193A MET* 1.3 76.2 - - - +
1195A SER* 1.3 62.6 + - - +
1196A LEU 3.3 2.0 - - - -
1197A GLY* 3.2 14.5 - - - +
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Residues in contact with SER1195 (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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1085A PHE* 3.5 16.1 - - - -
1093A ALA* 5.5 2.0 - - - -
1191A PRO 3.2 15.5 - - - -
1192A VAL* 2.7 5.5 + - - -
1194A GLN* 1.3 78.8 - - - +
1196A LEU* 1.3 69.6 + - - +
1197A GLY* 4.9 0.4 - - - -
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Residues in contact with LEU1196 (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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1083A LYS* 4.2 4.2 - - - +
1084A ILE 4.7 0.9 + - - -
1085A PHE* 2.8 31.7 - - + -
1089A GLU* 4.1 6.7 - - + +
1090A LEU* 3.4 30.1 - - + +
1093A ALA* 3.2 29.2 - - + -
1094A LEU* 3.3 11.4 - - + -
1150A PRO* 3.3 36.0 - - + +
1151A TRP* 5.0 0.5 - - - -
1192A VAL* 2.6 38.6 + - + +
1193A MET* 4.3 0.4 - - - +
1195A SER* 1.3 88.9 - - - +
1197A GLY* 1.3 56.8 + - - +
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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
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1082A LYS* 3.6 22.7 - - - +
1083A LYS* 5.7 0.2 - - - +
1150A PRO* 4.6 0.9 - - - -
1151A TRP* 3.1 42.9 - - - -
1193A MET* 3.0 22.6 + - - +
1194A GLN* 3.2 17.7 - - - +
1195A SER 4.9 0.3 - - - -
1196A LEU* 1.3 82.8 - - - +
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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
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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) + - + + + + + -
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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