Contacts of the helix formed by residues 1166 - 1189 (chain A) in PDB entry 1OFD
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 VAL1166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A THR* 3.7 6.4 - - - +
930A HIS* 3.7 29.8 - - + +
931A GLY* 4.1 8.7 - - - +
1165A GLY* 1.3 81.9 - - - +
1167A PRO* 1.3 77.3 - - + +
1168A GLY* 3.0 5.7 + - - +
1169A GLN* 3.0 50.7 + - + +
1170A VAL* 3.8 3.5 + - - +
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Residues in contact with PRO1167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A THR* 3.6 23.9 - - + +
890A ILE* 3.7 37.5 - - + -
891A ALA* 3.4 20.1 - - + +
894A ARG* 3.8 16.6 - - - +
929A LEU* 6.4 0.2 - - + -
930A HIS 3.3 17.9 - - - +
931A GLY 3.9 5.6 - - - +
932A LEU* 4.1 9.2 - - + -
1166A VAL* 1.3 85.4 - - + +
1168A GLY* 1.3 56.5 + - - +
1170A VAL* 3.1 4.1 + - + -
1171A VAL* 3.0 25.7 + - - +
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Residues in contact with GLY1168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A ARG* 3.7 15.7 - - - +
931A GLY 5.2 0.4 + - - -
1166A VAL* 3.0 7.8 + - - +
1167A PRO* 1.3 79.3 - - - +
1169A GLN* 1.3 55.3 + - - +
1171A VAL* 3.5 8.8 - - - +
1172A ASN* 3.0 37.3 + - - +
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Residues in contact with GLN1169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A HIS* 3.3 30.2 + - - -
809A VAL* 3.1 40.1 - - + +
810A ALA* 3.8 27.8 - - - +
1134A ALA 3.4 7.4 - - - +
1135A GLU* 4.3 1.6 - - - -
1164A LYS* 5.7 1.6 - - - +
1165A GLY* 3.5 19.7 - - - +
1166A VAL* 3.0 36.0 + - + +
1168A GLY* 1.3 75.4 - - - +
1170A VAL* 1.3 61.4 + - + +
1172A ASN 3.4 0.5 + - - -
1173A PHE* 3.1 20.8 + - - +
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Residues in contact with VAL1170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A THR* 4.5 5.6 - - + -
888A LEU* 4.1 18.8 - - + -
891A ALA* 3.4 23.3 - - + -
892A MET* 4.5 2.5 - - - -
1131A ALA* 4.9 1.1 - - + +
1134A ALA* 4.3 14.8 - - + -
1135A GLU* 3.8 29.8 - - + +
1166A VAL 4.1 9.0 - - - +
1167A PRO 3.1 7.7 + - - +
1169A GLN* 1.3 74.9 - - + +
1171A VAL* 1.3 65.8 + - - +
1173A PHE* 3.2 6.3 + - - +
1174A PHE* 3.1 46.9 + - + -
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Residues in contact with VAL1171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891A ALA* 3.6 28.3 - - - +
894A ARG* 4.2 19.5 - - + +
895A LEU* 3.8 16.5 - - + +
1167A PRO 3.0 19.3 + - - +
1168A GLY* 3.5 12.3 - - - +
1170A VAL* 1.3 75.6 - - - +
1172A ASN* 1.3 65.3 + - - +
1174A PHE* 3.2 5.2 + - - +
1175A TYR* 3.1 48.7 + - + +
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Residues in contact with ASN1172 (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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809A VAL* 3.2 31.3 + - + +
812A TYR* 3.5 33.2 - - - +
1168A GLY 3.0 24.5 + - - +
1169A GLN* 3.5 6.2 - - - +
1171A VAL* 1.3 76.1 - - - +
1173A PHE* 1.3 66.5 + - - +
1175A TYR* 3.2 11.8 + - - +
1176A PHE* 3.0 31.2 + - + -
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Residues in contact with PHE1173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A LEU* 3.8 42.0 - - + -
809A VAL* 3.5 12.0 - - + +
827A TYR* 5.2 3.6 - + - -
830A TYR* 4.7 2.9 - - - -
1109A LYS 3.5 21.3 - - - -
1127A PHE* 4.8 4.0 - + - -
1130A ILE* 3.6 27.8 - - + -
1131A ALA* 5.1 1.1 - - - -
1134A ALA* 4.0 16.8 - - + -
1169A GLN 3.1 14.3 + - - +
1170A VAL* 3.2 8.7 + - - +
1172A ASN* 1.3 75.3 - - - +
1174A PHE* 1.3 98.6 + + - +
1176A PHE* 3.1 16.6 + - - +
1177A ILE* 3.1 30.4 + - + +
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Residues in contact with PHE1174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867A VAL* 3.6 12.6 - - + +
870A PHE* 3.5 25.7 - + + -
872A THR* 4.2 8.7 - - - -
892A MET* 3.5 37.2 - - + -
895A LEU* 3.9 15.0 - - + -
1127A PHE* 3.5 47.1 - + + -
1131A ALA* 4.5 7.2 - - + -
1170A VAL* 3.1 32.4 + - + -
1171A VAL 3.2 5.6 + - - +
1173A PHE* 1.3 100.0 - + - +
1175A TYR* 1.3 60.4 + - - +
1177A ILE* 3.4 3.3 + - + +
1178A ALA* 3.0 28.9 + - - +
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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
----------------------------------------------------------
863A VAL* 2.9 36.8 - - + +
864A GLU* 4.1 26.3 + - + +
867A VAL* 3.9 14.1 - - + +
894A ARG 5.2 1.6 + - - -
895A LEU* 3.6 27.2 + - + +
1171A VAL* 3.1 37.4 + - + +
1172A ASN* 3.2 13.0 + - - +
1174A PHE* 1.3 74.3 - - - +
1176A PHE* 1.3 66.6 + - + +
1178A ALA* 3.3 1.0 + - - +
1179A GLU* 2.9 30.1 + - + +
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Residues in contact with PHE1176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808A ALA* 4.4 8.5 - - + -
809A VAL* 3.8 30.7 - - + -
812A TYR 3.6 24.5 - - - -
825A ASP* 5.8 2.0 - - - -
827A TYR* 3.7 52.5 + + + +
1172A ASN* 3.0 22.2 + - + -
1173A PHE* 3.1 8.5 + + - +
1175A TYR* 1.3 79.5 - - + +
1177A ILE* 1.3 62.8 + - + +
1179A GLU* 3.4 7.6 + - + +
1180A GLU* 3.2 20.4 + - - +
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Residues in contact with ILE1177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A TYR* 3.4 22.9 - - - +
830A TYR* 5.8 0.2 - - - +
870A PHE* 3.7 23.8 - - + -
1109A LYS 3.4 26.0 - - - +
1110A THR* 4.0 11.0 - - - +
1111A GLY* 3.6 18.4 - - - +
1114A VAL* 4.2 7.4 - - + -
1127A PHE* 4.7 6.1 - - + -
1173A PHE* 3.1 34.5 + - + +
1174A PHE* 3.8 8.5 - - + +
1175A TYR 3.3 0.2 - - - -
1176A PHE* 1.3 72.8 - - + +
1178A ALA* 1.3 61.1 + - - +
1180A GLU* 3.2 9.2 + - - +
1181A VAL* 2.9 26.0 + - + +
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Residues in contact with ALA1178 (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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863A VAL* 3.4 29.8 - - + -
866A ILE* 3.7 29.8 - - + +
867A VAL* 4.0 7.9 - - + -
870A PHE* 4.2 1.8 - - + -
1174A PHE 3.0 18.4 + - - +
1177A ILE* 1.3 78.2 - - - +
1179A GLU* 1.3 57.3 + - - +
1181A VAL* 3.1 6.2 + - - +
1182A ARG* 3.0 29.8 + - - +
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Residues in contact with GLU1179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A LEU* 4.9 9.5 - - - +
863A VAL* 3.4 13.9 - - + +
1175A TYR* 2.9 17.1 + - + +
1176A PHE* 3.6 7.9 - - + +
1178A ALA* 1.3 76.3 - - - +
1180A GLU* 1.3 62.1 + - - +
1182A ARG* 3.1 50.2 + - - +
1183A SER* 3.1 21.5 + - - -
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Residues in contact with GLU1180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A TYR* 4.1 8.7 + - - -
831A ARG* 2.8 46.9 + - - -
1110A THR* 3.4 1.7 + - - +
1111A GLY* 3.2 22.2 + - - -
1112A TRP* 3.2 21.2 + - - +
1176A PHE 3.2 8.6 + - - +
1177A ILE* 3.2 11.1 + - - +
1179A GLU* 1.3 76.4 - - - +
1181A VAL* 1.3 63.9 + - - +
1183A SER* 2.8 25.9 + - - +
1184A LEU* 3.2 14.7 + - + +
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Residues in contact with VAL1181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A ILE* 4.1 12.6 - - + -
870A PHE* 4.6 0.2 - - + -
1111A GLY* 3.7 19.5 - - - +
1114A VAL* 3.8 21.5 - - + -
1115A VAL* 4.2 9.6 - - + -
1177A ILE* 2.9 23.5 + - + +
1178A ALA* 3.1 12.3 + - - +
1180A GLU* 1.3 75.8 - - - +
1182A ARG* 1.3 57.0 + - - +
1184A LEU* 3.2 4.0 + - - +
1185A LEU* 2.9 35.3 + - + +
1193A LEU* 3.7 36.8 - - + -
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Residues in contact with ARG1182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A LEU* 2.9 54.0 + - + +
858A GLU* 4.4 6.5 + - - +
860A VAL* 3.0 28.2 + - + +
861A GLU 2.7 27.7 + - - +
862A SER* 4.0 5.5 - - - +
863A VAL* 3.7 19.3 - - - +
866A ILE* 3.4 9.4 - - + -
1178A ALA 3.0 16.2 + - - +
1179A GLU* 3.1 36.6 + - - +
1181A VAL* 1.3 75.2 - - - +
1183A SER* 1.3 62.6 + - - +
1185A LEU* 3.4 2.8 + - - +
1186A ALA* 3.0 24.9 + - - +
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Residues in contact with SER1183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A LEU* 3.9 15.2 - - - +
1179A GLU 3.1 12.0 + - - -
1180A GLU* 2.8 23.3 + - - +
1182A ARG* 1.3 75.0 - - - +
1184A LEU* 1.3 62.9 + - - +
1186A ALA* 3.5 3.3 + - - +
1187A HIS* 3.1 27.2 + - - +
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Residues in contact with LEU1184 (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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848A PHE* 3.9 22.4 - - + -
1111A GLY 3.8 2.7 - - - +
1112A TRP* 3.5 45.5 - - + +
1115A VAL* 3.8 28.7 - - + -
1180A GLU* 3.2 15.8 + - + +
1181A VAL 3.6 7.0 - - - +
1183A SER* 1.3 83.1 + - - +
1185A LEU* 1.3 64.6 + - - +
1187A HIS* 3.3 12.9 + - + +
1188A LEU* 3.0 30.5 + - + +
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Residues in contact with LEU1185 (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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860A VAL* 3.8 21.3 - - + -
861A GLU* 4.1 8.3 - - + +
866A ILE* 4.6 0.9 - - + -
1115A VAL* 5.3 2.2 - - + +
1181A VAL* 2.9 34.8 + - + +
1182A ARG* 3.7 4.7 - - - +
1184A LEU* 1.3 73.7 - - - +
1186A ALA* 1.3 58.4 + - - +
1188A LEU* 3.0 6.3 + - + +
1189A GLY 2.9 25.3 + - - -
1190A TYR* 3.1 23.7 + - + +
1192A SER* 3.8 26.0 - - - +
1193A LEU* 3.7 20.9 - - + +
1196A ILE* 3.9 34.1 - - + -
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Residues in contact with ALA1186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854A ALA* 3.2 1.7 - - - -
855A ILE* 2.9 47.9 + - - +
857A LEU* 4.1 17.5 - - + +
860A VAL* 3.8 19.2 - - + +
1182A ARG 3.0 17.2 + - - +
1183A SER* 3.7 5.2 - - - +
1184A LEU 3.3 0.2 - - - -
1185A LEU* 1.3 74.9 - - - +
1187A HIS* 1.3 62.4 + - - +
1189A GLY 3.2 4.5 + - - -
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Residues in contact with HIS1187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848A PHE* 4.7 25.5 - + + -
850A ALA* 4.7 10.3 - - + +
852A GLN 4.5 2.8 - - - +
854A ALA* 3.6 23.4 + - + +
1183A SER 3.1 14.7 + - - +
1184A LEU* 3.4 17.6 + - + +
1185A LEU 3.2 0.2 - - - -
1186A ALA* 1.3 77.7 - - - +
1188A LEU* 1.3 70.4 + - + +
1189A GLY 3.4 0.3 + - - -
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Residues in contact with LEU1188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848A PHE* 3.9 35.2 - - + -
850A ALA* 4.4 21.1 - - + +
851A ASP* 4.8 0.3 + - - +
852A GLN* 3.7 19.3 + - - +
1115A VAL* 4.4 14.8 - - + -
1119A LEU* 5.1 2.7 - - + -
1184A LEU* 3.0 22.8 + - + +
1185A LEU* 3.0 6.3 + - - +
1187A HIS* 1.3 83.1 - - - +
1189A GLY* 1.3 59.5 + - - +
1190A TYR* 3.4 23.6 - - + -
1196A ILE* 4.3 29.8 - - + -
1202A LEU* 4.8 16.4 - - + -
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Residues in contact with GLY1189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A GLN* 3.4 18.0 - - - +
853A PRO 3.4 22.9 - - - -
855A ILE* 4.0 21.2 - - - +
1185A LEU 2.9 3.4 + - - -
1186A ALA 3.2 11.6 + - - -
1187A HIS 3.2 0.4 - - - -
1188A LEU* 1.3 78.3 - - - +
1190A TYR* 1.3 61.0 + - - +
1191A ARG* 4.9 6.9 + - - -
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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