Contacts of the helix formed by residues 1166 - 1189 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887B THR* 3.7 6.2 - - - +
930B HIS* 3.7 25.8 - - + +
931B GLY* 4.1 10.3 - - - +
1165B GLY* 1.3 82.1 - - - +
1167B PRO* 1.3 73.2 - - + +
1168B GLY* 3.7 13.2 - - - +
1169B GLN* 3.0 45.4 + - + +
1170B VAL* 4.0 2.1 + - - +
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Residues in contact with PRO1167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887B THR* 3.6 24.0 - - + +
890B ILE* 3.5 39.3 - - + -
891B ALA* 3.5 16.3 - - + +
894B ARG* 3.8 13.7 - - - +
929B LEU* 6.1 0.9 - - + -
930B HIS 3.2 18.2 - - - +
931B GLY 3.9 5.8 - - - +
932B LEU* 4.1 8.3 - - + -
1165B GLY 4.7 0.2 - - - +
1166B VAL* 1.3 85.3 - - + +
1168B GLY* 1.3 60.8 + - - +
1170B VAL* 3.1 5.0 + - + -
1171B VAL* 3.0 24.5 + - - +
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Residues in contact with GLY1168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894B ARG* 3.8 15.5 - - - +
931B GLY 5.2 0.4 + - - -
1166B VAL* 3.2 10.5 + - - +
1167B PRO* 1.3 79.1 - - - +
1169B GLN* 1.3 55.8 + - - +
1171B VAL* 3.5 8.9 - - - +
1172B ASN* 2.9 40.6 + - - +
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Residues in contact with GLN1169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806B HIS* 2.9 33.3 + - + -
809B VAL* 3.2 45.9 - - + +
810B ALA* 4.7 8.3 - - - +
1134B ALA 3.1 7.5 - - - +
1135B GLU* 4.0 2.8 - - - -
1164B LYS* 5.5 1.6 - - - +
1165B GLY* 3.3 18.4 - - - +
1166B VAL* 3.0 45.3 + - + +
1168B GLY* 1.3 77.9 - - - +
1170B VAL* 1.3 59.4 - - + +
1172B ASN* 3.5 1.2 + - - +
1173B PHE 3.1 19.6 + - - -
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Residues in contact with VAL1170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887B THR* 4.6 4.9 - - + -
888B LEU* 4.0 18.8 - - + -
891B ALA* 3.5 21.8 - - + -
892B MET* 4.5 3.1 - - - -
1131B ALA* 4.7 2.7 - - + +
1134B ALA* 4.3 13.9 - - + -
1135B GLU* 3.8 28.9 - - + +
1166B VAL 4.4 7.4 - - - +
1167B PRO 3.1 7.1 + - - +
1169B GLN* 1.3 75.8 - - + +
1171B VAL* 1.3 65.6 + - - +
1173B PHE* 3.2 5.7 + - - +
1174B PHE* 3.1 47.2 + - + -
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Residues in contact with VAL1171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891B ALA* 3.8 27.6 - - - +
894B ARG* 4.2 18.8 - - + +
895B LEU* 4.0 16.3 - - + +
1167B PRO 3.0 20.3 + - - +
1168B GLY* 3.5 12.8 - - - +
1170B VAL* 1.3 78.0 - - - +
1172B ASN* 1.3 66.4 + - - +
1174B PHE* 3.3 3.3 + - - +
1175B TYR* 3.1 47.3 + - + +
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Residues in contact with ASN1172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809B VAL* 3.5 20.9 + - + +
810B ALA 5.7 0.2 + - - -
812B TYR* 3.4 45.3 - - - +
1168B GLY* 2.9 24.4 + - - +
1169B GLN* 3.7 4.7 - - - +
1170B VAL 3.2 0.2 - - - -
1171B VAL* 1.3 79.1 - - - +
1173B PHE* 1.3 66.1 + - - +
1175B TYR* 3.2 13.5 + - - +
1176B PHE* 3.0 31.1 + - + -
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Residues in contact with PHE1173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805B LEU* 4.0 30.7 - - + -
809B VAL* 3.6 16.3 - - + +
827B TYR* 5.3 1.1 - + - -
830B TYR* 4.6 2.9 - + - -
1109B LYS* 3.6 21.3 - - - -
1127B PHE* 4.7 6.3 - + - -
1130B ILE* 3.7 33.2 - - + -
1131B ALA* 5.1 1.8 - - - -
1134B ALA* 4.0 17.7 - - + -
1169B GLN 3.1 9.4 + - - +
1170B VAL* 3.4 8.3 - - - +
1172B ASN* 1.3 75.6 - - - +
1174B PHE* 1.3 93.8 + + - +
1176B PHE* 3.0 24.6 + + - +
1177B ILE* 3.2 32.6 + - + +
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Residues in contact with PHE1174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867B VAL* 4.0 4.9 - - + -
870B PHE* 3.4 32.5 - + + -
872B THR* 4.4 9.2 - - - -
892B MET* 3.4 36.8 - - + -
895B LEU* 3.8 20.0 - - + -
1127B PHE* 3.5 45.3 - + + -
1131B ALA* 4.6 5.4 - - + -
1170B VAL* 3.1 34.9 + - + +
1171B VAL 4.0 0.2 - - - +
1173B PHE* 1.3 102.1 - + - +
1175B TYR* 1.3 57.3 + - - +
1177B ILE* 4.4 3.1 - - + -
1178B ALA* 2.9 30.3 + - - +
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Residues in contact with TYR1175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863B VAL* 2.9 37.2 - - + +
864B GLU* 4.6 17.2 + - + +
867B VAL* 4.0 13.7 - - + +
894B ARG 5.4 1.6 + - - -
895B LEU* 3.5 28.9 + - + +
1171B VAL* 3.1 34.6 + - + +
1172B ASN* 3.6 14.4 - - - +
1174B PHE* 1.3 74.3 - - - +
1176B PHE* 1.3 64.9 + - + +
1178B ALA* 3.4 1.0 + - - +
1179B GLU* 2.9 29.9 + - + +
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Residues in contact with PHE1176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808B ALA* 4.0 23.1 - - + -
809B VAL* 4.0 20.2 - - + -
812B TYR 4.2 16.6 - - - -
825B ASP* 5.0 4.9 - - - -
827B TYR* 3.7 55.7 + + + +
1172B ASN* 3.0 23.3 + - + -
1173B PHE* 3.0 15.7 + + - +
1175B TYR* 1.3 76.5 - - + +
1177B ILE* 1.3 63.8 + - + +
1179B GLU* 3.4 6.4 + - - +
1180B GLU* 3.2 20.3 + - - +
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Residues in contact with ILE1177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827B TYR* 3.6 22.4 - - - +
830B TYR* 5.7 0.2 - - - +
831B ARG* 5.6 0.7 - - - +
870B PHE* 3.9 20.9 - - + -
1109B LYS 3.4 21.5 - - - +
1110B THR* 4.0 11.9 - - - +
1111B GLY* 3.7 19.6 - - - +
1114B VAL* 4.2 8.5 - - + -
1127B PHE* 4.6 7.4 - - + -
1173B PHE* 3.2 41.4 + - + +
1174B PHE* 3.7 8.7 - - + +
1176B PHE* 1.3 73.2 - - + +
1178B ALA* 1.3 59.3 + - - +
1180B GLU* 3.2 6.5 + - - +
1181B VAL* 3.0 26.7 + - + +
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Residues in contact with ALA1178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863B VAL* 3.7 33.7 - - + +
866B ILE* 3.7 26.6 - - + +
867B VAL* 4.2 2.0 - - + -
870B PHE* 4.2 5.8 - - + -
1174B PHE 2.9 17.8 + - - +
1175B TYR 3.8 0.4 - - - +
1177B ILE* 1.3 75.9 - - - +
1179B GLU* 1.3 57.4 + - - +
1181B VAL* 3.3 5.3 + - - +
1182B ARG* 3.0 30.8 + - - +
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Residues in contact with GLU1179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857B LEU* 4.6 11.7 - - - +
863B VAL* 3.6 15.1 - - + +
1175B TYR* 2.9 16.9 + - + +
1176B PHE* 3.7 7.2 - - - +
1178B ALA* 1.3 73.4 - - - +
1180B GLU* 1.3 60.5 + - - +
1182B ARG* 2.8 47.4 + - - +
1183B SER* 3.1 24.9 + - - -
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Residues in contact with GLU1180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827B TYR* 4.8 5.0 + - - -
831B ARG* 2.5 52.9 + - - -
1111B GLY* 3.4 13.8 + - - +
1112B TRP* 3.1 22.6 + - - +
1176B PHE 3.2 13.3 + - - +
1177B ILE* 3.2 10.2 + - + +
1179B GLU* 1.3 71.7 - - - +
1181B VAL* 1.3 65.8 + - - +
1183B SER* 2.9 26.5 + - - +
1184B LEU* 3.1 15.0 + - + +
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Residues in contact with VAL1181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866B ILE* 3.9 12.8 - - + -
870B PHE* 4.7 0.4 - - + -
1111B GLY* 3.8 21.5 - - - +
1114B VAL* 3.9 21.1 - - + -
1115B VAL* 4.4 10.1 - - + -
1177B ILE* 3.0 22.2 + - + +
1178B ALA* 3.5 12.1 - - - +
1180B GLU* 1.3 74.3 - - - +
1182B ARG* 1.3 63.4 + - - +
1184B LEU* 3.2 2.9 + - - +
1185B LEU* 3.0 41.4 + - + +
1193B LEU* 3.9 27.1 - - + -
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Residues in contact with ARG1182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857B LEU* 2.6 51.9 + - + +
858B GLU* 4.3 7.1 + - - +
860B VAL* 3.1 26.9 + - + +
861B GLU 2.8 21.3 + - - +
862B SER* 4.2 3.7 - - - +
863B VAL* 3.8 19.7 - - - +
866B ILE* 3.5 15.3 - - + -
1178B ALA 3.0 17.2 + - - +
1179B GLU* 2.8 46.1 + - - +
1180B GLU 3.2 0.2 - - - -
1181B VAL* 1.3 77.2 - - - +
1183B SER* 1.3 56.8 + - - +
1185B LEU* 3.4 3.6 + - - +
1186B ALA* 3.0 28.9 + - - +
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Residues in contact with SER1183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857B LEU* 4.0 15.0 - - - +
1179B GLU 3.1 13.0 + - - -
1180B GLU* 2.9 21.8 + - - +
1182B ARG* 1.3 74.9 - - - +
1184B LEU* 1.3 62.3 + - - +
1186B ALA* 3.4 3.8 + - - +
1187B HIS* 3.0 27.0 + - - +
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Residues in contact with LEU1184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848B PHE* 3.9 23.6 - - + -
1111B GLY 3.8 2.9 - - - +
1112B TRP* 3.6 43.7 - - + +
1115B VAL* 3.7 27.4 - - + -
1180B GLU* 3.1 17.1 + - + +
1181B VAL 3.6 6.5 - - - +
1183B SER* 1.3 84.1 + - - +
1185B LEU* 1.3 59.7 + - - +
1187B HIS* 3.3 12.8 + - + +
1188B LEU* 2.9 36.6 + - + +
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Residues in contact with LEU1185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860B VAL* 3.9 20.0 - - + -
861B GLU* 4.1 8.3 - - + +
866B ILE* 4.6 1.3 - - + -
1115B VAL* 5.3 2.0 - - + +
1181B VAL* 3.0 36.9 + - + +
1182B ARG 3.7 4.3 - - - +
1184B LEU* 1.3 73.7 - - - +
1186B ALA* 1.3 58.5 + - - +
1188B LEU* 3.2 5.4 + - + -
1189B GLY 3.0 23.2 + - - -
1190B TYR* 3.1 26.3 + - + +
1192B SER* 3.6 25.4 - - - +
1193B LEU* 3.8 18.8 - - + +
1196B ILE* 4.0 33.7 - - + -
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Residues in contact with ALA1186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854B ALA* 3.2 4.1 - - - +
855B ILE* 2.9 46.2 + - - +
857B LEU* 4.1 17.0 - - + -
860B VAL* 3.8 17.8 - - + +
1182B ARG 3.0 14.4 + - - +
1183B SER* 3.5 9.9 - - - +
1185B LEU* 1.3 76.4 - - - +
1187B HIS* 1.3 60.5 + - - +
1189B GLY 3.3 2.6 + - - -
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Residues in contact with HIS1187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848B PHE* 4.5 28.7 - + + -
850B ALA* 4.5 15.6 - - + +
852B GLN 4.6 0.3 - - - +
854B ALA* 3.8 20.3 + - + +
1183B SER 3.0 14.3 + - - +
1184B LEU* 3.3 16.7 + - + +
1186B ALA* 1.3 76.8 - - - +
1188B LEU* 1.3 73.6 + - + +
1189B GLY 3.4 0.5 + - - -
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Residues in contact with LEU1188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848B PHE* 4.0 35.0 - - + -
850B ALA* 4.3 24.2 - - + +
851B ASP* 4.7 0.5 + - - +
852B GLN* 3.8 18.1 + - - +
1115B VAL* 4.2 24.9 - - + -
1119B LEU* 5.1 2.5 - - + -
1184B LEU* 2.9 23.9 + - + +
1185B LEU* 3.2 7.6 + - - +
1187B HIS* 1.3 81.5 - - - +
1189B GLY* 1.3 61.2 + - - +
1190B TYR* 3.4 24.9 - - + -
1196B ILE* 4.4 18.6 - - + -
1202B LEU* 4.6 17.3 - - + -
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Residues in contact with GLY1189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852B GLN* 3.5 16.8 - - - +
853B PRO 3.2 23.7 - - - +
855B ILE* 3.9 20.5 - - - +
1185B LEU 3.0 4.7 + - - -
1186B ALA 3.3 7.0 + - - -
1187B HIS 3.2 4.2 + - - -
1188B LEU* 1.3 79.5 - - - +
1190B TYR* 1.3 62.5 + - - +
1191B ARG* 5.4 4.9 + - - -
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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