Contacts of the helix formed by residues 1178 - 1199 (chain A) in PDB entry 5ID6
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 ASN1178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837A ASN* 5.1 4.1 - - - +
840A TYR* 3.5 25.4 + - - -
1147A VAL* 6.3 1.1 - - + -
1148A ASP* 3.7 17.5 - - + +
1149A PHE* 5.1 0.2 - - - +
1150A LEU* 4.4 2.4 - - - +
1164A SER* 3.1 12.4 + - - -
1168A GLU* 6.0 3.4 - - + +
1176A PRO* 3.9 4.2 - - - +
1177A LYS* 1.3 83.6 + - - +
1179A ALA* 1.3 62.1 + - - +
1180A ASP* 3.2 10.8 + - - +
1181A ALA* 2.7 35.0 + - - +
1182A ASN* 3.3 20.1 + - - +
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Residues in contact with ALA1179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002A SER* 3.7 12.5 + - - +
1138A ARG* 3.3 49.6 - - + +
1148A ASP* 3.3 12.2 + - - +
1149A PHE* 5.0 0.4 - - - +
1150A LEU* 4.1 19.9 - - + +
1178A ASN* 1.3 74.8 - - - +
1180A ASP* 1.3 67.9 + - - +
1182A ASN* 3.3 10.0 + - - +
1183A GLY 3.3 8.0 + - - -
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Residues in contact with ASP1180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A ASP* 4.0 7.5 - - - +
834A GLY* 3.4 11.0 - - - -
835A GLU 3.2 18.6 + - - -
836A ARG* 3.1 20.1 + - - +
837A ASN* 2.7 35.4 + - - +
840A TYR* 4.0 15.6 - - + +
1002A SER* 5.4 0.2 - - - -
1138A ARG* 3.8 16.2 + - - +
1148A ASP* 4.4 6.4 + - - -
1178A ASN* 3.2 9.0 + - - +
1179A ALA* 1.3 77.7 - - - +
1181A ALA* 1.3 61.6 + - - +
1183A GLY* 3.3 10.2 + - - -
1184A ALA* 3.4 11.8 + - - +
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Residues in contact with ALA1181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840A TYR* 3.5 28.2 - - + -
842A VAL* 3.3 6.7 - - + +
853A GLN* 3.5 24.9 - - - +
1176A PRO* 4.1 2.2 - - + -
1177A LYS 3.9 7.0 - - - +
1178A ASN* 2.7 24.2 + - - +
1180A ASP* 1.3 70.0 - - - +
1182A ASN* 1.3 56.7 + - - +
1184A ALA 3.0 2.4 + - - -
1185A TYR* 2.6 38.0 + - - +
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Residues in contact with ASN1182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001A THR 3.5 0.9 + - - -
1002A SER 2.7 28.9 + - - -
1004A ILE* 2.9 19.7 + - - +
1006A PRO* 3.1 25.4 - - - +
1150A LEU* 3.4 22.7 - - + +
1176A PRO* 3.4 13.3 - - + +
1178A ASN 3.3 6.6 + - - +
1179A ALA 3.3 10.5 + - - +
1180A ASP 3.3 0.6 - - - -
1181A ALA* 1.3 78.1 - - - +
1183A GLY* 1.3 52.6 + - - +
1185A TYR* 3.2 0.9 + - - +
1186A ASN* 2.7 60.3 + - - +
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Residues in contact with GLY1183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A ASP* 3.5 20.0 - - - -
1001A THR* 3.3 17.6 + - - -
1002A SER* 3.7 11.1 + - - -
1179A ALA 3.3 3.8 + - - -
1180A ASP 3.3 4.3 + - - -
1181A ALA 3.1 0.8 - - - -
1182A ASN* 1.3 80.6 - - - +
1184A ALA* 1.3 56.2 + - - +
1186A ASN* 3.4 0.7 + - - -
1187A ILE* 2.9 34.1 + - - +
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Residues in contact with ALA1184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A GLY* 3.6 22.8 - - - +
832A ASP* 3.5 16.5 - - + +
840A TYR* 3.3 29.2 - - + +
842A VAL* 3.5 19.5 - - + +
1180A ASP 3.4 7.9 + - - +
1181A ALA 3.0 3.3 + - - +
1183A GLY* 1.3 71.7 - - - +
1185A TYR* 1.3 65.6 + - - +
1187A ILE* 3.5 4.1 + - - +
1188A ALA* 3.3 16.6 + - - +
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Residues in contact with TYR1185 (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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842A VAL* 3.4 14.1 - - + +
844A VAL* 3.6 13.7 - - + -
848A GLY* 2.9 30.3 + - - -
850A ILE* 3.5 28.3 - - + -
1006A PRO* 3.8 17.7 + - + -
1174A ILE 5.1 1.4 + - - -
1175A LEU* 4.8 8.8 - - + +
1176A PRO* 3.5 24.0 - - + -
1181A ALA 2.6 21.0 + - - +
1182A ASN* 3.4 9.0 - - - +
1184A ALA* 1.3 72.3 - - - +
1186A ASN* 1.3 69.8 + - - +
1188A ALA* 3.2 7.8 + - - +
1189A ARG* 3.1 57.3 + - - +
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Residues in contact with ASN1186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001A THR* 2.8 41.1 + - - +
1004A ILE* 3.6 9.3 + - - +
1006A PRO* 4.7 1.0 - - - +
1182A ASN* 2.7 43.8 + - - +
1185A TYR* 1.3 75.1 - - - +
1187A ILE* 1.3 66.6 + - - +
1188A ALA 3.3 0.3 + - - -
1189A ARG* 2.3 40.3 + - - +
1190A LYS* 3.3 24.9 + - - +
1218A TRP* 3.5 14.5 - - + -
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Residues in contact with ILE1187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831A ILE 4.0 14.1 - - - +
832A ASP* 3.6 26.2 - - - +
923A ALA* 3.5 37.8 - - + +
924A LEU* 4.2 3.6 - - - +
925A GLU* 5.0 10.8 - - + +
996A ILE* 3.9 23.7 - - + +
998A ALA* 4.6 13.7 - - + +
1001A THR* 4.1 20.8 - - + +
1183A GLY 2.9 22.2 + - - +
1184A ALA 3.9 5.4 - - - +
1185A TYR 3.4 0.4 - - - -
1186A ASN* 1.3 76.6 - - - +
1188A ALA* 1.3 63.4 + - - +
1190A LYS* 3.5 13.9 + - - +
1191A VAL 3.7 3.3 + - - -
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Residues in contact with ALA1188 (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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828A VAL* 3.9 23.1 - - + +
830A GLY* 3.9 13.7 - - - +
842A VAL 4.5 2.0 - - - +
844A VAL* 4.5 13.2 - - + -
923A ALA* 3.9 10.1 - - - -
1184A ALA 3.3 12.3 + - - +
1185A TYR* 3.2 11.4 + - - +
1186A ASN 3.1 0.6 - - - -
1187A ILE* 1.3 76.2 - - - +
1189A ARG* 1.3 60.0 + - - +
1191A VAL* 3.0 20.8 + - - +
1192A LEU* 3.0 14.3 + - - +
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Residues in contact with ARG1189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A VAL* 5.3 1.6 - - + -
848A GLY* 4.8 5.4 - - - -
1004A ILE* 5.4 2.4 - - - +
1005A ASP 5.5 0.2 + - - -
1006A PRO* 4.0 19.9 + - - +
1009A GLY* 5.6 1.0 - - - +
1185A TYR* 3.1 57.7 + - + +
1186A ASN* 2.3 38.8 + - - +
1188A ALA* 1.3 75.6 - - - +
1190A LYS* 1.3 57.3 + - - +
1192A LEU* 3.0 21.8 + - + +
1193A TRP* 2.8 27.9 + - - +
1218A TRP* 3.9 26.1 - - + -
1221A TYR* 3.7 15.3 + - + +
1222A ALA* 3.5 32.3 + - - +
1225A SER* 4.1 10.9 + - - -
1226A VAL* 5.0 5.1 - - - +
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Residues in contact with LYS1190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996A ILE* 3.5 33.0 - - + +
997A PRO* 2.9 22.1 + - - +
999A TRP* 2.6 32.3 + - - +
1001A THR* 3.7 10.9 - - + +
1186A ASN 3.3 9.9 + - - +
1187A ILE 3.6 8.7 - - - +
1188A ALA 3.2 0.6 - - - -
1189A ARG* 1.3 75.8 - - - +
1191A VAL* 1.3 58.8 + - - +
1193A TRP* 3.2 14.9 - - - +
1194A ALA* 2.9 24.3 + - - +
1213A ILE* 3.9 18.3 - - + +
1215A ASN* 4.9 2.8 + - - -
1218A TRP* 3.4 49.1 - - + +
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Residues in contact with VAL1191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828A VAL* 4.0 7.9 - - + -
921A VAL* 3.8 21.3 - - + -
922A ILE 4.8 0.2 - - - +
923A ALA* 3.4 27.1 - - + -
994A PHE* 3.7 35.2 - - + -
996A ILE* 3.9 11.9 - - + -
1187A ILE 3.7 0.4 + - - -
1188A ALA 3.0 10.4 + - - +
1190A LYS* 1.3 75.1 - - - +
1192A LEU* 1.3 54.7 + - - +
1194A ALA* 2.9 7.9 + - + +
1195A ILE* 2.7 52.1 + - + +
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Residues in contact with LEU1192 (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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826A PRO* 4.2 3.1 - - + +
828A VAL* 3.7 22.4 - - + -
844A VAL* 3.4 16.8 - - + -
845A ASP 3.3 26.9 - - - +
846A GLY* 4.1 18.8 - - - +
847A LYS 4.4 1.6 - - - +
848A GLY* 3.7 17.3 - - - +
1188A ALA 3.0 12.9 + - - +
1189A ARG* 3.0 16.0 + - + +
1191A VAL* 1.3 73.3 - - - +
1193A TRP* 1.3 58.8 + - - +
1195A ILE* 3.1 17.5 + - + +
1196A GLY* 2.8 26.7 + - - -
1221A TYR* 3.4 19.9 - - - +
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Residues in contact with TRP1193 (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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1189A ARG 2.8 16.2 + - - +
1190A LYS* 3.2 13.0 - - - +
1192A LEU* 1.3 72.7 - - - +
1194A ALA* 1.3 75.8 + - + +
1196A GLY* 3.0 12.8 + - - -
1197A GLN* 3.1 53.7 + - + +
1210A LYS* 4.2 12.6 - - + -
1211A ILE* 3.5 22.4 - - - -
1213A ILE* 3.5 44.4 - - + -
1217A GLU* 3.6 43.0 + - + +
1221A TYR* 3.9 40.5 - + + -
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Residues in contact with ALA1194 (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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994A PHE* 5.2 4.7 - - + -
996A ILE* 6.0 1.3 - - + -
1190A LYS 2.9 12.6 + - - +
1191A VAL* 2.9 16.1 + - + +
1193A TRP* 1.3 85.2 - - + +
1195A ILE* 1.3 66.0 + - + +
1197A GLN* 3.1 15.3 + - - +
1198A PHE* 3.2 22.8 + - + -
1211A ILE* 3.7 34.5 - - + +
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Residues in contact with ILE1195 (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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820A LEU* 4.0 38.8 - - + +
826A PRO* 4.2 20.9 - - + -
828A VAL* 4.1 7.6 - - + -
921A VAL* 4.8 1.3 - - + -
1191A VAL* 2.7 37.8 + - + +
1192A LEU* 3.4 27.6 - - + +
1194A ALA* 1.3 71.4 - - - +
1196A GLY* 1.3 59.1 + - - +
1198A PHE* 2.9 28.6 + - + +
1199A LYS* 3.1 38.2 + - + +
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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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1192A LEU 2.8 13.6 + - - -
1193A TRP* 3.0 6.5 + - - -
1195A ILE* 1.3 78.8 - - - +
1197A GLN* 1.3 63.1 + - - +
1199A LYS* 3.5 19.8 + - - +
1200A LYS* 3.5 22.9 + - - +
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Residues in contact with GLN1197 (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 TRP* 3.1 60.9 + - + +
1194A ALA* 3.1 9.0 + - - +
1196A GLY* 1.3 73.3 - - - +
1198A PHE* 1.3 66.6 + - - +
1200A LYS* 3.2 46.6 + - - +
1201A ALA* 3.6 9.2 + - - +
1209A VAL* 3.8 22.8 - - + +
1210A LYS* 4.5 5.6 + - - +
1217A GLU* 4.7 3.8 + - - -
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Residues in contact with PHE1198 (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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817A ARG* 3.8 43.1 - - + +
820A LEU* 4.2 29.4 - - + -
821A LYS* 3.6 18.4 - - + +
994A PHE* 4.3 13.0 - + - -
1194A ALA* 3.5 14.4 - - + -
1195A ILE* 2.9 17.1 + - + +
1197A GLN* 1.3 72.0 - - - +
1199A LYS* 1.3 60.0 + - - +
1200A LYS 2.9 10.8 + - - -
1201A ALA 2.9 15.9 + - - +
1206A LEU* 3.6 27.5 - - + +
1209A VAL* 3.9 17.7 - - + -
1211A ILE* 3.4 37.2 - - + -
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Residues in contact with LYS1199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A LEU 3.5 12.1 + - - -
821A LYS* 3.1 38.3 + - + +
822A HIS 4.7 0.2 - - - -
823A ASP 2.6 31.7 + - - -
824A ASP* 4.5 5.2 - - - +
826A PRO* 4.8 5.4 - - - -
1195A ILE* 3.1 30.8 + - + +
1196A GLY* 3.7 13.2 - - - +
1197A GLN 3.3 0.2 - - - -
1198A PHE* 1.3 79.8 - - - +
1200A LYS* 1.3 56.6 + - - +
1201A ALA 3.5 1.3 - - - +
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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