Contacts of the helix formed by residues 1108 - 1129 (chain A) in PDB entry 3LW0
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 SER1108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106A PRO 3.4 4.5 + - - -
1107A PRO* 1.3 76.5 - - - +
1109A LEU* 1.3 64.6 + - - +
1110A SER* 3.6 9.3 + - - -
1111A LYS* 3.1 34.7 + - - +
1112A MET* 3.0 21.5 + - - +
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Residues in contact with LEU1109 (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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1108A SER* 1.3 72.7 - - - +
1110A SER* 1.3 65.6 + - - +
1112A MET* 3.2 7.7 + - - +
1113A ILE* 2.9 50.4 + - + +
1238A PRO* 3.7 38.3 - - + +
1240A MET* 4.0 16.6 - - + -
1241A LEU* 3.9 14.8 - - + -
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Residues in contact with SER1110 (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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1108A SER* 3.2 8.5 + - - -
1109A LEU* 1.3 79.6 - - - +
1111A LYS* 1.3 63.3 + - - +
1113A ILE* 3.3 7.7 + - - +
1114A GLN* 3.0 44.7 + - - +
1269A GLU 5.0 1.4 + - - -
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Residues in contact with LYS1111 (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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1107A PRO* 4.3 11.5 - - + +
1108A SER* 3.1 34.2 + - - +
1110A SER* 1.3 77.5 - - - +
1112A MET* 1.3 62.1 + - - +
1114A GLN* 3.2 5.5 + - - +
1115A MET* 3.1 29.1 + - - +
1287A CCX 3.8 55.5 - - + +
1023D LYS* 5.4 5.3 - - - +
1024D ASP* 2.8 40.1 + - - -
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Residues in contact with MET1112 (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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1106A PRO* 6.2 0.7 - - + -
1107A PRO* 3.4 38.1 - - + +
1108A SER 3.0 16.6 + - - +
1109A LEU* 3.6 9.0 - - - +
1111A LYS* 1.3 74.6 - - - +
1113A ILE* 1.3 57.9 + - - +
1115A MET* 3.4 12.2 + - + +
1116A ALA* 3.0 28.4 + - - +
1202A LEU* 5.6 0.3 - - - +
1205A ILE* 3.7 41.6 - - + +
1206A ALA* 4.1 14.1 - - - +
1208A LEU* 5.7 0.7 - - + -
1238A PRO* 4.9 9.9 - - + -
1241A LEU* 3.8 32.2 - - + +
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Residues in contact with ILE1113 (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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1109A LEU* 2.9 41.9 + - + +
1110A SER* 3.6 7.9 - - - +
1112A MET* 1.3 73.5 - - - +
1114A GLN* 1.3 67.1 + - - +
1116A ALA* 3.2 6.7 + - - +
1117A GLY 2.9 20.8 + - - -
1240A MET* 3.7 31.4 - - + -
1241A LEU* 4.5 4.5 - - + -
1266A ILE* 4.6 14.8 - - + -
1269A GLU* 3.9 41.3 - - + +
1270A MET* 3.6 14.3 - - - +
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Residues in contact with GLN1114 (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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1110A SER* 3.0 42.0 + - - +
1111A LYS* 3.2 6.7 + - - +
1113A ILE* 1.3 78.9 - - - +
1115A MET* 1.3 64.2 + - - +
1117A GLY 3.4 0.3 + - - -
1118A GLU* 3.0 31.4 + - - +
1269A GLU 3.0 24.5 + - - -
1270A MET* 3.6 15.2 - - + +
1271A GLU* 2.8 50.8 + - - +
1287A CCX 3.7 25.1 - - + -
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Residues in contact with MET1115 (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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1087A LEU* 4.1 17.0 - - - -
1091A LEU* 5.1 1.1 - - + -
1107A PRO* 4.9 2.5 - - + -
1111A LYS 3.1 19.2 + - - +
1112A MET* 3.7 10.5 - - + +
1114A GLN* 1.3 76.1 - - - +
1116A ALA* 1.3 63.0 + - - +
1118A GLU* 3.4 7.9 + - - +
1119A ILE* 3.0 33.1 + - + +
1149A VAL* 3.7 27.1 - - + -
1205A ILE* 3.9 35.2 - - + -
1287A CCX 3.5 52.7 - - + +
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Residues in contact with ALA1116 (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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1112A MET 3.0 17.2 + - - +
1113A ILE* 3.5 8.5 - - - +
1115A MET* 1.3 76.4 - - - +
1117A GLY* 1.3 57.4 + - - +
1119A ILE* 4.7 3.1 - - - -
1120A ALA* 2.9 30.0 + - - +
1198A PHE* 3.5 15.4 - - + -
1202A LEU* 3.6 28.0 - - + -
1205A ILE* 4.8 1.7 - - - +
1241A LEU* 5.3 4.9 - - + -
1244A LEU* 5.2 4.7 - - + -
1266A ILE* 4.4 10.3 - - + -
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Residues in contact with GLY1117 (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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1113A ILE 2.9 11.8 + - - -
1116A ALA* 1.3 75.0 - - - +
1118A GLU* 1.3 59.5 + - - +
1120A ALA* 3.8 4.0 - - - +
1121A ASP* 2.9 31.2 + - - +
1263A ILE* 4.6 3.3 - - - +
1266A ILE* 3.8 16.1 - - - +
1270A MET* 3.8 21.1 - - - -
1274A PHE* 3.8 7.5 - - - -
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Residues in contact with GLU1118 (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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1061A HIS* 3.4 36.8 + - + +
1114A GLN* 3.0 21.9 + - - +
1115A MET* 3.7 5.4 - - - +
1117A GLY* 1.3 73.1 - - - +
1119A ILE* 1.3 66.4 + - - +
1121A ASP 3.3 0.5 + - - -
1122A GLY* 3.0 19.4 + - - -
1148A THR* 3.6 12.7 - - - +
1149A VAL* 3.0 46.2 + - - +
1270A MET* 4.1 7.1 - - + +
1271A GLU* 4.3 2.5 - - - +
1274A PHE* 5.2 1.3 - - + -
1287A CCX 3.5 39.5 - - - +
1287D CCX 5.8 0.3 + - - -
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Residues in contact with ILE1119 (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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1087A LEU* 4.2 9.2 - - + -
1115A MET* 3.0 22.8 + - + +
1116A ALA* 3.8 4.5 - - - +
1118A GLU* 1.3 75.4 - - - +
1120A ALA* 1.3 63.5 + - - +
1121A ASP 3.3 0.2 + - - -
1122A GLY 3.3 0.5 + - - -
1123A MET* 3.0 24.4 + - + +
1136A LEU* 4.3 14.1 - - + -
1141A CYS* 4.1 10.5 - - - -
1149A VAL* 3.6 30.5 - - + +
1151A ILE* 3.8 22.0 - - + +
1198A PHE* 3.7 22.2 - - + -
1201A VAL* 4.0 24.5 - - + -
1202A LEU* 6.4 0.2 - - + -
1205A ILE* 4.4 5.8 - - + -
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Residues in contact with ALA1120 (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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1116A ALA 2.9 19.1 + - - +
1117A GLY* 3.9 2.9 - - - +
1118A GLU 3.3 0.2 - - - -
1119A ILE* 1.3 77.1 - - - +
1121A ASP* 1.3 57.3 + - - +
1123A MET 3.4 0.5 + - - -
1124A ALA* 2.8 29.8 + - - +
1198A PHE* 4.0 15.5 - - + -
1259A PHE* 3.7 24.3 - - + +
1262A ILE* 4.2 9.2 - - + -
1263A ILE* 3.8 22.0 - - + -
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Residues in contact with ASP1121 (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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1059A CYS* 4.6 2.8 - - - -
1061A HIS* 2.8 29.5 + - - +
1117A GLY 2.9 18.8 + - - +
1118A GLU 3.7 0.7 - - - +
1119A ILE 3.2 0.2 - - - -
1120A ALA* 1.3 74.3 - - - +
1122A GLY* 1.3 65.8 + - - +
1124A ALA* 3.3 2.4 + - - +
1125A TYR* 3.0 22.9 + - - +
1263A ILE* 3.6 8.9 - - + +
1274A PHE* 4.0 6.7 - - + -
1278A SER* 3.3 11.5 - - - -
1279A PHE* 2.8 25.5 + - - +
1280A TYR* 2.9 34.0 + - - +
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Residues in contact with GLY1122 (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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1059A CYS* 4.3 4.0 - - - -
1061A HIS* 3.8 28.1 - - - +
1062A VAL* 3.9 8.9 - - - +
1118A GLU 3.0 12.1 + - - -
1119A ILE 3.8 2.2 - - - -
1121A ASP* 1.3 74.8 - - - +
1123A MET* 1.3 57.9 + - - +
1125A TYR* 3.4 3.8 + - - +
1126A LEU* 3.0 31.8 + - - +
1151A ILE* 4.2 8.1 - - - -
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Residues in contact with MET1123 (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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1119A ILE* 3.0 21.4 + - + +
1120A ALA 3.7 3.4 - - - +
1122A GLY* 1.3 73.9 - - - +
1124A ALA* 1.3 58.5 + - - +
1126A LEU* 3.7 9.7 - - + +
1127A ASN* 2.8 41.1 + - - +
1133A HIS* 3.8 22.7 - - + +
1136A LEU* 3.9 28.3 - - + -
1151A ILE* 3.9 23.3 - - + -
1194A ASP* 3.4 41.5 - - + +
1259A PHE* 3.6 25.1 - - + -
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Residues in contact with ALA1124 (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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1120A ALA 2.8 21.1 + - - +
1121A ASP 3.3 5.6 + - - +
1123A MET* 1.3 72.0 - - - +
1125A TYR* 1.3 56.8 + - - +
1127A ASN* 4.0 3.4 - - - +
1128A ALA* 2.9 31.5 + - - +
1259A PHE* 3.8 16.9 - - + +
1260A LEU* 3.8 30.8 - - + +
1263A ILE* 4.2 7.2 - - + -
1279A PHE* 3.7 7.9 - - + -
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Residues in contact with TYR1125 (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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1056A GLU* 3.9 4.3 + - - +
1057A PHE* 3.4 35.8 - + + -
1058A ASN* 3.0 34.5 + - - +
1059A CYS* 3.6 32.5 - - + -
1062A VAL* 4.5 2.0 - - + -
1121A ASP 3.0 12.9 + - - +
1122A GLY 3.5 8.3 - - - +
1124A ALA* 1.3 76.1 - - - +
1126A LEU* 1.3 72.9 + - + +
1128A ALA* 3.3 1.9 + - - +
1129A ASN* 2.9 50.7 + - - -
1279A PHE* 3.6 31.5 - + + -
1284A GLU* 3.5 21.4 + - - -
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Residues in contact with LEU1126 (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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1A CCX 6.0 0.9 - - + -
1054A MET* 4.7 2.9 - - + -
1057A PHE* 3.9 35.7 - - + -
1062A VAL* 4.2 17.7 - - + -
1122A GLY 3.0 20.7 + - - +
1123A MET* 3.3 17.5 + - + +
1125A TYR* 1.3 84.0 - - + +
1127A ASN* 1.3 64.9 + - - +
1129A ASN* 3.1 11.1 + - - +
1130A LYS 3.3 0.2 + - - -
1131A PHE* 2.9 55.6 + - + +
1133A HIS* 4.6 2.0 - - + -
1151A ILE* 4.2 25.1 - - + -
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Residues in contact with ASN1127 (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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1123A MET* 2.8 27.8 + - - +
1124A ALA* 4.0 4.9 - - - +
1126A LEU* 1.3 73.9 - - - +
1128A ALA* 1.3 60.9 + - - +
1130A LYS* 3.1 18.0 + - - +
1131A PHE 3.1 20.1 + - - +
1132A VAL* 4.2 0.4 - - - +
1191A THR* 3.4 39.9 - - + +
1194A ASP* 3.2 21.0 + - - -
1259A PHE* 3.2 26.1 - - - -
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Residues in contact with ALA1128 (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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1124A ALA 2.9 19.0 + - - +
1125A TYR 3.6 3.8 - - - +
1126A LEU 3.2 0.2 - - - -
1127A ASN* 1.3 76.3 - - - +
1129A ASN* 1.3 60.4 + - - +
1130A LYS* 3.2 15.5 + - - +
1260A LEU* 6.3 1.1 - - + -
1279A PHE* 3.6 27.4 - - + -
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Residues in contact with ASN1129 (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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1056A GLU* 3.7 22.5 - - - +
1057A PHE* 3.8 24.9 - - + -
1125A TYR* 2.9 52.1 + - - +
1126A LEU 3.1 5.2 + - - +
1128A ALA* 1.3 80.9 - - - +
1130A LYS* 1.3 70.4 + - - +
1131A PHE* 3.3 5.0 + - - +
1279A PHE* 5.2 2.0 - - - -
1284A GLU* 5.2 0.8 + - - -
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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
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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