Contacts of the helix formed by residues 1108 - 1129 (chain L) in PDB entry 3F5P
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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1107L PRO* 1.3 78.3 - - - +
1109L LEU* 1.3 64.6 + - - +
1110L SER* 3.6 8.5 + - - -
1111L LYS* 3.3 28.4 + - - +
1112L MET* 3.1 24.4 + - - +
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Residues in contact with LEU1109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108L SER* 1.3 74.5 - - - +
1110L SER* 1.3 59.0 + - - +
1112L MET* 3.3 2.5 + - - +
1113L ILE* 2.8 47.0 + - + +
1238L PRO* 3.9 37.5 - - + +
1240L MET* 4.1 25.4 - - + -
1241L LEU* 4.8 11.7 - - + -
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Residues in contact with SER1110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108L SER* 3.2 8.6 + - - -
1109L LEU* 1.3 77.1 - - - +
1111L LYS* 1.3 66.8 + - - +
1113L ILE* 3.2 8.1 + - - +
1114L GLN* 2.9 24.0 + - - +
1269L GLU* 4.4 17.0 + - - +
1271L GLU* 5.8 4.9 - - - +
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Residues in contact with LYS1111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107L PRO* 4.2 11.2 - - + -
1108L SER* 3.3 27.9 + - - +
1110L SER* 1.3 79.3 - - - +
1112L MET* 1.3 62.3 + - - +
1114L GLN* 3.0 22.9 + - + +
1115L MET* 3.1 19.4 + - + +
1147L PHE* 5.2 20.0 - - - +
1271L GLU* 5.5 6.9 + - - +
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Residues in contact with MET1112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107L PRO* 3.5 40.8 - - + +
1108L SER 3.1 20.6 + - - +
1109L LEU* 3.7 4.0 - - - +
1111L LYS* 1.3 76.4 - - - +
1113L ILE* 1.3 59.3 + - - +
1115L MET* 2.9 10.3 + - - +
1116L ALA* 2.8 28.0 + - - +
1205L ILE* 3.6 27.0 - - + +
1206L ALA* 3.6 31.6 - - + +
1238L PRO* 4.7 16.8 - - + -
1241L LEU* 3.6 34.8 - - + -
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Residues in contact with ILE1113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109L LEU* 2.8 37.5 + - + +
1110L SER* 3.5 7.4 - - - +
1112L MET* 1.3 75.0 - - - +
1114L GLN* 1.3 59.2 + - - +
1116L ALA* 3.5 5.1 - - + +
1117L GLY* 2.8 28.6 + - - -
1240L MET* 3.2 40.2 - - + -
1241L LEU* 4.2 10.1 - - + -
1244L LEU* 5.4 0.2 - - + -
1266L ILE* 3.7 29.6 - - + -
1269L GLU* 4.2 26.2 - - + +
1270L MET* 3.7 7.6 - - - +
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Residues in contact with GLN1114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110L SER* 2.9 14.1 + - - +
1111L LYS* 3.0 18.4 + - + +
1113L ILE* 1.3 77.8 - - - +
1115L MET* 1.3 56.2 + - + +
1118L GLU* 3.0 60.4 + - - +
1147L PHE 5.9 1.6 - - - +
1269L GLU 4.4 1.9 - - - +
1270L MET* 3.3 27.1 - - - +
1271L GLU* 3.0 56.4 + - + +
1274L PHE* 5.2 4.0 - - - +
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Residues in contact with MET1115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087L LEU* 4.2 15.5 - - + -
1090L TYR* 3.7 34.1 - - + +
1091L LEU* 4.7 4.0 - - + -
1094L LEU* 5.7 1.8 - - + -
1107L PRO* 5.9 6.1 - - + -
1111L LYS* 3.7 18.2 - - + +
1112L MET* 2.9 9.0 + - - +
1114L GLN* 1.3 74.3 - - + +
1116L ALA* 1.3 61.7 + - - +
1118L GLU* 3.9 3.1 - - - +
1119L ILE* 2.9 39.4 + - + +
1143L VAL* 5.7 1.6 - - + -
1147L PHE* 5.1 9.2 - - + +
1149L VAL* 3.5 27.6 - - + -
1205L ILE* 3.7 36.6 - - + -
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Residues in contact with ALA1116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112L MET 2.8 12.7 + - - +
1113L ILE* 3.5 13.9 - - + +
1115L MET* 1.3 77.5 - - - +
1117L GLY* 1.3 57.1 + - - +
1119L ILE* 4.7 0.9 - - - -
1120L ALA* 2.9 31.1 + - - +
1198L PHE* 3.5 12.0 - - + -
1202L LEU* 3.6 32.3 - - + -
1205L ILE* 4.7 2.2 - - - +
1241L LEU* 4.9 7.0 - - + -
1244L LEU* 5.3 3.8 - - + -
1262L ILE* 6.0 0.7 - - + -
1266L ILE* 4.3 8.7 - - + -
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Residues in contact with GLY1117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113L ILE 2.8 10.7 + - - -
1116L ALA* 1.3 74.9 - - - +
1118L GLU* 1.3 60.7 + - - +
1120L ALA* 3.8 5.0 - - - +
1121L ASP* 2.9 30.5 + - - +
1263L ILE* 4.4 3.9 - - - +
1266L ILE* 3.6 11.0 - - - +
1270L MET* 3.6 25.6 - - - -
1274L PHE* 4.0 7.1 - - - -
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Residues in contact with GLU1118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061L HIS* 3.3 47.9 + - + +
1114L GLN* 3.0 54.8 + - - +
1115L MET* 3.9 3.7 - - - +
1117L GLY* 1.3 77.1 - - - +
1119L ILE* 1.3 60.1 + - - +
1121L ASP* 3.4 1.8 + - - -
1122L GLY 3.3 6.6 + - - -
1147L PHE 3.9 3.5 - - - +
1148L THR* 3.3 29.7 + - - +
1149L VAL* 2.8 43.0 + - - +
1151L ILE* 5.0 0.2 - - - +
1270L MET* 4.2 3.6 - - + +
1274L PHE* 4.7 1.8 - - + -
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Residues in contact with ILE1119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087L LEU* 3.9 20.2 - - + -
1115L MET 2.9 24.8 + - - +
1116L ALA* 4.0 3.6 - - - +
1118L GLU* 1.3 73.5 - - - +
1120L ALA* 1.3 65.5 + - - +
1122L GLY 3.5 1.2 + - - -
1123L MET* 3.2 27.1 + - + +
1136L LEU* 4.6 9.6 - - + -
1141L CYS* 4.0 6.3 - - - -
1149L VAL* 4.0 18.8 - - + -
1151L ILE* 3.7 26.4 - - + +
1198L PHE* 3.7 23.3 - - + -
1201L VAL* 3.7 27.6 - - + -
1202L LEU* 6.4 0.2 - - + -
1205L ILE* 4.5 5.2 - - + -
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Residues in contact with ALA1120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116L ALA 2.9 21.1 + - - +
1117L GLY* 3.8 2.0 - - - +
1119L ILE* 1.3 77.3 - - - +
1121L ASP* 1.3 58.5 + - - +
1123L MET* 3.4 0.7 + - - +
1124L ALA* 2.9 28.6 + - - +
1198L PHE* 3.9 19.7 - - + -
1259L PHE* 3.6 21.0 - - + +
1262L ILE* 4.5 9.2 - - + -
1263L ILE* 3.7 21.5 - - + -
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Residues in contact with ASP1121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059L CYS* 4.0 3.1 - - - -
1061L HIS* 2.7 32.5 + - + +
1117L GLY 2.9 17.9 + - - +
1118L GLU 3.6 1.1 - - - +
1120L ALA* 1.3 75.9 - - - +
1122L GLY* 1.3 65.5 + - - +
1124L ALA* 3.2 2.9 + - - +
1125L TYR* 3.0 22.7 + - - +
1263L ILE* 3.5 10.0 - - + +
1274L PHE* 4.1 3.1 - - + -
1278L SER* 3.9 6.7 - - - -
1279L PHE* 2.7 26.7 + - - +
1280L TYR* 2.9 34.1 + - - +
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Residues in contact with GLY1122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059L CYS* 4.4 1.8 - - - -
1061L HIS* 3.8 27.0 - - - +
1062L VAL* 4.0 15.4 - - - +
1118L GLU 3.3 8.7 + - - -
1119L ILE 3.5 3.1 + - - -
1121L ASP* 1.3 78.8 - - - +
1123L MET* 1.3 58.6 + - - +
1125L TYR* 3.5 6.9 - - - +
1126L LEU* 3.0 25.3 + - - +
1151L ILE* 4.6 5.4 - - - -
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Residues in contact with MET1123 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1119L ILE* 3.2 17.9 + - + +
1120L ALA 3.4 0.4 + - - +
1121L ASP 3.2 0.6 - - - -
1122L GLY* 1.3 74.3 - - - +
1124L ALA* 1.3 60.6 + - - +
1126L LEU* 3.1 9.5 + - + +
1127L ASN* 2.8 37.1 + - - +
1133L HIS* 3.7 21.5 - - + +
1136L LEU* 3.9 30.3 - - + -
1151L ILE* 4.0 18.6 - - + -
1194L ASP* 3.1 43.5 - - + +
1259L PHE* 3.5 34.8 - - + -
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Residues in contact with ALA1124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120L ALA 2.9 13.9 + - - +
1121L ASP 3.4 9.6 - - - +
1123L MET* 1.3 77.2 - - - +
1125L TYR* 1.3 56.0 + - - +
1127L ASN* 3.3 3.6 + - - +
1128L ALA* 2.8 31.9 + - - +
1259L PHE* 3.9 19.2 - - + +
1260L LEU* 4.1 21.0 - - + +
1263L ILE* 4.2 6.1 - - + -
1279L PHE* 3.9 15.3 - - + -
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Residues in contact with TYR1125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056L GLU 3.7 5.7 + - - -
1057L PHE* 3.6 34.4 - + + -
1058L ASN* 3.0 29.4 + - - +
1059L CYS* 3.5 29.4 - - + -
1062L VAL* 4.6 4.5 - - + -
1121L ASP 3.0 13.2 + - - +
1122L GLY 3.5 9.6 - - - +
1124L ALA* 1.3 72.9 - - - +
1126L LEU* 1.3 67.6 + - + +
1128L ALA* 3.2 2.1 + - - +
1129L ASN* 2.7 54.2 + - - -
1279L PHE* 3.4 31.5 - + + -
1284L GLU* 3.7 28.7 + - - -
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Residues in contact with LEU1126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057L PHE* 3.6 46.7 - - + -
1062L VAL* 5.4 1.6 - - + -
1122L GLY 3.0 17.4 + - - +
1123L MET* 3.3 17.0 - - + +
1125L TYR* 1.3 78.3 - - + +
1127L ASN* 1.3 64.1 + - - +
1129L ASN* 3.1 14.7 + - - +
1131L PHE* 3.3 40.0 + - + +
1133L HIS* 4.0 33.4 - - + +
1151L ILE* 5.4 0.9 - - + -
1154L PHE* 4.2 21.5 - - + -
1157L THR* 4.8 2.2 - - + -
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Residues in contact with ASN1127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123L MET* 2.8 20.0 + - - +
1124L ALA* 4.0 3.8 - - - +
1126L LEU* 1.3 77.1 - - - +
1128L ALA* 1.3 58.5 + - - +
1130L LYS* 3.0 27.4 + - - +
1131L PHE 2.9 24.1 + - - +
1191L THR* 3.2 38.1 - - + +
1194L ASP* 3.6 16.8 + - - -
1259L PHE* 2.9 32.4 - - + -
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Residues in contact with ALA1128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124L ALA 2.8 18.7 + - - +
1125L TYR 3.4 6.3 - - - +
1126L LEU 3.1 0.2 - - - -
1127L ASN* 1.3 78.5 - - - +
1129L ASN* 1.3 60.4 + - - +
1130L LYS* 3.1 10.2 + - - +
1260L LEU* 6.5 0.4 - - + -
1279L PHE* 3.6 26.2 - - + -
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Residues in contact with ASN1129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056L GLU* 4.9 16.9 - - + +
1057L PHE* 5.0 4.9 - - + -
1125L TYR* 2.7 61.1 + - - -
1126L LEU* 3.1 8.8 + - - +
1128L ALA* 1.3 78.4 - - - +
1130L LYS* 1.3 72.2 + - - +
1131L PHE* 3.5 22.5 - - + -
1159L ASP* 4.6 1.2 - - - +
1279L PHE* 5.7 0.2 - - - -
1284L GLU* 5.0 4.0 + - - +
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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