Contacts of the helix formed by residues 1103 - 1130 (chain B) in PDB entry 6E5N
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 ASP1103 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101B SER* 3.2 3.5 + - - -
1102B CYS* 1.3 93.6 - - - +
1104B ILE* 1.3 65.1 + - + +
1105B GLU* 4.3 7.9 - - + +
1106B LEU* 3.3 18.4 + - + +
1107B LEU* 3.1 27.4 + - - +
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Residues in contact with ILE1104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1102B CYS 4.3 0.4 + - - -
1103B ASP* 1.3 72.1 - - - +
1105B GLU* 1.3 76.4 + - + +
1107B LEU* 3.2 15.9 + - + +
1108B ALA* 3.0 24.4 + - + +
1111B ARG* 6.0 3.1 - - - +
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Residues in contact with GLU1105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077B ALA* 5.6 4.3 - - + +
1080B GLY 6.5 0.2 - - - -
1081B THR* 3.5 29.9 - - - +
1084B TYR* 3.7 22.8 + - + -
1103B ASP* 3.2 6.7 - - + +
1104B ILE* 1.3 93.8 - - + +
1106B LEU* 1.3 61.6 + - - +
1108B ALA* 3.3 4.5 + - - +
1109B ALA* 3.0 18.5 + - - +
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Residues in contact with LEU1106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084B TYR* 4.8 6.9 - - + -
1086B LEU* 5.9 4.9 - - + -
1089B TRP* 6.3 1.6 - - + -
1097B THR* 3.6 29.4 - - + -
1101B SER* 2.9 38.4 - - - +
1102B CYS 5.8 0.2 - - - +
1103B ASP* 3.3 15.2 + - + +
1104B ILE 3.3 0.4 - - - -
1105B GLU* 1.3 76.5 - - - +
1107B LEU* 1.3 66.1 + - - +
1109B ALA* 3.1 9.2 + - + +
1110B CYS* 3.0 29.4 + - - -
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Residues in contact with LEU1107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1098B ILE* 3.7 27.3 - - + +
1101B SER* 3.2 31.2 - - - +
1102B CYS 5.4 0.9 - - - -
1103B ASP 3.1 20.4 + - - +
1104B ILE* 3.2 18.6 + - + +
1106B LEU* 1.3 78.1 - - - +
1108B ALA* 1.3 62.0 + - - +
1110B CYS* 3.3 5.6 + - - +
1111B ARG* 3.0 50.8 + - - +
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Residues in contact with ALA1108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1071B ALA* 5.0 1.3 - - + -
1073B LEU* 3.9 25.7 - - + +
1081B THR* 4.2 9.0 - - + -
1104B ILE* 3.0 15.2 + - + +
1105B GLU* 3.6 10.5 - - - +
1107B LEU* 1.3 76.0 - - - +
1109B ALA* 1.3 58.4 + - - +
1111B ARG* 3.2 15.4 + - - +
1112B GLU* 2.9 35.2 + - - +
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Residues in contact with ALA1109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1081B THR* 3.8 6.5 - - + +
1084B TYR* 3.6 25.1 - - + -
1086B LEU* 3.1 27.4 - - + +
1105B GLU 3.0 13.7 + - - +
1106B LEU* 3.1 11.2 + - + +
1108B ALA* 1.3 77.6 - - - +
1110B CYS* 1.3 62.7 + - - +
1112B GLU* 3.3 15.9 + - - +
1113B GLU* 3.0 17.7 + - - +
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Residues in contact with CYS1110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086B LEU* 3.7 15.5 - - - -
1094B LEU* 4.2 15.9 - - + -
1097B THR* 4.2 8.5 - - - -
1098B ILE* 3.3 37.7 - - + -
1106B LEU* 3.0 34.2 + - - -
1107B LEU 3.7 7.0 - - - +
1109B ALA* 1.3 73.2 - - - +
1111B ARG* 1.3 61.3 + - - +
1113B GLU* 3.2 3.9 + - - +
1114B PHE* 2.9 36.6 + - - -
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Residues in contact with ARG1111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065B PHE* 5.0 3.4 + - + +
1066B LEU* 3.4 28.2 - - + +
1068B ARG* 6.0 0.4 - - - +
1069B GLY* 2.7 43.4 + - - +
1070B PRO 3.7 11.5 + - - -
1071B ALA* 3.7 23.1 - - + +
1098B ILE* 6.0 4.7 - - + +
1104B ILE* 6.0 3.6 - - - +
1107B LEU* 3.0 38.9 + - - +
1108B ALA* 3.2 10.3 + - - +
1110B CYS* 1.3 77.4 - - + +
1112B GLU* 1.3 62.3 + - + +
1114B PHE* 3.3 3.5 + - - -
1115B HIS* 3.0 21.5 + - - +
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Residues in contact with GLU1112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073B LEU* 2.8 40.5 - - + +
1078B ALA* 4.6 2.1 - - - +
1081B THR* 3.8 6.5 - - - +
1082B LYS* 3.2 48.4 - - - +
1108B ALA 2.9 18.6 + - - +
1109B ALA* 3.5 15.5 - - - +
1110B CYS 3.2 0.2 - - - -
1111B ARG* 1.3 77.6 - - + +
1113B GLU* 1.3 61.7 + - - +
1115B HIS* 3.3 6.2 + - - +
1116B ARG* 3.0 32.6 + - + +
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Residues in contact with GLU1113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLY* 4.4 1.2 - - - +
1086B LEU* 3.9 23.8 + - + +
1087B SER* 3.2 35.0 + - - -
1094B LEU* 4.0 9.4 - - + -
1109B ALA 3.0 14.2 + - - +
1110B CYS* 3.2 9.2 + - - +
1112B GLU* 1.3 75.5 - - - +
1114B PHE* 1.3 59.8 + - + +
1116B ARG* 3.4 7.8 + - - +
1117B ARG* 2.8 74.3 + - - +
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Residues in contact with PHE1114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062B MET* 3.5 43.1 - - + -
1065B PHE* 4.2 19.1 - + + -
1066B LEU* 4.1 14.4 - - + -
1091B TYR* 4.3 19.1 - + - -
1094B LEU* 3.4 46.9 - - + -
1095B ARG* 4.5 4.9 - - + -
1098B ILE* 3.8 22.7 - - + -
1110B CYS 2.9 22.6 + - - +
1111B ARG* 3.5 5.8 - - - +
1113B GLU* 1.3 80.1 - - + +
1115B HIS* 1.3 57.2 + - - +
1117B ARG* 3.3 6.8 + - - +
1118B LEU* 2.8 37.1 + - - +
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Residues in contact with HIS1115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1066B LEU* 4.1 18.5 - - + +
1111B ARG 3.0 16.8 + - - +
1112B GLU* 3.6 7.0 - - - +
1113B GLU 3.3 0.2 - - - -
1114B PHE* 1.3 76.7 - - - +
1116B ARG* 1.3 63.2 + - + +
1118B LEU* 3.3 6.0 + - + +
1119B LYS* 2.9 36.6 + - + +
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Residues in contact with ARG1116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082B LYS* 5.6 6.9 - - - +
1112B GLU* 3.0 20.8 + - + +
1113B GLU* 3.8 11.9 - - - +
1115B HIS* 1.3 80.1 + - + +
1117B ARG* 1.3 63.4 + - - +
1119B LYS* 3.3 11.7 + - - +
1120B VAL* 3.1 29.6 + - + +
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Residues in contact with ARG1117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 3.5 27.9 - - - +
55A LEU* 3.9 13.1 + - + +
56A ASP* 2.7 37.1 + - - +
58A GLY* 3.2 14.9 - - - +
1062B MET* 4.6 5.6 - - - -
1086B LEU 3.6 0.6 + - - -
1087B SER 2.7 28.1 + - - -
1089B TRP 2.6 26.9 + - - -
1091B TYR* 3.9 7.5 - - - +
1094B LEU* 3.7 15.1 - - - +
1113B GLU* 2.8 46.8 + - - +
1114B PHE* 3.7 8.1 - - - +
1116B ARG* 1.3 76.0 - - - +
1118B LEU* 1.3 65.3 + - - +
1120B VAL* 3.3 4.6 + - - -
1121B TYR* 3.0 20.1 + - - +
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Residues in contact with LEU1118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.3 1.3 - - + -
1059B ALA* 3.4 44.6 - - + +
1062B MET* 3.3 29.8 - - + -
1063B SER* 3.9 9.4 - - - +
1066B LEU* 3.3 24.9 - - + -
1114B PHE 2.8 24.4 + - - +
1115B HIS* 3.6 8.1 - - + +
1117B ARG* 1.3 76.2 - - - +
1119B LYS* 1.3 64.7 + - - +
1121B TYR* 3.2 5.3 + - + +
1122B HIS* 2.9 41.2 + - + +
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Residues in contact with LYS1119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1115B HIS* 2.9 27.3 + - + +
1116B ARG* 3.5 14.6 - - - +
1117B ARG 3.3 0.2 - - - -
1118B LEU* 1.3 77.0 - - - +
1120B VAL* 1.3 65.8 + - + +
1122B HIS* 3.3 11.9 + - + +
1123B ALA* 3.0 25.4 + - + +
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Residues in contact with VAL1120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 3.4 16.2 - - + -
58A GLY 6.0 0.9 - - - +
59A ALA 3.6 5.6 - - - +
60A PRO* 3.1 38.8 - - + +
1116B ARG* 3.1 16.7 + - + +
1117B ARG* 3.7 9.0 - - - +
1119B LYS* 1.3 77.5 - - + +
1121B TYR* 1.3 56.1 + - - +
1123B ALA* 3.2 8.0 + - + +
1124B TRP* 2.8 28.1 + - - +
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Residues in contact with TYR1121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ALA* 3.8 20.0 - - + -
54A ILE* 3.3 10.4 - - + +
55A LEU* 3.2 30.7 - - + -
1055B PRO* 3.4 30.8 - - + +
1056B GLU* 3.1 33.4 + - + +
1059B ALA* 4.2 18.8 - - + -
1117B ARG 3.0 14.1 + - - +
1118B LEU* 3.2 9.6 + - - +
1120B VAL* 1.3 77.6 - - - +
1122B HIS* 1.3 75.5 + + - +
1124B TRP* 3.2 5.4 + + - +
1125B LYS* 3.0 55.7 + - + +
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Residues in contact with HIS1122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059B ALA* 5.5 3.8 - - + +
1118B LEU* 2.9 41.6 + - + +
1119B LYS* 3.6 13.9 - - + +
1120B VAL 3.3 0.2 - - - -
1121B TYR* 1.3 89.7 - + - +
1123B ALA* 1.3 64.2 + - - +
1125B LYS* 3.3 7.2 + - - +
1126B SER* 2.9 22.7 + - - -
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Residues in contact with ALA1123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1119B LYS* 3.0 17.9 + - + +
1120B VAL* 3.5 10.8 - - + +
1122B HIS* 1.3 76.1 - - - +
1124B TRP* 1.3 61.9 + - - +
1126B SER* 3.1 10.4 + - - -
1127B LYS* 3.1 36.3 + - - +
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Residues in contact with TRP1124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU* 2.8 49.6 - - + -
48A ASN* 4.4 4.7 - - - -
50A GLU* 2.9 25.3 + - + +
51A ALA* 3.2 25.8 - - + -
54A ILE* 3.3 31.2 - - + -
60A PRO 4.8 3.1 - - - +
61A GLY* 4.2 10.8 - - - -
1055B PRO* 5.7 0.2 - - + -
1120B VAL 2.8 9.2 + - - +
1121B TYR* 3.2 6.3 + + - +
1123B ALA* 1.3 75.7 - - - +
1125B LYS* 1.3 101.4 + - + +
1127B LYS* 3.1 27.7 + - + +
1128B ASN* 2.9 48.2 + - + +
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Residues in contact with LYS1125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056B GLU* 3.4 23.7 + - - +
1121B TYR* 3.0 51.4 + - + +
1122B HIS* 3.6 11.2 - - - +
1124B TRP* 1.3 99.8 - - + +
1126B SER* 1.3 53.7 + - - +
1128B ASN* 3.7 4.8 - - + +
1129B LYS* 2.7 71.5 + - + +
----------------------------------------------------------
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Residues in contact with SER1126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1122B HIS 2.9 13.6 + - - -
1123B ALA* 3.2 14.4 - - - -
1125B LYS* 1.3 77.4 - - - +
1127B LYS* 1.3 49.4 + - - +
1129B LYS* 4.4 4.5 - - - -
1130B LYS* 2.5 42.5 + - - +
1131B ARG* 4.1 16.3 + - - -
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Residues in contact with LYS1127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PRO 5.2 7.7 + - - -
1123B ALA* 3.1 25.6 + - - +
1124B TRP* 3.1 20.0 + - + +
1126B SER* 1.3 77.9 - - - +
1128B ASN* 1.3 64.7 + - - +
1130B LYS 2.5 20.9 - - - +
1131B ARG* 2.8 19.5 - - + +
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Residues in contact with ASN1128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU* 3.2 35.0 - - - +
50A GLU* 5.5 0.2 - - - +
1124B TRP* 2.9 62.8 + - + +
1125B LYS* 3.9 8.5 - - + +
1127B LYS* 1.3 78.9 - - - +
1129B LYS* 1.3 68.9 + - + +
1130B LYS* 4.6 0.2 - - - -
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Residues in contact with LYS1129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056B GLU* 5.9 0.2 - - - -
1125B LYS* 2.7 62.5 + - + +
1126B SER* 4.0 4.3 - - - +
1128B ASN* 1.3 77.5 - - + +
1130B LYS* 1.3 71.2 + - + +
----------------------------------------------------------
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Residues in contact with LYS1130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1126B SER* 2.5 26.8 + - - +
1127B LYS* 2.5 22.5 - - - +
1128B ASN 5.0 0.2 - - - -
1129B LYS* 1.3 85.3 - - + +
1131B ARG* 1.3 89.2 + - + +
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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