Contacts of the helix formed by residues 1055 - 1081 (chain B) in PDB entry 5UNG
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 SER1055 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1051B LYS* 3.7 17.9 - - - +
1052B SER* 3.3 25.7 + - - -
1053B PRO 3.3 0.8 - - - -
1054B ASP* 1.4 78.6 - - - +
1056B PRO* 1.4 69.6 - - - +
1057B GLU* 2.7 31.8 + - - +
1058B MET* 3.2 7.8 + - - +
1059B LYS* 3.1 20.3 + - - +
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Residues in contact with PRO1056 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1054B ASP 3.8 2.9 - - - +
1055B SER* 1.4 90.2 - - - +
1057B GLU* 1.3 63.6 + - - +
1059B LYS* 3.5 14.4 + - + +
1060B ASP* 3.1 26.9 + - - +
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Residues in contact with GLU1057 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1048B LEU* 4.3 23.9 - - + +
1051B LYS* 3.5 30.8 + - + +
1055B SER* 2.7 25.2 + - - +
1056B PRO* 1.3 86.9 - - - +
1058B MET* 1.3 60.2 + - - +
1060B ASP* 3.5 8.5 + - - +
1061B PHE* 3.2 23.2 + - - +
1105B TYR* 3.9 8.4 + - + -
1110B SER* 5.5 9.9 - - - +
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Residues in contact with MET1058 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043B ALA 5.0 0.9 - - - +
1044B THR* 4.2 21.3 - - + +
1045B PRO* 3.7 29.4 - - + -
1048B LEU* 3.8 21.1 - - + +
1051B LYS* 4.4 14.4 - - + +
1052B SER 3.5 20.6 - - - +
1053B PRO* 3.8 20.4 - - + +
1055B SER* 3.2 10.4 + - - +
1057B GLU* 1.3 75.4 - - - +
1059B LYS* 1.4 62.2 + - - +
1061B PHE* 3.3 21.6 + - + +
1062B ARG* 3.3 37.3 + - + +
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Residues in contact with LYS1059 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053B PRO 4.1 1.3 - - - +
1054B ASP* 3.4 30.0 + - - +
1055B SER 3.1 13.5 + - - +
1056B PRO* 3.6 15.5 - - + +
1058B MET* 1.4 73.3 - - - +
1060B ASP* 1.3 58.3 + - - +
1062B ARG* 3.5 25.9 + - - +
1063B HIS* 3.0 27.8 + - - +
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Residues in contact with ASP1060 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056B PRO 3.1 17.1 + - - +
1057B GLU* 3.6 10.1 - - - +
1059B LYS* 1.3 75.2 - - - +
1061B PHE* 1.4 58.1 + - - +
1063B HIS* 3.5 13.2 + - - +
1064B GLY* 3.0 24.3 + - - -
1104B LYS* 3.3 24.2 + - - -
1105B TYR* 2.8 21.7 + - - +
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Residues in contact with PHE1061 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003B LEU* 3.9 19.3 - - + -
1040B ALA 3.6 9.4 - - - -
1041B GLN 4.4 7.6 - - - -
1043B ALA 3.3 22.9 - - - -
1045B PRO* 3.7 24.5 - - + -
1048B LEU* 5.5 0.2 - - + -
1057B GLU 3.2 11.1 + - - +
1058B MET* 3.5 29.6 - - + +
1059B LYS 3.3 0.4 - - - -
1060B ASP* 1.4 76.1 - - - +
1062B ARG* 1.3 63.9 + - + +
1064B GLY* 3.4 8.1 + - - -
1065B PHE* 3.3 40.5 + + - -
1101B TYR* 3.7 24.2 - + - -
1105B TYR* 3.2 39.7 + + + +
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Residues in contact with ARG1062 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041B GLN* 2.8 64.6 + - + +
1042B LYS* 6.1 0.2 - - - +
1053B PRO* 2.8 46.4 + - - +
1058B MET* 3.3 24.0 + - + +
1059B LYS* 3.7 27.4 - - - +
1061B PHE* 1.3 78.4 - - + +
1063B HIS* 1.4 62.2 + - - +
1065B PHE 3.4 1.9 + - - -
1066B ASP* 3.1 9.4 + - - +
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Residues in contact with HIS1063 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059B LYS 3.0 17.7 + - - +
1060B ASP* 3.8 15.7 - - - +
1061B PHE 3.3 0.2 - - - -
1062B ARG* 1.4 73.6 - - - +
1064B GLY* 1.3 64.6 + - - +
1066B ASP* 3.1 27.8 + - + +
1067B ILE* 3.2 38.5 + - + +
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Residues in contact with GLY1064 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060B ASP 3.0 14.9 + - - -
1061B PHE* 3.4 5.8 + - - -
1062B ARG 3.3 0.8 - - - -
1063B HIS* 1.3 77.4 - - - +
1065B PHE* 1.3 61.1 + - - +
1067B ILE* 3.6 14.2 + - - +
1068B LEU* 3.4 18.0 + - - +
1097B THR* 4.0 10.1 - - - +
1105B TYR* 6.0 3.4 - - - -
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Residues in contact with PHE1065 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007B TRP* 3.5 43.1 - + - -
1010B LEU* 4.7 1.6 - - + -
1037B ALA* 3.4 25.6 - - - +
1040B ALA* 3.7 23.1 - - + -
1041B GLN* 3.5 31.2 - - + +
1061B PHE* 3.3 55.9 - + - -
1062B ARG 3.4 1.4 + - - -
1063B HIS 3.3 0.2 - - - -
1064B GLY* 1.3 74.5 - - - +
1066B ASP* 1.4 59.3 + - - +
1067B ILE 3.3 0.7 - - - -
1068B LEU* 3.3 21.6 + - + +
1069B VAL* 2.9 33.8 + - + +
1101B TYR* 4.3 4.9 - + - -
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Residues in contact with ASP1066 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038B LEU* 5.7 1.7 - - - +
1041B GLN* 3.1 19.3 + - - +
1062B ARG* 3.1 15.6 + - - +
1063B HIS* 3.1 28.7 + - + +
1065B PHE* 1.4 73.4 - - - +
1067B ILE* 1.4 58.9 + - - +
1069B VAL* 4.2 5.7 - - - +
1070B GLY* 3.2 22.0 + - - -
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Residues in contact with ILE1067 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063B HIS* 3.2 43.4 + - + +
1064B GLY* 3.7 13.2 - - - +
1065B PHE 3.3 0.4 - - - -
1066B ASP* 1.4 74.6 - - - +
1068B LEU* 1.4 55.8 + - - +
1070B GLY* 3.4 2.5 + - - -
1071B GLN* 2.9 57.1 + - + +
1097B THR* 4.5 9.0 - - + -
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Residues in contact with LEU1068 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007B TRP* 4.4 15.5 - - + -
1010B LEU* 3.9 20.0 - - + -
1033B MET* 5.3 2.2 - - + -
1037B ALA* 3.8 24.0 - - + -
1064B GLY 3.4 11.2 + - - +
1065B PHE* 3.3 23.5 + - + +
1067B ILE* 1.4 76.2 - - - +
1069B VAL* 1.4 58.9 + - - +
1071B GLN* 3.3 6.3 + - - +
1072B ILE* 2.9 38.5 + - + +
1094B LEU* 3.8 26.9 - - + +
1097B THR* 3.8 26.6 - - + +
1098B ARG* 5.0 3.6 - - + +
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Residues in contact with VAL1069 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034B ARG* 4.1 27.6 - - + +
1037B ALA* 3.8 24.5 - - + -
1038B LEU* 4.0 29.8 - - + +
1041B GLN* 5.4 0.4 - - - +
1065B PHE* 2.9 24.6 + - + +
1066B ASP* 4.3 5.2 - - - +
1068B LEU* 1.4 67.7 - - - +
1070B GLY* 1.3 59.5 + - - +
1072B ILE* 3.3 7.3 + - + +
1073B ASP* 3.0 48.5 + - - +
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Residues in contact with GLY1070 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1066B ASP 3.2 16.7 + - - -
1067B ILE* 3.6 4.5 - - - -
1068B LEU 3.3 0.2 - - - -
1069B VAL* 1.3 76.9 - - - +
1071B GLN* 1.4 57.6 + - - +
1073B ASP* 3.6 8.0 + - - +
1074B ASP* 3.0 30.2 + - - +
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Residues in contact with GLN1071 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067B ILE* 2.9 35.6 + - + +
1068B LEU* 3.3 6.0 + - - +
1070B GLY* 1.4 74.8 - - - +
1072B ILE* 1.4 61.9 + - - +
1074B ASP* 3.4 11.4 + - - +
1075B ALA* 3.3 21.0 + - - +
1090B ALA* 5.3 4.0 - - - +
1093B GLN* 3.3 36.4 + - + +
1094B LEU* 3.7 18.0 - - + +
1097B THR* 2.7 29.9 + - - -
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Residues in contact with ILE1072 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030B LEU* 3.4 39.0 - - + +
1033B MET* 3.9 38.4 - - + +
1034B ARG* 3.8 22.0 - - + +
1037B ALA* 4.5 2.5 - - + -
1068B LEU* 2.9 38.8 + - + +
1069B VAL* 3.6 7.9 - - - +
1071B GLN* 1.4 73.7 - - - +
1073B ASP* 1.4 53.2 - - - +
1075B ALA* 3.3 5.0 + - - +
1076B LEU* 2.8 42.3 + - + +
1094B LEU* 3.7 15.0 - - + -
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Residues in contact with ASP1073 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034B ARG* 2.8 44.6 + - - -
1069B VAL* 3.0 24.5 + - - +
1070B GLY* 3.7 8.1 - - - +
1072B ILE* 1.4 74.2 - - - +
1074B ASP* 1.4 59.6 + - - +
1076B LEU* 3.4 9.2 + - - +
1077B LYS* 3.1 28.9 + - - +
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Residues in contact with ASP1074 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070B GLY 3.0 20.5 + - - +
1071B GLN* 3.6 13.1 - - - +
1072B ILE 3.3 0.4 - - - -
1073B ASP* 1.4 78.1 - - - +
1075B ALA* 1.4 59.6 + - - +
1077B LYS* 3.6 12.9 + - - +
1078B LEU* 3.4 26.5 + - + +
1090B ALA* 5.4 2.9 - - + -
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Residues in contact with ALA1075 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030B LEU* 3.8 21.5 - - + -
1071B GLN 3.3 9.4 + - - +
1072B ILE* 3.3 8.2 + - - +
1074B ASP* 1.4 76.9 - - - +
1076B LEU* 1.4 59.3 + - - +
1078B LEU* 3.3 11.6 + - - -
1079B ALA* 3.0 24.1 + - - +
1087B ALA* 3.4 29.4 - - - +
1090B ALA* 4.2 10.5 - - + +
1091B ALA* 4.6 5.8 - - - +
1094B LEU* 5.4 0.9 - - + -
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Residues in contact with LEU1076 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027B LYS* 3.8 29.8 - - + +
1030B LEU* 3.7 23.3 - - + +
1031B THR* 4.2 14.4 - - - +
1034B ARG* 4.3 17.0 - - - +
1072B ILE* 2.8 34.8 + - + +
1073B ASP* 3.4 11.0 + - - +
1075B ALA* 1.4 75.5 - - - +
1077B LYS* 1.4 56.1 + - - +
1079B ALA* 3.4 2.9 + - - +
1080B ASN* 2.9 50.5 + - - +
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Residues in contact with LYS1077 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073B ASP 3.1 16.6 + - - +
1074B ASP* 3.8 17.6 + - - +
1075B ALA 3.3 0.2 - - - -
1076B LEU* 1.4 73.7 - - - +
1078B LEU* 1.4 74.6 + - - +
1080B ASN* 3.4 9.0 + - + +
1081B GLU* 3.1 64.1 + - + +
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Residues in contact with LEU1078 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074B ASP* 3.4 19.7 + - + +
1075B ALA* 3.3 7.3 + - - +
1077B LYS* 1.4 90.0 - - - +
1079B ALA* 1.4 60.6 + - - +
1081B GLU* 3.4 6.4 + - - +
1082B GLY 3.4 4.0 + - - -
1083B LYS* 3.0 60.1 + - + +
1086B GLU* 3.9 18.4 - - + +
1087B ALA* 3.9 10.5 - - + +
1090B ALA* 3.9 27.1 - - + -
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Residues in contact with ALA1079 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023B ALA* 3.4 36.6 - - - +
1026B VAL* 4.1 16.8 - - + -
1027B LYS* 4.4 12.4 - - + +
1030B LEU* 4.6 0.7 - - + -
1075B ALA 3.0 13.7 + - - +
1076B LEU* 3.5 13.0 - - - +
1077B LYS 3.3 0.2 - - - -
1078B LEU* 1.4 75.7 - - - +
1080B ASN* 1.4 60.2 + - - +
1082B GLY 3.4 5.4 + - - -
1083B LYS 4.0 7.9 - - - -
1084B VAL* 5.8 0.2 - - - +
1087B ALA* 3.9 9.1 - - + +
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Residues in contact with ASN1080 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027B LYS* 3.4 33.7 + - - +
1076B LEU* 2.9 40.6 + - - +
1077B LYS* 3.8 9.1 - - + +
1078B LEU 3.4 0.2 - - - -
1079B ALA* 1.4 76.2 - - - +
1081B GLU* 1.3 61.1 + - + +
1082B GLY 3.5 0.7 + - - -
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Residues in contact with GLU1081 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077B LYS* 3.1 50.1 + - + +
1078B LEU* 3.8 9.5 - - - +
1079B ALA 3.3 0.6 - - - -
1080B ASN* 1.3 77.8 - - - +
1082B GLY* 1.3 57.9 + - - +
1083B LYS* 3.5 27.8 + - + +
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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
------------------------------------------------------------
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