Contacts of the helix formed by residues 1008 - 1034 (chain F) in PDB entry 6C3P
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 GLY1008 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006F SER 4.2 0.4 + - - -
1007F ALA* 1.3 76.4 - - - +
1009F ILE* 1.3 66.8 + - - -
1010F LEU* 3.0 4.7 - - - -
1011F LEU* 2.9 31.3 + - - +
1012F LEU* 3.3 6.2 + - - +
1091F LYS* 5.0 5.9 - - - +
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Residues in contact with ILE1009 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007F ALA 3.6 2.0 + - - -
1008F GLY* 1.3 71.0 - - - -
1010F LEU* 1.3 62.2 + - + +
1012F LEU* 2.9 29.9 + - + +
1013F SER* 3.0 13.4 + - - -
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Residues in contact with LEU1010 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008F GLY* 3.0 2.6 - - - -
1009F ILE* 1.3 86.8 - - + +
1011F LEU* 1.3 58.4 + - + +
1013F SER* 3.4 8.3 + - - -
1014F LEU* 2.9 39.4 + - + +
1087F TRP* 5.4 12.6 - - + -
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Residues in contact with LEU1011 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007F ALA* 3.6 16.8 - - + -
1008F GLY* 2.9 20.2 + - - +
1010F LEU* 1.3 77.6 - - + +
1012F LEU* 1.3 58.6 + - + +
1014F LEU* 4.1 4.4 - - + +
1015F LEU* 2.9 34.2 + - - +
1084F THR* 4.0 19.5 - - + +
1087F TRP* 3.4 32.3 - - + -
1088F THR* 3.5 39.9 - - - +
1091F LYS* 3.6 28.9 - - + -
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Residues in contact with LEU1012 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004F LEU* 3.5 69.3 - - + +
1007F ALA* 4.5 3.6 - - + +
1008F GLY 3.6 11.0 - - - +
1009F ILE* 2.9 20.4 + - + +
1011F LEU* 1.3 77.5 - - + +
1013F SER* 1.3 62.9 + - - +
1015F LEU* 3.9 8.7 - - + +
1016F VAL* 3.0 40.6 + - + +
1088F THR* 5.9 0.2 - - - +
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Residues in contact with SER1013 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009F ILE* 3.0 12.2 + - - -
1010F LEU* 3.6 13.7 - - - -
1012F LEU* 1.3 77.1 - - - +
1014F LEU* 1.3 63.3 + - - +
1016F VAL* 3.9 2.0 - - - -
1017F PHE* 2.9 50.3 + - - -
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Residues in contact with LEU1014 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010F LEU* 2.9 32.0 + - + +
1011F LEU* 4.1 4.7 - - + +
1012F LEU 3.4 0.2 - - - -
1013F SER* 1.3 73.6 - - - +
1015F LEU* 1.3 55.7 + - - +
1017F PHE* 4.1 4.4 - - + -
1018F SER* 2.4 45.8 + - - +
1080F VAL* 4.1 17.0 - - + -
1084F THR* 3.2 35.0 - - + +
1087F TRP* 5.8 5.6 - - + -
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Residues in contact with LEU1015 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011F LEU 2.9 20.3 + - - +
1012F LEU* 3.9 9.6 - - + +
1014F LEU* 1.3 76.3 - - - +
1016F VAL* 1.3 76.7 + - + +
1018F SER* 3.2 4.5 + - - -
1019F GLN* 3.0 43.1 + - + +
1081F THR* 6.4 0.4 - - + -
1084F THR* 3.7 13.5 - - + +
1085F VAL* 4.8 17.9 - - + -
1088F THR* 4.2 24.5 - - + +
1139F LEU* 4.5 20.9 - - + -
1143F SER* 5.1 5.2 - - - +
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Residues in contact with VAL1016 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012F LEU* 3.0 29.0 + - + +
1013F SER* 4.0 2.7 - - - +
1015F LEU* 1.3 89.2 - - + +
1017F PHE* 1.3 68.0 + - + +
1018F SER 3.3 0.2 + - - -
1019F GLN* 3.9 2.9 - - - +
1020F LEU* 3.0 46.1 + - + +
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Residues in contact with PHE1017 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013F SER* 2.9 47.3 + - - +
1014F LEU* 4.1 5.2 - - + +
1016F VAL* 1.3 80.2 - - + +
1018F SER* 1.3 63.7 + - - +
1020F LEU* 4.7 6.7 - - + -
1021F LEU* 2.9 51.0 + - + +
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Residues in contact with SER1018 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014F LEU* 2.4 41.9 + - - +
1015F LEU* 3.5 6.7 - - - -
1016F VAL 3.2 0.2 - - - -
1017F PHE* 1.3 76.4 - - - +
1019F GLN* 1.3 63.1 - - - +
1022F LYS* 2.8 27.9 + - - +
1077F LEU* 4.0 11.6 - - - +
1080F VAL* 4.0 11.7 - - - +
1081F THR* 3.3 35.4 + - - -
1084F THR* 4.2 1.2 + - - -
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Residues in contact with GLN1019 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015F LEU* 3.0 32.5 + - + +
1016F VAL* 3.9 4.0 - - - +
1018F SER* 1.3 76.8 - - - +
1020F LEU* 1.3 65.2 + - + +
1022F LYS* 3.3 4.6 - - - +
1023F HIS* 3.0 49.5 + - - +
1081F THR* 3.1 27.4 - - - +
1085F VAL* 4.3 14.1 - - - +
1140F GLU* 5.7 2.6 - - - +
1143F SER* 3.0 35.2 + - - +
1144F ARG* 4.2 4.6 + - - +
1147F LEU* 4.2 12.4 - - + +
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Residues in contact with LEU1020 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1016F VAL* 3.0 41.7 + - + +
1017F PHE* 4.0 7.0 - - + +
1019F GLN* 1.3 80.0 - - + +
1021F LEU* 1.3 66.6 + - + +
1023F HIS* 4.5 0.3 - - - +
1024F MET* 2.9 44.9 + - - +
1147F LEU* 3.9 29.6 - - + -
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Residues in contact with LEU1021 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017F PHE* 2.9 42.8 + - + +
1020F LEU* 1.3 76.7 - - + +
1022F LYS* 1.3 65.0 + - - +
1024F MET* 3.8 9.5 - - + +
1025F VAL* 2.9 32.4 + - + +
1077F LEU* 3.5 22.0 - - + -
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Residues in contact with LYS1022 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548F THR* 3.4 25.2 - - - +
1018F SER 2.8 21.3 + - - +
1019F GLN* 3.3 4.3 - - - +
1020F LEU 3.2 0.2 - - - -
1021F LEU* 1.3 78.7 - - - +
1023F HIS* 1.3 94.2 + - + +
1025F VAL* 3.1 3.8 + - - +
1026F LEU* 2.9 40.8 + - + +
1074F GLY* 4.8 3.3 - - - +
1077F LEU* 3.3 17.6 - - + +
1078F CYS* 3.5 40.5 - - + +
1081F THR* 3.7 25.6 - - + +
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Residues in contact with HIS1023 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548F THR* 5.3 1.4 - - - +
1019F GLN* 3.0 26.9 + - - -
1022F LYS* 1.3 115.7 + - + +
1024F MET* 1.3 62.3 + - - +
1026F LEU* 3.2 17.2 + - + +
1027F VAL* 2.9 32.7 + - - +
1144F ARG* 4.0 14.1 - - + +
1147F LEU* 3.5 36.0 - - + +
1148F LEU* 3.2 41.8 - - + +
1151F SER* 5.2 3.1 - - - +
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Residues in contact with MET1024 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1020F LEU* 2.9 40.2 + - + +
1021F LEU* 4.0 10.3 - - + +
1023F HIS* 1.3 78.0 - - - +
1025F VAL* 1.3 58.3 + - + +
1027F VAL* 3.5 9.0 + - - +
1028F ALA* 2.8 26.9 + - - +
1147F LEU* 5.5 5.2 - - + -
1151F SER* 6.1 2.9 - - - -
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Residues in contact with VAL1025 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021F LEU* 2.9 27.9 + - + +
1022F LYS* 3.4 5.2 - - - +
1024F MET* 1.3 75.7 - - + +
1026F LEU* 1.3 59.4 + - - +
1028F ALA* 3.5 8.0 - - + +
1029F ILE* 2.8 33.4 + - + +
1070F LEU* 4.1 24.0 - - + +
1073F LEU* 3.6 36.8 - - + -
1074F GLY* 4.3 9.2 - - - +
1077F LEU* 4.6 0.2 - - + -
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Residues in contact with LEU1026 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552F ILE* 3.9 29.4 - - + -
584F HIS* 6.0 6.3 - - + -
1022F LYS* 2.9 46.3 + - + +
1023F HIS* 3.2 26.4 + - + +
1025F VAL* 1.3 75.5 - - + +
1027F VAL* 1.3 55.6 + - + +
1029F ILE* 3.0 23.7 - - + +
1030F ASP* 2.6 30.3 - - - +
1074F GLY* 5.1 14.4 - - - +
1148F LEU* 5.6 8.5 - - + -
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Residues in contact with VAL1027 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023F HIS* 2.9 19.4 + - + +
1024F MET* 3.7 7.9 - - - +
1026F LEU* 1.3 75.9 - - + +
1028F ALA* 1.3 63.9 + - - +
1030F ASP* 2.6 19.9 - - - +
1031F TYR* 2.9 27.6 + - + +
1148F LEU* 6.2 2.2 - - + -
1151F SER* 3.9 26.9 - - - +
1152F ALA* 5.9 0.4 - - - -
1155F VAL* 3.5 30.5 - - + -
1286F TYR* 4.8 7.2 - - + +
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Residues in contact with ALA1028 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024F MET 2.8 21.2 + - - +
1025F VAL* 3.2 12.5 + - + +
1027F VAL* 1.3 74.0 - - - +
1029F ILE* 1.3 58.0 + - - +
1031F TYR* 3.8 3.7 - - - +
1032F TRP* 2.9 35.4 + - - +
1070F LEU* 4.4 9.4 - - + -
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Residues in contact with ILE1029 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552F ILE* 6.2 3.1 - - + -
555F VAL* 6.2 1.1 - - + -
1025F VAL* 2.8 21.7 + - + +
1026F LEU* 3.0 35.4 - - + +
1028F ALA* 1.3 73.7 - - - +
1030F ASP* 1.3 61.0 + - + +
1032F TRP* 3.6 2.4 - - - +
1033F LEU* 2.8 24.1 + - - +
1067F PHE* 3.6 26.1 - - + +
1070F LEU* 3.6 25.7 - - + +
1071F CYS* 3.3 52.7 - - - +
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Residues in contact with ASP1030 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577F PHE* 5.4 3.6 - - + -
580F LEU* 4.3 25.1 - - + -
584F HIS* 4.3 13.2 + - - -
1026F LEU* 2.6 23.2 + - - +
1027F VAL* 2.6 31.7 - - - +
1029F ILE* 1.3 76.0 - - + +
1031F TYR* 1.3 60.2 + - - -
1032F TRP 3.0 0.9 - - - -
1033F LEU* 3.0 12.2 + - + +
1034F ALA 3.0 21.8 + - - -
1067F PHE* 5.5 0.4 - - - -
1282F LEU* 3.8 6.9 - - - +
1286F TYR* 2.5 33.1 + - - +
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Residues in contact with TYR1031 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027F VAL* 2.9 24.1 + - + +
1028F ALA* 4.2 3.4 - - - +
1030F ASP* 1.3 83.4 + - - +
1032F TRP* 1.3 59.2 + - + +
1034F ALA* 3.0 18.2 - - + +
1035F LYS* 3.8 13.8 + - + +
1155F VAL* 4.7 4.9 - - + -
1158F TYR* 3.1 34.1 + + - -
1159F VAL* 3.8 21.3 - - + -
1279F LEU* 3.6 30.1 - - + +
1282F LEU* 3.4 31.6 - - + +
1286F TYR* 5.0 0.9 - - - +
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Residues in contact with TRP1032 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028F ALA 2.9 21.3 + - - +
1029F ILE 3.7 1.1 - - - +
1031F TYR* 1.3 78.1 - - + +
1033F LEU* 1.3 59.8 + - - +
1034F ALA 3.1 0.7 - - - -
1035F LYS* 3.0 59.8 + - + +
1036F TRP* 3.3 8.1 + + + +
1063F TYR* 3.0 57.5 - + + -
1066F VAL* 3.3 22.7 - - + -
1067F PHE* 3.3 42.8 - + + -
1070F LEU* 4.1 17.9 - - + -
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Residues in contact with LEU1033 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559F PHE* 3.6 33.9 - - + -
576F ALA* 4.8 11.0 - - + -
577F PHE* 4.8 14.1 - - + -
580F LEU* 3.7 18.6 - - + -
1029F ILE 2.8 14.6 + - - +
1030F ASP* 3.1 13.0 - - - +
1032F TRP* 1.3 74.1 - - - +
1034F ALA* 1.3 59.0 + - - +
1036F TRP* 2.7 58.0 + - + +
1037F THR* 3.2 12.2 + - + +
1067F PHE* 3.9 26.7 - - + -
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Residues in contact with ALA1034 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577F PHE* 6.2 2.2 - - - -
1030F ASP 3.0 6.9 + - - -
1031F TYR* 3.0 19.3 - - + +
1033F LEU* 1.3 75.9 - - - +
1035F LYS* 1.3 57.4 + - + +
1037F THR* 2.9 26.3 + - - -
1038F ASP* 4.1 5.2 - - - +
1276F SER* 6.0 1.0 - - - -
1278F GLY* 4.7 9.1 - - - -
1279F LEU* 4.2 26.4 - - + +
1282F LEU* 3.6 23.3 - - + -
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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