Contacts of the helix formed by residues 1008 - 1034 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006E SER 4.2 0.6 + - - -
1007E ALA* 1.3 75.4 - - - +
1009E ILE* 1.3 66.5 + - - -
1010E LEU* 3.0 5.4 - - - -
1011E LEU* 2.9 30.2 + - - +
1012E LEU* 3.3 6.8 + - - +
1091E LYS* 5.0 6.1 - - - +
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Residues in contact with ILE1009 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007E ALA 3.6 2.0 + - - -
1008E GLY* 1.3 71.8 - - - -
1010E LEU* 1.3 62.0 + - + +
1012E LEU* 2.9 30.0 + - + +
1013E SER* 3.0 13.5 + - - -
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Residues in contact with LEU1010 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008E GLY* 3.0 2.4 - - - -
1009E ILE* 1.3 85.9 - - + +
1011E LEU* 1.3 58.4 + - + +
1013E SER* 3.6 8.4 - - - -
1014E LEU* 2.9 39.6 + - + +
1087E TRP* 5.4 12.3 - - + -
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Residues in contact with LEU1011 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007E ALA* 3.6 16.8 - - + -
1008E GLY* 2.9 19.3 + - - +
1010E LEU* 1.3 78.5 - - + +
1012E LEU* 1.3 58.3 + - + +
1014E LEU* 4.1 4.2 - - + +
1015E LEU* 2.9 34.4 + - - +
1084E THR* 4.0 18.0 - - + +
1087E TRP* 3.4 33.0 - - + -
1088E THR* 3.5 40.3 - - - +
1091E LYS* 3.6 30.1 - - + -
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Residues in contact with LEU1012 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004E LEU* 3.5 68.4 - - + +
1007E ALA* 4.8 3.4 - - + -
1008E GLY 3.6 11.0 - - - +
1009E ILE* 2.9 20.0 + - + +
1011E LEU* 1.3 76.8 - - + +
1013E SER* 1.3 63.6 + - - +
1015E LEU* 3.9 9.5 - - + +
1016E VAL* 3.0 39.8 + - + +
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Residues in contact with SER1013 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009E ILE* 3.0 11.3 + - - -
1010E LEU* 3.6 13.9 - - - -
1011E LEU 3.3 0.2 - - - -
1012E LEU* 1.3 77.2 - - - +
1014E LEU* 1.3 64.5 + - - +
1016E VAL* 3.9 2.0 - - - -
1017E PHE* 2.9 49.6 + - - -
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Residues in contact with LEU1014 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010E LEU* 2.9 33.8 + - + +
1011E LEU* 4.1 4.9 - - + +
1012E LEU 3.4 0.2 - - - -
1013E SER* 1.3 72.4 - - - +
1015E LEU* 1.3 55.8 + - - +
1017E PHE* 3.9 4.8 - - + +
1018E SER* 2.4 45.1 + - - +
1080E VAL* 4.1 17.3 - - + -
1084E THR* 3.2 33.7 - - + +
1087E TRP* 5.8 5.6 - - + -
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Residues in contact with LEU1015 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011E LEU 2.9 18.6 + - - +
1012E LEU* 3.9 9.9 - - + +
1014E LEU* 1.3 77.8 - - - +
1016E VAL* 1.3 76.6 + - + +
1018E SER* 3.2 4.3 + - - -
1019E GLN* 3.0 43.5 + - + +
1081E THR* 5.4 0.8 - - - +
1084E THR* 3.7 12.9 - - + +
1085E VAL* 4.8 17.0 - - + -
1088E THR* 4.2 24.7 - - + +
1139E LEU* 4.5 21.1 - - + -
1143E SER* 5.1 4.5 - - - +
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Residues in contact with VAL1016 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012E LEU* 3.0 29.7 + - + +
1013E SER* 4.0 2.7 - - - +
1015E LEU* 1.3 88.1 - - + +
1017E PHE* 1.3 68.0 + - + +
1019E GLN* 3.4 3.1 + - - +
1020E LEU* 3.0 45.9 + - + +
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Residues in contact with PHE1017 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013E SER* 2.9 46.6 + - - +
1014E LEU* 4.1 5.6 - - + +
1016E VAL* 1.3 80.2 - - + +
1018E SER* 1.3 62.9 + - - +
1020E LEU* 4.7 7.9 - - + -
1021E LEU* 2.9 50.5 + - + +
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Residues in contact with SER1018 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014E LEU* 2.4 41.6 + - - +
1015E LEU* 3.5 6.3 - - - -
1017E PHE* 1.3 75.0 - - - +
1019E GLN* 1.3 65.8 + - - +
1022E LYS* 2.8 27.5 + - - +
1077E LEU* 4.0 11.0 - - - +
1080E VAL* 4.0 11.7 - - - +
1081E THR* 3.3 32.9 + - - -
1084E THR* 4.2 1.4 + - - -
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Residues in contact with GLN1019 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015E LEU* 3.0 31.4 + - + +
1016E VAL* 3.9 4.3 - - - +
1018E SER* 1.3 75.9 - - - +
1020E LEU* 1.3 66.8 + - + +
1022E LYS* 3.3 4.5 - - - +
1023E HIS* 3.0 48.5 + - - +
1081E THR* 3.1 26.0 - - - +
1085E VAL* 4.3 14.5 - - - +
1140E GLU* 5.7 3.0 + - - +
1143E SER* 3.0 35.0 + - - +
1144E ARG* 4.2 4.9 + - - +
1147E LEU* 4.2 12.0 - - + +
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Residues in contact with LEU1020 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1016E VAL* 3.0 40.8 + - + +
1017E PHE* 4.0 7.2 - - + +
1019E GLN* 1.3 78.5 - - + +
1021E LEU* 1.3 67.3 + - + +
1023E HIS* 4.5 0.3 - - - +
1024E MET* 2.9 45.6 + - + +
1147E LEU* 3.9 28.9 - - + +
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Residues in contact with LEU1021 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017E PHE* 2.9 44.1 + - + +
1020E LEU* 1.3 75.9 - - + +
1022E LYS* 1.3 64.9 + - - +
1024E MET* 4.5 9.6 - - + -
1025E VAL* 2.9 33.0 + - + +
1077E LEU* 3.5 21.8 - - + -
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Residues in contact with LYS1022 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548E THR* 3.4 24.8 - - - +
1018E SER 2.8 19.6 + - - +
1019E GLN* 3.3 5.2 - - - +
1021E LEU* 1.3 79.0 - - - +
1023E HIS* 1.3 93.1 + - + +
1025E VAL* 3.1 3.8 + - - +
1026E LEU* 2.9 40.2 + - + +
1074E GLY* 4.8 3.4 + - - +
1077E LEU* 3.3 16.7 - - + +
1078E CYS* 3.5 41.6 - - + +
1081E THR* 3.7 25.6 - - + +
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Residues in contact with HIS1023 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548E THR* 5.3 1.2 - - - +
1019E GLN* 3.0 27.0 + - - -
1022E LYS* 1.3 115.7 + - + +
1024E MET* 1.3 61.7 + - - +
1026E LEU* 3.2 16.9 + - + +
1027E VAL* 2.9 33.1 + - - +
1144E ARG* 4.0 13.7 - - + -
1147E LEU* 3.5 36.4 - - + +
1148E LEU* 3.2 41.1 - - + +
1151E SER* 5.2 3.6 - - - +
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Residues in contact with MET1024 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1020E LEU* 2.9 39.3 + - + +
1021E LEU* 4.0 10.5 - - + +
1023E HIS* 1.3 78.9 - - - +
1025E VAL* 1.3 57.1 + - + +
1027E VAL* 3.5 8.3 + - - +
1028E ALA* 2.8 27.4 + - - +
1147E LEU* 5.5 5.2 - - + -
1151E SER* 6.1 3.1 - - - -
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Residues in contact with VAL1025 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021E LEU* 2.9 27.8 + - + +
1022E LYS* 3.4 5.4 - - - +
1024E MET* 1.3 76.5 - - + +
1026E LEU* 1.3 59.1 + - - +
1028E ALA* 3.9 7.9 - - + -
1029E ILE* 2.8 32.1 + - + +
1070E LEU* 4.1 24.2 - - + +
1073E LEU* 3.6 36.6 - - + -
1074E GLY* 4.3 9.9 - - - +
1077E LEU* 4.6 0.7 - - + -
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Residues in contact with LEU1026 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552E ILE* 3.9 27.1 - - + -
584E HIS* 6.0 6.3 - - + -
1022E LYS* 2.9 45.1 + - + +
1023E HIS* 3.2 26.2 + - + +
1025E VAL* 1.3 75.5 - - + +
1027E VAL* 1.3 53.4 + - + +
1029E ILE* 3.0 23.9 - - + +
1030E ASP* 2.6 30.4 - - - +
1074E GLY* 5.1 13.2 - - - +
1148E LEU* 5.6 8.3 - - + -
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Residues in contact with VAL1027 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023E HIS 2.9 19.9 + - - +
1024E MET* 3.7 7.4 - - - +
1026E LEU* 1.3 75.7 - - + +
1028E ALA* 1.3 63.5 + - - +
1030E ASP* 2.6 20.3 - - - +
1031E TYR* 2.9 27.2 + - + +
1148E LEU* 6.2 2.0 - - + -
1151E SER* 3.9 27.1 - - - +
1152E ALA* 5.4 0.7 - - - +
1155E VAL* 3.5 30.5 - - + -
1286E TYR* 4.8 6.5 - - + +
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Residues in contact with ALA1028 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024E MET 2.8 22.9 + - - +
1025E VAL* 3.2 11.6 + - + +
1027E VAL* 1.3 74.8 - - - +
1029E ILE* 1.3 57.6 + - - +
1031E TYR* 3.8 2.8 - - - +
1032E TRP* 2.9 36.4 + - - +
1070E LEU* 4.4 8.5 - - + -
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Residues in contact with ILE1029 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552E ILE* 6.2 2.9 - - + -
555E VAL* 6.2 1.1 - - + -
1025E VAL* 2.8 21.5 + - + +
1026E LEU* 3.0 35.0 - - + +
1028E ALA* 1.3 73.3 - - - +
1030E ASP* 1.3 61.4 + - + +
1032E TRP* 3.6 2.8 - - - +
1033E LEU* 2.8 24.3 + - - +
1067E PHE* 3.6 26.0 - - + +
1070E LEU* 3.6 25.3 - - + +
1071E CYS* 3.3 53.2 - - - +
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Residues in contact with ASP1030 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577E PHE* 5.4 4.5 - - + -
580E LEU* 4.3 25.4 - - + -
584E HIS* 4.3 13.5 + - - -
1026E LEU* 2.6 22.5 + - - +
1027E VAL* 2.6 32.2 - - - +
1029E ILE* 1.3 75.2 - - + +
1031E TYR* 1.3 61.9 + - - -
1032E TRP 3.0 1.6 - - - -
1033E LEU* 3.0 11.7 + - + +
1034E ALA 3.0 21.7 + - - -
1067E PHE* 5.5 0.7 - - - -
1282E LEU* 3.8 6.5 - - - +
1286E TYR* 2.5 33.3 + - - +
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Residues in contact with TYR1031 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027E VAL* 2.9 25.0 + - + +
1028E ALA* 4.2 2.5 - - - +
1030E ASP* 1.3 82.6 + - - +
1032E TRP* 1.3 59.0 + - + +
1034E ALA* 3.0 18.9 - - + +
1035E LYS* 3.8 13.8 + - + +
1155E VAL* 4.7 5.2 - - + -
1158E TYR* 3.1 33.7 + + - -
1159E VAL* 3.8 22.2 - - + -
1279E LEU* 3.6 29.8 - - + +
1282E LEU* 3.4 32.5 - - + -
1286E TYR* 5.0 0.9 - - - +
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Residues in contact with TRP1032 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028E ALA 2.9 20.8 + - - +
1029E ILE* 3.7 1.6 - - - +
1031E TYR* 1.3 77.8 - - + +
1033E LEU* 1.3 59.3 + - - +
1034E ALA 3.1 1.1 - - - -
1035E LYS* 3.0 57.8 + - + +
1036E TRP* 3.3 7.8 + + + +
1063E TYR* 3.0 57.0 - + + -
1066E VAL* 3.3 24.0 - - + -
1067E PHE* 3.3 42.0 - + + -
1070E LEU* 4.1 17.5 - - + -
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Residues in contact with LEU1033 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559E PHE* 3.6 35.2 - - + -
576E ALA* 4.8 10.5 - - + -
577E PHE* 4.8 14.4 - - + -
580E LEU* 3.7 17.9 - - + -
1029E ILE 2.8 14.6 + - - +
1030E ASP* 3.1 14.1 - - - +
1032E TRP* 1.3 74.9 - - - +
1034E ALA* 1.3 58.7 + - - -
1036E TRP* 2.7 57.3 + - + +
1037E THR* 3.2 13.0 + - + +
1067E PHE* 3.9 27.1 - - + -
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Residues in contact with ALA1034 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577E PHE* 6.2 1.7 - - - -
1030E ASP 3.0 7.1 + - - -
1031E TYR* 3.0 19.5 - - + +
1032E TRP 3.1 0.4 - - - -
1033E LEU* 1.3 77.9 - - - +
1035E LYS* 1.3 56.8 + - + +
1037E THR* 2.9 26.0 + - - -
1038E ASP* 4.1 5.2 - - - +
1276E SER* 6.0 0.7 - - - -
1278E GLY* 4.7 9.3 - - - +
1279E LEU* 4.2 27.1 - - + +
1282E LEU* 3.6 23.5 - - + +
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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