Contacts of the helix formed by residues 1009 - 1039 (chain E) in PDB entry 6BAA
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 GLY1009 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005E LEU 3.0 12.4 + - - +
1006E SER* 3.8 7.1 + - - -
1007E SER 3.5 2.0 - - - -
1008E ALA* 1.3 85.8 - - - +
1010E ILE* 1.3 64.3 + - - -
1011E LEU 3.3 3.0 + - - -
1012E LEU 4.0 1.5 + - - -
1013E LEU* 3.6 17.7 + - - +
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Residues in contact with ILE1010 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009E GLY* 1.3 72.9 - - - -
1011E LEU* 1.3 59.5 + - - +
1013E LEU* 3.3 8.6 - - - +
1014E SER* 2.9 28.8 + - - -
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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
----------------------------------------------------------
1009E GLY 3.3 0.8 - - - -
1010E ILE* 1.3 78.8 - - - +
1012E LEU* 1.3 58.4 + - - +
1014E SER* 3.2 8.8 + - - -
1015E LEU* 3.0 25.5 + - - +
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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
----------------------------------------------------------
1008E ALA* 4.7 14.8 - - + +
1009E GLY 4.0 2.2 + - - -
1011E LEU* 1.3 75.1 - - - +
1013E LEU* 1.3 61.6 + - - +
1015E LEU* 3.6 8.9 - - + +
1016E LEU* 2.9 30.8 + - - +
1085E THR* 5.2 6.1 - - - +
1089E THR* 4.7 21.4 - - - +
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Residues in contact with LEU1013 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005E LEU* 6.5 1.6 - - + -
1008E ALA* 5.9 3.5 - - + +
1009E GLY 3.6 14.1 + - - +
1010E ILE* 3.3 13.9 + - - +
1011E LEU 3.2 0.2 - - - -
1012E LEU* 1.3 77.5 - - - +
1014E SER* 1.3 57.0 + - - +
1016E LEU* 3.2 5.4 + - - +
1017E VAL* 2.9 33.8 + - - +
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Residues in contact with SER1014 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010E ILE 2.9 13.5 + - - -
1011E LEU* 3.2 11.0 + - - -
1013E LEU* 1.3 74.5 - - - +
1015E LEU* 1.3 63.5 + - - +
1017E VAL* 4.4 2.6 - - - +
1018E PHE* 3.0 30.0 + - - +
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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
----------------------------------------------------------
1011E LEU 3.0 13.1 + - - +
1012E LEU* 3.6 12.1 - - + +
1014E SER* 1.3 75.4 - - - +
1016E LEU* 1.3 56.7 + - - +
1018E PHE* 4.2 2.0 - - - +
1019E SER* 2.9 32.7 + - - -
1085E THR* 5.1 9.4 - - - -
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Residues in contact with LEU1016 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012E LEU 2.9 18.9 + - - +
1013E LEU* 3.2 6.0 + - - +
1015E LEU* 1.3 76.4 - - - +
1017E VAL* 1.3 58.2 + - - +
1019E SER* 3.3 3.7 + - - -
1020E GLN* 2.9 30.7 + - - +
1082E THR* 5.0 7.0 - - - +
1085E THR* 4.5 21.1 - - - -
1086E VAL* 5.5 2.0 - - - +
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Residues in contact with VAL1017 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013E LEU 2.9 16.4 + - - +
1014E SER* 4.4 2.9 - - - +
1016E LEU* 1.3 76.2 - - - +
1018E PHE* 1.3 58.3 + - - +
1020E GLN* 3.4 5.3 + - - +
1021E LEU* 3.0 31.7 + - - +
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Residues in contact with PHE1018 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014E SER 3.0 19.6 + - - +
1015E LEU* 4.2 2.5 - - - +
1017E VAL* 1.3 79.2 - - - +
1019E SER* 1.3 55.1 + - - +
1021E LEU* 3.6 4.3 + - - +
1022E LEU* 2.9 28.6 + - - +
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Residues in contact with SER1019 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015E LEU 2.9 20.6 + - - -
1016E LEU* 3.8 4.3 - - - -
1018E PHE* 1.3 73.7 - - - +
1020E GLN* 1.3 61.3 + - - +
1022E LEU* 3.3 7.7 - - - +
1023E LYS* 2.9 30.0 + - - +
1081E VAL* 4.8 12.1 - - - -
1082E THR* 4.6 20.7 - - - -
1085E THR* 6.0 0.4 - - - -
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Residues in contact with GLN1020 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016E LEU 2.9 19.0 + - - +
1017E VAL* 3.8 5.4 - - - +
1019E SER* 1.3 74.1 - - - +
1021E LEU* 1.3 61.3 + - - +
1023E LYS* 3.4 3.8 + - - +
1024E HIS* 2.9 31.2 + - - +
1082E THR* 4.7 13.2 - - - -
1144E SER* 5.9 3.8 - - - +
1148E LEU* 4.0 21.2 - - + +
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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
----------------------------------------------------------
1017E VAL 3.0 17.9 + - - +
1018E PHE* 4.0 4.9 - - - +
1020E GLN* 1.3 75.4 - - - +
1022E LEU* 1.3 58.0 + - - +
1024E HIS* 4.6 4.0 - - - +
1025E MET* 2.9 33.8 + - - +
1148E LEU* 4.6 7.0 - - + +
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Residues in contact with LEU1022 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018E PHE 2.9 20.3 + - - +
1019E SER* 3.3 10.8 - - - +
1021E LEU* 1.3 77.0 - - - +
1023E LYS* 1.3 58.4 + - - +
1025E MET* 3.8 2.9 - - - +
1026E VAL* 2.9 29.2 + - - +
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Residues in contact with LYS1023 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019E SER 2.9 16.7 + - - +
1020E GLN* 4.3 3.4 - - - +
1022E LEU* 1.3 76.6 - - - +
1024E HIS* 1.3 58.2 + - - +
1026E VAL* 3.5 8.3 - - - +
1027E LEU* 2.9 27.0 + - - +
1077E VAL 5.6 0.9 - - - +
1078E LEU* 4.6 24.2 - - + +
1079E CYS 4.9 8.5 - - - +
1082E THR* 6.3 2.0 - - - -
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Residues in contact with HIS1024 (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 GLN 2.9 18.1 + - - +
1021E LEU* 4.1 4.3 - - - +
1023E LYS* 1.3 75.2 - - - +
1025E MET* 1.3 61.1 + - - +
1027E LEU* 3.1 8.9 + - - +
1028E VAL* 3.0 26.0 + - - +
1148E LEU* 4.4 23.6 - - + +
1149E LEU* 6.2 3.8 - - + -
1152E SER* 4.4 15.3 + - - +
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Residues in contact with MET1025 (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 18.2 + - - +
1022E LEU* 4.0 3.1 - - - +
1024E HIS* 1.3 74.0 - - - +
1026E VAL* 1.3 59.9 + - - +
1028E VAL* 3.6 8.8 - - + +
1029E ALA* 2.9 30.5 + - - +
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Residues in contact with VAL1026 (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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1022E LEU 2.9 19.1 + - - +
1023E LYS* 3.5 10.5 - - - +
1024E HIS 3.2 0.2 - - - -
1025E MET* 1.3 76.5 - - - +
1027E LEU* 1.3 57.3 + - - +
1029E ALA* 3.2 6.4 + - - +
1030E ILE* 2.8 29.2 + - - +
1074E LEU* 4.8 12.2 - - + +
1077E VAL* 4.7 19.5 - - + -
1078E LEU* 5.2 7.0 - - + +
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Residues in contact with LEU1027 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552E ILE* 5.1 16.4 - - + -
1023E LYS 2.9 13.7 + - - +
1024E HIS* 3.1 11.4 + - - +
1026E VAL* 1.3 76.4 - - - +
1028E VAL* 1.3 62.4 + - - +
1030E ILE* 3.2 8.9 + - - +
1031E ASP* 3.1 22.7 + - - +
1149E LEU* 6.0 5.8 - - + -
1287E TYR* 4.4 4.8 + - - +
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Residues in contact with VAL1028 (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 HIS 3.0 13.4 + - - +
1025E MET* 3.6 13.0 - - + +
1027E LEU* 1.3 75.1 - - - +
1029E ALA* 1.3 57.1 + - - +
1031E ASP* 3.2 4.9 + - - +
1032E TYR* 2.9 28.2 + - - +
1152E SER* 5.2 12.1 - - - +
1156E VAL* 5.1 17.2 - - + +
1287E TYR* 4.6 9.6 - - + -
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Residues in contact with ALA1029 (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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1025E MET 2.9 18.4 + - - +
1026E VAL* 3.2 6.9 + - - +
1028E VAL* 1.3 75.5 - - - +
1030E ILE* 1.3 61.2 + - - +
1032E TYR* 3.7 8.1 - - - +
1033E TRP* 2.9 32.1 + - - +
1074E LEU* 5.6 4.3 - - + -
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Residues in contact with ILE1030 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552E ILE* 5.9 6.3 - - + -
1026E VAL 2.8 14.4 + - - +
1027E LEU* 3.2 14.1 + - - +
1029E ALA* 1.3 76.2 - - - +
1031E ASP* 1.3 57.3 + - - +
1033E TRP* 3.9 2.5 - - - +
1034E LEU* 2.9 28.6 + - - +
1071E LEU* 5.7 9.3 - - + +
1074E LEU* 4.9 17.6 - - + +
1075E GLY* 5.8 2.9 - - - +
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Residues in contact with ASP1031 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580E LEU* 5.6 6.1 - - + -
1027E LEU 3.1 9.5 + - - +
1028E VAL 3.7 5.8 - - - +
1030E ILE* 1.3 75.9 - - - +
1032E TYR* 1.3 57.8 + - - +
1034E LEU* 3.3 8.6 + - - +
1035E ALA 2.9 22.7 + - - -
1283E LEU* 3.3 34.7 - - + +
1287E TYR* 3.7 24.9 - - + +
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Residues in contact with TYR1032 (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 VAL 2.9 17.8 + - - +
1029E ALA* 3.7 9.0 - - - +
1030E ILE 3.2 0.2 - - - -
1031E ASP* 1.3 77.0 - - - +
1033E TRP* 1.3 58.2 + - - +
1035E ALA* 3.1 7.1 + - - +
1036E LYS* 2.9 25.5 + - - +
1283E LEU* 4.4 7.9 - - - -
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Residues in contact with TRP1033 (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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1029E ALA 2.9 16.4 + - - +
1030E ILE* 3.9 2.5 - - - +
1032E TYR* 1.3 72.7 - - - +
1034E LEU* 1.3 60.4 + - - +
1036E LYS* 3.7 9.0 - - + +
1037E TRP* 2.8 26.5 + - - +
1067E VAL* 5.1 14.8 - - + +
1070E LEU* 5.8 7.6 - - + -
1071E LEU* 5.9 8.1 - - + -
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Residues in contact with LEU1034 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577E PHE* 4.5 15.9 - - + -
1030E ILE 2.9 20.1 + - - +
1031E ASP* 3.3 10.8 - - - +
1033E TRP* 1.3 76.3 - - - +
1035E ALA* 1.3 60.1 + - - +
1037E TRP* 3.2 7.4 + - - +
1038E THR* 3.0 29.5 + - - -
1071E LEU* 6.1 2.2 - - + +
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Residues in contact with ALA1035 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577E PHE* 4.2 7.8 - - - -
1031E ASP 2.9 6.5 + - - -
1032E TYR* 3.4 9.0 - - - +
1034E LEU* 1.3 76.4 - - - +
1036E LYS* 1.3 60.4 + - - +
1038E THR* 3.3 1.8 + - - -
1039E ASP* 3.3 26.7 + - - +
1279E GLY* 4.1 22.1 - - - +
1280E LEU* 4.5 10.5 - - + +
1283E LEU* 3.7 26.0 - - + -
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Residues in contact with LYS1036 (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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1032E TYR 2.9 15.3 + - - +
1033E TRP* 3.7 8.7 - - + +
1035E ALA* 1.3 73.1 - - - +
1037E TRP* 1.3 66.2 + - - +
1039E ASP* 4.3 9.3 - - - +
1067E VAL* 5.9 1.3 - - - +
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Residues in contact with TRP1037 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571E LEU* 6.3 2.2 - - + -
1033E TRP 2.8 15.7 + - - +
1034E LEU* 3.2 13.5 - - - +
1036E LYS* 1.3 80.4 - - - +
1038E THR* 1.3 66.5 + - - +
1039E ASP 3.2 8.0 + - - +
1067E VAL* 5.1 15.9 - - + +
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Residues in contact with THR1038 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571E LEU* 3.2 31.3 - - - +
572E SER* 4.0 2.8 - - - -
573E PRO* 3.6 37.9 - - - +
576E ALA* 5.3 5.6 - - - -
577E PHE* 5.5 2.0 - - - -
1034E LEU 3.0 13.7 + - - -
1035E ALA* 3.3 3.9 + - - -
1037E TRP* 1.3 79.6 - - - +
1039E ASP* 1.3 59.2 + - - +
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Residues in contact with ASP1039 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573E PRO* 4.6 4.1 - - - +
1035E ALA 3.3 14.7 + - - +
1036E LYS* 4.3 7.6 - - - +
1037E TRP 3.2 9.7 + - - +
1038E THR* 1.3 81.5 - - - +
1277E SER* 4.5 21.8 - - - +
1278E ALA* 5.6 2.0 - - + +
1279E GLY* 5.2 6.5 - - - +
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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