Contacts of the helix formed by residues 1009 - 1039 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005G LEU 3.0 12.6 + - - +
1006G SER* 3.8 6.8 + - - -
1007G SER 3.5 1.4 - - - -
1008G ALA* 1.3 86.0 - - - +
1010G ILE* 1.3 64.2 + - - -
1011G LEU* 3.3 3.8 + - - -
1012G LEU 4.0 1.2 + - - -
1013G LEU* 3.6 17.7 + - - +
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Residues in contact with ILE1010 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009G GLY* 1.3 72.8 - - - -
1011G LEU* 1.3 59.4 + - - +
1013G LEU* 3.3 7.6 - - - +
1014G SER* 2.9 29.1 + - - -
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Residues in contact with LEU1011 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009G GLY 3.3 1.0 - - - -
1010G ILE* 1.3 78.8 - - - +
1012G LEU* 1.3 58.4 + - - +
1014G SER* 3.2 9.0 + - - -
1015G LEU* 3.0 25.6 + - - +
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Residues in contact with LEU1012 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008G ALA* 4.7 14.1 + - + +
1009G GLY 4.0 1.2 + - - -
1010G ILE 3.5 0.2 - - - -
1011G LEU* 1.3 75.7 - - - +
1013G LEU* 1.3 60.7 + - - +
1015G LEU* 3.6 8.6 - - + +
1016G LEU* 2.9 30.7 + - - +
1085G THR* 5.2 5.7 - - - +
1089G THR* 4.7 21.6 - - - -
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Residues in contact with LEU1013 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005G LEU* 6.5 1.1 - - + -
1008G ALA* 5.9 3.1 - - + +
1009G GLY 3.6 14.3 + - - +
1010G ILE* 3.3 13.2 - - - +
1011G LEU 3.2 0.2 - - - -
1012G LEU* 1.3 78.6 - - - +
1014G SER* 1.3 56.6 + - - +
1016G LEU* 3.2 4.8 + - - +
1017G VAL* 2.9 34.1 + - - +
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Residues in contact with SER1014 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010G ILE 2.9 14.0 + - - -
1011G LEU* 3.2 11.0 + - - -
1013G LEU* 1.3 75.0 - - - +
1015G LEU* 1.3 64.1 + - - +
1017G VAL* 4.4 2.4 - - - +
1018G PHE* 3.0 29.9 + - - +
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Residues in contact with LEU1015 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011G LEU 3.0 12.9 + - - +
1012G LEU* 3.6 11.4 - - - +
1014G SER* 1.3 75.9 - - - +
1016G LEU* 1.3 57.8 + - - +
1018G PHE* 4.1 2.1 - - - +
1019G SER* 2.9 33.2 + - - -
1085G THR* 5.1 9.2 - - - -
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Residues in contact with LEU1016 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012G LEU 2.9 18.8 + - - +
1013G LEU* 3.7 5.6 - - - +
1015G LEU* 1.3 76.6 - - - +
1017G VAL* 1.3 58.1 + - - +
1019G SER* 3.3 3.6 + - - -
1020G GLN* 2.9 31.3 + - - +
1082G THR* 5.0 6.6 - - - +
1085G THR* 4.5 21.5 - - - -
1086G VAL* 5.5 2.0 - - + +
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Residues in contact with VAL1017 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013G LEU 2.9 16.6 + - - +
1014G SER* 4.4 2.9 - - - +
1016G LEU* 1.3 76.1 - - - +
1018G PHE* 1.3 58.4 + - - +
1020G GLN* 3.8 4.7 - - - +
1021G LEU* 3.0 31.4 + - - +
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Residues in contact with PHE1018 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014G SER 3.0 20.2 + - - +
1015G LEU* 4.2 2.5 - - - +
1017G VAL* 1.3 78.6 - - - +
1019G SER* 1.3 56.4 + - - +
1021G LEU* 3.6 4.8 + - - +
1022G LEU* 2.9 28.8 + - - +
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Residues in contact with SER1019 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015G LEU 2.9 21.9 + - - -
1016G LEU* 3.8 4.3 - - - -
1018G PHE* 1.3 73.6 - - - +
1020G GLN* 1.3 61.3 + - - +
1022G LEU* 3.3 8.0 - - - +
1023G LYS* 2.9 30.0 + - - +
1081G VAL* 4.8 11.2 - - - -
1082G THR* 4.6 21.2 - - - -
1085G THR* 6.0 0.4 - - - -
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Residues in contact with GLN1020 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016G LEU 2.9 17.4 + - - +
1017G VAL* 3.8 6.1 - - - +
1019G SER* 1.3 75.2 - - - +
1021G LEU* 1.3 60.1 + - - +
1023G LYS* 3.4 3.4 + - - +
1024G HIS* 2.9 31.7 + - - +
1082G THR* 4.7 14.1 - - - -
1144G SER* 5.9 3.8 - - - +
1148G LEU* 4.0 21.3 - - + +
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Residues in contact with LEU1021 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017G VAL 3.0 17.7 + - - +
1018G PHE* 4.0 4.9 - - - +
1020G GLN* 1.3 76.0 - - - +
1022G LEU* 1.3 57.1 + - - +
1024G HIS* 4.1 4.8 - - - +
1025G MET* 2.9 33.8 + - - +
1148G LEU* 4.6 7.5 - - + +
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Residues in contact with LEU1022 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018G PHE 2.9 19.7 + - - +
1019G SER* 3.3 10.5 - - - +
1020G GLN 3.2 0.2 - - - -
1021G LEU* 1.3 77.0 - - - +
1023G LYS* 1.3 57.5 + - - +
1025G MET* 3.8 2.9 - - - +
1026G VAL* 2.9 28.9 + - - +
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Residues in contact with LYS1023 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019G SER 2.9 15.1 + - - +
1020G GLN* 4.3 3.6 - - - +
1022G LEU* 1.3 75.9 - - - +
1024G HIS* 1.3 58.1 + - - +
1026G VAL* 3.3 8.9 + - - +
1027G LEU* 2.9 26.5 + - - +
1077G VAL 5.6 0.4 - - - +
1078G LEU* 4.6 25.1 - - + +
1079G CYS 4.9 8.7 - - - +
1082G THR* 6.3 2.5 - - - -
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Residues in contact with HIS1024 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020G GLN 2.9 18.3 + - - +
1021G LEU* 4.1 4.0 - - - +
1023G LYS* 1.3 74.8 - - - +
1025G MET* 1.3 60.7 + - - +
1027G LEU* 3.1 8.4 + - - +
1028G VAL* 3.0 26.6 + - - +
1148G LEU* 4.4 23.8 - - + +
1149G LEU* 6.2 4.3 - - + -
1152G SER* 4.4 15.7 + - - +
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Residues in contact with MET1025 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021G LEU 2.9 18.8 + - - +
1022G LEU* 4.0 2.9 - - - +
1024G HIS* 1.3 74.2 - - - +
1026G VAL* 1.3 61.0 + - - +
1028G VAL* 3.6 9.0 - - + +
1029G ALA* 2.9 29.5 + - - +
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Residues in contact with VAL1026 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022G LEU 2.9 18.3 + - - +
1023G LYS* 3.5 10.8 - - - +
1024G HIS 3.2 0.2 - - - -
1025G MET* 1.3 75.5 - - - +
1027G LEU* 1.3 57.4 + - - +
1029G ALA* 3.2 6.2 + - - +
1030G ILE* 2.8 29.5 + - - +
1074G LEU* 4.8 12.9 - - + +
1077G VAL* 4.7 19.5 - - + -
1078G LEU* 5.2 6.7 - - + +
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Residues in contact with LEU1027 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552G ILE* 5.1 15.9 - - + -
1023G LYS 2.9 14.0 + - - +
1024G HIS* 3.1 11.0 + - - +
1026G VAL* 1.3 76.2 - - - +
1028G VAL* 1.3 62.6 + - - +
1030G ILE* 3.2 9.1 + - - +
1031G ASP* 3.1 22.5 + - - +
1149G LEU* 6.0 6.5 - - + -
1287G TYR* 4.4 4.2 + - - +
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Residues in contact with VAL1028 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1024G HIS 3.0 13.9 + - - +
1025G MET* 3.6 12.1 - - - +
1027G LEU* 1.3 74.9 - - - +
1029G ALA* 1.3 57.6 + - - +
1031G ASP* 3.2 5.1 + - - +
1032G TYR* 2.9 29.4 + - - +
1152G SER* 5.2 11.6 - - - +
1156G VAL* 5.1 15.7 - - + +
1287G TYR* 4.6 9.8 + - - -
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Residues in contact with ALA1029 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025G MET 2.9 17.5 + - - +
1026G VAL* 3.2 7.4 + - - +
1028G VAL* 1.3 73.4 - - - +
1030G ILE* 1.3 60.5 + - - +
1032G TYR* 3.7 7.7 - - - +
1033G TRP* 2.9 32.2 + - - +
1074G LEU* 5.6 4.9 - - + -
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Residues in contact with ILE1030 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552G ILE* 5.9 6.5 - - + -
1026G VAL 2.8 13.8 + - - +
1027G LEU* 3.2 12.8 + - - +
1029G ALA* 1.3 76.1 - - - +
1031G ASP* 1.3 58.6 + - - +
1033G TRP* 3.6 2.9 + - - +
1034G LEU* 2.9 28.3 + - - +
1071G LEU* 5.7 8.6 - - + +
1074G LEU* 4.9 17.6 - - + +
1075G GLY* 5.8 3.4 - - - +
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Residues in contact with ASP1031 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580G LEU* 5.6 5.6 - - + -
1027G LEU 3.1 8.5 + - - +
1028G VAL 3.2 6.5 + - - +
1030G ILE* 1.3 76.7 - - - +
1032G TYR* 1.3 56.8 + - - +
1034G LEU* 3.3 9.0 + - - +
1035G ALA 2.9 22.5 + - - -
1156G VAL* 6.5 0.2 - - + -
1283G LEU* 3.3 33.9 - - + +
1287G TYR* 3.7 25.4 - - + +
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Residues in contact with TYR1032 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028G VAL 2.9 16.3 + - - +
1029G ALA* 3.7 9.4 - - - +
1030G ILE 3.2 0.2 - - - -
1031G ASP* 1.3 78.9 - - - +
1033G TRP* 1.3 57.4 + - - +
1035G ALA* 3.1 6.4 + - - +
1036G LYS* 2.9 25.3 + - - +
1283G LEU* 4.4 7.4 - - - -
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Residues in contact with TRP1033 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029G ALA 2.9 16.5 + - - +
1030G ILE* 4.4 2.2 - - - +
1032G TYR* 1.3 72.1 - - - +
1034G LEU* 1.3 60.6 + - - +
1036G LYS* 3.7 10.3 - - + +
1037G TRP* 2.8 26.3 + - - +
1067G VAL* 5.1 13.9 - - + +
1070G LEU* 5.8 7.2 - - + -
1071G LEU* 5.9 8.7 - - + -
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Residues in contact with LEU1034 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577G PHE* 4.5 15.6 - - + -
1030G ILE 2.9 20.2 + - - +
1031G ASP* 3.3 10.8 - - - +
1032G TYR 3.1 0.2 - - - -
1033G TRP* 1.3 76.1 - - - +
1035G ALA* 1.3 59.2 + - - +
1037G TRP* 3.2 8.1 + - - +
1038G THR* 3.0 29.1 + - - -
1071G LEU* 6.1 2.9 - - + +
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Residues in contact with ALA1035 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577G PHE* 4.2 8.4 - - - -
1031G ASP 2.9 6.7 + - - -
1032G TYR* 3.1 8.7 + - - +
1034G LEU* 1.3 76.8 - - - +
1036G LYS* 1.3 61.6 + - - +
1038G THR* 3.3 1.7 + - - +
1039G ASP* 3.3 27.0 + - - +
1279G GLY* 4.1 22.8 - - - +
1280G LEU* 4.5 9.6 - - + +
1283G LEU* 3.7 26.9 - - + -
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Residues in contact with LYS1036 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032G TYR 2.9 16.1 + - - +
1033G TRP* 3.7 8.5 - - - +
1034G LEU 3.3 0.2 - - - -
1035G ALA* 1.3 72.7 - - - +
1037G TRP* 1.3 65.4 + - - +
1039G ASP* 4.3 9.6 - - - +
1067G VAL* 5.9 1.7 - - - +
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Residues in contact with TRP1037 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571G LEU* 6.3 2.0 - - + -
1033G TRP 2.8 15.7 + - - +
1034G LEU* 3.2 13.0 - - - +
1035G ALA 3.1 0.2 - - - -
1036G LYS* 1.3 80.3 - - - +
1038G THR* 1.3 66.3 + - - +
1039G ASP 3.2 7.6 + - - +
1067G VAL* 5.1 15.0 - - + +
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Residues in contact with THR1038 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571G LEU* 3.2 32.2 - - - +
572G SER* 4.0 2.4 - - - -
573G PRO* 3.6 38.4 - - - +
576G ALA* 5.3 5.6 - - - -
577G PHE* 5.5 2.0 - - - -
1034G LEU 3.0 13.3 + - - -
1035G ALA* 3.3 3.7 + - - -
1037G TRP* 1.3 80.2 - - - +
1039G ASP* 1.3 60.2 + - - +
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Residues in contact with ASP1039 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573G PRO* 4.6 3.9 - - - +
1035G ALA 3.3 14.7 + - - +
1036G LYS* 4.3 7.9 - - - +
1037G TRP 3.2 9.8 + - - +
1038G THR* 1.3 80.9 - - - +
1277G SER* 4.5 20.9 - - - +
1278G ALA* 5.6 2.2 - - + +
1279G 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