Contacts of the helix formed by residues 1080 - 1108 (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 LEU1080 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541G SER* 5.1 2.9 - - - +
545G PHE* 3.2 42.5 - - + +
548G THR* 5.8 0.2 - - - -
1079G CYS* 1.3 70.8 - - - +
1081G VAL* 1.3 58.8 + - - +
1082G THR 3.2 2.7 - - - -
1083G SER* 3.0 11.3 + - - -
1084G VAL* 3.0 28.8 + - + +
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Residues in contact with VAL1081 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019G SER* 4.8 13.2 - - - -
1079G CYS* 3.2 11.4 - - + +
1080G LEU* 1.3 78.1 - - - +
1082G THR* 1.3 58.1 + - - +
1084G VAL* 4.1 6.4 - - - +
1085G THR* 2.9 31.6 + - - -
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Residues in contact with THR1082 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016G LEU* 5.0 5.9 - - - +
1019G SER* 4.6 8.7 - - - -
1020G GLN* 4.7 26.5 - - - -
1079G CYS 4.3 5.0 + - - -
1080G LEU 3.2 0.8 - - - -
1081G VAL* 1.3 78.6 - - - +
1083G SER* 1.3 56.2 + - - +
1085G THR* 3.4 5.9 + - - -
1086G VAL* 2.9 29.8 + - - +
1141G GLU* 4.0 10.4 - - - -
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Residues in contact with SER1083 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541G SER* 3.8 31.4 - - - -
544G ILE* 4.1 11.7 - - - -
545G PHE* 4.6 3.8 - - - -
1080G LEU* 3.0 13.6 + - - -
1082G THR* 1.3 76.5 - - - +
1084G VAL* 1.3 58.5 + - - +
1086G VAL* 3.3 3.1 + - - +
1087G GLU* 3.0 29.6 + - - +
1141G GLU* 3.3 23.7 + - - +
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Residues in contact with VAL1084 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541G SER* 4.1 13.9 - - - -
1080G LEU* 3.0 15.9 + - + +
1081G VAL* 4.1 6.7 - - - +
1083G SER* 1.3 75.4 - - - +
1085G THR* 1.3 58.7 + - - +
1087G GLU* 3.4 3.3 + - - +
1088G TRP* 2.9 32.3 + - - +
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Residues in contact with THR1085 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012G LEU* 5.2 7.0 - - - +
1015G LEU* 5.1 7.4 - - - -
1016G LEU* 4.5 25.1 - - - -
1019G SER* 6.0 0.7 - - - -
1081G VAL 2.9 21.2 + - - -
1082G THR* 3.6 7.2 - - - -
1084G VAL* 1.3 75.5 - - - +
1086G VAL* 1.3 59.7 + - - +
1088G TRP* 3.8 5.1 - - - +
1089G THR* 2.9 31.9 + - - -
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Residues in contact with VAL1086 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016G LEU* 5.5 2.9 - - - +
1082G THR 2.9 18.2 + - - +
1083G SER 3.5 5.6 - - - +
1085G THR* 1.3 76.8 - - - +
1087G GLU* 1.3 56.9 + - - +
1089G THR* 3.3 6.5 + - - -
1090G GLY* 2.9 26.0 + - - -
1137G PRO* 4.6 15.9 - - + +
1141G GLU* 4.0 26.7 - - + +
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Residues in contact with GLU1087 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537G ALA* 3.6 44.5 - - + +
540G THR* 5.6 3.4 - - - -
541G SER* 4.8 2.7 - - - +
1083G SER 3.0 16.3 + - - +
1084G VAL* 3.9 5.8 - - - +
1085G THR 3.3 0.2 - - - -
1086G VAL* 1.3 75.1 - - - +
1088G TRP* 1.3 62.5 + - - +
1090G GLY* 3.2 3.1 + - - -
1091G LEU* 3.0 22.5 + - - +
1137G PRO* 5.5 5.6 - - - -
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Residues in contact with TRP1088 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537G ALA* 5.9 0.2 - - - -
1084G VAL 2.9 18.9 + - - +
1085G THR* 3.8 6.5 - - - +
1087G GLU* 1.3 76.4 - - - +
1089G THR* 1.3 56.4 + - - +
1091G LEU* 3.3 8.2 + - - +
1092G LYS* 3.0 27.6 + - - +
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Residues in contact with THR1089 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008G ALA* 5.4 14.8 - - - +
1012G LEU* 4.7 20.1 - - - +
1085G THR 2.9 19.9 + - - -
1086G VAL* 3.6 6.7 - - - -
1088G TRP* 1.3 75.6 - - - +
1090G GLY* 1.3 58.5 + - - +
1092G LYS* 3.3 8.6 + - - +
1093G VAL* 2.9 29.8 + - - +
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Residues in contact with GLY1090 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086G VAL 2.9 15.3 + - - -
1087G GLU 3.2 4.2 + - - -
1089G THR* 1.3 77.4 - - - +
1091G LEU* 1.3 56.7 + - - +
1093G VAL* 3.4 6.3 + - - +
1094G ALA* 2.9 30.0 + - - +
1132G ILE* 5.5 3.3 - - - +
1133G ASP* 5.0 0.7 - - - +
1137G PRO* 4.5 19.7 - - - -
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Residues in contact with LEU1091 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533G LEU* 5.9 10.5 - - + +
534G ARG* 6.1 2.7 - - + +
537G ALA* 5.8 5.2 - - + -
1087G GLU 3.0 13.3 + - - +
1088G TRP* 3.6 10.5 - - - +
1090G GLY* 1.3 75.7 - - - +
1092G LYS* 1.3 63.4 + - - +
1094G ALA* 3.4 6.6 + - - +
1095G LYS* 3.1 25.8 + - - +
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Residues in contact with LYS1092 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007G SER 4.8 3.4 - - - +
1008G ALA* 5.0 11.4 - - - +
1088G TRP 3.0 13.0 + - - +
1089G THR* 3.3 12.1 + - - +
1091G LEU* 1.3 77.8 - - - +
1093G VAL* 1.3 62.2 + - - +
1095G LYS* 3.4 2.3 + - - +
1096G ARG* 3.0 27.0 + - - +
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Residues in contact with VAL1093 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004G TYR* 5.2 4.3 - - + +
1007G SER* 4.2 26.2 - - - +
1008G ALA* 5.1 4.5 - - + +
1089G THR 2.9 16.2 + - - +
1090G GLY* 3.9 6.5 - - - +
1092G LYS* 1.3 76.7 - - - +
1094G ALA* 1.3 57.4 + - - +
1096G ARG* 4.0 1.5 - - - +
1097G LEU* 2.9 34.9 + - - +
1132G ILE* 5.4 8.5 - - + -
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Residues in contact with ALA1094 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533G LEU* 6.3 3.1 - - + -
1090G GLY 2.9 17.1 + - - +
1091G LEU* 3.6 7.4 - - - +
1092G LYS 3.2 0.2 - - - -
1093G VAL* 1.3 77.6 - - - +
1095G LYS* 1.3 57.7 + - - +
1097G LEU* 4.3 1.4 - - - +
1098G HIS* 3.0 32.6 + - - +
1132G ILE* 4.9 6.2 - - + +
1133G ASP* 3.3 33.4 - - - +
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Residues in contact with LYS1095 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530G MET* 6.0 7.0 - - + -
1091G LEU 3.1 13.4 + - - +
1092G LYS* 4.3 2.2 - - - +
1094G ALA* 1.3 78.9 - - - +
1096G ARG* 1.3 63.0 + - - +
1098G HIS* 3.8 4.7 - - - +
1099G ARG* 3.0 26.7 + - - +
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Residues in contact with ARG1096 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007G SER* 4.5 16.6 - - - +
1092G LYS 3.0 19.3 + - - +
1093G VAL* 4.0 2.7 - - - +
1095G LYS* 1.3 77.1 - - - +
1097G LEU* 1.3 58.4 + - - +
1099G ARG* 3.5 3.8 + - - +
1100G SER* 2.9 31.7 + - - -
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Residues in contact with LEU1097 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007G SER* 5.6 8.0 - - - -
1093G VAL 2.9 18.1 + - - +
1094G ALA* 4.3 2.5 - - - +
1096G ARG* 1.3 76.9 - - - +
1098G HIS* 1.3 57.5 + - - +
1100G SER* 3.9 5.1 - - - -
1101G LEU* 2.9 34.1 + - - +
1132G ILE* 5.7 9.0 - - + -
1315G ILE* 4.5 18.5 - - + +
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Residues in contact with HIS1098 (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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526G ARG* 5.9 7.4 - - + -
1094G ALA 3.0 20.7 + - - +
1095G LYS* 3.8 5.6 - - - +
1097G LEU* 1.3 78.2 - - - +
1099G ARG* 1.3 63.7 + - - +
1101G LEU* 4.2 2.0 - - - +
1102G LEU* 3.0 25.7 + - - +
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Residues in contact with ARG1099 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095G LYS 3.0 17.9 + - - +
1096G ARG* 4.0 3.4 - - - +
1098G HIS* 1.3 76.1 - - - +
1100G SER* 1.3 58.6 + - - +
1102G LEU* 3.4 5.9 + - - +
1103G ASN* 3.0 31.7 + - - +
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Residues in contact with SER1100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096G ARG 2.9 20.4 + - - -
1097G LEU* 3.9 5.6 - - - -
1098G HIS 3.3 0.2 - - - -
1099G ARG* 1.3 77.6 - - - +
1101G LEU* 1.3 57.8 + - - +
1103G ASN* 3.4 4.4 + - - +
1104G ARG* 2.9 31.9 + - - +
1318G LEU* 6.0 0.9 - - - -
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Residues in contact with LEU1101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097G LEU 2.9 17.9 + - - +
1098G HIS* 4.2 2.2 - - - +
1100G SER* 1.3 73.2 - - - +
1102G LEU* 1.3 60.2 + - - +
1104G ARG* 3.9 5.1 - - - +
1105G ILE* 2.9 33.6 + - - +
1315G ILE* 4.4 27.4 - - + +
1318G LEU* 5.1 6.5 - - + -
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Residues in contact with LEU1102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519G CYS* 5.8 9.0 - - + -
522G VAL* 6.1 5.6 - - + -
1098G HIS 3.0 19.3 + - - +
1099G ARG* 3.6 7.4 - - - +
1101G LEU* 1.3 76.9 - - - +
1103G ASN* 1.3 57.0 + - + +
1105G ILE* 4.0 3.1 - - - +
1106G ILE* 3.0 30.5 + - - +
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Residues in contact with ASN1103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099G ARG 3.0 16.7 + - - +
1100G SER* 4.1 3.8 - - - +
1102G LEU* 1.3 78.0 - - - +
1104G ARG* 1.3 57.0 + - - +
1106G ILE* 3.8 3.8 - - - +
1107G LEU* 3.0 30.0 + - - +
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Residues in contact with ARG1104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100G SER 2.9 18.0 + - - +
1101G LEU 3.9 2.7 - - - +
1103G ASN* 1.3 77.7 - - - +
1105G ILE* 1.3 60.9 + - - +
1107G LEU* 3.4 9.1 + - - +
1108G ALA* 3.4 17.8 + - - +
1318G LEU* 4.3 31.2 - - + -
1319G LEU* 5.1 8.8 - - - +
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Residues in contact with ILE1105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101G LEU 2.9 17.3 + - - +
1102G LEU* 4.1 3.4 - - - +
1104G ARG* 1.3 76.0 - - - +
1106G ILE* 1.3 64.4 + - - +
1107G LEU 3.1 0.2 - - - -
1108G ALA* 3.0 25.3 + - - +
1121G ILE* 6.0 6.5 - - + -
1319G LEU* 5.3 10.8 - - + +
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Residues in contact with ILE1106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515G GLU* 4.5 24.8 - - + +
519G CYS* 5.8 7.2 - - + -
1102G LEU 3.0 17.9 + - - +
1103G ASN* 4.3 4.5 - - - +
1105G ILE* 1.3 76.9 - - - +
1107G LEU* 1.3 60.8 + - - +
1108G ALA 3.9 4.7 - - - +
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Residues in contact with LEU1107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103G ASN 3.0 18.3 + - - +
1104G ARG* 3.5 9.2 - - - +
1105G ILE 3.1 0.2 - - - -
1106G ILE* 1.3 79.4 - - - +
1108G ALA* 1.3 62.6 + - - +
1109G PRO* 3.7 1.2 - - - +
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Residues in contact with ALA1108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104G ARG 3.4 7.6 + - - +
1105G ILE 3.0 18.2 + - - +
1106G ILE* 3.9 5.0 - - - +
1107G LEU* 1.3 82.6 - - - +
1109G PRO* 1.3 68.7 - - - +
1112G PHE* 4.6 4.0 - - + -
1319G LEU* 4.0 39.7 - - + +
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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