Contacts of the helix formed by residues 1080 - 1108 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541H SER* 5.1 3.1 - - - +
545H PHE* 3.2 41.5 - - + +
548H THR* 5.8 0.4 - - - -
1079H CYS* 1.3 71.6 - - - +
1081H VAL* 1.3 57.9 + - - +
1082H THR 3.2 2.7 - - - -
1083H SER* 3.0 10.8 + - - -
1084H VAL* 3.0 28.8 + - + +
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Residues in contact with VAL1081 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019H SER* 4.8 13.9 - - - -
1079H CYS* 3.2 11.4 - - + +
1080H LEU* 1.3 76.8 - - - +
1082H THR* 1.3 58.0 + - - +
1084H VAL* 4.1 6.2 - - - +
1085H THR* 2.9 31.4 + - - -
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Residues in contact with THR1082 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016H LEU* 5.0 6.0 - - - +
1019H SER* 4.6 8.7 - - - -
1020H GLN* 4.7 26.9 - - - -
1079H CYS 4.3 5.0 + - - -
1080H LEU 3.2 0.8 - - - -
1081H VAL* 1.3 79.7 - - - +
1083H SER* 1.3 56.2 + - - +
1085H THR* 3.4 5.6 + - - -
1086H VAL* 2.9 30.0 + - - +
1141H GLU* 4.0 11.1 - - - +
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Residues in contact with SER1083 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541H SER* 3.8 32.8 - - - -
544H ILE* 4.1 11.2 - - - -
545H PHE* 4.6 3.4 - - - -
1080H LEU* 3.0 13.0 + - - -
1082H THR* 1.3 77.3 - - - +
1084H VAL* 1.3 59.6 + - - +
1086H VAL* 3.3 4.2 + - - +
1087H GLU* 3.0 28.1 + - - +
1141H GLU* 3.3 23.4 + - - +
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Residues in contact with VAL1084 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541H SER* 4.1 14.0 - - - -
1080H LEU* 3.0 16.1 + - + +
1081H VAL* 4.1 7.0 - - - +
1083H SER* 1.3 77.1 - - - +
1085H THR* 1.3 57.7 + - - +
1087H GLU* 3.4 3.0 + - - +
1088H TRP* 2.9 31.9 + - - +
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Residues in contact with THR1085 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012H LEU* 5.2 6.1 - - - +
1015H LEU* 5.1 7.9 - - - -
1016H LEU* 4.5 25.1 - - - -
1019H SER* 6.0 0.7 - - - -
1081H VAL 2.9 20.9 + - - -
1082H THR* 3.6 7.4 - - - -
1083H SER 3.2 0.2 - - - -
1084H VAL* 1.3 75.5 - - - +
1086H VAL* 1.3 59.0 + - - +
1088H TRP* 3.5 5.5 + - - +
1089H THR* 2.9 31.7 + - - -
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Residues in contact with VAL1086 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016H LEU* 5.5 3.0 - - - +
1082H THR 2.9 18.6 + - - +
1083H SER 3.5 4.9 - - - +
1085H THR* 1.3 75.9 - - - +
1087H GLU* 1.3 57.4 + - - +
1089H THR* 3.3 6.4 + - - -
1090H GLY* 2.9 26.0 + - - -
1137H PRO* 4.6 16.1 - - + +
1141H GLU* 4.0 26.9 - - + +
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Residues in contact with GLU1087 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537H ALA* 3.6 44.8 - - + +
540H THR* 5.6 3.1 - - - -
541H SER* 4.8 2.2 - - - +
1083H SER 3.0 15.3 + - - +
1084H VAL* 3.9 6.1 - - - +
1085H THR 3.3 0.2 - - - -
1086H VAL* 1.3 77.3 - - - +
1088H TRP* 1.3 62.3 + - - +
1090H GLY* 3.2 2.6 + - - +
1091H LEU* 3.0 23.0 + - - +
1137H PRO* 5.5 4.5 - - - -
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Residues in contact with TRP1088 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537H ALA* 5.2 0.6 - - - +
1084H VAL 2.9 17.6 + - - +
1085H THR* 3.8 5.6 - - - +
1087H GLU* 1.3 74.3 - - - +
1089H THR* 1.3 57.6 - - - +
1091H LEU* 3.3 8.4 + - - +
1092H LYS* 3.0 27.0 + - - +
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Residues in contact with THR1089 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008H ALA* 5.4 15.3 - - - +
1012H LEU* 4.7 20.6 - - - +
1085H THR 2.9 19.5 + - - -
1086H VAL* 3.6 6.1 - - - -
1088H TRP* 1.3 76.4 - - - +
1090H GLY* 1.3 57.9 + - - +
1092H LYS* 3.3 8.7 + - - +
1093H VAL* 2.9 30.0 + - - +
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Residues in contact with GLY1090 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086H VAL 2.9 14.3 + - - -
1087H GLU 3.2 4.0 + - - -
1089H THR* 1.3 77.0 - - - +
1091H LEU* 1.3 55.5 + - - +
1093H VAL* 3.4 6.0 + - - +
1094H ALA* 2.9 30.9 + - - +
1132H ILE* 5.5 3.2 - - - +
1133H ASP* 5.0 0.3 - - - +
1137H PRO* 4.5 19.7 - - - -
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Residues in contact with LEU1091 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533H LEU* 5.9 10.5 - - + +
534H ARG* 6.1 2.2 - - - +
537H ALA* 5.8 5.2 - - + -
1087H GLU 3.0 13.3 + - - +
1088H TRP* 3.3 10.7 + - - +
1090H GLY* 1.3 75.4 - - - +
1092H LYS* 1.3 62.9 + - - +
1094H ALA* 3.4 6.4 + - - +
1095H LYS* 3.1 25.3 + - - +
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Residues in contact with LYS1092 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007H SER 4.8 3.6 - - - +
1008H ALA 5.0 11.7 - - - +
1088H TRP 3.0 13.6 + - - +
1089H THR* 3.3 12.1 + - - +
1091H LEU* 1.3 77.5 - - - +
1093H VAL* 1.3 61.8 + - - +
1095H LYS* 3.4 2.4 + - - +
1096H ARG* 3.0 27.4 + - - +
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Residues in contact with VAL1093 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004H TYR* 5.2 3.4 - - - +
1007H SER* 4.2 27.1 + - - +
1008H ALA* 5.1 5.4 - - + +
1089H THR 2.9 16.8 + - - +
1090H GLY* 3.4 6.3 + - - +
1092H LYS* 1.3 75.4 - - - +
1094H ALA* 1.3 58.2 + - - +
1096H ARG* 4.0 1.3 - - - +
1097H LEU* 2.9 35.0 + - - +
1132H ILE* 5.4 9.2 - - + -
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Residues in contact with ALA1094 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533H LEU* 6.3 3.4 - - + -
1090H GLY 2.9 17.3 + - - +
1091H LEU* 3.6 7.6 - - - +
1093H VAL* 1.3 76.0 - - - +
1095H LYS* 1.3 58.6 + - - +
1097H LEU* 4.1 1.6 - - - +
1098H HIS* 3.0 33.1 + - - +
1132H ILE* 4.9 5.8 - - + +
1133H ASP* 3.3 33.7 - - - +
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Residues in contact with LYS1095 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530H MET* 6.0 6.7 - - + -
1091H LEU 3.1 13.4 + - - +
1092H LYS* 4.3 2.2 - - - +
1094H ALA* 1.3 79.1 - - - +
1096H ARG* 1.3 62.6 + - - +
1098H HIS* 3.8 5.0 - - - +
1099H ARG* 3.0 26.9 + - - +
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Residues in contact with ARG1096 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007H SER* 4.5 17.5 - - - +
1092H LYS 3.0 19.2 + - - +
1093H VAL 4.0 2.2 - - - +
1095H LYS* 1.3 78.0 - - - +
1097H LEU* 1.3 58.1 + - - +
1099H ARG* 3.9 3.4 - - - +
1100H SER* 2.9 31.3 + - - -
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Residues in contact with LEU1097 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007H SER* 5.6 8.2 - - - -
1093H VAL 2.9 18.5 + - - +
1094H ALA* 4.3 1.8 - - - +
1096H ARG* 1.3 76.1 - - - +
1098H HIS* 1.3 58.6 + - - +
1100H SER* 3.9 4.7 - - - -
1101H LEU* 2.9 34.0 + - - +
1132H ILE* 5.7 9.2 - - + -
1315H ILE* 4.5 17.8 - - + +
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Residues in contact with HIS1098 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526H ARG* 5.9 7.4 - - + -
1094H ALA 3.0 21.4 + - - +
1095H LYS* 3.8 5.6 - - - +
1097H LEU* 1.3 77.0 - - - +
1099H ARG* 1.3 62.7 + - - +
1101H LEU* 4.1 2.2 - - - +
1102H LEU* 3.0 26.4 + - - +
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Residues in contact with ARG1099 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095H LYS 3.0 18.1 + - - +
1096H ARG* 4.0 3.1 - - - +
1098H HIS* 1.3 76.3 - - - +
1100H SER* 1.3 57.8 + - - +
1102H LEU* 3.4 6.2 + - - +
1103H ASN* 3.0 31.9 + - - +
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Residues in contact with SER1100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096H ARG 2.9 19.1 + - - -
1097H LEU* 3.9 5.6 - - - -
1098H HIS 3.3 0.2 - - - -
1099H ARG* 1.3 76.7 - - - +
1101H LEU* 1.3 57.5 + - - +
1103H ASN* 3.4 3.2 + - - +
1104H ARG* 2.9 32.0 + - - +
1318H LEU* 6.0 0.4 - - - -
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Residues in contact with LEU1101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097H LEU 2.9 17.5 + - - +
1098H HIS* 4.2 2.5 - - - +
1100H SER* 1.3 73.8 - - - +
1102H LEU* 1.3 61.2 + - - +
1104H ARG* 3.9 5.3 - - - +
1105H ILE* 2.9 33.8 + - - +
1315H ILE* 4.4 26.2 - - + +
1318H LEU* 5.1 7.0 - - + -
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Residues in contact with LEU1102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519H CYS* 5.8 8.7 - - + +
522H VAL* 6.1 5.6 - - + -
1098H HIS 3.0 20.7 + - - +
1099H ARG* 3.6 7.4 - - - +
1101H LEU* 1.3 76.6 - - - +
1103H ASN* 1.3 57.2 + - - +
1105H ILE* 4.0 2.6 - - - +
1106H ILE* 3.0 30.1 + - - +
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Residues in contact with ASN1103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099H ARG 3.0 17.8 + - - +
1100H SER* 4.1 3.6 - - - +
1102H LEU* 1.3 76.5 - - - +
1104H ARG* 1.3 58.5 + - - +
1106H ILE* 3.8 4.1 - - - +
1107H LEU* 3.0 29.5 + - - +
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Residues in contact with ARG1104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100H SER 2.9 18.8 + - - +
1101H LEU 3.9 3.4 - - - +
1103H ASN* 1.3 77.8 - - - +
1105H ILE* 1.3 59.3 + - - +
1107H LEU* 3.4 8.2 + - - +
1108H ALA* 3.4 18.2 + - - +
1318H LEU* 4.3 31.0 - - + -
1319H LEU* 5.1 8.8 + - - +
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Residues in contact with ILE1105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101H LEU 2.9 19.3 + - - +
1102H LEU* 4.1 3.1 - - - +
1104H ARG* 1.3 75.7 - - - +
1106H ILE* 1.3 64.6 + - - +
1107H LEU 3.1 0.2 - - - -
1108H ALA* 3.0 24.8 + - - +
1121H ILE* 6.0 6.7 - - + -
1319H LEU* 5.3 10.9 - - + +
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Residues in contact with ILE1106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515H GLU* 4.5 24.5 - - + +
519H CYS* 5.8 6.7 - - + -
1102H LEU 3.0 17.7 + - - +
1103H ASN* 4.3 4.0 - - - +
1105H ILE* 1.3 76.7 - - - +
1107H LEU* 1.3 62.4 + - - +
1108H ALA 3.9 4.8 - - - +
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Residues in contact with LEU1107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103H ASN 3.0 17.7 + - - +
1104H ARG* 3.5 9.6 - - - +
1105H ILE 3.1 0.6 - - - -
1106H ILE* 1.3 79.8 - - - +
1108H ALA* 1.3 62.4 + - - +
1109H PRO* 3.7 1.4 - - - +
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Residues in contact with ALA1108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104H ARG 3.4 7.6 + - - +
1105H ILE 3.0 18.4 + - - +
1106H ILE* 3.9 4.5 - - - +
1107H LEU* 1.3 81.9 - - - +
1109H PRO* 1.3 70.2 - - - +
1112H PHE* 4.6 4.5 - - + -
1319H LEU* 4.0 39.9 - - + +
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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