Contacts of the helix formed by residues 1080 - 1108 (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 LEU1080 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541E SER* 5.1 3.1 - - - +
545E PHE* 3.2 43.3 - - + +
548E THR* 5.8 0.4 - - - -
1079E CYS* 1.3 71.0 - - - +
1081E VAL* 1.3 57.8 + - - +
1082E THR 3.2 3.1 - - - -
1083E SER* 3.0 10.7 + - - -
1084E VAL* 3.0 28.6 + - + +
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Residues in contact with VAL1081 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019E SER* 4.8 14.5 - - - -
1079E CYS* 3.2 11.8 + - + -
1080E LEU* 1.3 77.7 - - - +
1082E THR* 1.3 57.2 + - - +
1084E VAL* 4.1 6.4 - - - +
1085E THR* 2.9 31.9 + - - -
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Residues in contact with THR1082 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016E LEU* 5.0 6.3 - - - +
1019E SER* 4.6 9.4 - - - -
1020E GLN* 4.7 26.2 - - - -
1079E CYS 4.3 5.6 + - - -
1080E LEU 3.2 0.6 - - - -
1081E VAL* 1.3 80.2 - - - +
1083E SER* 1.3 57.0 + - - +
1085E THR* 3.4 5.8 + - - -
1086E VAL* 2.9 29.5 + - - +
1141E GLU* 4.0 10.6 - - - +
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Residues in contact with SER1083 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541E SER* 3.8 32.3 - - - -
544E ILE* 4.1 11.4 - - - -
545E PHE 4.6 2.7 - - - -
1080E LEU* 3.0 13.1 + - - -
1082E THR* 1.3 76.5 - - - +
1084E VAL* 1.3 59.6 + - - +
1086E VAL* 3.3 4.0 + - - +
1087E GLU* 3.0 28.8 + - - +
1141E GLU* 3.3 24.3 + - - +
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Residues in contact with VAL1084 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541E SER* 4.1 14.1 - - - -
1080E LEU* 3.0 17.2 + - + +
1081E VAL* 4.1 6.5 - - - +
1083E SER* 1.3 75.4 - - - +
1085E THR* 1.3 57.8 + - - +
1087E GLU* 3.4 3.3 + - - +
1088E TRP* 2.9 32.1 + - - +
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Residues in contact with THR1085 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012E LEU* 5.2 6.3 - - - +
1015E LEU* 5.1 7.6 - - - -
1016E LEU* 4.5 25.8 - - - -
1019E SER* 6.0 0.7 - - - -
1081E VAL 2.9 21.1 + - - -
1082E THR* 3.6 7.2 - - - -
1084E VAL* 1.3 75.0 - - - +
1086E VAL* 1.3 59.6 + - - +
1088E TRP* 3.8 4.6 - - - +
1089E THR* 2.9 31.8 + - - -
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Residues in contact with VAL1086 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016E LEU* 5.5 2.8 - - - +
1082E THR 2.9 17.0 + - - +
1083E SER 3.5 5.4 - - - +
1085E THR* 1.3 76.8 - - - +
1087E GLU* 1.3 56.0 + - - +
1089E THR* 3.3 6.2 + - - -
1090E GLY* 2.9 26.5 + - - -
1137E PRO* 4.6 16.7 - - + +
1141E GLU* 4.0 26.2 - - + +
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Residues in contact with GLU1087 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537E ALA* 3.6 44.3 - - + +
540E THR* 5.6 3.1 - - - -
541E SER* 4.8 2.5 - - - +
1083E SER 3.0 15.9 + - - +
1084E VAL* 3.9 6.1 - - - +
1086E VAL* 1.3 75.3 - - - +
1088E TRP* 1.3 63.1 + - - +
1090E GLY* 3.2 2.1 + - - -
1091E LEU* 3.0 23.7 + - - +
1137E PRO* 5.5 5.2 - - - -
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Residues in contact with TRP1088 (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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537E ALA* 5.2 0.4 - - - +
1084E VAL 2.9 18.6 + - - +
1085E THR* 3.8 5.6 - - - +
1087E GLU* 1.3 75.3 - - - +
1089E THR* 1.3 58.6 + - - +
1091E LEU* 3.3 8.5 + - - +
1092E LYS* 3.0 27.0 + - - +
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Residues in contact with THR1089 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008E ALA* 5.4 14.6 - - - +
1012E LEU* 4.7 19.7 - - - +
1085E THR 2.9 19.3 + - - -
1086E VAL* 3.6 6.3 - - - -
1088E TRP* 1.3 75.8 - - - +
1090E GLY* 1.3 58.7 + - - +
1092E LYS* 3.3 8.1 + - - +
1093E VAL* 2.9 29.7 + - - +
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Residues in contact with GLY1090 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086E VAL 2.9 14.9 + - - -
1087E GLU* 3.2 3.8 + - - -
1089E THR* 1.3 76.1 - - - +
1091E LEU* 1.3 55.9 + - - +
1093E VAL* 3.4 6.3 + - - +
1094E ALA* 2.9 30.7 + - - +
1132E ILE* 5.5 3.4 - - - +
1133E ASP* 5.0 0.5 - - - +
1137E PRO* 4.5 20.2 - - - -
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Residues in contact with LEU1091 (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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533E LEU* 5.9 10.3 - - + +
534E ARG* 6.1 2.7 - - + +
537E ALA* 5.8 4.9 - - + -
1087E GLU 3.0 12.7 + - - +
1088E TRP* 3.3 10.7 + - - +
1090E GLY* 1.3 74.6 - - - +
1092E LYS* 1.3 62.4 + - - +
1094E ALA* 3.4 6.4 + - - +
1095E LYS* 3.1 25.6 + - - +
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Residues in contact with LYS1092 (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 SER 4.8 3.6 - - - +
1008E ALA* 5.0 11.2 - - - +
1088E TRP 3.0 12.7 + - - +
1089E THR* 3.4 12.6 - - - +
1091E LEU* 1.3 77.5 - - - +
1093E VAL* 1.3 62.9 + - - +
1095E LYS* 3.4 3.0 + - - +
1096E ARG* 3.0 26.8 + - - +
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Residues in contact with VAL1093 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004E TYR* 5.2 3.8 - - - +
1007E SER* 4.2 26.0 + - - +
1008E ALA* 5.1 5.4 - - + +
1089E THR 2.9 16.7 + - - +
1090E GLY* 3.9 6.5 - - - +
1092E LYS* 1.3 76.3 - - - +
1094E ALA* 1.3 58.3 + - - +
1096E ARG* 4.6 0.9 - - - -
1097E LEU* 2.9 35.2 + - - +
1132E ILE* 5.4 9.0 - - + -
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Residues in contact with ALA1094 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533E LEU* 6.3 2.9 - - + -
1090E GLY 2.9 16.9 + - - +
1091E LEU* 3.6 7.4 - - - +
1093E VAL* 1.3 77.2 - - - +
1095E LYS* 1.3 58.1 + - - +
1097E LEU* 4.1 1.6 - - - +
1098E HIS* 3.0 32.3 + - - +
1132E ILE* 4.9 6.0 - - + +
1133E ASP* 3.3 33.0 - - - +
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Residues in contact with LYS1095 (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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530E MET* 6.0 6.5 - - + -
1091E LEU 3.1 13.4 + - - +
1092E LYS* 4.3 2.7 - - - +
1094E ALA* 1.3 79.5 - - - +
1096E ARG* 1.3 62.5 + - - +
1098E HIS* 3.8 4.5 - - - +
1099E ARG* 3.0 26.9 + - - +
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Residues in contact with ARG1096 (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 SER* 4.5 17.3 - - - +
1092E LYS 3.0 19.3 + - - +
1093E VAL* 4.0 2.7 - - - +
1095E LYS* 1.3 78.5 - - - +
1097E LEU* 1.3 57.8 + - - +
1099E ARG* 3.9 3.2 - - - +
1100E SER* 2.9 31.8 + - - -
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Residues in contact with LEU1097 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007E SER* 5.6 8.0 - - - -
1093E VAL 2.9 17.9 + - - +
1094E ALA* 4.3 1.8 - - - +
1096E ARG* 1.3 77.4 - - - +
1098E HIS* 1.3 57.5 + - - +
1100E SER* 3.9 5.1 - - - -
1101E LEU* 2.9 33.6 + - - +
1132E ILE* 5.7 9.6 - - + -
1315E ILE* 4.5 19.4 - - + +
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Residues in contact with HIS1098 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526E ARG* 5.9 7.0 - - + -
1094E ALA 3.0 21.1 + - - +
1095E LYS* 3.8 5.4 - - - +
1097E LEU* 1.3 77.0 - - - +
1099E ARG* 1.3 61.6 + - - +
1101E LEU* 4.0 2.2 - - - +
1102E LEU* 3.0 26.2 + - - +
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Residues in contact with ARG1099 (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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1095E LYS 3.0 17.4 + - - +
1096E ARG* 4.0 3.6 - - - +
1098E HIS* 1.3 76.2 - - - +
1100E SER* 1.3 57.1 + - - +
1102E LEU* 3.4 5.8 + - - +
1103E ASN* 3.0 31.9 + - - +
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Residues in contact with SER1100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096E ARG 2.9 19.7 + - - -
1097E LEU* 3.9 5.8 - - - -
1099E ARG* 1.3 77.2 - - - +
1101E LEU* 1.3 58.5 + - - +
1103E ASN* 3.4 3.6 + - - +
1104E ARG* 2.9 32.3 + - - +
1318E LEU* 6.0 0.7 - - - -
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Residues in contact with LEU1101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097E LEU 2.9 18.3 + - - +
1098E HIS* 4.2 2.0 - - - +
1100E SER* 1.3 73.8 - - - +
1102E LEU* 1.3 60.1 + - - +
1104E ARG* 3.9 5.4 - - - +
1105E ILE* 2.9 33.6 + - - +
1315E ILE* 4.4 26.7 - - + +
1318E LEU* 5.1 7.9 - - + -
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Residues in contact with LEU1102 (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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519E CYS* 5.8 9.6 - - + +
522E VAL* 6.1 4.9 - - + -
1098E HIS 3.0 19.7 + - - +
1099E ARG* 3.6 7.2 - - - +
1101E LEU* 1.3 76.7 - - - +
1103E ASN* 1.3 57.9 + - - +
1105E ILE* 3.9 2.9 - - - +
1106E ILE* 3.0 30.1 + - - +
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Residues in contact with ASN1103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099E ARG 3.0 17.7 + - - +
1100E SER* 4.1 3.1 - - - +
1102E LEU* 1.3 78.5 - - - +
1104E ARG* 1.3 58.2 + - - +
1106E ILE* 3.8 3.7 - - - +
1107E LEU* 3.0 29.8 + - - +
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Residues in contact with ARG1104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100E SER 2.9 18.2 + - - +
1101E LEU 3.9 2.9 - - - +
1103E ASN* 1.3 77.7 - - - +
1105E ILE* 1.3 61.0 + - - +
1107E LEU* 3.4 8.1 + - - +
1108E ALA* 3.4 18.7 + - - +
1318E LEU* 4.3 30.7 - - + -
1319E LEU* 5.1 8.9 - - - +
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Residues in contact with ILE1105 (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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1101E LEU 2.9 19.4 + - - +
1102E LEU* 4.1 3.1 - - - +
1104E ARG* 1.3 74.2 - - - +
1106E ILE* 1.3 63.7 + - - +
1107E LEU 3.1 0.2 - - - -
1108E ALA* 3.0 26.1 + - - +
1121E ILE* 6.0 6.5 - - + -
1319E LEU* 5.3 11.3 - - + +
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Residues in contact with ILE1106 (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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515E GLU* 4.5 24.5 - - + +
519E CYS* 5.8 7.0 - - + -
1102E LEU 3.0 17.3 + - - +
1103E ASN* 4.3 4.0 - - - +
1105E ILE* 1.3 76.7 - - - +
1107E LEU* 1.3 59.7 - - - +
1108E ALA 3.3 4.6 - - - +
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Residues in contact with LEU1107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103E ASN 3.0 18.8 + - - +
1104E ARG* 3.5 9.9 - - - +
1105E ILE 3.1 0.4 - - - -
1106E ILE* 1.3 78.9 - - - +
1108E ALA* 1.3 63.0 + - - +
1109E PRO* 3.7 1.2 - - - +
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Residues in contact with ALA1108 (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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1104E ARG 3.4 7.4 + - - +
1105E ILE 3.0 18.1 + - - +
1106E ILE 3.9 4.5 - - - +
1107E LEU* 1.3 81.7 - - - +
1109E PRO* 1.3 69.4 - - - +
1112E PHE* 4.6 3.4 - - + -
1319E LEU* 4.0 40.2 - - + +
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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