Contacts of the helix formed by residues 95 - 135 (chain A) in PDB entry 1G1J
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 ILE 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLU* 1.3 73.1 + - - +
97A LYS* 3.1 4.2 - - - +
98A GLN* 3.0 20.0 + - - +
99A MET* 2.9 25.6 + - + +
95B ILE* 3.9 19.5 - - + -
96B GLU* 4.2 12.1 - - + -
99B MET* 3.2 44.0 - - + -
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 1.3 83.7 - - + +
97A LYS* 1.3 82.0 + - - +
99A MET* 3.4 10.2 + - - +
100A ASP* 3.0 24.6 + - - +
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 3.1 1.7 - - - +
96A GLU* 1.3 95.4 - - - +
98A GLN* 1.3 65.9 + - + +
100A ASP* 3.4 7.9 + - - +
101A ARG* 3.3 37.8 + - - +
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Residues in contact with GLN 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 3.0 13.2 + - - +
97A LYS* 1.3 76.0 - - + +
99A MET* 1.3 66.5 + - - +
101A ARG* 3.1 36.0 + - - +
102A VAL* 3.1 18.3 + - - +
96B GLU* 3.6 33.5 + - - +
99B MET* 2.9 47.9 - - + +
100B ASP* 4.4 12.2 - - - +
103B VAL* 4.1 8.1 - - + +
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Residues in contact with MET 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 2.9 18.4 + - + +
96A GLU* 3.6 12.3 - - - +
98A GLN* 1.3 78.0 - - - +
100A ASP* 1.3 61.0 + - - +
102A VAL* 3.3 17.1 + - + +
103A VAL* 3.1 39.6 + - + +
99B MET* 4.2 24.2 - - + -
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Residues in contact with ASP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLU* 3.0 15.9 + - - +
97A LYS* 3.5 12.1 - - - +
98A GLN 3.2 0.2 - - - -
99A MET* 1.3 75.1 - - - +
101A ARG* 1.3 65.8 + - + +
103A VAL* 3.3 9.2 + - - +
104A LYS* 3.1 58.7 + - - +
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Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LYS* 3.3 24.4 + - - +
98A GLN* 3.1 26.6 + - - +
100A ASP* 1.3 78.8 - - + +
102A VAL* 1.3 61.6 + - - +
104A LYS* 3.4 7.2 + - - +
105A GLU* 3.1 29.2 + - - +
100B ASP* 5.8 1.8 + - - -
103B VAL* 4.3 18.5 - - + +
107B ARG* 4.1 26.4 - - - +
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLN 3.1 16.2 + - - +
99A MET* 3.5 20.2 - - + +
100A ASP 3.2 0.2 - - - -
101A ARG* 1.3 77.6 - - - +
103A VAL* 1.3 64.6 + - + +
105A GLU* 3.3 2.6 + - - -
106A MET* 3.1 35.5 + - - +
99B MET* 5.0 4.0 - - + +
102B VAL* 4.3 18.2 - - + -
103B VAL* 3.8 20.0 - - + -
106B MET* 3.6 24.7 - - - +
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Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A MET* 3.1 29.1 + - + +
100A ASP* 3.3 12.1 + - - +
102A VAL* 1.3 77.0 - - + +
104A LYS* 1.3 66.9 + - + +
106A MET* 3.3 14.0 + - + +
107A ARG* 3.1 22.8 + - + +
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Residues in contact with LYS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ASP* 3.1 41.5 + - - +
101A ARG* 3.9 7.0 - - - +
102A VAL 3.3 0.2 - - - -
103A VAL* 1.3 78.5 - - + +
105A GLU* 1.3 67.1 + - - +
107A ARG* 3.3 32.9 + - - +
108A ARG* 3.0 21.8 + - - +
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Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG 3.1 21.1 + - - +
102A VAL* 3.3 3.6 + - - +
104A LYS* 1.3 78.3 - - - +
106A MET* 1.3 59.1 + - - +
108A ARG* 3.2 7.1 + - - +
109A GLN* 2.8 28.9 + - - +
103B VAL* 5.1 4.0 - - + -
106B MET* 3.4 28.0 - - + -
107B ARG* 3.1 47.5 + - + +
110B LEU* 2.9 31.7 - - + +
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Residues in contact with MET 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 3.1 28.8 + - - +
103A VAL* 3.5 14.8 - - + +
105A GLU* 1.3 78.5 - - - +
107A ARG* 1.3 57.6 + - - +
109A GLN* 3.3 11.2 + - - +
110A LEU* 2.9 28.2 + - - +
106B MET* 3.4 17.7 - - + -
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 3.1 15.5 + - + +
104A LYS* 3.6 40.0 - - - +
105A GLU 3.2 0.2 - - - -
106A MET* 1.3 76.4 - - - +
108A ARG* 1.3 63.6 + - - +
110A LEU* 3.4 10.0 + - + +
111A GLU* 3.3 19.8 + - - +
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Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LYS 3.0 14.7 + - - +
105A GLU* 3.4 13.2 - - - +
106A MET 3.2 0.2 - - - -
107A ARG* 1.3 76.4 - - - +
109A GLN* 1.3 65.8 + - - +
111A GLU* 3.2 16.4 + - - +
112A MSE 3.3 19.1 + - + +
110B LEU* 4.3 10.8 - - + -
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Residues in contact with GLN 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLU 2.8 17.4 + - - +
106A MET* 3.6 12.9 - - - +
108A ARG* 1.3 77.4 - - - +
110A LEU* 1.3 63.0 + - - +
112A MSE 3.0 5.9 + - - +
113A ILE* 2.9 45.2 + - + +
106B MET* 5.1 12.0 - - - +
109B GLN* 5.5 5.7 - - - +
110B LEU* 3.5 26.3 - - + +
113B ILE* 4.0 20.1 - - + +
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A MET 2.9 16.7 + - - +
107A ARG* 3.6 11.7 - - + +
108A ARG 3.2 0.2 - - - -
109A GLN* 1.3 76.8 - - - +
111A GLU* 1.3 62.4 + - - +
113A ILE* 3.3 14.2 + - + +
114A ASP* 2.9 43.2 + - - +
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG 3.3 9.3 + - - +
108A ARG* 3.2 13.1 + - - +
110A LEU* 1.3 79.2 - - - +
112A MSE 1.3 67.3 + - + +
114A ASP* 3.4 10.6 + - - +
115A LYS* 3.1 32.0 + - - +
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Residues in contact with MSE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 3.3 18.2 - - + +
109A GLN* 3.0 9.4 + - - +
111A GLU* 1.3 79.6 - - - +
113A ILE* 1.3 60.0 + - - +
115A LYS* 3.3 24.7 + - - +
116A LEU* 3.0 32.5 + - - +
110B LEU* 4.6 7.6 - - + +
113B ILE* 3.7 19.7 - - + -
114B ASP* 3.5 38.6 - - + +
117B THR* 3.4 32.1 + - + +
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Residues in contact with ILE 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLN* 2.9 47.9 + - + +
110A LEU* 3.3 14.3 + - + +
112A MSE 1.3 73.3 - - + +
114A ASP* 1.3 62.2 + - - +
116A LEU* 3.2 13.1 + - + +
117A THR* 2.7 47.5 + - - +
113B ILE* 5.4 6.3 - - + -
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Residues in contact with ASP 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 2.9 39.0 + - - +
111A GLU* 3.5 12.7 - - - +
113A ILE* 1.3 80.5 - - - +
115A LYS* 1.3 62.2 + - + +
117A THR* 3.3 6.0 + - - -
118A THR* 3.0 31.5 + - + +
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Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLU* 3.1 19.8 + - - +
112A MSE 3.5 28.4 - - - +
113A ILE 3.2 0.2 - - - -
114A ASP* 1.3 78.4 - - + +
116A LEU* 1.3 62.3 + - - +
118A THR* 3.0 8.9 + - - -
119A ARG* 2.9 62.4 + - - +
117B THR* 4.4 9.5 - - + +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A MSE 3.0 18.9 + - - +
113A ILE* 3.6 15.3 - - + +
115A LYS* 1.3 76.2 - - - +
117A THR* 1.3 59.0 + - - +
119A ARG* 3.5 4.9 + - - +
120A GLU* 2.9 31.5 + - - +
113B ILE* 4.0 23.1 - - + -
116B LEU* 4.0 21.8 - - + -
117B THR* 3.8 26.2 - - + +
120B GLU* 3.7 30.7 - - + +
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Residues in contact with THR 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 2.7 35.2 + - - +
114A ASP* 3.6 7.6 - - - -
116A LEU* 1.3 78.6 - - - +
118A THR* 1.3 62.4 + - + +
120A GLU* 3.5 7.5 + - - +
121A ILE* 3.3 32.6 + - + +
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Residues in contact with THR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASP* 3.0 18.7 + - + +
115A LYS* 3.0 17.0 + - - -
117A THR* 1.3 75.5 - - + +
119A ARG* 1.3 67.7 + - - +
121A ILE* 3.4 14.4 + - + +
122A GLU* 3.3 26.1 + - - +
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Residues in contact with ARG 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LYS* 2.9 50.1 + - - +
116A LEU* 4.0 4.7 - - - +
118A THR* 1.3 79.0 - - - +
120A GLU* 1.3 66.7 + - - +
122A GLU* 3.2 8.9 + - - +
123A GLN* 2.9 38.9 + - - +
117B THR* 2.8 49.8 + - - +
120B GLU* 4.4 14.6 - - + -
121B ILE* 2.9 34.4 - - - +
124B VAL* 4.3 8.2 - - + +
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Residues in contact with GLU 120 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU 2.9 19.7 + - - +
117A THR* 3.6 7.3 - - - +
119A ARG* 1.3 76.7 - - - +
121A ILE* 1.3 73.5 + - - +
123A GLN* 3.2 17.2 + - - +
124A VAL* 3.0 34.6 + - - +
120B GLU* 5.8 1.1 - - - +
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A THR* 3.3 25.7 + - + +
118A THR* 3.6 15.5 - - + +
119A ARG 3.2 0.4 - - - -
120A GLU* 1.3 87.9 - - - +
122A GLU* 1.3 71.6 + - - +
124A VAL* 3.1 10.5 - - + +
125A GLU* 3.1 36.1 + - + +
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Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR 3.3 14.1 + - - +
119A ARG* 3.2 12.4 + - - +
121A ILE* 1.3 86.5 - - - +
123A GLN* 1.3 62.9 + - - +
125A GLU* 3.7 6.6 + - - +
126A LEU* 3.2 32.5 + - + +
129A ARG* 5.9 0.5 + - - -
124B VAL* 4.9 14.6 - - + -
----------------------------------------------------------
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Residues in contact with GLN 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ARG 2.9 23.1 + - - +
120A GLU* 3.5 11.4 - - - +
121A ILE 3.2 0.2 - - - -
122A GLU* 1.3 74.7 - - - +
124A VAL* 1.3 60.6 + - - +
126A LEU* 3.1 5.8 + - - +
127A LEU* 2.8 37.3 + - + +
120B GLU* 2.8 47.4 + - - +
123B GLN* 3.3 10.9 - - - +
124B VAL* 3.6 16.2 - - + +
127B LEU* 3.6 20.1 - - + +
201B SR 2.4 31.2 - - - -
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU* 3.0 29.7 + - - +
121A ILE* 3.1 20.2 - - + +
123A GLN* 1.3 77.1 - - - +
125A GLU* 1.3 78.9 + - - +
127A LEU* 3.1 14.9 + - + +
128A LYS* 2.9 46.6 + - + +
----------------------------------------------------------
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.1 27.9 + - + +
122A GLU* 4.0 7.9 - - - +
124A VAL* 1.3 94.0 - - + +
126A LEU* 1.3 61.6 + - - +
128A LYS* 3.5 24.2 + - - +
129A ARG* 3.2 34.0 + - - +
----------------------------------------------------------
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU* 3.2 24.3 + - + +
123A GLN* 3.1 8.4 + - - +
125A GLU* 1.3 75.8 - - + +
127A LEU* 1.3 59.6 + - - +
129A ARG* 2.9 41.7 + - - +
130A ILE* 2.9 35.2 + - + +
124B VAL* 4.2 11.2 - - + +
127B LEU* 3.7 35.2 - - + +
128B LYS* 4.1 25.4 - - + -
131B TYR* 4.6 17.5 - - + -
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLN* 2.8 23.9 + - + +
124A VAL* 3.1 19.5 + - + +
126A LEU* 1.3 77.5 - - - +
128A LYS* 1.3 57.8 - - + +
130A ILE* 3.3 9.5 + - + +
131A TYR* 2.9 29.9 + - - +
127B LEU* 3.5 25.8 - - + -
----------------------------------------------------------
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Residues in contact with LYS 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 2.9 38.1 + - + +
125A GLU* 3.8 26.4 + - - +
127A LEU* 1.3 76.3 - - + +
129A ARG* 1.3 58.4 + - + +
131A TYR* 3.3 7.1 + - - +
132A ASP* 2.9 38.4 + - - +
----------------------------------------------------------
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU* 5.9 0.4 + - - -
125A GLU* 3.2 20.0 + - - +
126A LEU* 2.9 41.8 + - - +
128A LYS* 1.3 76.0 - - + +
130A ILE* 1.3 66.0 + - - +
132A ASP* 3.4 10.4 + - - +
133A LYS* 3.1 26.9 + - - +
131B TYR* 3.8 44.6 + - + -
----------------------------------------------------------
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Residues in contact with ILE 130 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 2.9 22.8 + - + +
127A LEU* 3.6 9.9 - - + +
129A ARG* 1.3 74.0 - - - +
131A TYR* 1.3 66.3 + - - +
133A LYS* 3.1 11.7 + - - +
134A LEU* 3.4 24.6 + - + +
127B LEU* 3.7 45.1 - - + +
130B ILE* 3.7 20.2 - - + -
131B TYR* 4.0 26.2 - - + -
134B LEU* 3.8 17.9 - - + -
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Residues in contact with TYR 131 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU 2.9 17.3 + - - +
128A LYS* 3.6 7.2 - - - +
130A ILE* 1.3 77.8 - - - +
132A ASP* 1.3 73.3 + - - +
134A LEU* 3.1 17.8 + - + +
135A THR* 2.9 51.1 + - + +
----------------------------------------------------------
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Residues in contact with ASP 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LYS* 2.9 26.6 + - - +
129A ARG* 3.6 9.3 - - - +
130A ILE 3.2 0.2 - - - -
131A TYR* 1.3 87.5 - - - +
133A LYS* 1.3 62.3 + - + +
134A LEU 3.1 0.9 + - - -
135A THR* 3.2 6.4 + - - -
137A GLN* 2.5 46.7 + - - +
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Residues in contact with LYS 133 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ARG 3.1 18.5 + - - +
130A ILE 3.1 8.7 + - - +
132A ASP* 1.3 75.4 - - + +
134A LEU* 1.3 62.0 + - - +
135A THR 3.5 0.2 - - - -
137A GLN* 4.9 0.2 - - - +
131B TYR* 3.1 39.9 + - + -
134B LEU* 4.0 34.7 + - + +
135B THR* 4.3 8.9 - - - +
----------------------------------------------------------
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Residues in contact with LEU 134 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ILE* 3.5 29.4 - - + +
131A TYR* 3.1 14.7 + - + +
132A ASP 3.0 0.6 - - - -
133A LYS* 1.3 81.4 - - - +
135A THR* 1.3 61.7 + - - +
136A VAL 4.4 0.5 + - - -
134B LEU* 3.7 30.3 - - + -
----------------------------------------------------------
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Residues in contact with THR 135 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TYR* 2.9 53.4 + - + +
132A ASP* 3.2 2.1 + - - +
133A LYS 3.5 0.6 - - - -
134A LEU* 1.3 82.5 + - - +
136A VAL* 1.3 77.5 + - + +
137A GLN* 2.6 39.1 + - - +
----------------------------------------------------------
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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