Contacts of the helix formed by residues 125 - 150 (chain V) in PDB entry 2BKC
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 ASP 125 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136O LYS* 5.3 1.2 + - - -
9V THR* 3.6 20.6 - - - +
63V ARG* 3.0 26.8 + - - -
67V ILE* 4.0 9.7 - - - +
120V THR* 3.1 18.9 + - - +
123V GLU* 3.3 8.7 - - + +
124V GLY* 1.3 74.0 - - - +
126V ASP* 1.3 64.7 + - - +
127V VAL 3.6 0.9 + - - -
128V THR* 2.8 27.1 + - - -
129V ASN* 3.1 21.7 + - - +
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Residues in contact with ASP 126 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114O LYS* 2.8 30.4 + - - +
117O ILE* 3.2 21.6 - - + +
133O ILE* 3.8 30.0 - - + +
136O LYS* 5.9 3.5 - - + +
120V THR 5.2 0.7 - - - +
121V ASP* 5.5 2.3 - - - +
124V GLY* 3.3 15.3 + - - +
125V ASP* 1.3 70.2 + - - +
127V VAL* 1.3 67.4 + - + +
129V ASN* 3.3 8.6 - - - +
130V ASP* 3.0 23.0 + - - +
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Residues in contact with VAL 127 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133O ILE* 3.7 15.9 - - + +
136O LYS* 3.6 43.4 - - + +
137O ALA* 3.4 35.2 - - + +
140O ASP* 4.1 0.7 - - - +
63V ARG* 3.4 36.3 - - - +
125V ASP* 3.3 1.4 + - - -
126V ASP* 1.3 76.0 - - + +
128V THR* 1.3 61.6 + - - +
130V ASP* 3.1 7.3 + - - +
131V MET* 3.0 22.1 + - + +
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Residues in contact with THR 128 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9V THR* 4.0 6.1 - - + +
13V LEU* 3.7 34.2 - - + +
63V ARG* 2.9 22.3 + - - +
67V ILE* 4.6 0.3 - - - +
120V THR* 3.6 17.3 - - - +
125V ASP* 2.8 26.9 + - - -
127V VAL* 1.3 73.2 - - - +
129V ASN* 1.3 66.7 + - - +
131V MET* 3.2 15.2 + - + +
132V LEU* 3.2 27.8 + - + +
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Residues in contact with ASN 129 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117V ILE* 3.0 40.4 + - - +
120V THR* 3.1 21.7 - - + +
121V ASP* 3.9 14.4 - - - +
125V ASP 3.1 12.7 + - - +
126V ASP* 3.3 14.7 - - - +
127V VAL 3.2 0.2 - - - -
128V THR* 1.3 77.8 - - - +
130V ASP* 1.3 64.0 + - - +
132V LEU* 3.3 3.1 + - - +
133V ILE* 3.1 39.3 + - - +
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Residues in contact with ASP 130 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130O ASP* 3.8 13.0 - - - +
133O ILE* 4.1 19.2 - - + +
134O ALA* 5.6 7.3 - - - +
130T ASP* 3.7 21.5 - - - +
126V ASP 3.0 12.7 + - - +
127V VAL 3.1 8.5 + - - +
129V ASN* 1.3 79.5 + - - +
131V MET* 1.3 63.1 + - - +
133V ILE* 3.4 9.8 + - - +
134V ALA* 3.1 24.6 + - - +
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Residues in contact with MET 131 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13V LEU* 4.8 4.9 - - + -
59V GLU* 3.7 27.1 - - - +
60V VAL* 4.1 17.0 - - + -
63V ARG* 4.0 20.0 - - + -
127V VAL* 3.0 15.9 + - + +
128V THR* 3.2 21.7 + - + +
130V ASP* 1.3 78.0 + - - +
132V LEU* 1.3 82.4 + - + +
134V ALA* 3.3 6.6 + - - +
135V PHE* 3.1 54.8 + - + -
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Residues in contact with LEU 132 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12V PHE* 3.8 26.9 - - + -
13V LEU* 4.9 2.0 - - + -
16V GLN* 5.9 0.9 - - + -
60V VAL* 5.2 4.0 - - + -
113V TYR* 4.2 18.1 - - + +
116V GLY 3.7 30.5 - - - +
117V ILE* 3.6 17.5 - - + +
120V THR* 4.5 2.9 - - + +
128V THR* 3.2 29.0 + - + +
129V ASN 3.7 0.9 - - - +
131V MET* 1.3 100.4 - - + +
133V ILE* 1.3 61.8 + - - +
135V PHE* 3.2 14.7 + - + +
136V LYS* 2.9 28.8 + - - +
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Residues in contact with ILE 133 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126T ASP* 3.7 40.8 - - + +
127T VAL* 3.7 11.4 - - + +
130T ASP* 4.0 22.7 - - + +
117V ILE* 3.8 25.6 - - + -
129V ASN* 3.1 39.9 + - - +
130V ASP* 3.7 9.0 - - - +
132V LEU* 1.3 77.1 - - - +
134V ALA* 1.3 57.0 + - - +
136V LYS* 3.3 3.8 + - - +
137V ALA* 3.0 26.7 + - + +
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Residues in contact with ALA 134 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130T ASP* 5.5 7.2 - - - +
130V ASP* 3.1 17.2 + - - +
131V MET* 3.7 9.6 - - - +
132V LEU 3.2 0.4 - - - -
133V ILE* 1.3 78.3 - - - +
135V PHE* 1.3 67.9 + - + +
137V ALA* 3.5 9.1 - - - +
138V SER* 3.3 18.9 + - - -
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Residues in contact with PHE 135 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56V GLN* 3.6 46.1 + - + +
59V GLU* 3.4 28.3 - - + -
60V VAL* 3.7 24.0 - - + -
113V TYR* 3.5 25.4 - + + -
131V MET* 3.1 41.6 + - + -
132V LEU* 3.2 10.7 + - + +
134V ALA* 1.3 79.7 - - + +
136V LYS* 1.3 59.5 + - - +
138V SER* 3.2 5.4 + - - -
139V ILE* 2.9 33.1 + - - +
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Residues in contact with LYS 136 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63T ARG* 4.1 10.5 - - - +
125T ASP* 5.3 1.2 + - - -
126T ASP* 6.1 2.2 - - + +
127T VAL* 4.0 11.9 - - + +
110V ARG* 4.0 34.7 - - + +
113V TYR* 4.3 5.8 - - + -
114V LYS* 4.7 19.3 - - + -
117V ILE* 4.1 20.0 - - + -
132V LEU 2.9 16.1 + - - +
133V ILE* 3.3 6.5 + - - +
135V PHE* 1.3 77.6 - - - +
137V ALA* 1.3 53.7 + - - +
139V ILE* 3.1 10.6 + - - +
140V ASP* 2.6 66.8 + - - +
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Residues in contact with ALA 137 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63T ARG* 5.0 0.9 + - - -
127T VAL* 3.6 30.3 - - + +
133V ILE* 3.0 12.6 + - + +
134V ALA* 3.5 13.2 - - - +
136V LYS* 1.3 77.6 - - - +
138V SER* 1.3 64.6 + - - +
140V ASP* 3.5 4.8 + - - +
141V LYS* 3.5 18.0 + - - +
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Residues in contact with SER 138 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52V GLU* 2.6 28.6 + - - -
56V GLN* 5.0 3.8 + - - -
134V ALA 3.3 8.1 + - - -
135V PHE* 3.2 10.2 + - - -
137V ALA* 1.3 81.9 - - - +
139V ILE* 1.3 62.9 + - - +
141V LYS* 3.4 12.1 + - - +
142V HIS* 3.1 34.5 + - - -
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Residues in contact with ILE 139 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53V PHE* 3.9 27.1 - - + -
56V GLN* 4.0 8.3 - - - +
106V LEU* 3.6 30.3 - - + +
109V LEU* 4.4 10.8 - - + -
110V ARG* 3.8 15.3 - - + +
113V TYR* 3.8 33.7 - - + -
135V PHE 2.9 21.5 + - - +
136V LYS* 3.5 5.8 - - - +
138V SER* 1.3 75.5 - - - +
140V ASP* 1.3 58.2 + - - +
142V HIS* 3.3 8.2 + - - +
143V ILE* 3.0 39.3 + - + +
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Residues in contact with ASP 140 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63T ARG* 3.0 34.2 + - - +
66T ALA* 4.0 17.2 - - + +
67T ILE* 6.1 0.4 - - - -
127T VAL* 4.1 1.6 - - - +
110V ARG* 3.2 32.6 + - - +
136V LYS* 2.6 49.3 + - - +
137V ALA 3.9 2.7 - - - +
138V SER 3.3 0.2 - - - -
139V ILE* 1.3 70.6 - - - +
141V LYS* 1.3 57.7 + - - +
143V ILE* 3.4 10.0 + - - +
144V TRP* 3.1 24.4 + - - +
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Residues in contact with LYS 141 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59T GLU* 5.1 8.2 + - - -
62T GLU* 3.9 24.5 - - + +
66T ALA* 4.5 6.0 - - + +
137V ALA 3.5 9.0 + - - +
138V SER* 3.4 16.7 + - - +
139V ILE 3.3 0.4 - - - -
140V ASP* 1.3 75.1 - - - +
142V HIS* 1.3 70.2 + - + +
143V ILE 3.1 1.1 - - - -
144V TRP* 3.4 22.6 + - + +
145V MET* 3.0 50.8 + - + +
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Residues in contact with HIS 142 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45V LYS* 4.9 4.7 + - - -
48V ASP* 6.6 0.2 - - + -
49V LEU* 3.6 24.2 - - + +
52V GLU* 2.8 27.8 + - - -
53V PHE* 4.4 13.9 - + - -
106V LEU* 4.0 17.7 - - + -
138V SER* 3.1 34.5 + - - -
139V ILE* 3.8 9.2 - - - +
141V LYS* 1.3 80.3 + - + +
143V ILE* 1.3 57.1 + - - +
145V MET* 3.2 23.4 + - + +
146V PHE* 2.9 42.8 + - + +
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Residues in contact with ILE 143 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66T ALA 6.0 0.4 - - - +
103V VAL* 4.8 4.7 - - + +
106V LEU* 3.9 20.0 - - + +
107V GLU* 4.0 24.9 - - + +
110V ARG* 4.0 31.9 - - - +
139V ILE* 3.0 35.8 + - + +
140V ASP* 3.4 10.8 - - - +
141V LYS 3.1 0.2 - - - -
142V HIS* 1.3 73.7 - - - +
144V TRP* 1.3 66.6 + - - +
146V PHE* 4.1 1.5 - - - -
147V LYS* 3.0 38.9 + - + +
154V PRO* 3.9 25.1 - - + +
155V LEU* 5.4 1.1 - - + -
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Residues in contact with TRP 144 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R HIS* 4.6 17.5 - + - -
32R TRP* 4.3 9.6 + - - -
34R MET 5.6 0.4 + - - -
39R PHE* 3.8 25.9 - + - -
62T GLU* 3.8 44.9 - - + -
65T LEU* 3.8 35.8 - - + +
66T ALA* 4.2 9.6 - - - -
140V ASP 3.1 13.2 + - - +
141V LYS* 3.7 19.7 - - + +
143V ILE* 1.3 75.6 - - - +
145V MET* 1.3 80.7 + - + +
147V LYS* 3.7 1.4 - - - +
148V ALA* 2.9 36.8 + - + +
152V LYS 5.0 1.0 - - - +
154V PRO* 3.9 33.6 - - + +
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Residues in contact with MET 145 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R PHE* 3.5 36.3 - - + -
40R PHE* 3.9 12.4 - - + -
45V LYS* 3.9 21.3 - - - +
141V LYS* 3.0 38.0 + - + +
142V HIS* 3.2 31.8 + - + +
144V TRP* 1.3 98.5 - - + +
146V PHE* 1.3 59.8 + - + +
148V ALA* 3.4 4.3 + - - +
149V PHE* 3.1 21.7 + - - +
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Residues in contact with PHE 146 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R PHE* 3.7 30.7 - + - -
42V LEU* 4.1 3.1 - - + -
45V LYS* 4.0 13.9 - - + -
46V MET* 3.7 22.2 - - + -
49V LEU* 4.2 11.7 - - + -
99V MET* 3.7 33.9 - - + -
102V LEU* 3.7 15.5 - - + -
103V VAL* 3.6 22.7 - - + -
106V LEU* 4.4 5.4 - - + -
142V HIS* 2.9 49.3 + - + +
143V ILE* 4.4 0.4 - - - +
145V MET* 1.3 74.1 - - + +
147V LYS* 1.3 65.5 + - - +
149V PHE* 3.1 16.3 + - + +
150V LEU* 3.1 17.5 + - - +
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Residues in contact with LYS 147 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103V VAL* 3.5 22.3 - - + +
107V GLU* 3.1 28.8 + - - -
143V ILE* 3.0 29.9 + - + +
144V TRP 3.7 2.9 - - - +
146V PHE* 1.3 75.8 - - - +
148V ALA* 1.3 57.2 + - - +
150V LEU* 3.0 25.0 + - + +
152V LYS* 3.0 40.7 + - - +
153V ALA 3.7 20.6 - - - +
154V PRO* 3.3 18.8 + - + +
155V LEU 4.8 0.2 - - - -
156V GLU 3.0 33.9 + - - -
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Residues in contact with ALA 148 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34R MET 4.1 7.9 - - - +
35R ARG* 3.4 10.8 - - + +
36R GLY 2.7 30.2 + - - -
39R PHE* 3.8 26.7 - - + -
144V TRP* 2.9 28.5 + - + +
145V MET 3.6 5.6 - - - +
147V LYS* 1.3 75.7 - - - +
149V PHE* 1.3 56.0 + - - +
151V GLY 3.2 6.1 + - - +
152V LYS 3.5 10.7 + - - +
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Residues in contact with PHE 149 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36R GLY* 3.2 27.4 - - - -
37R HIS* 3.2 53.3 - + - -
39R PHE* 4.2 3.5 - - + +
40R PHE* 3.9 29.8 - + + -
38V ASN* 3.5 21.8 - - + -
42V LEU* 3.7 25.4 - - + -
95V MET* 4.3 7.0 - - + -
96V ASP* 4.1 11.7 - - - -
99V MET* 4.0 26.7 - - + -
145V MET 3.1 13.8 + - - +
146V PHE* 3.1 11.2 + + - +
148V ALA* 1.3 75.8 - - - +
150V LEU* 1.3 65.4 + - + +
151V GLY 3.4 2.1 + - - -
----------------------------------------------------------
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Residues in contact with LEU 150 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R HIS* 5.4 1.6 - - - -
96V ASP* 3.5 50.7 - - - +
99V MET* 4.1 12.3 - - + +
100V GLU* 3.9 30.7 - - + +
103V VAL* 3.9 23.8 - - + -
146V PHE 3.1 16.9 + - - +
147V LYS* 3.0 15.4 + - + +
149V PHE* 1.3 80.2 - - + +
151V GLY* 1.3 59.9 + - - +
152V LYS* 3.5 17.2 - - + +
----------------------------------------------------------
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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