Contacts of the helix formed by residues 125 - 151 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R THR* 3.8 18.3 - - + +
63R ARG* 2.9 27.1 + - - -
67R ILE* 4.1 9.2 - - - +
120R THR* 2.9 36.9 + - + +
123R GLU* 3.2 10.3 - - + +
124R GLY* 1.3 73.7 - - - +
126R ASP* 1.3 62.4 + - - +
127R VAL* 3.3 3.3 + - - +
128R THR* 2.5 30.3 + - - -
129R ASN* 3.2 2.6 + - - +
136X LYS* 5.8 0.7 + - - -
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Residues in contact with ASP 126 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124R GLY* 3.3 15.4 + - - +
125R ASP* 1.3 72.4 + - - +
127R VAL* 1.3 63.3 + - + +
129R ASN* 3.5 7.2 + - - +
130R ASP* 3.1 24.1 + - - +
114X LYS* 3.5 18.1 + - - +
117X ILE* 3.7 28.8 - - + +
118X GLU* 5.2 4.2 - - - +
129X ASN* 5.5 0.3 + - - -
133X ILE* 3.5 30.7 - - + +
136X LYS* 5.3 6.0 - - - +
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Residues in contact with VAL 127 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63R ARG* 3.2 38.1 - - - +
125R ASP* 3.3 1.6 + - - -
126R ASP* 1.3 74.9 - - + +
128R THR* 1.3 65.9 + - - +
130R ASP* 3.4 2.9 + - - +
131R MET* 3.2 22.8 + - + +
117X ILE* 6.1 0.2 - - + -
133X ILE* 4.0 13.9 - - + +
136X LYS* 4.0 19.7 - - + +
137X ALA* 3.6 40.4 - - + +
140X ASP* 3.7 18.2 - - - +
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Residues in contact with THR 128 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R THR* 4.0 6.6 - - + +
12R PHE* 5.8 0.2 - - + -
13R LEU* 3.9 32.9 - - + +
63R ARG* 3.3 20.5 + - - +
67R ILE* 4.6 0.7 - - - +
120R THR* 3.8 17.5 - - - +
125R ASP* 2.5 30.9 + - - -
127R VAL* 1.3 78.3 - - - +
129R ASN* 1.3 62.4 + - - +
131R MET* 3.2 11.0 + - + +
132R LEU* 2.9 31.0 + - + +
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Residues in contact with ASN 129 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117R ILE* 2.8 43.2 + - - +
120R THR* 3.1 24.3 - - + +
121R ASP* 3.7 16.5 - - - +
125R ASP 3.2 8.2 + - - +
126R ASP* 3.6 9.6 - - - +
128R THR* 1.3 75.3 - - - +
130R ASP* 1.3 63.0 + - - +
132R LEU* 3.4 5.6 + - - +
133R ILE* 3.2 42.9 + - - +
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Residues in contact with ASP 130 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130P ASP* 3.5 19.3 - - - +
126R ASP 3.1 13.8 + - - +
127R VAL 3.7 4.5 - - - +
129R ASN* 1.3 80.4 - - - +
131R MET* 1.3 65.7 + - - +
133R ILE* 3.3 9.0 + - - +
134R ALA* 3.1 24.6 + - - +
130X ASP* 3.3 23.5 - - - +
133X ILE* 4.1 18.7 - - + +
134X ALA* 6.1 2.3 - - - +
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Residues in contact with MET 131 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R LEU* 4.2 10.1 - - + -
59R GLU* 3.8 26.2 - - - +
60R VAL* 4.1 13.5 - - + -
63R ARG* 4.0 27.1 - - + -
127R VAL* 3.2 13.7 + - + +
128R THR* 3.2 8.5 + - + +
130R ASP* 1.3 79.0 + - - +
132R LEU* 1.3 85.2 + - + +
134R ALA* 3.4 5.5 + - - +
135R PHE* 3.2 57.3 + - + -
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Residues in contact with LEU 132 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R PHE* 3.5 35.2 - - + -
13R LEU* 4.4 6.1 - - + -
16R GLN* 5.9 0.9 - - + -
60R VAL* 5.3 2.7 - - + -
113R TYR* 4.0 19.4 - - + +
116R GLY 3.7 23.1 - - - +
117R ILE* 3.7 16.8 - - + +
120R THR* 4.2 1.8 - - - +
128R THR* 2.9 29.2 + - + +
129R ASN 3.7 4.9 - - - +
131R MET* 1.3 97.1 - - + +
133R ILE* 1.3 63.6 + - - +
135R PHE* 3.6 15.8 + - + +
136R LYS* 3.1 22.0 + - - +
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Residues in contact with ILE 133 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P ASP* 3.6 46.4 - - + +
127P VAL* 3.7 11.1 - - + +
130P ASP* 4.2 19.1 - - + +
117R ILE* 3.6 25.6 - - + -
129R ASN* 3.2 37.2 + - - +
130R ASP* 3.3 10.3 + - - +
132R LEU* 1.3 76.7 - - - +
134R ALA* 1.3 60.5 + - - +
136R LYS* 3.2 4.1 + - - +
137R ALA* 3.0 25.7 + - + +
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Residues in contact with ALA 134 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130P ASP* 5.9 4.0 - - - +
130R ASP* 3.1 16.7 + - - +
131R MET* 3.7 10.5 - - - +
132R LEU 3.3 0.2 - - - -
133R ILE* 1.3 74.1 - - - +
135R PHE* 1.3 70.4 + - + +
137R ALA* 3.5 8.6 + - - +
138R SER* 3.5 18.4 + - - -
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Residues in contact with PHE 135 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56R GLN* 3.6 36.3 + - + +
59R GLU* 3.5 33.2 - - + -
60R VAL* 3.8 23.1 - - + -
113R TYR* 3.4 32.8 - + + -
131R MET* 3.2 43.2 + - + -
132R LEU* 3.7 9.9 - - + +
133R ILE 3.3 0.2 - - - -
134R ALA* 1.3 79.1 - - + +
136R LYS* 1.3 65.2 + - - +
138R SER* 3.3 5.6 + - - -
139R ILE* 3.1 28.2 + - - +
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Residues in contact with LYS 136 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63P ARG* 5.0 3.2 - - - +
125P ASP* 5.8 1.3 + - - -
126P ASP* 5.7 4.7 - - - +
127P VAL* 4.1 14.6 - - + +
110R ARG* 4.0 36.4 - - + +
113R TYR* 4.7 4.3 - - + -
114R LYS* 4.7 24.0 - - + +
117R ILE* 3.9 20.4 - - + -
132R LEU 3.1 12.0 + - - +
133R ILE* 3.2 10.5 + - - +
135R PHE* 1.3 76.8 - - - +
137R ALA* 1.3 61.1 + - - +
139R ILE* 3.1 8.8 + - - +
140R ASP* 2.8 61.6 + - - +
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Residues in contact with ALA 137 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63P ARG* 4.9 1.4 + - - -
127P VAL* 3.3 34.4 - - + +
133R ILE* 3.0 11.6 + - + +
134R ALA* 3.8 11.0 - - - +
135R PHE 3.3 0.2 - - - -
136R LYS* 1.3 77.9 - - - +
138R SER* 1.3 59.9 + - - +
140R ASP* 3.7 5.1 - - - +
141R LYS* 3.3 29.0 + - + +
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Residues in contact with SER 138 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52R GLU* 2.5 32.8 + - - -
56R GLN* 5.0 2.6 + - - -
134R ALA 3.5 9.0 + - - -
135R PHE* 3.3 10.2 + - - -
136R LYS 3.1 0.8 - - - -
137R ALA* 1.3 79.2 - - - +
139R ILE* 1.3 58.1 + - - +
141R LYS* 3.4 8.5 + - - +
142R HIS* 3.1 35.6 + - - -
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Residues in contact with ILE 139 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53R PHE* 3.9 28.0 - - + -
56R GLN* 4.2 7.6 - - - +
106R LEU* 3.4 32.7 - - + +
109R LEU* 4.5 10.5 - - + -
110R ARG* 3.9 12.1 - - + +
113R TYR* 3.7 33.2 - - + -
135R PHE 3.1 18.4 + - - +
136R LYS* 3.6 5.4 - - - +
138R SER* 1.3 73.4 - - - +
140R ASP* 1.3 60.8 + - - +
142R HIS* 3.3 8.0 + - - +
143R ILE* 2.9 37.9 + - + +
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Residues in contact with ASP 140 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63P ARG* 3.0 36.5 + - - +
66P ALA* 3.9 13.8 - - + +
127P VAL* 3.9 2.4 - - - +
110R ARG* 3.2 32.1 + - - +
136R LYS* 2.8 40.3 + - - +
137R ALA 3.7 3.8 - - - +
139R ILE* 1.3 74.0 - - - +
141R LYS* 1.3 65.0 + - - +
143R ILE* 3.3 8.8 + - - +
144R TRP* 3.1 21.0 + - - +
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Residues in contact with LYS 141 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59P GLU* 3.1 39.6 + - - +
62P GLU* 3.7 41.8 + - - +
63P ARG* 3.7 17.9 - - - +
66P ALA* 4.6 4.9 - - - +
131P MET* 4.5 5.1 - - - -
137R ALA* 3.3 17.9 + - + +
138R SER* 3.6 10.8 - - - +
139R ILE 3.4 0.4 - - - -
140R ASP* 1.3 77.3 - - - +
142R HIS* 1.3 58.0 - - + +
144R TRP* 3.1 19.7 + - + +
145R MET* 3.0 42.3 + - + +
----------------------------------------------------------
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Residues in contact with HIS 142 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R LYS* 4.9 7.6 + - - -
48R ASP* 6.3 1.3 - - + -
49R LEU* 3.3 31.7 - - + +
52R GLU* 2.8 25.0 + - - -
53R PHE* 4.4 13.9 - + - -
106R LEU* 4.2 15.7 - - + -
138R SER* 3.1 32.9 + - - -
139R ILE* 3.6 9.9 - - - +
141R LYS* 1.3 76.4 - - + +
143R ILE* 1.3 57.8 + - - +
145R MET* 4.0 21.2 - - + +
146R PHE* 3.0 44.0 + + + +
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Residues in contact with ILE 143 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66P ALA 6.0 0.4 - - - +
103R VAL* 4.7 5.8 - - + +
106R LEU* 3.7 45.8 - - + +
107R GLU* 3.9 12.3 - - + +
110R ARG* 4.0 30.5 - - - +
139R ILE* 2.9 27.6 + - + +
140R ASP* 3.6 7.4 - - - +
141R LYS 3.3 0.2 - - - -
142R HIS* 1.3 74.5 - - - +
144R TRP* 1.3 64.8 - - - +
146R PHE* 5.0 1.6 - - - -
147R LYS* 3.1 31.9 + - + +
154R PRO* 3.8 25.6 - - + +
155R LEU* 5.5 0.9 - - + -
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Residues in contact with TRP 144 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N HIS* 4.9 14.6 - + - -
32N TRP* 4.3 9.2 + - - -
39N PHE* 3.8 25.9 - + - -
62P GLU* 3.8 51.4 - - + -
65P LEU* 3.8 36.5 - - + +
66P ALA* 4.1 10.8 - - + -
140R ASP 3.1 11.6 + - - +
141R LYS* 3.1 19.0 + - + +
143R ILE* 1.3 78.1 - - - +
145R MET* 1.3 78.9 + - + +
147R LYS* 3.8 1.4 - - - +
148R ALA* 2.9 36.7 + - + +
152R LYS 5.9 0.9 - - - -
154R PRO* 3.9 32.7 - - + +
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Residues in contact with MET 145 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39N PHE* 3.6 35.2 - - + -
40N PHE* 3.9 21.6 - - + -
62P GLU* 5.9 0.7 - - - +
45R LYS* 4.8 5.4 - - - +
141R LYS* 3.0 26.3 + - + +
142R HIS* 4.0 29.8 - - + +
143R ILE 3.3 0.2 - - - -
144R TRP* 1.3 100.1 - - + +
146R PHE* 1.3 61.1 + - + +
148R ALA* 3.4 3.5 + - - +
149R PHE* 3.0 25.5 + - - +
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Residues in contact with PHE 146 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N PHE* 3.6 31.0 - + - -
42R LEU* 4.9 2.5 - - + -
45R LYS* 4.5 10.3 - - + -
46R MET* 3.7 23.1 - - + -
49R LEU* 3.9 25.8 - - + -
99R MET* 3.8 33.2 - - + +
102R LEU* 3.8 15.7 - - + -
103R VAL* 3.6 22.4 - - + -
106R LEU* 4.3 8.1 - - + -
142R HIS* 3.0 36.8 + - + +
143R ILE* 4.6 0.4 - - - +
145R MET* 1.3 77.3 - - + +
147R LYS* 1.3 61.8 + - - +
149R PHE* 3.2 19.5 - + + +
150R LEU* 3.3 14.0 + - - +
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Residues in contact with LYS 147 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103R VAL* 3.9 21.5 - - + -
107R GLU* 3.4 23.9 + - - -
143R ILE* 3.1 25.4 + - + +
144R TRP 3.8 2.0 - - - +
146R PHE* 1.3 73.3 - - - +
148R ALA* 1.3 65.8 + - - +
150R LEU* 2.9 19.7 + - + +
151R GLY 3.1 0.3 + - - -
152R LYS* 3.0 46.7 + - + +
153R ALA 3.4 15.0 + - - +
154R PRO* 2.3 37.7 + - + +
155R LEU* 4.0 1.2 - - - +
156R GLU 3.3 23.7 + - - +
----------------------------------------------------------
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Residues in contact with ALA 148 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N MET 4.0 7.4 - - - +
35N ARG* 3.7 10.3 - - - +
36N GLY 2.9 22.7 + - - -
39N PHE* 3.5 34.1 - - + -
144R TRP* 2.9 26.0 + - + +
145R MET 3.6 2.0 - - - +
147R LYS* 1.3 75.2 - - - +
149R PHE* 1.3 64.2 + - - +
151R GLY* 3.1 7.8 + - - -
152R LYS 3.3 9.7 + - - +
----------------------------------------------------------
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Residues in contact with PHE 149 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N GLY* 3.2 28.3 - - - -
37N HIS* 3.1 47.9 + + - -
39N PHE* 4.3 2.6 - - + +
40N PHE* 3.9 25.8 - + + -
38R ASN* 3.9 20.0 - - - -
41R THR* 6.0 0.4 - - - -
42R LEU* 3.8 29.2 - - + -
95R MET* 4.8 2.5 - - + -
96R ASP* 4.1 17.5 - - - -
99R MET* 4.1 23.1 - - + -
145R MET 3.0 14.2 + - - +
146R PHE* 3.2 13.5 - + + +
148R ALA* 1.3 75.7 - - - +
150R LEU* 1.3 70.2 + - + +
151R GLY 3.3 2.0 + - - -
----------------------------------------------------------
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Residues in contact with LEU 150 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N GLY* 5.5 0.2 - - - -
37N HIS* 5.7 2.2 - - - -
96R ASP* 4.0 35.4 - - + +
99R MET* 4.0 17.0 - - + -
100R GLU* 4.1 27.1 - - + +
103R VAL* 4.2 20.6 - - + -
146R PHE 3.3 15.7 - - - +
147R LYS* 2.9 14.0 + - + +
149R PHE* 1.3 89.0 - - + +
151R GLY* 1.3 59.0 + - - +
152R LYS* 3.5 26.3 - - + +
----------------------------------------------------------
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Residues in contact with GLY 151 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35N ARG* 3.8 23.2 + - - -
36N GLY* 4.5 9.0 - - - -
148R ALA 3.1 13.3 + - - -
149R PHE 3.3 1.4 + - - -
150R LEU* 1.3 78.1 - - - +
152R LYS* 1.3 61.4 + - - +
156R GLU* 5.1 0.7 - - - +
----------------------------------------------------------
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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