Contacts of the helix formed by residues 94 - 123 (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 THR 94 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93R LYS* 1.3 76.5 - - - +
95R MET* 1.3 66.1 + - - +
96R ASP* 3.6 9.6 + - - +
97R GLN* 2.9 42.9 + - - +
98R LEU* 3.1 22.8 + - - +
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Residues in contact with MET 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N HIS* 5.9 1.8 - - + -
34R MET* 3.5 40.8 - - + -
35R ARG 4.1 23.3 + - - +
36R GLY* 6.0 0.4 - - - -
38R ASN* 3.3 49.1 - - + +
39R PHE* 3.5 11.2 - - - +
42R LEU* 3.3 27.8 - - + -
94R THR* 1.3 73.4 - - - +
96R ASP* 1.3 60.5 + - - +
98R LEU* 3.1 10.1 + - - +
99R MET* 2.9 30.7 + - + +
149R PHE* 4.8 4.5 - - + -
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Residues in contact with ASP 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N HIS* 3.6 32.3 + - - -
94R THR* 3.9 7.6 - - - +
95R MET* 1.3 76.4 - - - +
97R GLN* 1.3 65.2 + - - +
99R MET* 3.9 0.9 - - - +
100R GLU* 3.0 34.3 + - - +
149R PHE* 4.1 5.9 - - - -
150R LEU* 4.0 29.7 - - + +
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Residues in contact with GLN 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92R PRO 4.4 2.7 + - - +
93R LYS* 3.4 32.0 - - + +
94R THR* 2.9 50.7 + - - +
96R ASP* 1.3 75.7 - - - +
98R LEU* 1.3 62.2 + - - +
100R GLU* 3.3 13.1 + - - +
101R ASP* 3.2 22.5 + - - +
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Residues in contact with LEU 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R GLN* 5.8 4.9 - - + +
30R ILE* 3.7 34.0 - - + +
33R TYR* 4.6 3.6 - - + +
34R MET* 3.8 37.0 - - + +
35R ARG 5.2 0.4 - - - +
89R TYR* 4.2 17.5 - - + +
93R LYS* 3.9 28.7 - - + +
94R THR 3.1 18.8 + - - +
95R MET* 3.4 11.9 - - - +
97R GLN* 1.3 73.7 - - - +
99R MET* 1.3 71.2 + - + +
101R ASP* 3.4 7.1 + - + +
102R LEU* 3.1 25.3 + - - +
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Residues in contact with MET 99 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R ILE* 3.7 29.8 - - + -
34R MET* 4.3 3.4 - - + -
42R LEU* 3.8 31.6 - - + -
46R MET* 4.3 6.1 - - + -
95R MET* 2.9 18.6 + - - +
96R ASP 4.1 0.2 - - - +
98R LEU* 1.3 79.7 - - + +
100R GLU* 1.3 56.8 + - - +
102R LEU* 3.3 16.2 + - + +
103R VAL* 2.9 38.3 + - + +
146R PHE* 3.8 32.1 - - + -
149R PHE* 4.1 14.8 - - + -
150R LEU* 4.0 23.1 - - + -
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Residues in contact with GLU 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96R ASP* 3.0 27.8 + - - +
97R GLN* 3.7 12.2 - - - +
98R LEU 3.2 0.2 - - - -
99R MET* 1.3 76.0 - - - +
101R ASP* 1.3 60.0 + - - +
103R VAL* 4.0 5.1 - - + +
104R GLY* 2.9 26.5 + - - -
150R LEU* 4.1 17.9 - - + +
152R LYS* 2.8 29.9 + - - +
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Residues in contact with ASP 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26R LYS* 2.6 41.4 + - + +
29R GLN* 5.2 3.8 + - - -
30R ILE* 5.5 3.6 - - + +
97R GLN 3.2 13.8 + - - +
98R LEU* 3.8 10.1 - - + +
100R GLU* 1.3 76.2 - - - +
102R LEU* 1.3 63.7 + - - +
104R GLY* 3.6 2.1 - - - -
105R THR* 3.0 24.4 + - - -
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Residues in contact with LEU 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R PHE* 3.9 16.8 - - + -
26R LYS* 5.5 2.0 - - - -
27R ILE* 5.6 1.3 - - + -
30R ILE* 4.2 16.1 - - + +
46R MET* 3.8 32.5 - - + -
49R LEU* 3.8 16.2 - - + -
98R LEU 3.1 13.8 + - - +
99R MET* 3.4 21.5 - - + +
100R GLU 3.2 0.2 - - - -
101R ASP* 1.3 76.2 - - - +
103R VAL* 1.3 56.4 + - - +
105R THR* 3.2 7.3 + - - -
106R LEU* 2.9 46.4 + - + +
146R PHE* 3.8 23.3 - - + -
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Residues in contact with VAL 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99R MET 2.9 25.5 + - - +
100R GLU* 4.0 5.8 - - + +
102R LEU* 1.3 76.2 - - + +
104R GLY* 1.3 57.0 + - - +
106R LEU* 3.1 12.7 + - + +
107R GLU* 2.9 38.7 + - + +
143R ILE* 4.9 9.2 - - + +
146R PHE* 3.6 34.5 - - + -
147R LYS* 3.9 33.0 - - + +
150R LEU* 4.2 14.4 - - + -
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Residues in contact with GLY 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100R GLU 2.9 19.2 + - - -
101R ASP* 3.6 2.9 - - - -
103R VAL* 1.3 77.4 - - - +
105R THR* 1.3 58.7 + - - +
107R GLU* 3.5 14.4 + - - +
108R LEU* 3.2 21.0 + - - +
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Residues in contact with THR 105 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R PHE* 3.6 34.5 - - + -
26R LYS* 3.6 20.2 - - - +
84R VAL* 3.8 31.5 - - + +
101R ASP* 3.0 18.7 + - - -
102R LEU 3.2 7.2 + - - -
104R GLY* 1.3 69.9 - - - +
106R LEU* 1.3 60.8 + - - +
108R LEU* 3.4 8.5 + - + +
109R LEU* 3.0 30.0 + - + +
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Residues in contact with LEU 106 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R PHE* 3.9 12.6 - - + -
49R LEU* 5.2 1.6 - - + -
53R PHE* 3.7 31.6 - - + -
102R LEU* 2.9 36.4 + - + +
103R VAL* 3.1 15.2 + - + +
105R THR* 1.3 78.7 - - - +
107R GLU* 1.3 55.7 + - - +
109R LEU* 3.4 4.0 + - + +
110R ARG* 2.9 24.9 + - - +
139R ILE* 3.4 25.0 - - + +
142R HIS* 4.2 24.7 - - + +
143R ILE* 3.7 20.2 - - + -
146R PHE* 4.3 11.7 - - + -
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Residues in contact with GLU 107 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103R VAL* 2.9 27.9 + - - +
104R GLY* 3.7 14.3 + - - +
106R LEU* 1.3 72.4 - - - +
108R LEU* 1.3 59.5 + - - +
110R ARG* 3.4 26.2 + - - +
111R ASP* 2.9 38.0 + - - +
143R ILE* 4.1 17.7 - - + +
147R LYS* 3.4 26.6 + - - -
154R PRO 4.5 1.7 - - - +
155R LEU* 5.8 0.5 - - - +
156R GLU 5.2 0.2 - - - +
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Residues in contact with LEU 108 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R ASN* 4.3 2.5 - - - +
83R SER* 3.7 26.7 - - - +
84R VAL* 3.7 27.8 - - + -
85R GLU* 4.1 14.8 - - - +
104R GLY 3.2 11.3 + - - +
105R THR* 3.5 10.5 - - - +
107R GLU* 1.3 78.9 - - - +
109R LEU* 1.3 62.5 + - + +
111R ASP* 3.9 4.5 - - - +
112R GLU* 3.0 60.5 + - + +
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Residues in contact with LEU 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16R GLN* 3.6 24.5 - - - +
19R ASN* 4.1 19.5 - - + +
20R LEU* 4.3 14.1 - - + -
23R PHE* 3.4 42.0 - - + -
53R PHE* 4.4 8.1 - - + -
84R VAL* 4.6 1.6 - - + -
105R THR* 3.0 24.7 + - + +
106R LEU* 3.8 5.4 - - - +
107R GLU 3.3 0.2 - - - -
108R LEU* 1.3 77.4 - - + +
110R ARG* 1.3 57.4 + - - +
112R GLU* 3.4 1.5 + - - -
113R TYR* 2.8 52.2 + - + +
139R ILE* 4.5 11.0 - - + -
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Residues in contact with ARG 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106R LEU 2.9 18.0 + - - +
107R GLU* 3.5 30.9 + - - +
109R LEU* 1.3 76.0 - - - +
111R ASP* 1.3 84.5 + - - +
113R TYR* 3.6 6.3 + - - +
114R LYS* 3.0 26.1 + - + +
136R LYS* 4.0 24.0 - - + +
139R ILE* 3.9 15.7 - - + +
140R ASP* 3.2 27.5 + - - +
143R ILE* 4.0 20.3 - - + +
155R LEU* 3.6 29.1 - - - +
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Residues in contact with ASP 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107R GLU* 2.9 22.1 + - - +
108R LEU* 3.9 4.3 - - - +
109R LEU 3.2 0.4 - - - -
110R ARG* 1.3 106.2 + - - +
112R GLU* 1.3 66.5 + - + +
114R LYS* 3.2 17.3 + - - +
115R GLN* 3.4 18.7 + - - +
----------------------------------------------------------
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Residues in contact with GLU 112 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R PHE* 3.2 13.0 - - + -
15R HIS* 3.1 10.1 + - - -
16R GLN* 3.0 30.6 + - - +
19R ASN* 3.1 13.0 + - - -
83R SER* 2.4 28.7 + - - -
108R LEU* 3.0 33.5 + - + +
109R LEU* 3.9 3.8 - - - +
111R ASP* 1.3 73.1 - - + +
113R TYR* 1.3 65.3 + - - +
115R GLN* 3.1 19.4 + - - +
116R GLY 3.1 16.6 + - - -
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Residues in contact with TYR 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R PHE* 3.9 9.0 - + - -
16R GLN* 3.6 37.4 - - + +
20R LEU* 3.6 23.4 - - - +
56R GLN* 2.9 18.2 + - - -
60R VAL* 4.8 1.2 - - + +
109R LEU* 2.8 33.2 + - + +
110R ARG* 3.8 5.4 - - - +
112R GLU* 1.3 73.1 - - - +
114R LYS* 1.3 56.4 + - - +
116R GLY* 3.7 0.2 - - - -
117R ILE* 3.0 37.7 + - + +
132R LEU* 4.0 23.7 - - + +
135R PHE* 3.4 42.9 - + + -
136R LYS* 4.4 6.5 - - + -
139R ILE* 3.7 22.2 - - + -
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Residues in contact with LYS 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124P GLY 4.4 12.1 + - - -
126P ASP* 3.3 24.6 + - - -
110R ARG* 3.0 15.6 + - + +
111R ASP* 3.4 14.6 - - - +
112R GLU 3.1 0.8 - - - -
113R TYR* 1.3 77.2 - - - +
115R GLN* 1.3 63.1 + - + +
117R ILE* 3.6 11.8 + - - +
118R GLU* 3.5 40.2 + - - +
136R LYS* 4.7 19.8 - - + +
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Residues in contact with GLN 115 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R PHE* 5.2 3.7 - - + -
111R ASP 3.4 11.4 + - - +
112R GLU* 3.1 22.3 + - - +
114R LYS* 1.3 78.1 - - + +
116R GLY* 1.3 60.1 + - - +
118R GLU* 3.3 11.2 + - - +
119R LEU* 3.0 30.3 + - - +
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Residues in contact with GLY 116 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R PHE* 3.5 38.0 - - - -
112R GLU 3.1 9.9 + - - -
113R TYR 3.3 1.0 + - - -
115R GLN* 1.3 75.3 - - - +
117R ILE* 1.3 57.2 + - - +
119R LEU* 3.5 5.3 + - - +
120R THR* 3.0 34.7 + - - -
132R LEU* 3.7 6.7 - - - -
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Residues in contact with ILE 117 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P ASP* 3.3 32.1 - - + +
113R TYR 3.0 22.7 + - - +
114R LYS* 3.6 11.0 - - - +
115R GLN 3.2 0.2 - - - -
116R GLY* 1.3 77.2 - - - +
118R GLU* 1.3 57.7 + - + +
121R ASP* 3.1 14.9 + - - +
129R ASN* 2.8 36.8 + - - +
132R LEU* 3.7 33.2 - - + +
133R ILE* 3.6 26.7 - - + -
136R LYS* 3.9 23.8 - - + -
----------------------------------------------------------
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Residues in contact with GLU 118 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P ASP* 5.8 0.2 - - - +
114R LYS* 3.5 35.7 + - - +
115R GLN* 3.3 13.1 + - - +
117R ILE* 1.3 74.3 - - + +
119R LEU* 1.3 66.8 + - - +
121R ASP* 3.2 21.4 - - - +
122R LYS* 3.3 13.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 119 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R ASP* 3.7 45.5 - - - +
9R THR* 4.2 7.4 - - - +
12R PHE* 3.9 22.9 - - + -
115R GLN 3.0 17.0 + - - +
116R GLY* 3.6 5.4 - - - +
118R GLU* 1.3 77.6 - - - +
120R THR* 1.3 58.1 + - - +
122R LYS* 3.4 7.1 + - + +
123R GLU* 3.1 29.2 + - - +
----------------------------------------------------------
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Residues in contact with THR 120 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R THR* 3.4 20.6 + - - +
12R PHE* 5.5 1.2 - - - -
116R GLY* 3.0 20.4 + - - -
117R ILE 3.9 3.4 - - - -
119R LEU* 1.3 77.2 - - - +
121R ASP* 1.3 61.9 + - - +
123R GLU* 3.7 1.3 + - - +
124R GLY* 3.3 2.1 + - - -
125R ASP* 2.9 60.3 + - + +
128R THR* 3.8 18.7 - - - +
129R ASN* 3.1 28.2 - - + +
132R LEU* 4.2 2.1 - - - +
----------------------------------------------------------
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Residues in contact with ASP 121 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117R ILE* 3.1 14.0 + - + +
118R GLU* 3.2 15.6 - - - +
120R THR* 1.3 73.8 - - - +
122R LYS* 1.3 76.0 + - - +
124R GLY* 2.9 20.8 + - - -
129R ASN* 3.7 12.5 + - - +
----------------------------------------------------------
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Residues in contact with LYS 122 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118R GLU 3.3 10.8 + - - +
119R LEU* 3.6 11.2 - - + +
120R THR 3.3 0.2 - - - -
121R ASP* 1.3 97.1 + - - +
123R GLU* 1.3 60.4 + - - +
124R GLY 3.1 5.6 + - - -
----------------------------------------------------------
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Residues in contact with GLU 123 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R ASP* 3.5 16.5 + - - +
9R THR* 3.2 46.4 + - - +
10R LYS* 5.1 0.3 + - - +
119R LEU* 3.1 19.1 + - - +
120R THR 4.3 2.7 - - - +
121R ASP 3.4 0.4 - - - -
122R LYS* 1.3 75.7 - - - +
124R GLY* 1.3 62.5 + - - +
125R ASP* 3.3 7.1 + - + +
----------------------------------------------------------
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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