Contacts of the helix formed by residues 82 - 111 (chain R) in PDB entry 2X17
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 SER 82 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R TYR* 3.3 7.9 + - - -
80R TRP* 3.3 2.0 - - - +
81R GLU* 1.3 80.0 - - - +
83R PRO* 1.4 71.1 - - - +
84R LEU* 3.6 13.3 + - - +
85R LYS* 3.0 28.1 + - - +
86R ALA* 2.9 27.0 + - - +
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Residues in contact with PRO 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R TYR* 3.7 8.1 - - - +
31R PHE* 3.7 21.5 - - + -
34R LEU* 4.0 20.9 - - + -
36R LEU* 4.1 14.8 - - + -
39R PHE* 5.1 0.9 - - + -
82R SER* 1.4 86.7 - - - +
84R LEU* 1.3 60.8 + - - +
86R ALA* 3.4 5.8 + - + +
87R PHE* 3.3 19.6 + - - -
141R LEU* 3.5 17.8 - - + +
151R LEU* 4.2 27.4 - - + -
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Residues in contact with LEU 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82R SER* 3.6 10.9 + - - +
83R PRO* 1.3 80.7 - - - +
85R LYS* 1.3 67.0 + - + +
87R PHE* 3.3 5.5 + - - +
88R GLU* 3.1 44.1 + - + +
138R LEU* 4.0 5.7 - - + +
141R LEU* 3.8 29.7 - - + +
142R LYS* 3.7 42.8 - - + +
145R LYS* 5.0 14.1 - - + -
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Residues in contact with LYS 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80R TRP* 3.8 12.1 - - + -
81R GLU* 4.3 29.1 + - + +
82R SER* 3.0 30.3 + - - +
84R LEU* 1.3 83.3 - - + +
86R ALA* 1.3 62.8 + - - +
88R GLU* 3.4 28.4 + - + +
89R ALA* 3.3 17.3 + - - +
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Residues in contact with ALA 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27R MET* 3.5 19.8 - - - +
30R TYR* 4.0 15.5 - - + -
31R PHE* 3.7 23.8 - - + -
80R TRP* 3.9 19.3 - - + +
82R SER 2.9 11.7 + - - +
83R PRO 3.5 10.5 - - - +
84R LEU 3.2 0.4 - - - -
85R LYS* 1.3 78.9 - - - +
87R PHE* 1.3 57.4 + - - +
89R ALA* 3.7 1.4 + - - +
90R ALA* 3.3 18.0 + - - +
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Residues in contact with PHE 87 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R PHE* 3.8 13.5 - + - -
39R PHE* 3.7 30.5 - + - -
42R TRP* 4.3 13.7 - + + -
43R MET* 3.7 24.9 - - + -
83R PRO 3.3 6.4 + - - -
84R LEU 3.3 4.4 + - - +
86R ALA* 1.3 77.8 - - - +
88R GLU* 1.3 59.1 + - - +
89R ALA 3.3 0.7 - - - -
90R ALA* 3.6 5.0 - - + +
91R TYR* 3.0 23.6 + - - +
134R VAL* 3.9 31.9 - - + +
137R ILE* 3.7 39.0 - - + -
138R LEU* 3.4 19.8 - - - +
141R LEU* 3.6 28.5 - - + -
158R LEU* 4.8 1.6 - - + -
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Residues in contact with GLU 88 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R LEU* 3.1 34.3 + - + +
85R LYS* 3.4 40.9 + - + +
86R ALA 3.4 0.2 - - - -
87R PHE* 1.3 78.3 - - - +
89R ALA* 1.3 57.4 + - - +
91R TYR* 3.6 3.3 + - - +
92R GLU* 3.1 27.1 + - - +
138R LEU* 3.8 23.8 - - + -
142R LYS* 4.1 14.4 - - - -
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Residues in contact with ALA 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R LEU* 5.4 0.5 - - - +
27R MET* 4.4 6.2 - - + +
80R TRP* 3.5 29.6 - - + +
85R LYS 3.3 9.1 + - - +
86R ALA 3.9 2.9 - - - +
87R PHE 3.3 0.2 - - - -
88R GLU* 1.3 77.0 - - - +
90R ALA* 1.3 60.6 + - - +
92R GLU* 3.6 13.1 + - - +
93R HIS* 3.0 28.1 + - - +
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Residues in contact with ALA 90 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24R TYR* 3.8 17.3 + - + +
27R MET* 3.9 17.9 - - + +
43R MET* 4.9 2.5 - - + -
86R ALA 3.3 13.5 + - - +
87R PHE* 3.6 16.2 - - + +
88R GLU 3.3 0.4 - - - -
89R ALA* 1.3 76.7 - - - +
91R TYR* 1.3 60.1 + - - +
93R HIS* 3.2 6.6 + - - +
94R GLU* 2.9 32.3 + - - +
134R VAL* 4.0 14.6 - - + -
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Residues in contact with TYR 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MET* 3.7 24.3 + - + +
65H ASN* 4.6 6.2 - - - +
87R PHE 3.0 16.8 + - - +
88R GLU 4.0 2.9 - - - +
90R ALA* 1.3 72.5 - - - +
92R GLU* 1.3 64.7 + - - +
94R GLU* 3.5 3.1 + - + +
95R LYS* 3.2 54.1 + - + +
131R GLU* 3.9 40.3 + - + -
134R VAL* 3.8 8.9 - - + +
135R LYS* 3.6 47.0 - - + +
138R LEU* 3.6 21.5 - - + -
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Residues in contact with GLU 92 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88R GLU 3.1 17.6 + - - +
89R ALA* 3.7 14.2 - - - +
91R TYR* 1.3 78.9 - - - +
93R HIS* 1.3 57.4 + - - +
95R LYS* 3.5 16.7 + - - +
96R PHE* 3.1 24.9 + - - +
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Residues in contact with HIS 93 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R TYR* 3.8 27.6 - + - -
20R SER* 2.8 34.0 + - - -
23R LEU* 3.5 25.9 - - + +
24R TYR* 3.9 19.7 - + - -
89R ALA 3.0 18.6 + - - +
90R ALA* 3.2 5.8 + - - +
92R GLU* 1.3 76.1 - - - +
94R GLU* 1.3 58.8 + - - +
96R PHE* 3.2 20.9 + + - +
97R ILE* 2.9 44.4 + - + +
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Residues in contact with GLU 94 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24R TYR* 2.5 31.8 + - - +
46R GLN* 5.1 0.3 + - - -
50R GLU* 3.8 5.4 - - - +
90R ALA 2.9 20.3 + - - +
91R TYR* 3.8 8.3 - - + +
92R GLU 3.3 0.2 - - - -
93R HIS* 1.3 77.9 - - - +
95R LYS* 1.3 53.5 + - - +
97R ILE* 4.5 5.3 - - - +
98R SER* 2.8 37.6 + - - -
127R GLN* 2.8 29.6 + - - +
130R GLU* 3.3 28.9 - - + +
131R GLU* 3.9 18.6 - - + -
134R VAL* 4.1 19.4 - - + +
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Residues in contact with LYS 95 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MET* 4.7 18.8 - - + +
91R TYR* 3.2 48.3 + - + +
92R GLU* 3.7 15.6 - - - +
94R GLU* 1.3 74.3 - - - +
96R PHE* 1.3 60.7 + - - +
98R SER* 3.9 1.1 - - - -
99R LYS* 3.1 29.5 + - - +
102R TYR* 5.7 0.2 - - - -
131R GLU* 3.9 24.0 - - - +
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Residues in contact with PHE 96 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16R ARG* 4.3 26.9 - - + -
19R TYR* 5.9 3.1 - + - -
92R GLU 3.1 13.9 + - - +
93R HIS* 3.2 34.0 + + - +
95R LYS* 1.3 75.3 - - - +
97R ILE* 1.3 78.5 + - + +
99R LYS* 3.4 9.8 + - + +
100R SER* 3.1 24.2 + - - -
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Residues in contact with ILE 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R GLN* 4.0 7.0 - - - +
16R ARG* 4.0 25.8 - - + +
17R GLU* 3.9 18.8 - - - +
20R SER* 3.4 26.9 - - - +
50R GLU* 5.7 1.3 - - - +
93R HIS* 2.9 36.0 + - + +
94R GLU* 3.9 8.3 - - - +
96R PHE* 1.3 80.4 - - + +
98R SER* 1.3 65.3 + - - +
100R SER* 2.7 20.0 + - - +
101R ILE* 3.0 14.2 + - + +
127R GLN* 3.5 28.5 - - - +
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Residues in contact with SER 98 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94R GLU 2.8 17.4 + - - -
95R LYS* 3.9 4.3 - - - -
97R ILE* 1.3 76.6 - - - +
99R LYS* 1.3 56.2 + - - +
101R ILE* 3.2 9.7 + - - +
102R TYR* 2.9 52.5 + - - -
127R GLN* 3.2 28.1 + - - +
131R GLU* 2.7 26.4 + - - -
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Residues in contact with LYS 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95R LYS 3.1 19.5 + - - +
96R PHE* 3.6 10.8 - - + +
97R ILE 3.2 0.2 - - - -
98R SER* 1.3 77.6 - - - +
100R SER* 1.3 55.3 - - - +
102R TYR* 3.2 18.0 + - + +
103R GLU* 3.1 52.2 + - + +
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Residues in contact with SER 100 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R GLN* 2.9 23.0 + - - -
16R ARG* 3.9 26.7 + - - -
96R PHE* 3.1 17.3 + - - -
97R ILE* 2.7 24.4 + - - -
99R LYS* 1.3 74.5 - - - +
101R ILE* 1.3 61.0 + - - +
103R GLU* 4.1 13.5 - - - +
104R LEU* 3.4 27.7 + - - +
----------------------------------------------------------
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Residues in contact with ILE 101 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R GLN* 3.8 31.9 - - + +
17R GLU* 4.5 4.9 - - - +
57R PHE* 4.2 10.3 - - + -
97R ILE* 3.0 25.1 + - + +
98R SER* 3.4 11.4 - - - +
100R SER* 1.3 75.2 - - - +
102R TYR* 1.3 67.5 + - + +
103R GLU 3.3 0.2 - - - -
104R LEU* 3.3 6.5 + - + +
105R ALA* 3.0 21.0 + - - +
120R LEU* 4.3 12.5 - - + +
123R PHE* 4.1 29.8 - - + +
124R ILE* 3.9 30.1 - - + +
127R GLN* 4.7 6.1 - - + -
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Residues in contact with TYR 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H ARG* 3.4 16.8 + - - -
112H LYS 5.6 2.0 - - - -
113H ASP* 5.2 1.7 + - - -
114H TYR* 3.5 54.6 - + + -
115H SER* 2.8 26.5 + - - -
98R SER* 2.9 40.1 + - - -
99R LYS* 3.2 18.8 + - + +
101R ILE* 1.3 80.4 - - + +
103R GLU* 1.3 57.9 + - + +
105R ALA* 3.3 6.4 + - - +
106R ALA* 2.9 24.5 + - - +
124R ILE* 4.5 9.6 - - + -
131R GLU* 5.0 0.7 + - - -
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Residues in contact with GLU 103 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99R LYS* 3.1 43.9 + - + +
100R SER* 4.2 9.9 - - - +
101R ILE 3.3 0.2 - - - -
102R TYR* 1.3 74.0 - - + +
104R LEU* 1.3 61.3 + - - +
106R ALA* 3.5 8.6 - - - +
107R LEU* 2.8 29.3 + - - +
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Residues in contact with LEU 104 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6R MET* 4.1 15.4 - - - +
9R ALA* 3.7 36.3 - - + +
10R LEU* 4.0 17.7 - - + -
13R GLN* 3.6 37.9 - - + +
16R ARG* 5.1 2.0 - - - +
57R PHE* 4.7 1.8 - - + -
100R SER 3.4 17.8 + - - +
101R ILE* 3.3 9.8 + - - +
103R GLU* 1.3 76.8 - - - +
105R ALA* 1.3 56.8 + - - +
107R LEU* 3.4 7.3 + - + +
108R ALA* 3.0 28.9 + - - +
120R LEU* 3.6 24.8 - - + +
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Residues in contact with ALA 105 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H TYR* 4.1 16.4 - - + -
101R ILE 3.0 13.2 + - - +
102R TYR* 3.5 11.2 - - - +
104R LEU* 1.3 74.6 - - - +
106R ALA* 1.3 58.4 + - - +
108R ALA* 3.5 0.8 + - - -
109R GLU* 3.0 32.7 + - - +
117R ARG* 3.7 27.4 - - - +
120R LEU* 3.7 12.7 - - + +
124R ILE* 4.6 9.6 - - + -
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Residues in contact with ALA 106 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H TYR* 3.4 20.3 + - + +
102R TYR 2.9 11.7 + - - +
103R GLU* 3.3 12.3 + - - +
105R ALA* 1.3 76.1 - - - +
107R LEU* 1.3 58.7 + - - +
109R GLU* 3.5 5.7 + - - +
110R GLU* 3.1 29.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU 107 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R ARG* 4.2 34.1 - - + +
6R MET* 3.9 21.3 - - + -
9R ALA* 3.9 28.5 - - + -
103R GLU 2.8 16.8 + - - +
104R LEU* 3.6 7.9 - - + +
105R ALA 3.4 0.2 - - - -
106R ALA* 1.3 76.0 - - - +
108R ALA* 1.3 57.6 + - - +
110R GLU* 3.6 16.2 + - - +
111R GLU* 3.1 38.8 + - + +
----------------------------------------------------------
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Residues in contact with ALA 108 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6R MET* 3.7 16.4 - - + +
104R LEU 3.0 17.8 + - - +
105R ALA* 3.8 6.1 - - - +
106R ALA 3.3 0.2 - - - -
107R LEU* 1.3 75.5 - - - +
109R GLU* 1.3 58.9 + - - +
111R GLU 3.6 0.2 + - - -
112R LYS* 3.1 6.6 + - - -
113R ASP* 2.9 46.2 + - - +
116R THR* 4.3 5.2 - - + -
117R ARG* 3.8 22.0 - - + +
120R LEU* 4.6 0.4 - - + -
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Residues in contact with GLU 109 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H TYR* 3.0 33.7 + - - -
105R ALA 3.0 17.7 + - - +
106R ALA* 3.9 4.9 - - - +
108R ALA* 1.3 75.8 - - - +
110R GLU* 1.3 61.5 + - - +
112R LYS* 3.5 15.6 + - - +
117R ARG* 3.2 34.0 + - + -
----------------------------------------------------------
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Residues in contact with GLU 110 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106R ALA 3.1 17.7 + - - +
107R LEU* 3.9 17.6 - - - +
108R ALA 3.3 0.2 - - - -
109R GLU* 1.3 74.9 - - - +
111R GLU* 1.3 60.8 + - + +
112R LYS* 3.1 14.1 + - - +
----------------------------------------------------------
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Residues in contact with GLU 111 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3R SER* 2.7 32.2 + - - -
5R ARG* 3.7 27.4 - - - +
6R MET* 3.6 19.7 + - - +
107R LEU* 3.1 27.6 + - + +
108R ALA 3.6 2.7 + - - +
110R GLU* 1.3 77.8 - - + +
112R LYS* 1.3 69.2 + - - +
113R ASP* 3.3 10.9 + - + +
----------------------------------------------------------
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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