Contacts of the helix formed by residues 56 - 85 (chain E) in PDB entry 3BZE
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 GLY 56 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E GLN 3.6 3.8 + - - -
55E GLU* 1.3 83.1 + - - +
57E SER* 1.3 65.1 - - - +
58E GLU* 3.3 3.1 - - - -
59E TYR* 3.0 24.8 - - - +
60E TRP* 3.8 3.3 + - - -
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Residues in contact with SER 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E ARG* 6.3 0.4 - - - -
55E GLU 4.2 4.8 + - - -
56E GLY* 1.3 73.0 - - - -
58E GLU* 1.3 58.4 + - - +
59E TYR 2.4 17.4 + - - -
60E TRP* 2.7 24.8 + - - +
61E ASP* 3.1 19.5 + - - +
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Residues in contact with GLU 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E GLY* 3.3 1.5 - - - -
57E SER* 1.3 78.8 - - - +
59E TYR* 1.3 59.0 + - - +
61E ASP* 4.1 10.2 + - - +
62E ARG* 3.3 26.4 + - + +
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Residues in contact with TYR 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E TYR* 4.6 0.3 + - - -
33E PHE* 4.1 6.2 - - - -
34E VAL* 4.5 3.3 - - + +
52E MET* 3.4 18.4 - - + +
55E GLU* 3.9 15.9 - - + +
56E GLY 3.0 17.8 + - - +
57E SER 2.4 11.9 + - - -
58E GLU* 1.3 68.4 - - - +
60E TRP* 1.3 100.7 + + - -
62E ARG* 3.4 12.1 + - - +
63E GLU* 3.0 46.7 + - + +
167E TRP* 3.7 25.6 - + - -
171E TYR* 2.6 30.5 + + - -
1R VAL* 3.6 15.1 - - + +
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Residues in contact with TRP 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E VAL* 4.0 14.8 - - + -
44E ARG* 3.7 22.7 - - - +
45E MET* 3.5 36.9 - - + +
46E VAL 4.2 4.3 - - - -
47E PRO* 3.3 36.6 - - + +
52E MET* 3.6 28.2 + - + -
53E GLU* 5.9 1.0 - - - +
55E GLU* 3.6 28.1 + - + +
56E GLY 3.9 9.4 - - - -
57E SER* 2.7 19.9 + - - +
59E TYR* 1.3 100.9 - + - +
61E ASP* 1.3 51.8 + - - +
63E GLU* 4.0 1.1 - - - +
64E THR* 2.5 39.4 + - - -
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Residues in contact with ASP 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E ARG* 2.5 29.8 + - - +
57E SER* 3.1 23.3 + - - +
58E GLU* 4.1 7.5 - - - +
60E TRP* 1.3 76.3 - - - +
62E ARG* 1.3 58.4 - - - +
64E THR* 3.3 5.4 + - - +
65E ARG* 2.9 26.9 + - - +
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Residues in contact with ARG 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E GLU* 3.3 21.1 + - + +
59E TYR* 3.8 16.6 - - - +
60E TRP 3.3 0.2 - - - -
61E ASP* 1.3 76.4 - - - +
63E GLU* 1.3 88.2 + - - +
64E THR 3.1 0.9 - - - -
65E ARG* 2.9 33.8 + - - +
66E SER* 2.9 18.8 + - - +
163E THR* 5.9 1.0 - - - +
167E TRP* 3.9 31.3 - - - +
1R VAL* 4.2 18.3 - - - +
4R PRO* 6.0 3.4 - - - +
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Residues in contact with GLU 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E TYR* 4.0 3.3 + - - -
34E VAL* 6.1 0.3 - - - +
45E MET* 3.6 35.9 - - + +
59E TYR* 3.0 46.0 + - + +
60E TRP* 4.0 1.3 - - - +
62E ARG* 1.3 95.5 + - - +
64E THR* 1.3 61.2 + - - +
66E SER* 3.3 9.5 + - - +
67E ALA* 3.0 24.6 + - - +
1R VAL* 2.9 39.8 - - - +
2R MET* 2.9 14.8 + - - +
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Residues in contact with THR 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E PHE* 4.5 0.4 - - + -
44E ARG* 3.1 33.9 - - + +
45E MET* 3.0 23.2 + - - +
60E TRP 2.5 26.1 + - - -
61E ASP* 3.4 8.7 - - - +
63E GLU* 1.3 79.1 - - - +
65E ARG* 1.3 61.4 + - - +
67E ALA* 3.5 3.5 + - - +
68E ARG* 3.0 53.8 + - + +
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Residues in contact with ARG 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E ASP 2.9 14.5 + - - +
62E ARG* 2.9 20.9 + - - +
64E THR* 1.3 78.1 - - - +
66E SER* 1.3 57.1 + - - +
68E ARG* 3.3 6.9 + - - +
69E ASP* 2.9 50.6 + - - +
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Residues in contact with SER 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E ARG* 2.9 17.1 + - - +
63E GLU* 3.7 14.7 + - - -
64E THR 3.3 0.2 - - - -
65E ARG* 1.3 78.0 + - - +
67E ALA* 1.3 60.2 + - - +
69E ASP* 3.4 7.0 + - - +
70E THR* 2.8 31.0 + - - -
2R MET* 3.9 23.5 + - - -
3R ALA 4.1 6.7 - - - -
4R PRO* 3.5 27.7 + - - +
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Residues in contact with ALA 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E PHE* 3.8 8.7 - - + -
24E SER* 4.8 0.7 - - - +
36E PHE* 3.4 45.1 - - + -
45E MET* 4.3 2.2 - - + -
63E GLU 3.0 16.5 + - - +
64E THR 3.9 0.7 - - - +
66E SER* 1.3 75.6 - - - +
68E ARG* 1.3 57.5 + - - +
70E THR* 3.5 2.5 + - - -
71E ALA* 3.0 28.8 + - - +
2R MET* 3.7 18.1 - - - -
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Residues in contact with ARG 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E PHE* 4.1 14.8 - - + -
43E PRO* 3.2 25.9 + - - +
44E ARG* 4.7 5.7 - - - +
64E THR* 3.0 39.5 + - - +
65E ARG* 3.7 5.8 - - - +
67E ALA* 1.3 76.0 - - - +
69E ASP* 1.3 66.8 + - - +
71E ALA* 3.4 6.3 + - - +
72E GLN* 3.0 26.5 + - - +
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Residues in contact with ASP 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E ARG* 2.9 41.6 + - - +
66E SER* 3.9 6.2 + - - +
67E ALA 3.4 0.2 - - - -
68E ARG* 1.3 78.7 - - - +
70E THR* 1.3 64.3 + - - +
72E GLN* 3.2 8.6 + - - +
73E ILE* 3.0 32.8 + - + +
4R PRO 5.4 6.2 - - - +
6R THR* 5.3 0.4 - - + -
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Residues in contact with THR 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E PHE* 3.4 25.4 - - + -
66E SER 2.8 20.8 + - - -
67E ALA 3.6 4.5 - - - -
69E ASP* 1.3 77.5 - - - +
71E ALA* 1.3 62.5 + - - +
73E ILE* 3.3 1.0 + - - +
74E PHE* 2.9 50.4 + - + -
97E TRP* 3.8 21.4 - - + -
2R MET* 3.3 16.9 - - + +
3R ALA 4.6 2.4 + - - -
4R PRO 5.9 0.9 - - - -
5R ARG 5.7 0.5 + - - -
6R THR* 4.1 14.5 + - + +
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Residues in contact with ALA 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E SER* 5.3 0.9 + - - -
22E PHE* 3.5 38.3 - - + -
36E PHE* 5.1 2.5 - - + -
38E ASN* 4.4 7.2 - - - +
67E ALA 3.0 18.2 + - - +
68E ARG* 3.6 7.9 - - - +
69E ASP 3.3 0.2 - - - -
70E THR* 1.3 76.9 - - - +
72E GLN* 1.3 56.9 + - - +
74E PHE* 3.3 2.3 + - - +
75E ARG* 2.8 30.2 + - - +
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Residues in contact with GLN 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ARG 3.0 16.2 + - - +
69E ASP* 3.4 12.3 - - - +
71E ALA* 1.3 77.0 - - - +
73E ILE* 1.3 64.8 + - + +
75E ARG* 3.1 39.5 + - - +
76E VAL* 3.2 16.8 + - - +
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Residues in contact with ILE 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ASP* 3.0 20.8 + - + +
70E THR 3.7 3.8 - - - +
72E GLN* 1.3 77.7 - - + +
74E PHE* 1.3 52.2 + - - +
76E VAL* 2.9 10.0 + - - +
77E ASN* 2.7 34.0 + - - +
6R THR* 3.9 20.6 - - + -
7R LEU 3.6 25.8 - - - +
8R PHE* 3.2 50.3 - - + -
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Residues in contact with PHE 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E HIS* 4.7 3.8 - - + -
11E SER* 4.0 22.0 - - - -
22E PHE* 3.9 13.7 - + - -
70E THR* 2.9 31.0 + - + +
71E ALA* 3.7 4.9 - - - +
73E ILE* 1.3 74.8 - - + +
75E ARG* 1.3 66.2 + - - +
77E ASN* 3.6 21.4 - - - +
78E LEU* 3.0 29.1 + - - +
95E LEU* 3.6 30.0 - - + +
97E TRP* 3.6 45.3 - + + -
116E PHE* 3.8 10.3 - + - -
6R THR* 3.2 22.9 - - + -
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Residues in contact with ARG 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E SER* 4.9 0.9 + - - -
19E GLU* 2.8 44.1 + - - +
20E PRO* 3.7 30.8 - - + +
71E ALA 2.8 13.4 + - - +
72E GLN* 3.2 30.3 + - - +
74E PHE* 1.3 80.8 - - - +
76E VAL* 1.3 59.8 + - + +
78E LEU* 3.7 9.9 + - - +
79E ARG* 3.8 9.5 + - - +
----------------------------------------------------------
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Residues in contact with VAL 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E GLN* 3.2 18.1 + - - +
73E ILE* 2.9 11.7 + - - +
75E ARG* 1.3 77.0 - - + +
77E ASN* 1.3 66.3 + - - +
79E ARG* 3.0 20.6 + - + +
80E THR* 3.0 20.4 + - - +
8R PHE* 4.4 25.1 - - + -
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Residues in contact with ASN 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E ILE* 2.7 18.6 + - - +
74E PHE* 3.3 27.0 + - - +
76E VAL* 1.3 73.4 - - - +
78E LEU* 1.3 53.7 + - - +
80E THR* 3.2 6.3 + - - -
81E LEU* 2.7 39.3 + - - +
95E LEU* 3.5 18.1 - - + +
116E PHE* 5.3 0.2 - - - -
7R LEU 2.9 21.0 + - - -
8R PHE* 3.4 8.5 - - - +
9R LEU* 2.6 46.6 + - + +
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Residues in contact with LEU 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E SER* 3.5 26.9 - - - +
13E SER* 4.2 18.6 - - - +
20E PRO* 4.2 20.6 - - + -
74E PHE 3.0 18.4 + - - +
75E ARG* 3.9 5.6 - - - +
76E VAL 3.2 0.4 - - - -
77E ASN* 1.3 75.1 - - - +
79E ARG* 1.3 62.9 + - - +
81E LEU* 3.9 4.0 - - - +
82E ARG* 3.0 36.6 + - - +
93E HIS* 4.2 14.1 - - + +
95E LEU* 3.8 31.0 - - + +
118E TYR* 4.0 22.6 + - + -
----------------------------------------------------------
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Residues in contact with ARG 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E ARG 3.8 7.1 + - - +
76E VAL* 3.0 16.7 + - + +
78E LEU* 1.3 76.7 - - - +
80E THR* 1.3 69.2 + - - +
82E ARG* 2.9 53.3 + - - +
83E GLY* 3.1 4.2 + - - -
89E GLU* 4.8 5.1 + - - -
----------------------------------------------------------
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Residues in contact with THR 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E VAL* 3.0 19.0 + - - +
77E ASN* 3.4 9.3 - - - -
79E ARG* 1.3 81.2 - - - +
81E LEU* 1.3 59.6 + - - +
83E GLY* 2.8 21.4 + - - -
84E TYR* 3.1 46.5 + - + +
146E LYS* 5.0 3.5 + - - +
9R LEU* 3.6 20.4 + - - +
----------------------------------------------------------
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Residues in contact with LEU 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E ASN 2.7 25.2 + - - +
78E LEU* 4.1 1.3 - - - +
80E THR* 1.3 72.7 - - - +
82E ARG* 1.3 64.9 + - - +
84E TYR* 3.2 13.6 + - + -
85E TYR* 3.1 24.4 - - + -
95E LEU* 3.9 14.4 - - + -
118E TYR* 3.5 47.1 - - + -
123E TYR* 3.0 42.8 - - + +
9R LEU* 3.8 33.0 - - + -
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Residues in contact with ARG 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E SER* 5.3 9.9 - - - -
78E LEU* 3.0 19.3 + - - +
79E ARG* 2.9 56.8 + - - +
81E LEU* 1.3 74.9 - - - +
83E GLY* 1.3 57.0 + - - +
85E TYR* 3.0 4.9 + - - +
86E ASN 2.8 23.2 + - - -
87E GLN* 3.1 51.3 + - + +
88E SER 3.4 18.2 + - - +
89E GLU* 3.4 39.8 + - - +
91E GLY 5.3 1.1 - - - -
93E HIS* 4.5 14.6 - - - -
118E TYR* 4.1 1.3 + - - -
----------------------------------------------------------
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Residues in contact with GLY 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E ARG 3.1 3.9 + - - -
80E THR* 2.8 10.5 + - - -
82E ARG* 1.3 77.6 - - - +
84E TYR* 1.3 66.8 + - - +
86E ASN* 2.8 23.7 + - - +
87E GLN 5.6 0.2 - - - -
----------------------------------------------------------
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Residues in contact with TYR 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E THR* 3.1 31.7 + - + +
81E LEU* 3.2 14.8 + - + +
83E GLY* 1.3 75.3 - - - +
85E TYR* 1.3 70.0 + - + +
86E ASN* 3.9 8.3 + - - +
123E TYR* 3.1 18.4 - + - -
139E ALA* 3.2 27.0 - - + +
142E ILE* 3.5 42.4 - - + +
143E SER* 3.2 22.2 - - - -
146E LYS* 4.1 6.8 + - - -
9R LEU* 2.9 18.4 + - - -
----------------------------------------------------------
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Residues in contact with TYR 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E LEU* 3.1 16.6 - - + -
82E ARG 3.0 3.7 + - - +
84E TYR* 1.3 80.8 - - + +
86E ASN* 1.3 81.9 + - - +
87E GLN* 3.2 32.4 - - + +
118E TYR* 4.0 21.5 - + - +
123E TYR* 3.4 31.4 - + - -
137E ASP* 3.0 35.4 + - - -
139E ALA* 3.5 21.1 - - + -
----------------------------------------------------------
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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