Contacts of the helix formed by residues 47 - 75 (chain B) in PDB entry 2YW7
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 PHE 47 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 3.5 14.4 - - + +
43B VAL* 3.3 26.5 - - - +
44B GLY 2.8 30.3 - - - +
45B PRO 3.0 9.1 + - - -
46B ASN* 1.3 76.4 - - - +
48B ILE* 1.3 80.4 + - + +
50B VAL* 3.2 18.9 + - - +
51B HIS* 3.1 34.0 - + - -
102B VAL* 3.4 9.6 - - - +
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Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PRO 4.9 4.5 - - - +
46B ASN* 4.7 12.3 - - - +
47B PHE* 1.3 94.9 - - + +
49B GLY* 1.3 68.5 + - - +
50B VAL 3.1 2.2 - - - -
51B HIS* 3.9 13.1 - - + +
52B GLU* 3.1 39.4 + - - +
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Residues in contact with GLY 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASN* 3.1 13.4 + - - -
48B ILE* 1.3 85.0 - - - +
50B VAL* 1.3 58.5 + - - +
52B GLU* 3.4 18.6 - - - +
53B MET* 3.8 12.5 + - - +
151B PHE* 5.9 0.7 - - - -
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Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 4.5 1.1 - - + -
39B HIS* 5.4 1.1 - - + -
42B VAL* 4.2 20.4 - - + -
46B ASN 4.1 0.4 + - - +
47B PHE 3.2 10.6 + - - +
48B ILE 3.1 0.4 - - - -
49B GLY* 1.3 74.5 - - - +
51B HIS* 1.3 72.5 + - + +
52B GLU 2.9 1.3 - - - -
53B MET* 2.6 22.0 + - + +
54B ILE* 2.9 38.8 + - + -
102B VAL* 3.6 39.9 - - + +
105B HIS* 6.1 0.7 - - + -
106B LEU* 3.9 23.3 - - + -
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Residues in contact with HIS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B HIS* 2.6 76.5 + + + +
42B VAL* 4.7 10.0 + - + +
47B PHE* 3.1 50.1 - + - -
48B ILE* 3.9 13.5 - - + +
50B VAL* 1.3 78.0 - - + +
52B GLU* 1.3 58.1 + - - +
55B ASP* 2.8 41.1 + - - +
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ILE* 3.1 34.5 + - - +
49B GLY* 3.4 14.5 - - - +
50B VAL 2.8 0.4 + - - -
51B HIS* 1.3 80.6 - - - +
53B MET* 1.3 55.4 + - + +
55B ASP* 5.0 0.8 - - - +
56B PRO* 3.5 17.0 - - - +
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Residues in contact with MET 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLY 4.2 9.9 - - - +
50B VAL* 2.6 20.8 + - - +
52B GLU* 1.3 74.2 - - + +
54B ILE* 1.3 72.3 + - + +
55B ASP 3.5 0.4 - - - -
56B PRO* 3.3 15.7 - - - +
57B GLN* 3.7 2.1 + - - +
106B LEU* 4.0 25.6 - - - -
148B PHE* 3.4 37.4 - - + -
151B PHE* 3.6 59.1 - - + -
152B VAL* 3.7 24.7 - - + +
154B ALA* 6.5 0.9 - - - -
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Residues in contact with ILE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.8 29.4 - - + +
38B VAL* 3.1 37.2 - - + -
39B HIS* 3.9 20.6 - - + +
50B VAL* 2.9 30.9 + - + +
53B MET* 1.3 82.5 - - + +
55B ASP* 1.3 68.3 + - - +
57B GLN* 2.7 19.3 + - - -
58B VAL* 2.9 33.0 + - + -
106B LEU* 6.1 0.7 - - + -
109B LEU* 4.5 7.4 - - + -
148B PHE* 4.6 5.2 - - + -
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Residues in contact with ASP 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LYS* 5.2 8.2 - - - +
39B HIS* 2.8 35.7 + - - -
51B HIS* 2.8 26.0 + - - +
52B GLU* 5.0 0.8 - - - +
54B ILE* 1.3 76.0 - - - +
56B PRO* 1.4 65.4 - - + +
58B VAL* 3.5 7.6 + - - +
59B GLU* 3.5 23.7 + - - +
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Residues in contact with PRO 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLU 3.5 17.5 - - - +
53B MET* 3.3 18.6 - - - +
55B ASP* 1.4 94.5 - - + +
57B GLN* 1.3 57.4 + - - +
59B GLU* 3.7 7.7 + - + +
60B LEU* 3.2 24.8 + - - +
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Residues in contact with GLN 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 4.5 6.3 - - + -
53B MET 3.8 1.1 - - - +
54B ILE* 2.7 14.7 + - - +
56B PRO* 1.3 74.8 - - + +
58B VAL* 1.3 54.4 + - - +
60B LEU* 3.1 21.3 + - - +
61B VAL* 2.7 46.2 + - + +
113B TYR* 2.4 48.0 + - - +
144B GLU* 4.7 2.8 - - - +
145B LEU* 4.1 13.1 - - - +
148B PHE* 3.2 52.5 - - + +
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B HIS* 4.3 7.0 - - + +
35B LEU* 3.4 32.3 - - + +
36B LYS* 4.0 22.0 - - + +
54B ILE* 2.9 26.4 + - + +
55B ASP* 3.6 9.4 - - - +
57B GLN* 1.3 77.1 - - - +
59B GLU* 1.3 62.3 + - - +
61B VAL* 3.2 3.8 + - - +
62B ARG* 2.9 67.9 + - - +
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LYS* 5.9 0.3 + - - -
55B ASP 3.5 14.4 + - - +
56B PRO* 3.8 10.1 - - + +
57B GLN 3.3 0.4 - - - -
58B VAL* 1.3 82.9 - - - +
60B LEU* 1.3 57.0 + - - +
62B ARG* 3.1 35.5 + - - +
63B GLY* 3.1 22.3 + - - -
59G GLU* 4.8 4.9 - - - +
62G ARG* 4.3 4.7 + - - -
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PRO 3.2 14.9 + - - +
57B GLN* 3.1 29.5 + - - +
59B GLU* 1.3 74.5 - - - +
61B VAL* 1.3 59.9 + - + +
63B GLY* 3.0 4.0 + - - -
64B TYR* 3.0 71.7 + - + +
144B GLU* 3.3 26.9 - - + +
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Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR* 3.4 31.9 - - + +
31B LEU* 3.2 37.7 - - + -
32B HIS* 4.0 10.0 - - + -
35B LEU* 4.6 0.7 - - + -
57B GLN* 2.7 31.8 + - + +
58B VAL* 3.9 3.6 - - - +
60B LEU* 1.3 69.6 - - + +
62B ARG* 1.3 59.4 + - - +
64B TYR* 3.6 9.5 - - + +
65B ALA* 3.1 25.3 + - - +
113B TYR* 3.8 11.9 - - - +
145B LEU* 4.2 11.2 - - + -
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Residues in contact with ARG 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B HIS* 3.4 39.1 + - + +
36B LYS* 3.6 35.6 - - - +
58B VAL* 2.9 34.4 + - - +
59B GLU* 3.1 32.4 + - - +
60B LEU 3.2 0.2 - - - -
61B VAL* 1.3 75.1 - - - +
63B GLY* 1.3 67.0 + - - +
65B ALA* 3.2 6.2 - - - +
66B ASP* 3.1 22.8 + - - +
32G HIS* 4.8 5.5 - - - -
59G GLU* 5.0 1.6 + - - -
62G ARG* 3.3 60.4 - - - +
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Residues in contact with GLY 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU 3.1 12.4 + - - -
60B LEU* 3.0 8.9 + - - -
62B ARG* 1.3 73.9 - - - +
64B TYR* 1.3 55.5 + - - +
66B ASP* 2.6 33.2 + - - +
67B GLU* 2.8 20.2 + - - +
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Residues in contact with TYR 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR* 3.4 23.8 - + + -
60B LEU* 3.0 46.3 + - + +
61B VAL* 3.6 13.2 - - - +
63B GLY* 1.3 72.1 - - - +
65B ALA* 1.3 55.2 + - - +
67B GLU* 3.0 15.9 + - - +
68B VAL* 2.7 38.6 + - - +
140B ALA* 4.2 1.5 + - + -
141B HIS* 3.3 53.0 - + + -
144B GLU* 3.0 33.6 - - - +
145B LEU* 4.0 22.0 - - + -
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.5 12.8 - - + +
28B TYR* 3.5 19.0 - - + -
29B ASN* 3.6 23.8 - - - +
32B HIS* 4.6 3.4 - - + +
61B VAL 3.1 11.9 + - - +
62B ARG* 3.2 14.6 - - - +
64B TYR* 1.3 77.7 - - - +
66B ASP* 1.3 52.4 + - - +
68B VAL* 3.6 0.5 + - - +
69B ALA* 2.8 35.0 + - - +
40G TRP* 4.2 7.4 - - + -
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Residues in contact with ASP 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 3.1 14.2 + - - +
63B GLY* 2.6 21.4 + - - +
65B ALA* 1.3 67.3 - - - +
67B GLU* 1.3 55.6 + - + +
68B VAL 3.0 1.3 - - - -
69B ALA 2.9 0.9 + - - -
70B GLU* 2.7 52.9 + - + +
36G LYS* 3.2 31.8 + - - +
39G HIS* 5.7 2.6 - - - -
40G TRP* 3.2 30.4 + - - +
62G ARG* 5.7 0.3 + - - -
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Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LYS* 5.5 11.7 - - - +
63B GLY* 2.8 18.6 + - - +
64B TYR* 3.5 23.2 + - - +
66B ASP* 1.3 73.7 - - + +
68B VAL* 1.3 61.8 + - - +
70B GLU* 3.7 8.3 + - - +
71B ARG* 3.3 20.3 + - - +
137B LEU* 3.0 26.9 - - + +
140B ALA* 5.4 1.9 - - - +
141B HIS* 3.0 25.0 + - - +
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 3.4 33.4 - - + +
24B GLN* 4.5 3.1 - - + -
25B LEU* 3.7 21.8 - - + -
28B TYR* 3.5 27.6 - - + -
64B TYR 2.7 15.5 + - - +
65B ALA 3.8 1.8 - - - +
67B GLU* 1.3 71.8 - - - +
69B ALA* 1.3 65.5 + - - +
71B ARG* 3.0 9.3 + - - +
72B ILE* 3.0 26.8 + - + +
137B LEU* 4.4 7.2 - - + -
138B LEU* 4.2 14.4 - - + -
141B HIS* 4.0 9.6 - - + -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 4.2 3.8 - - + -
65B ALA 2.8 22.8 + - - +
66B ASP 3.5 2.5 - - - +
68B VAL* 1.3 76.0 - - - +
70B GLU* 1.3 63.3 + - - +
71B ARG 3.2 0.2 + - - -
72B ILE* 3.3 0.6 + - - -
73B ALA* 3.0 7.5 + - - +
79B PRO* 2.9 36.4 - - + +
40G TRP* 3.3 46.2 - - + -
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LYS* 3.3 36.3 + - + +
150A TRP* 4.7 19.1 - - + -
66B ASP* 2.7 40.4 + - - +
67B GLU* 4.1 4.9 - - - +
69B ALA* 1.3 72.4 - - - +
71B ARG* 1.3 50.3 + - - +
73B ALA* 3.2 9.1 - - - +
74B THR* 2.6 38.9 + - - +
39G HIS* 5.5 6.2 - - - -
40G TRP* 4.7 13.2 - - + -
----------------------------------------------------------
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Residues in contact with ARG 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 3.8 2.4 - - - +
143A GLY* 5.1 3.6 + - - -
146A GLU* 3.2 31.3 + - - +
147A LYS* 5.9 0.9 - - - +
21B LEU* 3.6 21.1 - - + -
67B GLU 3.3 12.9 + - - +
68B VAL* 3.0 10.4 + - - +
70B GLU* 1.3 75.3 - - - +
72B ILE* 1.3 65.7 + - - +
73B ALA 3.0 1.1 - - - -
74B THR* 2.9 24.7 + - - +
75B LEU* 2.9 44.4 + - - +
131B ASP* 3.0 33.3 + - - -
133B VAL* 3.5 18.1 - - - +
134B SER* 2.8 16.0 + - - +
137B LEU* 3.9 20.4 - - + -
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ALA* 3.9 19.3 - - + +
21B LEU* 3.7 26.0 - - + +
22B GLN* 3.6 36.3 - - + +
25B LEU* 4.2 4.9 - - + -
68B VAL* 3.0 24.9 + - + +
69B ALA 3.7 4.9 - - - +
71B ARG* 1.3 74.3 - - - +
73B ALA* 1.3 63.0 + - - +
75B LEU* 3.1 16.7 + - - +
76B GLY 3.6 0.7 + - - -
77B LYS 3.2 34.5 + - - +
78B SER 4.0 2.0 - - - +
79B PRO* 3.7 27.6 - - + -
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A TRP* 3.7 28.8 - - + -
69B ALA 3.0 13.7 + - - +
70B GLU* 3.2 14.6 - - - +
71B ARG 3.0 0.2 - - - -
72B ILE* 1.3 77.7 - - - +
74B THR* 1.3 60.6 + - - +
75B LEU 3.2 0.9 + - - -
76B GLY 3.6 3.6 + - - -
79B PRO* 3.7 12.0 - - + +
40G TRP* 4.4 5.8 - - + +
99G ARG* 2.7 39.8 + - - +
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Residues in contact with THR 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLU* 3.6 35.4 - - + +
147A LYS* 4.1 15.7 - - + +
150A TRP* 3.9 23.3 - - + +
70B GLU 2.6 28.0 + - - -
71B ARG* 2.9 30.9 + - - +
73B ALA* 1.3 72.0 - - - +
75B LEU* 1.3 61.4 + - + +
76B GLY 3.4 1.4 + - - -
----------------------------------------------------------
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 5.0 5.8 - - - +
146A GLU* 5.5 0.7 - - - +
11B ASP* 4.7 3.5 - - - +
14B ALA* 4.3 31.8 - - + +
17B VAL* 3.6 23.8 - - + -
18B ALA* 4.7 10.4 - - + +
21B LEU* 3.9 10.3 - - + -
71B ARG* 2.9 45.8 + - - +
72B ILE* 3.1 9.0 + - - +
74B THR* 1.3 78.5 - - + +
76B GLY* 1.3 55.8 + - - +
77B LYS 3.8 1.6 - - - -
131B ASP* 3.4 22.4 - - - +
134B SER* 3.8 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