Contacts of the helix formed by residues 48 - 76 (chain D) in PDB entry 6WYG
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 LEU 48 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ASN* 4.2 13.2 - - - +
41D PHE* 3.1 24.7 + - + +
46D VAL* 3.8 25.6 - - + +
47D ALA* 1.3 73.6 - - - +
49D LYS* 1.3 65.5 + - - +
50D ASN 3.2 3.2 + - - -
51D PHE* 3.3 19.3 + - + +
52D ALA* 3.2 17.0 + - - +
96D GLY 5.2 0.2 - - - +
164D GLY 5.8 0.2 - - - +
167D GLU* 4.0 25.6 - - + +
168D TYR* 3.9 31.0 - - + +
171D ASP* 3.3 22.0 - - + +
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Residues in contact with LYS 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ASP* 5.7 5.2 - - - +
41D PHE 5.0 0.4 - - - -
42D ASP* 5.9 3.8 - - - +
47D ALA* 3.7 7.8 + - - +
48D LEU* 1.3 73.1 - - - +
50D ASN* 1.3 64.7 + - - +
52D ALA* 3.3 8.7 - - - +
53D LYS* 3.0 31.6 + - + +
171D ASP* 3.6 4.1 + - - +
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Residues in contact with ASN 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LYS* 1.3 78.9 - - - +
51D PHE* 1.3 60.1 + - - +
53D LYS* 3.8 12.4 - - + +
54D TYR* 2.9 30.1 + - - +
171D ASP* 2.8 45.3 + - - +
172D LYS* 4.3 7.7 + - - +
175D LEU* 3.4 26.7 - - + +
176D GLY* 3.7 14.9 - - - -
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Residues in contact with PHE 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PHE* 3.7 17.7 - + + -
48D LEU* 3.5 23.1 - - + +
50D ASN* 1.3 77.2 - - - +
52D ALA* 1.3 61.4 + - - +
54D TYR* 3.4 1.7 + - - +
55D PHE* 3.0 51.5 + + - -
96D GLY* 3.5 35.9 - - - -
100D MET* 3.7 17.3 - - + -
155D LEU* 3.9 12.3 - - + -
167D GLU* 3.9 10.1 - - + -
170D PHE* 3.7 23.3 - + - -
171D ASP* 2.9 35.1 + - + -
175D LEU* 3.6 16.6 - - + -
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Residues in contact with ALA 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D SER* 2.9 46.6 + - - +
41D PHE* 3.8 11.6 - - + +
42D ASP* 4.3 10.3 - - + +
48D LEU 3.2 9.6 + - - +
49D LYS* 3.3 13.5 - - - +
50D ASN 3.2 0.2 - - - -
51D PHE* 1.3 79.6 - - - +
53D LYS* 1.3 62.2 + - + +
56D LEU* 3.0 13.3 + - - +
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Residues in contact with LYS 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LYS* 3.0 23.6 + - + +
50D ASN* 3.8 14.6 - - + +
51D PHE 3.4 0.2 - - - -
52D ALA* 1.3 74.6 - - + +
54D TYR* 1.3 63.9 + - - +
56D LEU* 3.2 8.2 + - - +
57D HIS* 3.0 24.1 + - - +
175D LEU 6.0 0.4 - - - +
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Residues in contact with TYR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D ASN 2.9 19.0 + - - +
51D PHE* 3.6 5.2 - - - +
52D ALA 3.3 0.2 - - - -
53D LYS* 1.3 77.9 - - - +
55D PHE* 1.3 80.8 + + - +
57D HIS* 3.3 6.4 + + + +
58D GLN* 3.0 58.3 + - + +
100D MET* 3.9 21.1 - - + -
147D GLU* 2.5 38.6 + - - +
148D LEU* 3.7 13.3 - - + +
151D HIS* 3.7 19.1 - - - -
175D LEU* 3.7 21.8 - - + +
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Residues in contact with PHE 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR* 3.5 51.3 - + - +
37D MET* 3.3 30.3 - - + -
38D SER* 3.7 10.5 - - - +
41D PHE* 3.5 35.7 - + - -
51D PHE* 3.0 38.6 + + - +
54D TYR* 1.3 95.4 - + - +
56D LEU* 1.3 57.7 + - - +
58D GLN* 3.4 1.5 + - - -
59D SER* 2.9 24.4 + - - -
99D ALA* 3.9 7.9 - - + -
100D MET* 3.8 25.8 - - + -
103D ALA* 4.3 4.7 - - + -
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Residues in contact with LEU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D LEU* 4.2 24.9 - - + -
38D SER* 3.5 19.2 - - - +
39D TYR* 4.5 15.9 - - + +
52D ALA 3.0 11.5 + - - +
53D LYS* 3.7 7.2 - - - +
55D PHE* 1.3 75.9 - - - +
57D HIS* 1.3 58.7 + - - +
59D SER* 3.2 7.8 + - - -
60D HIS* 3.0 61.5 + - + +
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Residues in contact with HIS 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D LYS 3.0 16.1 + - - +
54D TYR* 3.7 6.3 - + + +
56D LEU* 1.3 74.7 - - - +
58D GLN* 1.3 76.4 + - - +
60D HIS* 3.3 12.3 + - + +
61D GLU* 2.9 46.2 + - + +
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Residues in contact with GLN 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR* 3.7 37.9 + - + -
54D TYR* 3.0 60.1 + - + +
55D PHE* 3.6 7.2 - - - +
57D HIS* 1.3 87.7 - - - +
59D SER* 1.3 62.1 - - - +
61D GLU* 3.2 8.7 + - - +
62D GLU* 2.9 30.1 + - - +
107D GLU* 5.0 2.1 - - - +
144D ALA* 5.3 8.7 - - - +
147D GLU* 4.2 5.9 + - - +
148D LEU* 5.3 5.2 - - - +
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Residues in contact with SER 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D SER* 2.8 40.3 + - - +
34D TYR* 3.6 10.9 - - - +
35D LEU* 3.7 17.0 - - - +
55D PHE 2.9 15.1 + - - -
56D LEU* 3.3 14.7 - - - +
57D HIS 3.1 0.2 - - - -
58D GLN* 1.3 76.3 - - - +
60D HIS* 1.3 69.1 + - - +
62D GLU 3.2 1.4 + - - -
63D ARG* 3.0 19.5 + - - +
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Residues in contact with HIS 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D LEU* 3.0 51.1 + - + +
57D HIS* 3.8 11.6 + - + +
59D SER* 1.3 80.2 - - - +
61D GLU* 1.3 58.0 + - + +
63D ARG* 3.2 8.7 + - + +
64D GLU* 2.9 35.4 + - + +
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Residues in contact with GLU 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D HIS* 2.9 48.1 + - + +
58D GLN* 3.6 9.6 - - - +
60D HIS* 1.3 75.5 - - + +
62D GLU* 1.3 65.8 + - - +
64D GLU* 3.2 10.2 + - - +
65D HIS* 3.0 37.9 + - + +
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Residues in contact with GLU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLU* 2.6 22.7 - - - +
30D ALA* 3.6 13.6 - - + +
31D SER* 3.5 24.2 - - - +
34D TYR* 3.8 20.9 - - + -
58D GLN* 2.9 20.5 + - - +
59D SER 3.6 0.2 - - - +
61D GLU* 1.3 78.4 - - - +
63D ARG* 1.3 63.0 + - - +
65D HIS* 3.1 11.3 + - - +
66D ALA* 2.9 22.7 + - - +
107D GLU* 3.4 8.8 - - - +
110D VAL* 5.0 1.4 - - - +
201D FE 2.4 21.5 - - - -
202D FE 2.4 24.7 - - - -
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Residues in contact with ARG 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLU 5.2 0.2 - - - -
28D LEU* 4.4 16.2 - - + -
31D SER* 3.7 14.7 - - - +
59D SER 3.0 13.5 + - - +
60D HIS* 3.2 11.9 + - + +
62D GLU* 1.3 75.9 - - - +
64D GLU* 1.3 56.4 + - + +
66D ALA* 3.2 6.6 + - - +
67D GLU* 2.9 55.8 + - + +
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Residues in contact with GLU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D HIS* 2.9 20.4 + - + +
61D GLU* 3.2 11.0 + - - +
63D ARG* 1.3 75.6 - - + +
65D HIS* 1.3 60.9 + - + +
67D GLU* 3.4 15.6 + - - +
68D LYS* 2.9 26.2 + - - +
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Residues in contact with HIS 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLU* 3.7 9.3 + - - +
61D GLU* 3.0 28.1 + - + +
62D GLU* 3.1 12.9 + - - +
64D GLU* 1.3 78.7 - - + +
66D ALA* 1.3 67.3 + - - +
68D LYS* 3.0 4.0 + - + -
69D LEU* 2.9 22.6 + - - +
136D HIS 4.9 6.9 + - - -
137D TYR* 3.0 37.9 + + + -
140D GLU* 5.1 14.1 - - + +
141D GLN* 4.5 5.4 - - - -
201D FE 3.2 24.4 - - - -
202D FE 4.6 0.9 - - - -
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ILE* 4.0 8.4 - - + +
27D GLU* 3.8 17.6 - - + +
28D LEU* 3.6 37.2 - - + +
62D GLU 2.9 12.4 + - - +
63D ARG 3.5 8.1 - - - +
65D HIS* 1.3 76.2 - - - +
67D GLU* 1.3 58.4 + - + +
69D LEU* 3.1 8.9 + - - +
70D MET* 2.9 33.2 + - - +
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Residues in contact with GLU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LEU* 6.3 1.1 - - + -
63D ARG* 2.9 46.0 + - + +
64D GLU* 3.7 13.4 - - - +
66D ALA* 1.3 78.4 - - + +
68D LYS* 1.3 57.0 + - - +
70D MET* 3.3 18.3 + - - +
71D LYS* 2.9 26.9 + - - +
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Residues in contact with LYS 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D GLU 2.9 15.3 + - - +
65D HIS* 3.0 7.4 + - + +
67D GLU* 1.3 76.4 - - - +
69D LEU* 1.3 55.8 + - - +
71D LYS* 3.2 14.2 + - + +
72D LEU* 2.9 27.3 + - - +
132D PHE* 4.0 19.4 - - + -
136D HIS* 5.3 7.6 - - + -
137D TYR* 3.4 20.2 - - + +
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Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ILE* 3.9 28.3 - - + +
23D GLN* 3.5 47.6 - - + +
24D ILE* 3.6 13.9 - - + +
27D GLU* 3.9 14.1 - - + -
65D HIS 2.9 8.9 + - - +
66D ALA* 3.5 6.5 - - - +
68D LYS* 1.3 71.7 - - - +
70D MET* 1.3 61.3 + - - +
72D LEU* 3.2 5.8 + - + +
73D GLN* 2.9 29.5 + - - +
132D PHE* 4.3 9.4 - - + -
133D ILE* 4.8 6.3 - - + -
137D TYR* 3.2 34.8 - - + +
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Residues in contact with MET 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ILE* 3.7 33.2 - - + -
28D LEU* 5.6 4.9 - - - -
66D ALA* 2.9 22.2 + - - +
67D GLU* 3.5 20.9 - - - +
69D LEU* 1.3 76.3 - - - +
71D LYS* 1.3 62.4 + - - +
73D GLN* 3.2 4.8 + - - +
74D ASN* 3.0 21.3 + - - +
80D ILE* 3.6 40.6 - - + +
82D LEU* 4.3 16.2 - - + -
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Residues in contact with LYS 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D GLU 2.9 14.2 + - - +
68D LYS* 3.2 16.1 + - + +
70D MET* 1.3 76.4 - - - +
72D LEU* 1.3 57.7 + - - +
74D ASN* 3.4 6.9 + - - +
75D GLN* 2.8 52.6 + - + +
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D TYR* 4.4 11.9 - - - +
20D ILE* 4.5 10.8 - - + -
68D LYS 2.9 13.8 + - - +
69D LEU* 3.6 7.9 - - - +
70D MET 3.2 0.2 - - - -
71D LYS* 1.3 74.8 - - - +
73D GLN* 1.3 66.9 + - - +
75D GLN* 3.1 18.4 + - + +
76D ARG* 2.9 31.9 + - + +
128D HIS* 3.6 30.7 - - + -
129D LEU* 3.6 27.6 - - + -
132D PHE* 3.7 33.7 - - + -
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Residues in contact with GLN 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D TYR* 2.7 42.6 + - - -
17D GLU* 3.3 16.7 + - - +
20D ILE* 3.7 11.1 - - + +
21D ASN* 3.2 35.4 + - - +
24D ILE* 4.7 1.3 - - + +
69D LEU 2.9 13.4 + - - +
70D MET* 3.3 9.6 - - - +
72D LEU* 1.3 76.5 - - - +
74D ASN* 1.3 63.0 + - - +
76D ARG* 3.1 6.9 + - - +
78D GLY* 3.0 30.3 + - - -
79D ARG 3.4 8.0 + - - -
80D ILE* 3.6 30.5 - - + +
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Residues in contact with ASN 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 4.6 5.7 - - - +
70D MET 3.0 12.6 + - - +
71D LYS* 3.8 7.0 - - - +
73D GLN* 1.3 76.3 - - - +
75D GLN* 1.3 60.9 + - - +
76D ARG 3.3 0.7 + - - -
77D GLY* 3.3 10.4 + - - -
78D GLY 4.0 11.4 - - - +
79D ARG* 5.5 0.2 - - - -
80D ILE* 3.6 30.4 + - - +
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Residues in contact with GLN 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 4.3 12.1 - - - +
71D LYS* 2.8 41.1 + - + +
72D LEU* 3.1 32.5 + - + +
74D ASN* 1.3 77.9 - - - +
76D ARG* 1.3 62.5 + - + +
77D GLY 3.6 0.3 + - - -
128D HIS* 5.6 3.3 + - + -
132D PHE* 4.9 6.6 - - - -
----------------------------------------------------------
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Residues in contact with ARG 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 4.4 3.3 - - - +
9D ARG* 3.5 24.9 - - - +
10D GLN 4.3 12.9 + - - +
11D ASN* 3.7 7.9 + - - +
12D TYR* 3.0 54.5 - - + +
72D LEU* 2.9 30.1 + - + +
73D GLN 3.1 1.1 + - - +
75D GLN* 1.3 78.6 - - - +
77D GLY* 1.3 60.3 + - - +
78D GLY 3.7 0.2 + - - -
126D ASP* 2.3 44.8 + - - -
127D PRO* 5.4 0.2 - - - +
128D HIS* 3.0 43.9 + - - +
129D LEU* 3.4 3.3 - - - +
----------------------------------------------------------
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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