Contacts of the helix formed by residues 13 - 41 (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 HIS 13 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASN 3.8 3.0 + - - -
12D TYR* 1.3 77.7 - - - +
14D GLN* 1.3 74.6 + - + +
15D ASP* 3.2 44.2 + - - +
16D SER* 3.0 25.8 + - - +
17D GLU* 3.3 10.9 + - - +
124D LYS* 4.4 23.6 - - + +
126D ASP* 5.2 1.4 + - - +
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Residues in contact with GLN 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ARG* 3.9 14.6 - - - +
13D HIS* 1.3 80.3 + - + +
15D ASP* 1.3 69.0 + - - +
17D GLU* 2.9 32.1 - - - +
18D ALA* 3.0 25.1 + - - +
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Residues in contact with ASP 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D HIS* 3.2 30.5 + - - +
14D GLN* 1.3 79.7 - - - +
16D SER* 1.3 59.1 + - - +
18D ALA* 3.3 6.6 + - - +
19D ALA* 2.9 28.1 + - - +
22D ARG* 4.1 4.2 + - - +
120D LEU* 3.7 29.0 - - + +
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Residues in contact with SER 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D TYR* 4.2 8.3 - - - -
13D HIS* 3.0 28.5 + - - +
15D ASP* 1.3 76.0 - - - +
17D GLU* 1.3 60.2 + - - +
19D ALA* 3.7 3.4 - - - +
20D ILE* 2.8 35.7 + - - +
117D LEU* 5.0 2.0 - - - +
120D LEU* 3.7 18.4 - - - +
121D ALA* 5.4 3.4 - - - -
124D LYS* 5.5 3.9 - - - +
126D ASP* 4.5 3.7 + - - +
129D LEU* 3.6 28.0 - - - +
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Residues in contact with GLU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ARG* 2.7 35.6 + - - -
12D TYR* 3.5 21.0 + - + -
13D HIS 3.3 10.0 + - - +
14D GLN* 2.9 24.0 - - - +
16D SER* 1.3 76.1 - - - +
18D ALA* 1.3 62.2 + - - +
20D ILE 3.2 1.6 + - - -
21D ASN* 3.0 24.0 + - - +
73D GLN* 3.3 29.4 + - - +
78D GLY* 4.0 1.6 - - - -
79D ARG* 3.1 32.1 + - - +
81D PHE* 4.7 5.0 - - - -
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Residues in contact with ALA 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D GLN 3.0 16.5 + - - +
15D ASP* 3.7 6.3 - - - +
17D GLU* 1.3 77.8 - - - +
19D ALA* 1.3 57.7 + - - +
21D ASN* 3.2 11.3 + - - +
22D ARG* 2.9 41.8 + - - +
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Residues in contact with ALA 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ASP 2.9 17.4 + - - +
16D SER* 3.8 4.5 - - - +
17D GLU 3.3 0.2 - - - -
18D ALA* 1.3 74.4 - - - +
20D ILE* 1.3 60.4 + - - +
22D ARG* 3.3 29.3 + - - +
23D GLN* 2.8 30.5 + - - +
117D LEU* 4.2 19.7 - - + +
120D LEU* 4.1 16.2 - - + -
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Residues in contact with ILE 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D TYR* 3.5 16.2 - - - +
16D SER 2.8 21.4 + - - +
17D GLU 3.5 4.7 - - - +
19D ALA* 1.3 73.9 - - - +
21D ASN* 1.3 60.1 + - - +
23D GLN* 3.1 2.7 + - + +
24D ILE* 2.8 35.4 + - + +
69D LEU* 3.9 40.4 - - + +
72D LEU* 4.5 4.0 - - + -
73D GLN* 3.7 18.2 - - + +
117D LEU* 3.5 27.4 - - + -
129D LEU* 4.2 23.3 - - + -
132D PHE* 6.2 0.2 - - + -
133D ILE* 5.0 1.6 - - + -
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Residues in contact with ASN 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLU* 3.0 17.8 + - - +
18D ALA* 3.2 11.1 + - - +
20D ILE* 1.3 75.6 - - - +
22D ARG* 1.3 63.7 + - + +
24D ILE* 3.3 11.7 + - - +
25D ASN* 3.1 21.1 + - - +
73D GLN* 3.2 13.9 + - - +
79D ARG 2.9 21.2 + - - -
80D ILE* 3.3 12.0 - - - +
81D PHE* 2.6 53.2 + - + +
82D LEU* 5.8 0.2 - - - +
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Residues in contact with ARG 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ASP* 4.1 5.9 + - - +
18D ALA* 2.9 19.9 + - - +
19D ALA* 3.5 44.8 + - - +
21D ASN* 1.3 76.7 - - + +
23D GLN* 1.3 58.3 + - - +
25D ASN* 3.2 8.0 + - - +
26D LEU* 2.9 28.3 + - - +
120D LEU* 5.6 1.8 - - - +
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Residues in contact with GLN 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ALA 2.8 17.2 + - - +
20D ILE* 3.1 5.6 + - - +
22D ARG* 1.3 73.5 - - - +
24D ILE* 1.3 60.8 + - - +
26D LEU* 3.2 17.4 + - - +
27D GLU* 2.9 41.0 + - + +
69D LEU* 3.5 21.1 - - + -
110D VAL* 3.9 11.7 + - - +
113D SER* 2.8 31.5 + - - +
114D LEU* 3.4 38.4 - - + +
117D LEU* 4.1 15.8 - - + +
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Residues in contact with ILE 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ILE* 2.8 32.1 + - + +
21D ASN* 3.3 22.6 + - - +
23D GLN* 1.3 75.7 - - - +
25D ASN* 1.3 63.8 + - - +
27D GLU* 3.2 4.2 + - - +
28D LEU* 3.0 45.0 + - + +
66D ALA* 4.0 4.9 - - + +
69D LEU* 3.6 23.1 - - + +
70D MET* 3.7 44.2 - - + +
73D GLN* 4.7 3.6 - - + -
80D ILE* 4.7 5.8 - - + -
82D LEU* 4.1 15.0 - - + -
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Residues in contact with ASN 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ASN 3.1 13.0 + - - +
22D ARG* 3.6 9.6 - - - +
24D ILE* 1.3 77.5 - - - +
26D LEU* 1.3 59.0 + - - +
28D LEU* 3.4 9.8 + - - +
29D TYR* 2.9 29.3 + - - +
82D LEU* 6.4 0.2 - - - -
83D GLN* 3.0 29.6 + - + +
84D ASP 2.7 31.4 + - - +
85D ILE* 3.9 10.1 - - - +
86D GLN* 5.2 2.8 + - - +
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Residues in contact with LEU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ARG 2.9 17.1 + - - +
23D GLN* 3.6 19.7 - - - +
24D ILE 3.2 0.2 - - - -
25D ASN* 1.3 79.2 + - - +
27D GLU* 1.3 57.7 + - - +
29D TYR* 3.1 23.5 + - + +
30D ALA* 2.8 26.3 + - - +
106D LEU* 5.5 1.1 - - + -
109D ASN* 4.9 2.2 - - + +
110D VAL* 4.1 28.0 - - + +
113D SER* 3.6 32.8 - - - +
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Residues in contact with GLU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLN* 2.9 31.2 + - + +
26D LEU* 1.3 71.5 - - + +
28D LEU* 1.3 65.4 + - - +
30D ALA* 3.3 6.6 + - - +
31D SER* 3.0 19.6 + - - -
62D GLU* 2.6 39.8 - - - +
65D HIS* 3.7 14.3 - - - +
66D ALA* 3.8 24.9 - - + +
69D LEU* 3.9 13.4 - - + +
110D VAL* 3.9 17.2 - - - +
114D LEU* 4.4 1.4 - - - +
137D TYR* 3.8 19.2 - - - -
201D FE 2.8 13.7 - - - -
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Residues in contact with LEU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ILE* 3.0 36.2 + - + +
25D ASN* 3.8 8.5 - - - +
27D GLU* 1.3 77.3 - - - +
29D TYR* 1.3 61.7 + - - +
31D SER* 3.4 8.2 + - - +
32D TYR* 3.0 22.9 + - - +
63D ARG* 4.4 18.8 - - + -
66D ALA* 3.6 20.0 - - + -
67D GLU* 6.3 1.1 - - + -
70D MET* 5.6 4.5 - - - -
82D LEU* 4.5 13.7 - - + -
83D GLN 5.7 1.1 - - - +
85D ILE* 3.8 34.6 - - + +
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Residues in contact with TYR 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ASN* 2.9 18.7 + - - +
26D LEU* 3.3 24.2 - - + +
28D LEU* 1.3 76.8 - - - +
30D ALA* 1.3 63.6 + - - +
32D TYR* 3.1 4.8 + - + +
33D VAL* 2.9 47.3 + - + +
85D ILE* 3.7 12.0 - - + +
86D GLN* 3.2 40.2 - - + +
87D LYS 4.2 10.1 - - - -
88D PRO* 4.4 0.9 - - + -
89D ASP* 4.3 14.4 + - - +
106D LEU* 3.9 21.3 - - + -
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Residues in contact with ALA 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LEU 2.8 12.9 + - - +
27D GLU* 3.3 6.9 + - - +
29D TYR* 1.3 80.3 - - - +
31D SER* 1.3 63.1 + - - +
33D VAL* 3.2 4.0 + - - +
34D TYR* 3.0 29.1 + - + -
62D GLU* 3.6 26.5 - - + +
106D LEU* 4.1 27.3 - - + +
107D GLU* 5.1 0.9 - - - +
110D VAL* 4.6 8.1 - - + -
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Residues in contact with SER 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLU 3.0 9.9 + - - -
28D LEU* 3.4 8.3 + - - +
30D ALA* 1.3 77.0 - - - +
32D TYR* 1.3 59.8 + - - +
34D TYR 3.3 0.3 + - - -
35D LEU* 2.9 18.5 + - - +
59D SER* 2.8 53.0 + - - +
62D GLU* 3.5 14.5 - - - +
63D ARG* 3.7 19.8 - - - +
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Residues in contact with TYR 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LEU 3.0 14.0 + - - +
29D TYR* 3.1 9.6 + - - +
31D SER* 1.3 78.5 + - - +
33D VAL* 1.3 63.6 + - + +
35D LEU* 3.2 24.9 + - + +
36D SER* 3.0 24.2 + - - -
85D ILE* 4.1 20.2 - - + -
86D GLN 3.8 12.1 - - - +
87D LYS* 3.8 22.9 - - + +
88D PRO* 3.7 19.9 - - + +
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Residues in contact with VAL 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D TYR* 2.9 50.1 + - + +
30D ALA 3.6 7.0 - - - +
32D TYR* 1.3 74.6 - - - +
34D TYR* 1.3 64.5 + - - +
36D SER* 3.2 3.5 + - - -
37D MET* 3.0 45.9 + - - +
88D PRO* 3.8 22.7 - - + -
93D TRP* 4.0 17.0 - - + -
102D ALA* 6.0 2.0 - - + +
106D LEU* 4.0 19.1 - - + -
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Residues in contact with TYR 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ALA 3.0 22.7 + - - +
31D SER* 4.4 0.2 - - - -
33D VAL* 1.3 77.8 - - - +
35D LEU* 1.3 58.2 + - - +
37D MET* 3.4 7.5 + - - +
38D SER* 2.9 29.3 + - - -
55D PHE* 3.5 42.5 - + - +
58D GLN* 3.7 29.5 + - + -
59D SER* 3.6 12.1 - - - +
62D GLU* 3.8 22.2 - - + -
103D ALA* 3.7 29.1 + - + +
106D LEU* 3.9 16.6 - - + -
107D GLU* 2.9 44.0 + - - +
148D LEU* 3.9 5.5 - - + +
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Residues in contact with LEU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D SER 2.9 17.0 + - - +
32D TYR* 3.2 26.4 + - + +
34D TYR* 1.3 73.2 - - - +
36D SER* 1.3 66.5 + - - +
38D SER* 3.3 4.3 + - - -
39D TYR* 3.1 50.7 + - + +
56D LEU* 4.2 13.5 - - + -
59D SER* 3.7 13.0 + - - +
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Residues in contact with SER 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D TYR* 3.0 16.0 + - - -
33D VAL* 3.5 7.9 - - - -
35D LEU* 1.3 79.9 - - - +
37D MET* 1.3 63.6 + - - +
39D TYR* 3.3 3.1 + - - +
40D TYR* 2.9 22.5 + - - +
88D PRO* 3.9 22.6 - - - +
90D GLU 4.3 3.5 + - - -
91D ASP* 4.5 5.4 + - - +
93D TRP* 3.1 17.1 + - - -
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Residues in contact with MET 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D VAL* 3.0 38.9 + - - +
34D TYR* 3.7 14.8 - - - +
36D SER* 1.3 74.8 - - - +
38D SER* 1.3 64.3 + - - +
40D TYR* 3.2 2.4 + - - +
41D PHE* 3.0 31.8 + - + -
55D PHE* 3.3 37.2 - - + -
93D TRP* 3.5 36.8 - - + -
99D ALA* 3.1 37.5 - - + +
102D ALA* 5.2 0.4 - - - -
103D ALA* 4.2 9.2 - - + -
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Residues in contact with SER 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR 2.9 17.8 + - - -
35D LEU* 3.6 7.0 - - - -
36D SER 3.2 0.2 - - - -
37D MET* 1.3 75.7 - - - +
39D TYR* 1.3 70.1 + - - +
41D PHE 3.1 13.7 + - - -
42D ASP* 3.4 8.0 + - - +
52D ALA* 2.9 40.7 + - - +
55D PHE* 3.7 8.7 - - - +
56D LEU* 3.5 25.4 - - - +
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Residues in contact with TYR 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D LEU* 3.1 43.0 + - + +
36D SER* 4.3 2.2 - - - +
38D SER* 1.3 84.2 - - - +
40D TYR* 1.3 67.0 + - - +
42D ASP* 3.1 37.6 + - + +
43D ARG* 3.3 13.2 + - - +
56D LEU* 4.5 18.4 - - + +
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Residues in contact with TYR 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B RFT 5.5 1.4 + - - -
36D SER 2.9 15.0 + - - +
37D MET 3.4 6.5 - - - +
39D TYR* 1.3 75.9 - - - +
41D PHE* 1.3 88.4 + + - +
43D ARG* 3.1 55.4 + - - +
46D VAL* 3.7 30.6 - - + +
91D ASP 4.4 5.2 - - - +
92D ASP* 3.5 25.8 + - - -
93D TRP* 3.6 32.5 - - + -
94D GLU* 3.0 41.3 + - - -
95D SER* 4.2 2.8 - - - -
----------------------------------------------------------
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Residues in contact with PHE 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D MET* 3.0 27.3 + - + -
38D SER 3.1 7.1 + - - +
40D TYR* 1.3 93.0 - + - +
42D ASP* 1.3 56.1 + - - +
43D ARG 3.4 0.4 - - - -
46D VAL* 3.6 19.3 - - + -
47D ALA* 3.4 6.4 + - - -
48D LEU* 3.1 39.3 + - + +
49D LYS* 5.0 0.2 - - - -
51D PHE* 3.7 15.9 - + + -
52D ALA* 3.8 17.7 - - - +
55D PHE* 3.5 23.8 - + - -
95D SER* 3.6 6.7 - - - -
96D GLY* 3.4 30.3 - - - -
99D ALA* 3.3 35.9 - - + -
----------------------------------------------------------
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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