Contacts of the helix formed by residues 11 - 38 (chain D) in PDB entry 2WP9
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 ASN 11 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B SER* 3.5 20.0 - - - +
199B ASP* 4.8 6.7 - - - +
200B ALA* 4.5 3.6 - - - +
237B ASN* 5.5 8.7 + - - +
12D GLY* 1.3 57.1 + - - +
13D VAL* 2.8 25.2 + - - +
14D HIS* 2.9 36.6 + - - +
15D ASP* 3.5 11.9 + - - +
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Residues in contact with GLY 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B SER 2.9 16.9 + - - -
199B ASP 3.6 7.1 - - - -
200B ALA* 3.6 23.7 - - - +
204B PHE* 3.7 15.8 - - - +
11D ASN* 1.3 67.9 - - - +
13D VAL* 1.3 62.1 + - - -
14D HIS 3.2 1.1 - - - -
15D ASP* 3.8 7.8 - - - +
16D PHE* 3.1 24.1 + - - +
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Residues in contact with VAL 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B SER* 3.8 9.6 + - - +
204B PHE* 3.7 24.7 - - + -
233B LEU* 4.1 14.6 - - + +
234B LEU* 3.6 24.9 - - + -
237B ASN* 4.1 44.4 - - + +
238B ALA* 4.3 1.8 - - + -
11D ASN* 2.8 12.4 + - - +
12D GLY* 1.3 72.9 - - - +
14D HIS* 1.3 66.4 + - - +
16D PHE* 3.4 3.6 + - - +
17D ILE* 3.0 30.9 + - + +
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Residues in contact with HIS 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASN* 2.9 31.7 + - - +
13D VAL* 1.3 77.4 - - - +
15D ASP* 1.3 66.2 + - - +
17D ILE* 3.3 7.3 + - + +
18D LEU* 3.0 57.7 + - + +
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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
----------------------------------------------------------
200B ALA* 4.3 11.3 - - - +
11D ASN 3.5 11.3 + - - +
12D GLY* 3.9 7.9 - - - +
13D VAL 3.3 0.4 - - - -
14D HIS* 1.3 83.3 + - - +
16D PHE* 1.3 65.6 + - - +
17D ILE 2.9 0.5 + - - -
18D LEU* 5.4 1.3 - - - +
19D VAL* 2.8 28.4 + - - +
74D ILE* 3.9 35.6 - - + +
77D TRP* 4.2 22.5 - - - -
78D GLN* 4.9 6.3 - - - +
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Residues in contact with PHE 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PHE* 3.3 34.1 - + + -
230B LYS* 4.2 21.3 - - + -
234B LEU* 4.0 35.7 - - + -
95C ASP* 3.8 21.3 - - + -
96C PHE* 5.4 4.3 - + - -
12D GLY 3.1 16.3 + - - +
13D VAL* 3.5 5.4 - - - +
15D ASP* 1.3 80.3 - - - +
17D ILE* 1.3 64.9 + - + +
19D VAL* 5.0 0.4 - - - -
20D ARG* 3.2 78.4 + - - +
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Residues in contact with ILE 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 3.8 19.7 - - + -
238B ALA* 3.5 32.5 - - + -
13D VAL* 3.0 24.5 + - + +
14D HIS* 3.9 5.6 - - + +
16D PHE* 1.3 78.0 - - + +
18D LEU* 1.3 67.6 + - + +
20D ARG* 3.0 5.6 + - - +
21D ALA* 2.8 33.4 + - + +
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Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D HIS* 3.0 52.9 + - + +
15D ASP* 5.4 1.1 - - - +
17D ILE* 1.3 80.5 - - + +
19D VAL* 1.3 65.5 + - - +
21D ALA* 4.3 7.4 - - + -
22D THR* 2.8 32.4 + - + +
70D ILE* 4.2 24.2 - - + -
74D ILE* 3.7 16.4 - - + -
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Residues in contact with VAL 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ASP 2.8 15.2 + - - +
16D PHE 4.0 0.2 - - - +
18D LEU* 1.3 79.1 - - - +
20D ARG* 1.3 88.3 + - + +
22D THR* 3.1 7.2 + - - -
23D ALA* 3.2 7.9 + - + +
71D HIS* 3.0 48.5 + - + +
74D ILE* 3.3 39.2 - - + +
75D GLY* 4.6 3.8 - - - +
78D GLN* 5.2 5.2 - - - +
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Residues in contact with ARG 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C HIS* 3.5 25.9 + - - -
92C MET* 4.1 29.3 - - + +
95C ASP* 2.8 29.3 + - - -
96C PHE* 4.9 13.2 - - + -
16D PHE* 3.2 65.5 + - - +
17D ILE* 3.0 6.4 + - - +
19D VAL* 1.3 97.2 - - + +
21D ALA* 1.3 64.8 - - - +
23D ALA* 3.1 6.5 + - + +
24D ILE* 3.0 30.2 + - + +
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Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ILE* 2.8 22.1 + - + +
18D LEU* 3.8 11.4 - - + +
20D ARG* 1.3 75.4 - - - +
22D THR* 1.3 64.3 + - + +
24D ILE* 3.1 22.3 + - - +
25D VAL* 3.1 17.8 + - + +
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Residues in contact with THR 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D LEU* 2.8 22.5 + - + +
19D VAL* 3.1 6.4 + - - -
21D ALA* 1.3 77.1 - - + +
23D ALA* 1.3 56.1 + - - +
25D VAL* 3.3 8.4 + - - +
26D LEU* 2.8 34.4 + - - +
67D SER* 3.7 37.5 - - - +
70D ILE* 4.1 22.9 - - + -
71D HIS* 3.0 21.1 - - - +
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Residues in contact with ALA 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C MET* 4.1 17.9 - - - -
19D VAL* 3.2 15.8 + - + +
20D ARG* 3.1 7.9 + - - +
22D THR* 1.3 82.1 + - - +
24D ILE* 1.3 57.2 + - - +
26D LEU* 4.0 6.1 - - - +
27D THR* 2.8 34.5 + - - +
71D HIS* 3.8 18.6 - - + -
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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
----------------------------------------------------------
92C MET* 3.8 22.7 - - + -
96C PHE* 5.1 10.1 - - + -
20D ARG* 3.0 22.2 + - + +
21D ALA* 3.1 10.7 + - - +
23D ALA* 1.3 74.9 - - - +
25D VAL* 1.3 69.3 + - + +
27D THR* 3.2 7.0 + - - -
28D LEU* 3.0 35.9 + - + +
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Residues in contact with VAL 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ALA* 3.1 12.5 + - + +
22D THR* 3.6 7.6 - - - +
24D ILE* 1.3 79.9 - - + +
26D LEU* 1.3 59.2 + - + +
28D LEU* 2.9 27.9 + - + +
29D TYR* 3.0 11.8 + - + +
60D PHE* 4.3 8.3 - - + -
63D LEU* 4.1 29.4 - - + +
64D ALA* 5.1 2.5 - - - -
67D SER* 3.3 24.9 - - - +
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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 THR 2.8 23.4 + - - +
23D ALA* 4.0 4.5 - - - +
25D VAL* 1.3 70.8 - - - +
27D THR* 1.3 57.9 + - - +
29D TYR* 3.3 7.3 + - + +
30D ILE* 2.9 41.8 + - + +
64D ALA* 3.4 43.1 - - + +
67D SER* 3.7 16.4 - - - +
68D ILE* 3.7 30.5 - - + +
71D HIS* 4.5 17.3 - - + +
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Residues in contact with THR 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C VAL* 4.4 16.9 - - + +
89C ILE* 4.3 24.5 - - + +
23D ALA* 2.8 23.6 + - - +
24D ILE* 3.2 7.8 + - - -
26D LEU* 1.3 75.5 - - - +
28D LEU* 1.3 65.4 + - + +
30D ILE* 3.4 9.4 + - + +
31D ILE* 3.1 38.1 + - + +
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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 29.3 + - + +
25D VAL* 2.9 14.5 + - + +
27D THR* 1.3 78.4 - - + +
29D TYR* 1.3 63.2 + - - +
31D ILE* 3.1 20.2 + - + +
32D TYR* 3.0 21.5 + - - +
60D PHE* 3.8 15.8 - - + -
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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 VAL* 3.0 9.4 + - + +
26D LEU* 3.6 13.5 - - + +
28D LEU* 1.3 76.3 - - - +
30D ILE* 1.3 63.3 + - + +
32D TYR* 3.3 5.2 + + - +
33D MET* 3.0 62.3 + - + +
52D PHE* 4.9 1.9 - - - -
57D THR 5.0 0.2 - - - -
60D PHE* 3.5 44.7 - + + -
61D THR* 2.8 52.0 + - + +
64D ALA* 3.6 21.3 - - + -
68D ILE* 6.2 1.8 - - + -
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Residues in contact with ILE 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 4.3 25.8 - - + -
85C VAL* 4.0 30.1 - - + -
26D LEU* 2.9 29.2 + - + +
27D THR* 3.9 6.7 - - + +
28D LEU 3.2 0.4 - - - -
29D TYR* 1.3 79.9 - - + +
31D ILE* 1.3 62.9 + - + +
33D MET* 4.1 4.6 - - - +
34D VAL* 2.8 44.8 + - + +
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Residues in contact with ILE 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D THR* 3.1 30.9 + - + +
28D LEU* 3.1 20.7 + - + +
30D ILE* 1.3 77.1 - - + +
32D TYR* 1.3 58.5 + - - +
34D VAL* 4.0 4.9 - - - +
35D GLY* 2.9 26.2 + - - -
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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 11.9 + - - +
29D TYR* 3.5 10.8 - + - +
30D ILE 3.1 0.2 - - - -
31D ILE* 1.3 75.6 - - - +
33D MET* 1.3 77.4 + - + +
35D GLY* 3.3 3.2 + - - -
36D PHE* 3.0 20.8 + - - +
51D PHE* 3.3 27.5 - + - -
54D SER* 4.9 1.0 + - - -
56D PHE* 3.4 36.0 - + - +
57D THR* 2.5 35.1 + - + -
60D PHE* 3.8 28.9 - + + -
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Residues in contact with MET 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D TYR* 3.0 59.6 + - + +
30D ILE* 4.1 4.7 - - + +
32D TYR* 1.3 77.6 - - + +
34D VAL* 1.3 64.9 + - + +
36D PHE* 3.5 3.7 + - - +
37D PHE* 3.1 50.6 + - + -
51D PHE* 3.8 24.9 - - + -
52D PHE* 3.8 28.0 - - + -
57D THR* 5.0 0.7 - - - -
61D THR* 4.9 1.8 - - - -
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Residues in contact with VAL 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C LEU* 5.8 3.1 - - + +
30D ILE* 2.8 37.9 + - + +
31D ILE* 4.0 5.4 - - - +
33D MET* 1.3 69.6 - - + +
35D GLY* 1.3 69.2 + - - +
36D PHE 3.2 0.2 + - - -
37D PHE* 3.2 7.0 + - + +
38D ALA* 2.8 31.1 + - + +
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Residues in contact with GLY 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ILE 2.9 17.1 + - - -
32D TYR* 3.3 4.5 + - - -
34D VAL* 1.3 79.5 - - - +
36D PHE* 1.3 63.3 + - - +
38D ALA* 3.1 7.8 + - - -
39D THR* 2.9 25.7 + - - +
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Residues in contact with PHE 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D TYR 3.0 9.7 + - - +
33D MET 3.7 6.1 - - - +
34D VAL 3.2 0.2 - - - -
35D GLY* 1.3 73.5 - - - +
37D PHE* 1.3 89.4 + + - +
39D THR* 2.9 21.7 + - - +
40D SER* 3.3 26.1 + - - -
43D LEU* 4.2 20.4 - - + -
47D VAL* 4.4 13.0 - - + -
48D TRP* 3.9 28.7 - + - -
51D PHE* 3.4 68.0 - + + -
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Residues in contact with PHE 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C LEU* 4.0 39.4 - - + +
33D MET* 3.1 44.3 + - + +
34D VAL* 3.8 6.5 - - + +
36D PHE* 1.3 89.6 - + - +
38D ALA* 1.3 58.0 + - - +
39D THR 3.2 1.4 + - - -
40D SER* 4.1 9.2 + - - -
41D GLY 5.3 1.9 + - - -
43D LEU* 4.4 24.9 - - + +
48D TRP* 3.5 37.5 - + - -
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Residues in contact with ALA 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C LEU* 5.2 6.5 - - + -
34D VAL* 2.8 29.3 + - + +
35D GLY* 3.1 4.5 + - - +
36D PHE 3.0 0.6 + - - -
37D PHE* 1.3 73.8 - - - +
39D THR* 1.3 69.6 + - + +
40D SER 4.0 0.9 - - - -
41D GLY 5.6 0.2 - - - -
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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