Contacts of the helix formed by residues 6 - 29 (chain D) in PDB entry 5OA3
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 SER 6 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15512 U 4.8 6.7 - - - -
15782 U 3.1 45.3 + - - -
15792 A 4.3 14.0 + - - -
5D ILE* 1.3 80.8 - - - +
7D LYS* 1.3 63.1 + - - +
8D LYS* 3.3 13.0 + - - +
9D ARG* 3.3 15.5 + - - +
10D LYS* 2.8 26.0 + - - +
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Residues in contact with LYS 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15782 U 4.2 2.0 + - - -
15792 A 3.5 22.8 + - - +
5D ILE 3.8 2.6 + - - +
6D SER* 1.3 76.9 + - - +
8D LYS* 1.3 66.5 + - + +
10D LYS* 2.8 45.1 + - + +
11D PHE* 2.9 36.3 + - + -
23U THR* 5.7 1.1 - - - -
25U THR* 3.4 41.8 + - + +
84U ILE* 4.7 7.4 - - + -
86U LYS* 5.5 6.7 - - + +
112U VAL 6.3 0.2 - - - -
113U GLU* 3.7 24.8 + - - +
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Residues in contact with LYS 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15492 U 2.8 36.2 + - - -
15502 G 4.0 18.3 + - - +
15792 A 5.9 5.3 + - - -
6D SER* 3.3 10.3 - - - +
7D LYS* 1.3 80.4 - - + +
9D ARG* 1.3 60.9 + - + +
11D PHE* 3.2 2.3 + - - +
12D VAL* 2.9 34.1 + - - +
59U LYS* 5.2 15.0 - - + -
60U THR 5.4 1.5 + - - +
61U LEU* 3.8 28.3 - - + +
84U ILE* 4.2 13.0 - - + +
34d TYR* 3.8 23.3 - - + -
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Residues in contact with ARG 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15502 G 5.0 5.3 + - - -
15512 U 2.5 44.3 + - - -
15782 U 6.0 0.7 - - - -
5D ILE* 3.8 29.6 - - + +
6D SER* 3.3 12.6 + - - +
8D LYS* 1.3 81.2 - - + +
10D LYS* 1.3 58.9 + - - +
12D VAL* 3.7 7.8 - - - +
13D ALA* 2.9 31.7 + - - +
33d LYS 4.9 8.1 + - - -
34d TYR* 3.4 30.8 + - + +
35d GLY* 5.2 5.8 - - - +
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Residues in contact with LYS 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ILE* 4.7 14.1 - - + +
6D SER 2.8 14.6 + - - +
7D LYS* 2.8 46.8 - - + +
8D LYS 3.1 0.2 - - - -
9D ARG* 1.3 77.5 - - - +
11D PHE* 1.3 64.5 + - + +
13D ALA* 3.3 6.7 + - - +
14D ASP* 3.0 22.2 + - + +
111U GLU* 3.6 32.5 + - - +
112U VAL 5.5 5.1 + - - -
113U GLU* 5.2 4.0 + - - +
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Residues in contact with PHE 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D LYS* 2.9 33.4 + - + +
8D LYS 3.7 3.6 - - - +
10D LYS* 1.3 78.6 - - + +
12D VAL* 1.3 62.9 + - + +
14D ASP* 3.1 11.5 + - - +
15D GLY* 2.9 19.9 + - - -
25U THR* 3.8 20.6 - - - -
26U SER* 3.8 25.4 - - - -
27U ARG* 3.9 43.8 + - + +
61U LEU* 5.8 0.2 - - + -
82U MET* 5.1 10.4 - - - +
84U ILE* 4.0 32.3 - - + -
109U GLY 5.5 2.5 - - - -
111U GLU* 3.5 33.2 - - - -
50d ILE 5.1 1.4 - - - +
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Residues in contact with VAL 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LYS 2.9 24.2 + - - +
9D ARG* 3.7 6.7 - - - +
11D PHE* 1.3 75.6 - - - +
13D ALA* 1.3 59.0 + - - +
15D GLY* 3.0 5.0 + - - -
16D ILE* 2.9 37.1 + - + +
61U LEU* 4.5 17.0 - - + -
82U MET* 5.6 4.9 - - + -
34d TYR* 4.1 29.8 - - + +
35d GLY 5.2 0.9 - - - -
36d LEU* 3.5 33.0 - - + +
50d ILE* 4.9 6.0 - - + +
52d PHE* 5.0 10.5 - - + -
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Residues in contact with ALA 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ILE* 6.2 3.6 - - + -
9D ARG 2.9 19.7 + - - +
10D LYS* 3.6 5.2 - - - +
12D VAL* 1.3 76.7 - - - +
14D ASP* 1.3 57.3 + - - +
16D ILE* 3.3 15.4 + - + +
17D PHE* 2.9 27.9 + - - +
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Residues in contact with ASP 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LYS* 3.0 14.5 + - + +
11D PHE* 3.2 17.1 - - - +
13D ALA* 1.3 75.3 - - - +
15D GLY* 1.3 65.2 + - - +
17D PHE* 3.1 20.2 + - - +
18D LYS* 2.9 41.9 + - - +
39D VAL* 5.9 0.2 - - - +
41D VAL* 5.6 5.8 - - - +
27U ARG* 5.7 3.9 + - - -
111U GLU* 3.3 23.1 - - - +
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Residues in contact with GLY 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D PHE 2.9 12.2 + - - -
12D VAL 3.0 4.5 + - - -
14D ASP* 1.3 76.7 - - - +
16D ILE* 1.3 56.5 + - - +
18D LYS* 3.1 7.9 + - - +
19D ALA* 2.9 29.5 + - - +
27U ARG* 5.0 4.9 - - - +
49d ASP 4.0 5.3 - - - +
50d ILE* 3.6 32.3 - - - -
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Residues in contact with ILE 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D VAL* 2.9 29.8 + - + +
13D ALA* 3.6 13.0 - - - +
15D GLY* 1.3 74.8 - - - +
17D PHE* 1.3 58.4 + - - +
19D ALA* 3.9 5.5 - - - +
20D GLU* 2.9 37.0 + - - +
77D PHE* 5.3 0.2 - - - -
64K TRP* 3.7 28.7 - - + -
22d ARG* 3.5 46.4 - - - +
35d GLY 4.9 0.4 - - - +
36d LEU* 3.9 16.2 - - + -
38d MET* 5.5 2.2 - - - -
50d ILE* 4.9 6.5 - - + +
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Residues in contact with PHE 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ALA 2.9 14.7 + - - +
14D ASP* 3.1 24.5 - - - +
16D ILE* 1.3 77.3 - - - +
18D LYS* 1.3 78.4 + - + +
20D GLU* 3.9 0.3 - - - -
21D LEU* 2.9 43.1 + - + +
39D VAL* 3.8 36.1 - - + -
41D VAL* 6.0 0.7 - - + -
46D THR* 4.9 8.1 - - + -
48D ILE* 4.5 9.2 - - + -
73D VAL* 4.8 2.7 - - + -
77D PHE* 3.5 51.3 - + + -
79D PHE* 4.7 13.5 - + - -
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Residues in contact with LYS 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ASP* 2.9 35.7 + - - +
15D GLY* 3.1 8.0 + - - +
17D PHE* 1.3 89.0 - - + +
19D ALA* 1.3 58.2 + - - +
21D LEU* 3.8 4.0 - - - +
22D ASN* 2.9 32.9 + - - +
37D VAL* 5.4 2.4 - - - +
39D VAL* 4.5 33.8 + - + +
41D VAL* 6.1 1.8 - - - -
27U ARG* 4.4 19.5 - - - +
109U GLY* 6.2 2.4 - - - -
49d ASP* 4.5 14.8 - - + +
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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 GLY 2.9 16.7 + - - +
16D ILE* 3.9 7.0 - - - +
18D LYS* 1.3 75.8 - - - +
20D GLU* 1.3 60.0 + - - +
22D ASN* 3.5 3.9 + - - +
23D GLU* 2.9 30.0 + - - +
64K TRP* 4.5 14.9 + - + -
46d TYR* 4.7 12.9 - - + -
49d ASP* 4.1 27.5 - - + +
50d ILE* 4.7 8.5 - - + +
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Residues in contact with GLU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ILE* 2.9 25.2 + - - +
17D PHE 4.0 1.8 - - - +
19D ALA* 1.3 74.1 - - - +
21D LEU* 1.3 60.2 + - - +
23D GLU* 3.5 5.0 - - - +
24D PHE* 2.9 31.4 + - + +
76D ARG* 3.2 40.5 + - + +
77D PHE* 4.5 15.9 - - + -
63K ALA* 4.5 3.1 - - + +
64K TRP* 3.1 60.1 - - + +
66K HIS* 4.5 0.2 - - - -
68K TYR* 5.1 3.3 + - - +
22d ARG* 4.7 1.6 + - - -
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D PHE* 2.9 25.6 + - + +
18D LYS* 3.8 3.1 - - - +
20D GLU* 1.3 74.9 - - - +
22D ASN* 1.3 65.9 + - - +
24D PHE* 3.2 11.2 + - + +
25D LEU* 2.9 42.1 + - + +
37D VAL* 3.7 29.8 - - + -
39D VAL* 4.1 10.8 - - + -
48D ILE* 3.7 26.7 - - + -
73D VAL* 4.4 22.7 - - + -
77D PHE* 4.3 17.6 - - + -
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Residues in contact with ASN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D LYS 2.9 20.2 + - - +
19D ALA* 3.7 6.5 - - - +
21D LEU* 1.3 76.2 - - - +
23D GLU* 1.3 53.3 + - - +
26D THR* 2.7 39.4 + - - -
34D TYR* 2.2 41.2 + - - -
35D SER 5.1 0.3 - - - +
36D GLY* 4.0 5.9 - - - -
37D VAL* 3.9 24.4 + - + +
49d ASP* 4.3 22.2 + - - +
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Residues in contact with GLU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ALA 2.9 19.5 + - - +
20D GLU 3.5 4.7 - - - +
21D LEU 3.1 0.2 - - - -
22D ASN* 1.3 75.3 - - - +
24D PHE* 1.3 60.1 + - - +
26D THR* 3.0 20.4 + - - +
27D ARG* 2.9 62.5 + - + +
63K ALA* 4.8 0.9 - - + -
64K TRP* 3.4 33.9 - - + +
45d GLN* 5.6 0.5 + - - -
46d TYR* 3.6 23.5 + - + +
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Residues in contact with PHE 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D GLU* 2.9 18.3 + - + +
21D LEU* 3.8 10.1 - - + +
23D GLU* 1.3 75.1 - - - +
25D LEU* 1.3 67.6 + - + +
27D ARG* 3.0 4.9 + - - +
28D GLU* 3.0 33.7 + - - +
69D LEU* 3.5 24.5 - - + -
72D VAL* 3.8 15.5 - - + -
61K GLN* 3.5 26.2 - - + -
63K ALA* 3.7 28.9 - - + +
68K TYR* 3.5 38.4 - + + +
70K TYR* 3.2 22.2 - + - -
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Residues in contact with LEU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 2.9 31.1 + - + +
24D PHE* 1.3 86.9 - - + +
26D THR* 1.3 59.4 + - - +
28D GLU* 4.5 2.2 - - - +
29D LEU* 2.9 54.3 + - + +
34D TYR* 3.5 24.9 - - + -
37D VAL* 3.5 19.5 - - + -
50D ILE* 3.5 33.7 - - + -
69D LEU* 4.2 19.5 - - + -
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Residues in contact with THR 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ASN* 2.7 23.6 + - - -
23D GLU* 3.0 24.4 + - - +
25D LEU* 1.3 77.3 - - - +
27D ARG* 1.3 62.8 + - - +
30D ALA* 3.4 20.3 + - - +
34D TYR* 3.2 20.2 - - + -
103D GLU* 6.0 1.8 - - + +
106D ARG* 6.3 1.3 - - - +
173D ARG* 3.6 33.9 + - - +
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Residues in contact with ARG 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14972 G 3.8 7.4 + - - -
14982 A 2.4 46.5 + - - -
23D GLU* 2.9 42.4 + - - +
24D PHE 3.0 5.8 + - - +
26D THR* 1.3 80.4 - - - +
28D GLU* 1.3 62.2 + - - +
30D ALA* 3.7 10.6 - - - +
61K GLN* 3.1 25.6 + - + +
62K PHE 3.3 20.8 + - - +
63K ALA* 3.6 19.3 - - + +
64K TRP* 4.0 20.0 - - - +
23d VAL* 5.5 2.2 - - - +
46d TYR* 5.3 2.8 + - - -
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Residues in contact with GLU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D PHE* 3.0 15.7 + - + +
25D LEU* 4.7 1.9 - - - +
27D ARG* 1.3 75.3 - - - +
29D LEU* 1.3 70.4 + - + +
30D ALA* 3.2 8.0 + - - +
31D GLU* 4.5 5.0 + - - +
32D ASP* 5.6 0.2 - - - -
65D ARG* 4.0 34.8 + - - +
69D LEU* 3.3 23.7 - - - +
61K GLN* 3.4 28.9 - - + +
70K TYR* 3.3 37.8 + - + -
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Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D LEU* 2.9 42.8 + - + +
28D GLU* 1.3 88.6 - - + +
30D ALA* 1.3 63.6 + - - +
31D GLU 3.1 3.4 - - - -
32D ASP* 2.9 39.9 + - + +
34D TYR* 3.5 30.1 + - + +
50D ILE* 4.0 24.2 - - + -
58D VAL* 4.1 19.1 - - + +
65D ARG* 4.1 9.9 - - - +
69D LEU* 4.7 11.2 - - + -
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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