Contacts of the helix formed by residues 9 - 36 (chain D) in PDB entry 2Q7M
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 VAL 9 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET* 5.0 9.9 - - + -
5D THR* 3.1 20.4 - - - +
6D VAL* 3.2 17.5 - - + +
7D GLY 3.2 0.8 + - - -
8D ASN* 1.3 75.6 - - - +
10D VAL* 1.3 57.9 + - - +
11D LEU 2.7 17.5 + - - -
12D LEU* 2.8 21.6 + - + -
13D ALA* 2.9 9.9 + - + +
72D TRP* 3.3 34.8 - - + -
76D LEU* 5.2 4.3 - - + -
80D GLN* 3.2 5.9 - - - +
77F LEU* 5.7 4.7 - - + -
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Residues in contact with VAL 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D VAL* 2.9 35.7 + - + +
7D GLY 3.9 8.1 - - - +
9D VAL* 1.3 75.9 - - - +
11D LEU* 1.3 63.8 + - + +
13D ALA* 3.7 9.5 - - + +
14D ILE* 3.0 29.2 + - + +
80D GLN* 3.3 0.4 - - - +
77F LEU* 5.7 1.3 - - + -
130F ILE* 3.8 21.2 - - + +
133F TYR* 3.8 26.2 - - + -
134F TYR* 3.1 33.4 - - + +
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Residues in contact with LEU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D GLY 4.7 2.9 - - - +
9D VAL 2.7 1.0 + - - -
10D VAL* 1.3 87.3 - - + +
12D LEU* 1.3 58.4 + - - +
13D ALA 3.1 1.1 - - - -
14D ILE* 3.2 13.5 + - + +
15D VAL* 2.9 31.4 + - - +
80D GLN* 2.7 39.2 - - - +
81D VAL* 4.7 12.6 - - + -
84D ALA* 3.4 27.7 - - + +
134F TYR* 4.6 4.5 - - - +
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Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D VAL* 2.8 32.9 + - + +
11D LEU* 1.3 70.0 - - - +
13D ALA* 1.3 60.1 + - - +
15D VAL* 3.6 8.3 - - - +
16D THR* 2.8 35.5 + - - -
71D LEU* 3.6 28.9 - - + +
72D TRP* 3.5 25.6 - - + +
75D GLY* 3.8 14.1 - - - -
76D LEU* 3.8 25.1 - - + -
80D GLN* 3.8 22.2 - - + +
83D ALA* 4.0 11.2 - - + -
84D ALA 4.1 3.1 - - - +
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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
----------------------------------------------------------
9D VAL* 2.9 17.5 + - + +
10D VAL* 3.7 9.4 - - - +
12D LEU* 1.3 75.7 - - - +
14D ILE* 1.3 56.7 + - - +
16D THR* 3.0 4.8 + - - -
17D LEU* 2.7 45.9 + - + +
72D TRP* 3.8 12.7 - - + -
73F SER* 5.2 3.4 - - - +
77F LEU* 3.6 32.3 - - + -
130F ILE* 4.5 2.7 - - + -
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Residues in contact with ILE 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D VAL* 3.0 26.4 + - + +
11D LEU* 3.5 15.9 - - + +
13D ALA* 1.3 77.9 - - - +
15D VAL* 1.3 69.1 + - + +
17D LEU* 3.0 7.2 + - - +
18D ILE* 2.7 41.5 + - + +
130F ILE* 3.0 36.8 - - + -
134F TYR* 4.1 11.9 - - + +
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Residues in contact with VAL 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU 2.9 13.9 + - - +
12D LEU* 3.6 10.5 - - - +
14D ILE* 1.3 79.3 - - + +
16D THR* 1.3 61.1 + - - +
18D ILE* 3.0 13.9 - - + +
19D SER* 2.8 28.3 + - - +
67D PHE* 5.4 0.9 - - + -
71D LEU* 3.7 32.1 - - + -
84D ALA* 3.6 15.3 - - + +
87D GLY 3.8 4.9 - - - +
88D LEU* 3.5 40.2 - - + +
91D LEU* 3.3 14.1 - - + +
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Residues in contact with THR 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LEU 2.8 24.1 + - - -
13D ALA 3.3 2.5 - - - -
15D VAL* 1.3 79.1 - - - +
17D LEU* 1.3 65.1 + - + +
19D SER* 2.5 22.2 + - - -
20D VAL* 2.7 22.2 + - - +
64D TYR* 3.5 8.9 + - - +
68D LEU* 4.5 6.6 - - + +
71D LEU* 3.5 7.6 - - - +
72D TRP* 3.2 30.4 + - + -
69F ALA* 4.4 15.3 - - + -
73F SER* 4.4 9.2 - - - +
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Residues in contact with LEU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ALA* 2.7 29.5 + - + +
14D ILE* 3.6 6.3 - - - +
16D THR* 1.3 76.0 - - + +
18D ILE* 1.3 66.4 + - - +
20D VAL* 3.6 10.6 - - + +
21D VAL* 3.2 14.6 + - - +
70F VAL* 5.6 3.8 - - - +
73F SER* 3.6 26.9 - - - +
77F LEU* 5.5 1.3 - - + -
123F PHE* 3.3 36.4 - - + -
126F SER* 3.1 42.0 - - - +
127F VAL* 4.0 6.7 - - + +
130F ILE* 5.4 5.2 - - + -
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Residues in contact with ILE 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ILE* 2.7 50.4 + - + +
15D VAL* 3.0 11.9 - - + +
16D THR 3.0 0.2 - - - -
17D LEU* 1.3 75.5 - - - +
19D SER* 1.3 59.8 + - - +
21D VAL* 2.8 32.1 + - + +
22D GLN* 2.9 14.6 + - + +
88D LEU* 5.4 7.0 - - + -
91D LEU* 3.0 27.4 - - + -
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Residues in contact with SER 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D VAL* 2.8 10.6 + - - +
16D THR* 2.5 27.0 + - - -
18D ILE* 1.3 74.5 - - - +
20D VAL* 1.3 54.2 + - - +
22D GLN* 3.7 6.8 - - - +
23D ASN* 2.6 38.1 + - - +
64D TYR* 2.9 26.1 + - - -
67D PHE* 4.5 3.6 - - - -
68D LEU* 4.8 0.3 - - - +
91D LEU* 3.4 36.8 - - - -
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D THR* 2.7 19.2 + - + +
17D LEU* 3.6 12.6 - - + +
18D ILE 3.0 0.4 + - - -
19D SER* 1.3 74.7 + - - +
21D VAL* 1.3 59.4 + - - +
23D ASN* 3.2 16.8 - - - +
24D GLY* 3.3 6.6 + - - -
64D TYR* 3.6 8.7 - - - +
504D 2CS 5.4 4.7 - - + +
66F THR* 3.3 28.3 - - + +
69F ALA* 3.2 35.4 - - + -
70F VAL* 3.7 21.1 - - + -
123F PHE* 3.9 15.9 - - + -
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Residues in contact with VAL 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU 3.2 11.0 + - - +
18D ILE* 2.8 19.6 + - + +
20D VAL* 1.3 70.5 - - - +
22D GLN* 1.3 71.0 + - + +
23D ASN 3.0 2.1 + - - -
24D GLY 3.2 1.4 + - - -
25D PHE* 3.2 16.6 + - - +
504D 2CS 3.0 61.4 - - + +
123F PHE* 4.6 9.2 - - + -
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Residues in contact with GLN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ILE* 2.9 9.2 + - + +
19D SER* 3.7 8.4 - - - +
21D VAL* 1.3 84.4 - - + +
23D ASN* 1.3 61.9 + - - +
25D PHE* 3.1 23.2 + - + +
26D PHE* 3.1 33.5 + - + -
91D LEU* 3.2 27.0 + - + +
94D ARG* 2.9 61.0 + - - +
95D GLN* 3.2 16.0 + - + +
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Residues in contact with ASN 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D SER 2.6 22.4 + - - +
20D VAL 3.2 8.1 - - - +
22D GLN* 1.3 73.2 - - - +
24D GLY* 1.3 62.3 + - - +
25D PHE 2.9 5.9 + - - -
26D PHE* 3.0 18.4 + - - +
27D ALA 3.0 0.2 + - - -
60D CYS 5.6 1.0 + - - -
61D VAL* 5.5 5.9 - - - +
64D TYR* 3.4 23.6 - - - +
94D ARG* 2.4 31.8 + - - +
504D 2CS 2.8 30.5 - - + -
62F ASP 5.4 0.4 + - - -
65F PRO* 5.5 0.6 - - - +
66F THR* 3.0 31.8 + - + -
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Residues in contact with GLY 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D VAL 3.3 7.2 + - - -
21D VAL 3.2 5.3 + - - -
23D ASN* 1.3 78.1 - - - +
25D PHE* 1.3 59.7 + - - +
27D ALA 3.6 1.1 + - - -
28D HIS* 3.2 14.2 + - - +
504D 2CS 2.8 64.4 - - - -
66F THR* 5.9 0.2 - - - -
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Residues in contact with PHE 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D VAL 3.2 2.9 + - - +
22D GLN* 3.1 13.2 + - + +
23D ASN 2.9 0.6 - - - -
24D GLY* 1.3 75.3 - - - +
26D PHE* 1.3 79.3 + + - +
27D ALA 3.0 0.9 - - - -
28D HIS* 2.6 30.6 + + - +
29D LYS* 2.9 50.8 + - + -
95D GLN* 3.4 29.2 - - - -
98D PHE* 4.2 8.5 - + - -
99D VAL* 6.2 1.3 - - + -
504D 2CS 3.1 32.7 - + + -
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Residues in contact with PHE 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D GLN* 3.2 29.8 - - + -
23D ASN* 3.0 13.2 + - - +
25D PHE* 1.3 87.0 - + - +
27D ALA* 1.3 57.4 + - - +
28D HIS 3.2 2.6 + - - -
29D LYS 3.5 1.2 + - - -
30D VAL* 3.0 27.7 + - - +
57D ASN* 3.4 17.3 - - - +
60D CYS* 3.9 25.1 - - + -
61D VAL* 6.2 0.2 - - + -
94D ARG* 3.5 32.5 - - - -
95D GLN* 3.0 28.9 - - - -
98D PHE* 3.0 51.4 - + + -
504D 2CS 4.6 0.4 - + + -
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ASN 3.0 3.6 + - - +
24D GLY* 3.7 5.6 - - - +
25D PHE 3.0 1.0 - - - -
26D PHE* 1.3 75.6 - - - +
28D HIS* 1.3 58.4 + - - +
30D VAL* 3.9 3.1 - - - -
31D GLU* 3.9 7.6 + - - +
57D ASN* 4.5 0.2 - - - +
504D 2CS 3.0 62.8 - - + +
112F TYR* 3.7 29.2 - - + +
113F ILE* 5.7 1.7 + - - -
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Residues in contact with HIS 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLY 3.2 12.7 + - - +
25D PHE* 2.6 25.1 + + - +
27D ALA* 1.3 72.4 - - - +
29D LYS* 1.3 87.9 + - + -
30D VAL 2.8 4.7 - - - -
31D GLU* 2.9 25.6 + - + +
32D HIS* 3.2 31.2 + + - +
504D 2CS 3.9 35.8 + + + -
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Residues in contact with LYS 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D PHE* 2.9 39.5 + - + +
26D PHE 4.0 4.9 - - - +
28D HIS* 1.3 99.9 + - + +
30D VAL* 1.3 59.7 + - - +
31D GLU 3.5 0.4 - - - -
32D HIS* 3.9 28.4 + - + +
33D GLU* 3.5 16.6 + - - +
53D VAL* 3.4 20.5 - - + +
98D PHE* 4.3 13.9 - - + -
102D LEU* 5.3 8.3 - - + -
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Residues in contact with VAL 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D PHE 3.0 23.5 + - - +
27D ALA 4.0 1.1 - - - +
28D HIS 2.8 0.6 - - - -
29D LYS* 1.3 79.7 - - - +
31D GLU* 1.3 63.3 + - - +
32D HIS 3.4 0.4 - - - -
33D GLU* 3.7 2.6 + - - +
34D SER* 3.3 21.8 + - - -
50D PHE* 4.8 5.3 - - + -
53D VAL* 3.4 24.9 - - + +
54D TYR* 4.5 13.7 - - + -
57D ASN* 3.5 27.6 - - + -
98D PHE* 5.0 0.2 - - + -
112F TYR* 3.0 39.0 - - + -
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Residues in contact with GLU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ALA 3.9 8.8 + - - +
28D HIS* 2.9 15.0 + - + +
30D VAL* 1.3 79.2 - - - +
32D HIS* 1.3 66.8 + - + +
34D SER* 3.2 6.6 + - - -
35D ARG* 3.0 60.2 + - + +
111F GLY* 3.6 3.6 - - - -
112F TYR* 2.9 37.6 + - - +
113F ILE* 3.8 21.6 - - + +
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Residues in contact with HIS 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D HIS* 3.2 31.9 + + - +
29D LYS* 3.9 34.2 + - + +
31D GLU* 1.3 80.9 - - + +
33D GLU* 1.3 67.1 + - - +
35D ARG* 4.1 4.2 - - + +
36D THR* 2.8 37.2 + - + +
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Residues in contact with GLU 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LYS 3.5 18.6 + - - +
30D VAL 3.7 4.1 + - - +
31D GLU 3.2 0.6 - - - -
32D HIS* 1.3 85.0 + - - +
34D SER* 1.3 61.5 + - - +
35D ARG 3.2 2.2 - - - -
36D THR* 3.8 14.5 + - - +
37D GLN* 3.4 18.5 + - - +
47D THR* 4.9 0.5 + - - +
49D ALA* 2.9 44.1 - - - +
50D PHE* 3.3 35.6 + - + +
53D VAL* 4.3 9.0 - - + -
102D LEU* 6.5 0.2 - - - -
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Residues in contact with SER 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D VAL* 3.3 17.8 + - - -
31D GLU* 3.2 15.8 + - - -
33D GLU* 1.3 75.7 - - - +
35D ARG* 1.3 68.0 + - - +
37D GLN* 4.1 1.8 - - - -
38D ASN 3.0 22.3 + - - +
41D SER 3.9 3.5 + - - -
42D PHE* 3.8 28.3 - - - +
43D GLN* 3.8 7.4 + - - +
50D PHE* 3.7 20.4 - - - -
112F TYR* 5.5 2.2 - - - -
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Residues in contact with ARG 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D GLU* 3.0 49.6 + - + +
32D HIS* 4.1 4.0 - - - +
34D SER* 1.3 95.8 + - - +
36D THR* 1.3 53.8 + - + +
37D GLN 2.9 4.9 - - - -
38D ASN* 2.7 26.7 + - - +
39D GLY* 3.3 20.4 - - - +
41D SER 2.5 31.7 + - - -
42D PHE* 6.0 0.2 - - - -
109F THR* 2.9 22.0 + - - +
110F PRO 3.6 2.0 + - - -
111F GLY* 3.6 18.6 - - - -
112F TYR 4.7 0.2 - - - +
113F ILE* 5.8 0.2 - - - +
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Residues in contact with THR 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D HIS* 2.8 28.3 + - + +
33D GLU* 3.8 19.4 + - - +
35D ARG* 1.3 77.2 - - + +
37D GLN* 1.3 56.9 + - - +
38D ASN* 3.1 12.3 + - - -
47D THR* 5.0 6.4 + - - +
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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