Contacts of the helix formed by residues 9 - 33 (chain D) in PDB entry 1QGH
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 THR 9 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ASP* 1.3 72.2 - - - +
10D LYS* 1.3 67.3 + - - +
12D PHE* 2.9 2.8 + - + +
13D LEU* 2.8 45.5 + - + +
67D ILE* 3.9 7.4 - - + -
119D LEU* 3.4 8.2 - - - +
120D THR* 3.8 20.3 + - - +
123D GLU* 2.7 32.8 + - - +
125D ASP* 3.9 22.3 - - - +
128D THR* 4.0 11.0 - - + -
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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
----------------------------------------------------------
8D ASP* 3.2 13.4 + - - +
9D THR* 1.3 76.8 - - - +
11D GLU* 1.3 75.5 + - - +
13D LEU* 3.3 1.2 + - - +
14D ASN* 3.0 25.0 + - - +
64D LEU* 3.7 17.1 - - + +
67D ILE* 3.5 38.4 + - + -
68D GLY* 3.8 14.1 + - - -
69D GLY* 4.0 15.9 - - - -
155F LEU* 6.0 0.2 - - - +
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Residues in contact with GLU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 3.2 32.0 - - + +
8D ASP* 2.6 31.5 + - - +
10D LYS* 1.3 84.0 - - - +
12D PHE* 1.3 62.2 + - - +
14D ASN* 3.4 5.7 + - - +
15D HIS* 3.0 23.7 + - - +
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Residues in contact with PHE 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 5.0 4.7 - - + +
8D ASP 2.8 16.3 + - - +
9D THR* 2.9 4.9 + - + +
11D GLU* 1.3 75.5 - - - +
13D LEU* 1.3 84.3 + - + +
15D HIS* 3.0 18.2 + - - +
16D GLN* 3.1 46.7 + - + +
112D GLU* 3.1 30.7 - - + -
113D TYR* 3.9 11.2 - + - -
115D GLN* 4.6 4.3 - - + -
116D GLY* 3.4 28.0 - - - -
119D LEU* 3.6 15.5 - - + -
132D LEU* 3.8 20.6 - - + -
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D THR* 2.8 33.3 + - + +
10D LYS 3.7 2.9 - - - +
12D PHE* 1.3 101.6 - - + +
14D ASN* 1.3 55.4 + - - +
16D GLN* 2.6 27.9 + - + +
17D VAL* 2.9 9.5 + - - -
60D VAL* 3.6 24.3 - - + +
63D ARG* 4.3 9.0 - - + -
64D LEU* 4.2 21.3 - - + -
67D ILE* 3.9 18.6 - - + -
128D THR* 3.8 25.4 - - + -
131D MET* 4.4 9.0 - - + -
132D LEU* 4.4 4.9 - - + -
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Residues in contact with ASN 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 17.2 + - - +
11D GLU* 4.0 5.6 - - - +
13D LEU* 1.3 77.9 - - - +
15D HIS* 1.3 65.0 + - - +
17D VAL* 3.0 16.3 + - - +
18D ALA 3.1 9.4 + - - -
64D LEU* 3.6 13.5 - - + +
70D SER 3.0 21.8 + - - -
71D PRO* 3.2 5.5 - - - +
72D PHE* 2.8 72.2 + - + +
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Residues in contact with HIS 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D GLU 3.0 13.9 + - - +
12D PHE* 3.4 12.7 - - + +
13D LEU 3.0 0.2 - - - -
14D ASN* 1.3 81.3 - - - +
16D GLN* 1.3 65.6 + - - +
18D ALA* 3.4 4.1 + - - +
19D ASN* 3.0 29.2 + - - -
72D PHE* 4.4 6.3 - - - -
81D ASN* 2.8 33.0 + - + -
83D SER* 2.8 40.0 + - - -
112D GLU* 3.0 21.1 + - - -
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Residues in contact with GLN 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D PHE* 3.1 48.8 + - + +
13D LEU* 2.6 15.8 + - + +
15D HIS* 1.3 80.5 + - - +
17D VAL* 1.3 59.4 + - - +
19D ASN* 3.1 16.4 + - - +
20D LEU* 2.7 46.5 + - + +
60D VAL* 4.2 12.3 - - + -
109D LEU* 3.6 9.2 - - - +
112D GLU* 2.9 28.1 + - - +
113D TYR* 3.5 24.4 - - + +
132D LEU* 6.0 0.9 - - + -
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Residues in contact with VAL 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TRP* 4.5 6.1 - - + -
13D LEU 2.9 17.8 + - - +
14D ASN* 3.4 21.3 - - - +
16D GLN* 1.3 77.8 - - - +
18D ALA* 1.3 64.4 + - - +
20D LEU* 3.8 4.3 - - - +
21D ASN* 2.9 42.7 + - - +
57D MET* 4.5 12.1 - - - +
60D VAL* 3.8 17.5 - - + +
61D ALA* 4.0 20.4 - - + +
64D LEU* 4.9 1.6 - - + -
71D PRO* 4.6 3.1 - - + -
72D PHE* 3.8 12.6 - - + +
78D PHE* 3.8 15.5 - - + -
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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 ASN 3.1 10.5 + - - +
15D HIS 3.6 8.1 - - - +
17D VAL* 1.3 81.6 - - - +
19D ASN* 1.3 65.0 + - - +
21D ASN* 3.2 8.5 + - - +
22D VAL* 3.2 17.0 + - - +
72D PHE* 4.2 4.2 - - + -
78D PHE* 3.6 38.6 - - - +
81D ASN* 4.0 11.7 - - + -
82D ALA* 3.8 15.3 - - - +
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Residues in contact with ASN 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D HIS* 3.0 17.2 + - - -
16D GLN* 3.1 23.3 + - - +
18D ALA* 1.3 77.9 - - - +
20D LEU* 1.3 57.9 + - - +
22D VAL* 3.1 3.6 + - - +
23D PHE* 2.9 29.9 + - - +
82D ALA* 3.3 5.8 - - - -
83D SER* 2.5 38.4 + - - -
84D VAL* 3.0 24.0 + - + +
108D LEU* 4.1 4.9 - - - +
109D LEU* 4.1 5.6 - - + +
112D GLU* 2.9 29.9 + - - -
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Residues in contact with LEU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLN* 2.7 29.6 + - + +
17D VAL 4.9 0.2 - - - +
19D ASN* 1.3 72.3 - - - +
21D ASN* 1.3 64.6 + - - +
23D PHE* 3.2 4.6 + - + +
24D THR* 3.0 26.3 + - - -
53D PHE* 4.2 25.9 - - + +
56D GLN* 4.2 3.8 - - + -
57D MET* 3.5 42.2 - - + +
60D VAL* 4.2 14.8 - - + -
109D LEU* 4.2 27.6 - - + -
113D TYR* 3.4 26.7 - - - +
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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
----------------------------------------------------------
25B VAL* 4.6 8.3 - - - +
28B HIS* 5.4 1.2 - - - -
50B TYR* 5.4 1.4 + - - -
75B LEU* 4.2 3.2 - - + +
17D VAL* 2.9 29.9 + - - +
18D ALA 3.7 2.2 - - - +
20D LEU* 1.3 78.3 - - - +
22D VAL* 1.3 60.3 + - - +
24D THR* 3.1 24.9 - - - +
25D VAL* 3.3 13.5 - - - +
57D MET* 3.4 37.2 - - - +
78D PHE* 3.1 50.0 - - + -
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Residues in contact with VAL 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 4.0 25.6 - - + -
18D ALA 3.2 12.7 + - - +
19D ASN 3.1 7.7 + - - +
21D ASN* 1.3 73.5 - - - +
23D PHE* 1.3 66.6 + - - +
25D VAL* 3.3 3.8 + - - +
26D LYS* 3.0 20.5 + - - +
78D PHE 4.7 4.3 - - - +
79D LEU* 5.0 6.5 - - + -
82D ALA* 3.7 18.8 - - + -
84D VAL* 3.8 32.3 - - + +
85D GLU 4.7 0.2 - - - +
86D GLU* 3.9 31.2 - - + +
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Residues in contact with PHE 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ASN 2.9 16.8 + - - +
20D LEU* 3.2 8.0 + - + +
22D VAL* 1.3 78.6 - - - +
24D THR* 1.3 62.6 + - - +
26D LYS* 3.0 13.2 + - + +
27D ILE* 2.9 42.7 + - + +
49D LEU* 5.2 0.9 - - + -
53D PHE* 3.8 35.0 - + + -
84D VAL* 4.4 4.9 - - + +
102D LEU* 3.4 35.0 - - + -
105D THR* 3.4 31.2 - - + -
106D LEU* 3.7 22.0 - - + -
109D LEU* 3.5 24.2 - - + -
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Residues in contact with THR 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TYR* 5.8 3.1 - - - +
20D LEU 3.0 13.7 + - - +
21D ASN* 3.1 27.4 - - - +
22D VAL 3.2 0.2 - - - -
23D PHE* 1.3 77.6 - - - +
25D VAL* 1.3 72.0 + - + +
27D ILE* 3.1 15.4 + - - +
28D HIS 3.1 17.2 + - - -
50D TYR* 3.6 49.4 + - + +
53D PHE* 4.7 3.3 - - - -
54D GLY* 4.3 12.7 + - - -
57D MET* 6.0 4.3 - - + -
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Residues in contact with VAL 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASN* 4.6 7.0 - - - +
73B SER* 3.6 22.8 - - - +
74B THR* 3.8 7.4 - - - -
75B LEU* 3.6 21.3 - - + -
78B PHE* 3.5 33.7 - - + -
21D ASN 3.3 15.5 - - - +
22D VAL 3.3 3.3 + - - +
23D PHE 3.2 0.2 - - - -
24D THR* 1.3 79.7 - - + +
26D LYS* 1.3 69.6 + - - +
28D HIS* 3.1 13.8 + - + +
29D GLN* 2.9 19.8 + - - +
50D TYR* 6.1 0.2 - - + -
86D GLU* 4.8 1.1 - - - +
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Residues in contact with LYS 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B SER 5.2 1.6 - - - -
22D VAL* 3.0 11.8 + - + +
23D PHE* 3.0 20.5 + - + +
25D VAL* 1.3 80.6 - - - +
27D ILE* 1.3 61.0 + - - +
29D GLN* 2.9 25.9 + - - +
30D ILE* 3.0 26.9 + - + +
84D VAL* 4.3 10.1 - - - -
85D GLU 2.8 29.3 + - - -
86D GLU* 4.0 12.4 - - + +
87D ALA 4.7 3.0 - - - +
101D ASP* 3.2 38.9 + - - +
102D LEU* 5.1 0.7 - - - -
105D THR* 3.6 24.9 - - - +
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Residues in contact with ILE 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE* 2.9 56.5 + - + +
24D THR* 3.1 13.2 + - - +
26D LYS* 1.3 75.4 - - - +
28D HIS* 1.3 64.5 + - - +
30D ILE* 3.2 11.7 + - - +
31D HIS* 2.9 23.3 + - + +
46D MET* 3.3 41.2 - - + +
49D LEU* 3.9 30.1 - - + +
50D TYR* 3.9 13.7 - - + +
53D PHE* 4.4 3.6 - - + -
102D LEU* 4.8 5.8 - - + -
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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
----------------------------------------------------------
21B ASN* 5.3 1.6 - - - -
54B GLY 5.3 1.4 + - - -
57B MET* 3.6 29.2 - - + +
58B ASP* 3.8 27.8 + - + +
24D THR 3.1 7.5 + - - +
25D VAL* 3.5 13.5 - - + +
27D ILE* 1.3 80.5 - - - +
29D GLN* 1.3 63.2 + - - +
31D HIS* 3.2 13.3 + + - +
32D TRP* 2.9 49.7 + + + -
47D ASP* 4.8 4.7 + - - -
50D TYR* 3.0 52.9 + + + +
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Residues in contact with GLN 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B SER* 3.0 45.9 + - - +
74B THR* 4.1 0.7 - - - +
25D VAL 2.9 12.8 + - - +
26D LYS* 2.9 19.8 + - - +
28D HIS* 1.3 77.2 - - - +
30D ILE* 1.3 70.3 + - - +
32D TRP* 4.4 1.3 - - - -
33D TYR* 2.9 40.8 + - + +
87D ALA 3.1 28.2 + - - +
89D TYR* 3.9 22.0 + - + +
93D LYS* 5.6 4.2 - - - +
98D LEU* 5.3 5.8 - - + +
101D ASP* 4.7 12.3 + - - -
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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
----------------------------------------------------------
26D LYS* 3.0 27.3 + - + +
27D ILE* 3.2 10.7 + - - +
29D GLN* 1.3 81.4 - - + +
31D HIS* 1.3 58.0 + - - +
34D MET* 2.9 49.7 + - + +
46D MET* 4.0 7.2 - - - -
98D LEU* 3.9 45.3 - - + +
99D MET* 3.4 25.4 - - + -
101D ASP* 5.3 3.1 - - + +
102D LEU* 3.9 28.0 - - + +
----------------------------------------------------------
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Residues in contact with HIS 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASP* 3.6 6.7 - - - -
62B GLU* 3.1 2.0 + - - -
27D ILE* 2.9 18.8 + - + +
28D HIS* 3.3 13.7 - - - +
30D ILE* 1.3 78.2 - - - +
32D TRP* 1.3 82.3 + + - +
34D MET* 3.7 10.6 - - - +
39D PHE* 4.5 1.7 - - - -
43D HIS* 2.8 79.4 + + - -
46D MET* 3.8 18.5 - - + +
47D ASP* 3.3 22.7 + - - -
144G TRP* 4.7 0.2 - - - -
157J FE 2.3 29.0 - - - -
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Residues in contact with TRP 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 4.4 5.8 - - + -
21B ASN* 5.0 1.6 - - - -
57B MET* 3.6 29.6 - - + -
58B ASP* 2.6 27.8 + - - -
61B ALA* 3.5 24.0 - - + +
62B GLU* 3.9 16.8 - - + +
65B LEU* 3.4 32.4 - - + +
71B PRO* 3.8 18.8 - - + -
72B PHE 3.6 20.2 - - - -
73B SER* 4.2 15.0 - - - -
78B PHE* 4.9 4.5 - + - -
25D VAL 5.7 0.2 - - - -
28D HIS* 2.9 43.0 + + + +
29D GLN* 3.8 2.9 - - - +
31D HIS* 1.3 93.3 - + - +
33D TYR* 1.3 66.8 + + + +
34D MET 3.6 2.5 - - - +
144G TRP* 4.2 10.7 + - - -
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Residues in contact with TYR 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 4.7 4.5 - - + -
70B SER* 3.2 21.2 - - - -
71B PRO* 2.5 52.4 + - + -
73B SER* 3.5 23.3 - - - -
29D GLN* 2.9 29.6 + - + +
30D ILE* 4.5 1.1 - - - +
32D TRP* 1.3 83.0 - - + +
34D MET* 1.3 67.9 + - - +
35D ARG* 3.5 13.2 + - - +
89D TYR* 3.5 70.5 + + + +
93D LYS 5.6 0.5 - - - +
98D LEU* 4.6 3.4 - - + +
----------------------------------------------------------
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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