Contacts of the helix formed by residues 9 - 33 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASP* 1.3 72.6 - - - +
10B LYS* 1.3 55.1 + - - +
12B PHE* 3.0 2.6 + - + +
13B LEU* 2.6 55.6 + - + +
67B ILE* 3.9 8.3 - - + -
119B LEU* 4.1 10.9 - - - +
120B THR* 4.1 17.4 - - - +
123B GLU* 3.8 20.1 + - - +
125B ASP* 3.7 26.8 - - - +
128B THR* 3.9 12.1 - - + -
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Residues in contact with LYS 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASP* 3.2 15.8 + - - +
9B THR* 1.3 77.7 - - - +
11B GLU* 1.3 72.9 + - - +
14B ASN* 2.9 26.2 + - - +
64B LEU* 3.7 18.7 - - + +
67B ILE* 3.4 37.8 + - + -
68B GLY* 3.7 15.5 + - - -
69B GLY* 3.9 18.2 - - - +
155G LEU* 6.0 0.2 - - - +
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 3.2 29.9 - - + +
8B ASP* 2.6 34.9 + - - +
10B LYS* 1.3 81.5 - - - +
12B PHE* 1.3 63.5 + - - +
14B ASN* 4.0 5.5 - - - +
15B HIS* 3.0 23.7 + - - +
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Residues in contact with PHE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 5.4 1.7 - - + +
8B ASP 2.7 7.0 + - - +
9B THR* 3.5 7.0 - - + +
11B GLU* 1.3 77.9 - - - +
13B LEU* 1.3 82.1 + - + +
15B HIS* 3.1 17.4 + - - +
16B GLN* 3.1 45.7 + - + +
112B GLU* 3.1 29.8 - - + -
113B TYR* 3.9 11.2 - + - -
115B GLN* 4.6 4.7 - - + -
116B GLY* 3.5 27.6 - - - -
119B LEU* 3.6 23.3 - - + -
120B THR* 6.4 0.2 - - - -
132B LEU* 3.8 20.9 - - + -
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR* 2.6 37.3 + - + +
10B LYS 3.7 3.4 - - - +
12B PHE* 1.3 95.9 - - + +
14B ASN* 1.3 58.4 + - - +
16B GLN* 2.8 21.7 + - + +
17B VAL* 3.0 10.2 + - - -
60B VAL* 3.5 25.9 - - + +
63B ARG* 4.2 5.4 - - + -
64B LEU* 4.1 23.3 - - + +
67B ILE* 3.9 16.8 - - + -
128B THR* 3.8 25.4 - - + -
131B MET* 4.5 10.3 - - + -
132B LEU* 4.5 3.6 - - + -
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Residues in contact with ASN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS 2.9 16.9 + - - +
11B GLU* 4.0 5.4 - - - +
13B LEU* 1.3 76.3 - - - +
15B HIS* 1.3 64.5 + - - +
17B VAL* 2.9 19.3 + - - +
18B ALA 3.1 9.4 + - - -
64B LEU* 3.6 13.7 - - + +
70B SER 3.0 21.0 + - - -
71B PRO* 3.1 6.2 - - - +
72B PHE* 2.7 67.2 + - + +
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Residues in contact with HIS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU 3.0 19.6 + - - +
12B PHE* 3.1 9.2 + - - +
14B ASN* 1.3 78.8 - - - +
16B GLN* 1.3 66.7 + - - +
18B ALA* 3.2 5.7 + - - +
19B ASN* 2.9 29.9 + - - -
72B PHE* 4.2 6.5 - - - -
81B ASN* 2.9 32.4 + - + -
82B ALA 4.0 0.2 - - - -
83B SER* 2.9 38.5 + - - -
112B GLU* 3.1 20.8 + - - -
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Residues in contact with GLN 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.1 48.9 + - + +
13B LEU* 2.8 12.6 + - + +
15B HIS* 1.3 80.1 + - - +
17B VAL* 1.3 59.9 + - - +
19B ASN* 3.0 23.4 + - - +
20B LEU* 2.7 47.7 + - + +
60B VAL* 4.3 12.6 - - + -
109B LEU* 3.7 5.0 - - - +
112B GLU* 3.0 26.7 + - - +
113B TYR* 3.6 25.9 - - + +
132B LEU* 5.9 0.9 - - + -
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Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU 3.0 15.9 + - - +
14B ASN* 2.9 21.4 + - - +
16B GLN* 1.3 78.3 - - - +
18B ALA* 1.3 63.2 + - - +
20B LEU* 3.9 4.2 - - - +
21B ASN* 2.8 41.3 + - - +
57B MET* 4.4 6.1 - - - +
60B VAL* 3.7 18.1 - - + +
61B ALA* 4.0 20.2 - - + +
64B LEU* 4.8 1.8 - - + -
71B PRO* 4.6 3.4 - - + -
72B PHE* 3.9 22.0 - - + +
78B PHE* 3.9 4.9 - - + -
32D TRP* 4.4 12.6 - - + -
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASN 3.1 9.0 + - - +
15B HIS 3.5 8.5 - - - +
17B VAL* 1.3 78.3 - - - +
19B ASN* 1.3 62.1 + - - +
21B ASN* 3.4 2.9 + - - +
22B VAL* 3.3 24.8 + - - +
72B PHE* 4.1 4.7 - - + -
78B PHE* 3.6 40.2 - - - +
81B ASN* 3.9 13.0 - - + -
82B ALA* 3.7 14.4 - - - +
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Residues in contact with ASN 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B HIS* 2.9 16.9 + - - -
16B GLN* 3.0 30.6 + - - +
18B ALA* 1.3 76.4 - - - +
20B LEU* 1.3 60.9 + - - +
22B VAL* 3.0 4.5 + - - +
23B PHE* 2.8 29.6 + - - +
82B ALA* 3.4 3.8 - - - -
83B SER* 2.7 36.5 + - - -
84B VAL* 3.1 22.5 + - + +
109B LEU* 4.1 10.2 - - + +
112B GLU* 3.0 23.8 + - - -
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLN* 2.7 27.9 + - + +
19B ASN* 1.3 74.1 - - - +
21B ASN* 1.3 58.3 + - - +
23B PHE* 3.3 4.6 + - + +
24B THR* 2.9 32.5 + - - -
53B PHE* 4.2 28.9 - - + +
56B GLN* 4.0 4.0 - - + -
57B MET* 3.5 46.4 - - + +
60B VAL* 4.0 17.3 - - + -
109B LEU* 4.2 20.9 - - + -
113B TYR* 3.4 27.8 - - - +
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Residues in contact with ASN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 2.8 29.4 + - - +
18B ALA 3.8 2.9 - - - +
19B ASN 3.3 0.2 - - - -
20B LEU* 1.3 76.6 - - - +
22B VAL* 1.3 62.1 + - - +
24B THR* 3.2 25.0 - - - +
25B VAL* 3.4 13.7 - - - +
57B MET* 3.3 38.9 - - - +
78B PHE* 3.4 48.7 - - + -
25D VAL* 4.6 8.3 - - - +
28D HIS* 5.3 1.4 - - - -
50D TYR* 5.4 1.4 + - - -
75D LEU* 4.1 3.5 - - + +
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ALA 3.3 14.3 + - - +
19B ASN 3.0 7.5 + - - +
21B ASN* 1.3 79.4 - - - +
23B PHE* 1.3 63.6 + - - +
25B VAL* 3.3 4.3 + - - +
26B LYS* 3.0 20.6 + - - +
78B PHE 4.7 3.4 - - - +
79B LEU* 5.0 7.2 - - + -
82B ALA* 3.5 19.7 - - + -
84B VAL* 3.6 31.2 - - + +
85B GLU 4.5 0.4 - - - +
86B GLU* 3.9 30.9 - - + +
75D LEU* 4.2 24.5 - - + -
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Residues in contact with PHE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASN 2.8 16.6 + - - +
20B LEU* 3.6 7.6 - - + +
22B VAL* 1.3 75.3 - - - +
24B THR* 1.3 60.3 + - - +
26B LYS* 3.0 13.7 + - + +
27B ILE* 2.8 48.1 + - + +
49B LEU* 5.2 0.9 - - + -
53B PHE* 3.7 40.6 - + + -
84B VAL* 4.3 4.4 - - + +
102B LEU* 3.4 33.9 - - + -
105B THR* 3.3 33.4 - - + -
106B LEU* 3.7 19.7 - - + -
109B LEU* 3.6 21.8 - - + -
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Residues in contact with THR 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU 2.9 14.7 + - - +
21B ASN* 3.2 24.2 - - - +
22B VAL 3.2 0.2 - - - -
23B PHE* 1.3 77.9 - - - +
25B VAL* 1.3 71.5 + - + +
27B ILE* 3.1 21.7 + - - +
28B HIS 3.1 9.4 + - - -
50B TYR* 3.5 48.7 + - + +
53B PHE* 4.7 4.5 - - - +
54B GLY* 4.3 13.1 + - - -
57B MET* 6.0 4.0 - - + -
50D TYR* 5.9 3.1 - - - +
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Residues in contact with VAL 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASN 3.4 14.1 - - - +
22B VAL 3.3 7.3 + - - +
24B THR* 1.3 81.1 - - + +
26B LYS* 1.3 63.4 + - - +
28B HIS* 3.2 13.3 + - + +
29B GLN* 3.0 19.8 + - - +
32B TRP* 6.1 0.4 - - + -
50B TYR* 6.1 0.2 - - + -
86B GLU* 4.7 1.1 - - - +
21D ASN* 4.6 7.2 - - - +
73D SER* 3.6 30.0 - - - +
74D THR* 3.8 8.1 - - - +
75D LEU* 3.6 18.4 - - + -
78D PHE* 3.8 25.6 - - + -
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL 3.0 13.6 + - - +
23B PHE* 3.0 20.2 + - + +
25B VAL* 1.3 75.9 - - - +
27B ILE* 1.3 67.5 + - - +
29B GLN* 3.2 15.3 + - - +
30B ILE* 3.0 34.1 + - + +
84B VAL* 4.2 10.5 - - - -
85B GLU 2.8 29.7 + - - -
86B GLU* 4.0 12.6 - - + +
87B ALA 4.8 2.6 - - - +
101B ASP* 3.3 36.7 + - - +
102B LEU* 5.2 0.2 - - - -
105B THR* 3.5 25.4 - - - +
73D SER 5.4 1.3 - - - -
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Residues in contact with ILE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 2.8 58.5 + - + +
24B THR* 3.1 12.1 + - - +
26B LYS* 1.3 77.8 - - + +
28B HIS* 1.3 63.4 + - - +
30B ILE* 3.1 10.7 + - + +
31B HIS* 3.0 24.2 + - + +
46B MET* 3.5 39.6 - - + +
49B LEU* 4.0 33.7 - - + +
50B TYR* 3.9 11.7 - - + +
53B PHE* 4.5 2.9 - - + -
102B LEU* 4.8 4.3 - - + -
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Residues in contact with HIS 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR 3.1 8.0 + - - +
25B VAL* 3.4 13.5 - - + +
27B ILE* 1.3 73.4 - - - +
29B GLN* 1.3 66.2 + - - +
31B HIS* 3.2 13.0 + + - +
32B TRP* 2.9 48.5 + + + -
47B ASP* 4.8 5.8 - - - -
50B TYR* 2.9 52.1 + + + +
21D ASN* 5.4 1.6 - - - -
54D GLY 5.3 1.8 + - - -
57D MET* 3.6 29.5 - - + +
58D ASP* 3.7 27.6 + - + +
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Residues in contact with GLN 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL 3.0 13.5 + - - +
26B LYS* 3.4 19.0 - - - +
27B ILE 3.2 0.2 - - - -
28B HIS* 1.3 75.9 - - - +
30B ILE* 1.3 65.7 + - - +
32B TRP* 4.2 3.5 - - - -
33B TYR* 2.9 40.5 + - + +
87B ALA 3.1 28.1 + - - +
89B TYR* 3.9 22.5 + - + -
93B LYS* 5.9 1.8 - - - +
98B LEU* 5.2 5.2 - - + +
101B ASP* 4.7 11.5 + - - -
73D SER* 2.9 45.3 + - - +
74D THR* 4.3 0.5 - - - +
----------------------------------------------------------
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Residues in contact with ILE 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LYS* 3.0 27.0 + - + +
27B ILE* 3.1 9.6 + - - +
29B GLN* 1.3 83.2 - - + +
31B HIS* 1.3 57.1 + - - +
34B MET* 2.8 50.3 + - + +
46B MET* 4.0 7.6 - - - -
98B LEU* 3.8 47.3 - - + +
99B MET* 3.6 23.6 - - + -
101B ASP* 5.2 3.1 - - + +
102B LEU* 4.1 27.6 - - + +
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Residues in contact with HIS 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 3.0 18.1 + - + +
28B HIS* 3.2 16.2 - - - +
30B ILE* 1.3 79.3 - - - +
32B TRP* 1.3 85.5 + + - +
34B MET* 3.7 16.2 - - - +
39B PHE* 4.5 1.6 - - - -
43B HIS* 2.9 75.8 + + - -
46B MET* 3.9 12.2 - - + +
47B ASP* 3.2 24.2 + - - -
58D ASP* 3.7 3.4 - - - -
62D GLU* 3.1 2.6 + - - -
144F TRP* 4.7 0.2 - - - -
157L FE 2.3 28.6 - - - -
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Residues in contact with TRP 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 5.5 0.7 - - + -
28B HIS* 2.9 42.5 + + + +
29B GLN* 3.7 2.7 - - - +
31B HIS* 1.3 91.6 - + - +
33B TYR* 1.3 66.2 + + + +
34B MET 3.6 2.3 + - - +
17D VAL* 4.5 5.6 - - + -
21D ASN* 5.0 1.8 - - - -
57D MET* 3.7 28.9 - - + -
58D ASP* 2.6 28.3 + - - -
61D ALA* 3.4 26.8 - - + +
62D GLU* 3.8 17.1 + - + +
65D LEU* 3.5 33.7 - - + +
71D PRO* 3.9 16.4 - - + -
72D PHE 3.7 18.4 - - - -
73D SER* 4.1 16.8 - - - -
78D PHE* 5.0 3.6 - + - -
144F TRP* 3.9 12.1 + + - -
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Residues in contact with TYR 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLN* 2.9 29.5 + - + +
30B ILE* 4.6 1.8 - - - +
32B TRP* 1.3 81.2 - - + +
34B MET* 1.3 67.7 + - - +
35B ARG* 3.5 12.5 + - - +
89B TYR* 3.3 70.3 + + + +
98B LEU* 4.6 2.6 - - + +
65D LEU* 4.6 6.3 - - + -
70D SER* 3.2 21.1 - - - -
71D PRO* 2.4 56.4 + - + -
73D SER* 3.7 24.0 - - - -
----------------------------------------------------------
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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