Contacts of the helix formed by residues 9 - 33 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ASP* 1.3 72.8 - - - +
10G LYS* 1.3 53.9 + - - +
12G PHE* 2.9 8.3 + - + +
13G LEU* 2.6 59.1 + - + +
67G ILE* 3.9 7.9 - - + -
119G LEU* 3.9 7.8 - - - +
120G THR* 4.1 15.3 + - - +
123G GLU* 2.8 30.1 + - - +
125G ASP* 3.7 24.5 + - - +
128G THR* 3.9 11.4 - - + -
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Residues in contact with LYS 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ASP* 3.3 13.3 + - - +
9G THR* 1.3 78.1 - - - +
11G GLU* 1.3 69.9 + - - +
13G LEU 3.2 0.2 + - - -
14G ASN* 2.8 32.1 + - - +
64G LEU* 3.6 19.5 - - + +
67G ILE* 3.5 37.4 + - + -
68G GLY* 3.8 14.9 + - - -
69G GLY* 4.0 16.2 - - - -
155L LEU* 6.1 0.4 - - - +
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Residues in contact with GLU 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G VAL* 3.0 32.9 - - + +
8G ASP* 2.7 34.2 + - - +
10G LYS* 1.3 79.6 - - - +
12G PHE* 1.3 64.1 - - - +
14G ASN* 4.0 6.1 + - - +
15G HIS* 3.0 24.1 + - - +
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Residues in contact with PHE 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G VAL* 4.4 10.7 - - + +
8G ASP 2.8 13.6 + - - +
9G THR* 3.4 7.4 - - + +
11G GLU* 1.3 75.4 - - - +
13G LEU* 1.3 83.0 + - + +
15G HIS* 3.0 17.9 + - + +
16G GLN* 3.1 43.6 + - + +
112G GLU* 3.1 29.4 - - + -
113G TYR* 3.9 12.8 - + - -
115G GLN* 4.7 4.3 - - + -
116G GLY* 3.4 28.3 - - - -
119G LEU* 3.8 15.7 - - + -
120G THR* 5.8 1.1 - - - -
132G LEU* 3.9 21.5 - - + -
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Residues in contact with LEU 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G THR* 2.6 38.4 + - + +
10G LYS 3.7 3.1 - - - +
12G PHE* 1.3 96.8 - - + +
14G ASN* 1.3 63.8 + - - +
16G GLN* 2.9 14.4 + - + -
17G VAL* 3.1 9.0 + - - -
60G VAL* 3.5 28.7 - - + +
63G ARG* 4.3 11.0 - - + -
64G LEU* 4.2 14.8 - - + -
67G ILE* 3.9 17.0 - - + -
128G THR* 3.7 27.6 - - + +
131G MET* 4.3 12.1 - - + -
132G LEU* 4.3 3.8 - - + -
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Residues in contact with ASN 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G LYS 2.8 20.9 + - - +
11G GLU* 4.0 6.3 + - - +
13G LEU* 1.3 72.9 - - - +
15G HIS* 1.3 64.5 + - - +
17G VAL* 2.9 16.1 + - - +
18G ALA 3.1 9.7 + - - -
64G LEU* 3.6 13.6 - - + +
70G SER 3.2 20.0 + - - -
71G PRO* 3.2 5.7 - - - +
72G PHE* 2.7 72.4 + - + +
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Residues in contact with HIS 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G GLU 3.0 13.7 + - - +
12G PHE* 3.0 14.3 + - + +
14G ASN* 1.3 76.4 - - - +
16G GLN* 1.3 67.6 + - - +
18G ALA* 3.2 6.2 + - - +
19G ASN* 2.9 27.2 + - - -
72G PHE* 4.3 6.2 - - - -
81G ASN* 2.8 31.4 + - + -
83G SER* 2.8 40.7 + - - -
112G GLU* 3.0 20.2 + - - -
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Residues in contact with GLN 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G PHE* 3.1 48.0 + - + +
13G LEU* 2.9 7.4 + - + +
15G HIS* 1.3 84.3 + - - +
17G VAL* 1.3 61.0 + - - +
19G ASN* 3.0 24.0 + - - +
20G LEU* 2.7 47.1 + - + +
60G VAL* 4.3 12.3 - - + -
109G LEU* 3.7 4.7 - - - +
112G GLU* 3.0 27.3 + - - +
113G TYR* 3.6 25.6 - - + +
132G LEU* 6.0 0.7 - - + -
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Residues in contact with VAL 17 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E TRP* 4.3 13.0 - - + -
13G LEU 3.1 16.2 + - - +
14G ASN* 2.9 22.8 + - - +
16G GLN* 1.3 80.3 - - - +
18G ALA* 1.3 62.3 + - - +
20G LEU* 3.9 3.6 - - - +
21G ASN* 2.9 34.3 + - - +
57G MET* 4.4 5.4 - - - +
60G VAL* 3.7 17.9 - - + -
61G ALA* 3.9 22.0 - - + +
64G LEU* 4.9 1.3 - - + -
71G PRO* 4.6 3.4 - - + -
72G PHE* 3.8 22.9 - - + +
78G PHE* 3.8 10.8 - - + -
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Residues in contact with ALA 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ASN 3.1 8.8 + - - +
15G HIS 3.4 8.7 - - - +
17G VAL* 1.3 79.9 - - - +
19G ASN* 1.3 63.7 + - - +
21G ASN* 3.3 3.3 + - - +
22G VAL* 3.2 22.5 + - - +
72G PHE* 4.3 3.8 - - + -
78G PHE* 3.6 38.5 - - - +
81G ASN* 3.9 13.2 - - + -
82G ALA* 3.7 13.9 - - - +
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Residues in contact with ASN 19 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G HIS* 2.9 15.6 + - - -
16G GLN* 3.0 24.4 + - - +
18G ALA* 1.3 75.6 - - - +
20G LEU* 1.3 60.3 + - - +
22G VAL* 3.1 4.2 + - - +
23G PHE* 2.8 29.7 + - - +
82G ALA* 3.4 5.1 - - - -
83G SER* 2.7 36.8 + - - -
84G VAL* 3.2 20.7 + - + +
108G LEU* 4.1 5.9 - - - +
109G LEU* 4.0 6.2 - - + +
112G GLU* 2.9 29.3 + - - -
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Residues in contact with LEU 20 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G GLN* 2.7 27.0 + - + +
19G ASN* 1.3 72.9 - - - +
21G ASN* 1.3 57.5 + - - +
23G PHE* 3.2 4.8 + - + +
24G THR* 2.9 33.0 + - - -
53G PHE* 4.2 23.8 - - + +
56G GLN* 4.1 5.2 - - + -
57G MET* 3.6 45.5 - - + +
60G VAL* 4.1 14.8 - - + -
109G LEU* 4.1 27.1 - - + -
113G TYR* 3.5 28.0 - - - +
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Residues in contact with ASN 21 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E VAL* 4.5 8.3 - - - +
28E HIS* 5.4 1.2 - - - -
50E TYR* 5.4 1.6 + - - -
75E LEU* 4.2 4.1 - - + +
17G VAL* 2.9 25.8 + - - +
18G ALA 3.7 5.4 - - - +
19G ASN 3.2 0.2 - - - -
20G LEU* 1.3 78.1 - - - +
22G VAL* 1.3 60.8 + - - +
24G THR* 3.3 24.1 - - - +
25G VAL* 3.3 13.9 - - - +
57G MET* 3.2 38.4 - - - +
78G PHE* 3.2 49.9 - - + -
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Residues in contact with VAL 22 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E LEU* 4.1 23.7 - - + +
18G ALA 3.2 13.9 + - - +
19G ASN 3.1 6.6 + - - +
21G ASN* 1.3 75.6 - - - +
23G PHE* 1.3 68.1 + - - +
25G VAL* 3.2 4.7 + - - +
26G LYS* 3.0 20.1 + - - +
78G PHE* 4.6 3.8 - - + +
79G LEU* 5.0 6.3 - - + -
82G ALA* 3.5 21.5 - - + -
84G VAL* 3.7 30.3 - - + +
85G GLU 4.5 0.2 - - - +
86G GLU* 3.9 31.5 - - + +
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Residues in contact with PHE 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ASN 2.8 16.5 + - - +
20G LEU* 3.2 8.3 + - + +
22G VAL* 1.3 79.5 - - - +
24G THR* 1.3 57.0 + - - +
26G LYS* 2.9 14.5 + - + +
27G ILE* 2.8 44.1 + - + +
49G LEU* 5.2 1.1 - - + -
53G PHE* 3.7 40.4 - + + -
84G VAL* 4.3 5.4 - - + +
102G LEU* 3.5 33.9 - - + -
105G THR* 3.5 29.6 - - + -
106G LEU* 3.8 17.5 - - + -
109G LEU* 3.5 22.7 - - + -
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Residues in contact with THR 24 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E TYR* 5.8 3.6 - - - +
20G LEU 2.9 15.8 + - - +
21G ASN* 3.3 23.6 - - - +
23G PHE* 1.3 80.1 - - - +
25G VAL* 1.3 71.3 + - + +
27G ILE* 3.2 9.2 + - - +
28G HIS 3.1 16.6 + - - -
50G TYR* 3.4 54.4 + - + +
53G PHE* 4.7 4.2 - - - +
54G GLY* 4.3 12.4 + - - -
57G MET* 6.1 3.6 - - + -
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Residues in contact with VAL 25 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ASN* 4.5 8.1 - - - +
73E SER* 3.7 21.3 - - - +
74E THR* 3.9 7.4 - - - +
75E LEU* 3.7 17.3 - - + -
78E PHE* 3.5 34.3 - - + -
21G ASN 3.3 14.4 - - - +
22G VAL 3.2 6.8 + - - +
24G THR* 1.3 80.8 - - + +
26G LYS* 1.3 65.8 + - - +
28G HIS* 3.1 12.7 + - + +
29G GLN* 3.0 21.3 + - - +
32G TRP* 6.0 0.4 - - + -
50G TYR* 5.2 0.7 - - + -
86G GLU* 4.8 0.7 - - - +
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Residues in contact with LYS 26 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E SER 5.3 1.1 - - - -
22G VAL* 3.0 11.8 + - + +
23G PHE* 2.9 20.0 + - + +
25G VAL* 1.3 79.5 - - - +
27G ILE* 1.3 61.9 + - - +
29G GLN* 3.1 25.4 + - - +
30G ILE* 3.1 25.3 + - + +
84G VAL* 4.3 9.4 - - - -
85G GLU 2.8 29.5 + - - -
86G GLU* 3.9 13.3 - - + +
87G ALA 4.8 2.8 - - - +
101G ASP* 3.3 39.2 + - - +
102G LEU* 5.2 0.2 - - - -
105G THR* 3.5 26.0 - - - +
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Residues in contact with ILE 27 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G PHE* 2.8 56.0 + - + +
24G THR* 3.2 13.4 + - - +
26G LYS* 1.3 76.4 - - - +
28G HIS* 1.3 65.4 + - - +
30G ILE* 3.3 9.1 + - + +
31G HIS* 3.0 23.3 + - + +
46G MET* 3.3 40.5 - - + +
49G LEU* 4.0 30.1 - - + +
50G TYR* 3.9 12.3 - - + +
53G PHE* 4.4 3.6 - - + -
102G LEU* 4.8 6.1 - - + -
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Residues in contact with HIS 28 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ASN* 5.4 1.3 - - - -
54E GLY 5.3 1.4 + - - -
57E MET* 3.5 30.1 - - + +
58E ASP* 3.7 27.7 + - + +
24G THR 3.1 6.5 + - - +
25G VAL* 3.1 16.4 + - + +
27G ILE* 1.3 79.7 - - - +
29G GLN* 1.3 56.5 + - - +
31G HIS* 3.1 12.7 + + - +
32G TRP* 2.9 55.7 + + + -
47G ASP* 4.8 5.8 + - - -
50G TYR* 3.1 52.8 + + + +
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Residues in contact with GLN 29 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E SER* 2.9 48.2 + - - +
74E THR* 4.1 0.7 - - - +
25G VAL 3.0 10.1 + - - +
26G LYS* 3.1 20.3 + - - +
28G HIS* 1.3 76.2 - - - +
30G ILE* 1.3 61.9 + - - +
32G TRP* 3.2 1.9 + - - -
33G TYR* 2.8 46.4 + - + +
87G ALA 3.0 28.2 + - - +
89G TYR* 3.9 17.9 + - + +
93G LYS* 4.3 18.6 - - - +
98G LEU* 5.3 3.9 - - + +
101G ASP* 4.7 8.3 + - - -
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Residues in contact with ILE 30 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G PHE* 6.3 0.2 - - + -
26G LYS* 3.1 25.8 + - + +
27G ILE* 3.5 8.5 - - - +
29G GLN* 1.3 81.3 - - + +
31G HIS* 1.3 60.2 + - - +
33G TYR* 4.6 0.4 - - - +
34G MET* 2.9 46.1 + - + +
46G MET* 3.8 9.6 - - - -
98G LEU* 3.7 46.7 - - + +
99G MET* 3.5 25.1 - - + -
101G ASP* 5.3 3.1 - - + +
102G LEU* 3.9 28.0 - - + +
----------------------------------------------------------
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Residues in contact with HIS 31 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B FE 2.4 28.1 - - - -
58E ASP* 3.7 5.4 - - - -
62E GLU* 3.1 2.6 + - - -
27G ILE* 3.0 16.6 + - + +
28G HIS* 3.2 11.4 - - - +
30G ILE* 1.3 81.8 - - - +
32G TRP* 1.3 81.1 + + - +
34G MET* 3.9 8.9 - - - +
39G PHE* 4.7 0.3 - - - -
43G HIS* 2.9 76.3 + + - -
46G MET* 3.7 18.5 - - + +
47G ASP* 3.2 25.2 + - - -
144I TRP* 4.6 1.4 - - - -
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Residues in contact with TRP 32 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E VAL* 4.4 4.5 - - + -
21E ASN* 5.0 2.0 - - - -
57E MET* 3.6 29.6 - - + -
58E ASP* 2.6 29.3 + - - -
61E ALA* 3.5 26.9 - - + +
62E GLU* 3.8 17.8 - - + +
65E LEU* 3.5 34.0 - - + +
71E PRO* 3.8 17.0 - - + -
72E PHE 3.5 20.9 - - - -
73E SER* 4.1 15.5 - - - -
78E PHE* 4.9 3.4 - + - -
25G VAL* 5.7 0.9 - - + -
28G HIS* 2.9 42.3 + + + +
29G GLN* 3.8 2.7 - - - +
31G HIS* 1.3 96.0 - + - +
33G TYR* 1.3 67.9 + - + +
34G MET 3.5 2.6 - - - +
43G HIS* 5.4 0.2 - + - -
144I TRP* 4.1 10.0 + - - -
----------------------------------------------------------
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Residues in contact with TYR 33 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E LEU* 4.7 6.3 - - + -
70E SER* 3.0 23.5 + - - -
71E PRO* 2.5 51.8 + - + -
73E SER* 3.5 23.6 - - - -
29G GLN* 2.8 31.6 + - + +
30G ILE* 5.2 1.1 - - - -
32G TRP* 1.3 82.2 - - + +
34G MET* 1.3 67.2 + - - +
35G ARG* 3.5 11.1 + - - +
89G TYR* 3.4 69.5 + + + -
93G LYS 5.4 0.7 - - - +
98G LEU* 4.6 1.8 - - + -
----------------------------------------------------------
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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