Contacts of the helix formed by residues 9 - 33 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ASP* 1.3 71.5 - - - +
10E LYS* 1.3 60.1 + - - +
12E PHE* 2.9 8.4 + - + +
13E LEU* 2.8 49.4 + - + +
67E ILE* 3.8 7.9 - - + -
119E LEU* 4.2 3.1 - - - +
120E THR* 4.0 20.7 + - - +
123E GLU* 2.9 29.3 + - - +
125E ASP* 3.8 23.4 + - - +
128E THR* 3.9 11.7 - - + -
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Residues in contact with LYS 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ASP* 3.1 14.1 + - - +
9E THR* 1.3 76.1 - - - +
11E GLU* 1.3 72.2 + - - +
14E ASN* 3.0 25.1 + - - +
64E LEU* 3.7 19.5 - - + +
67E ILE* 3.5 37.8 + - + -
68E GLY* 3.7 15.3 + - - -
69E GLY* 4.0 17.0 - - - +
155I LEU* 6.0 0.4 - - - +
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Residues in contact with GLU 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E VAL* 3.2 31.0 - - + -
8E ASP* 2.5 32.0 + - - +
10E LYS* 1.3 83.4 - - - +
12E PHE* 1.3 63.2 - - - +
14E ASN* 3.4 5.3 + - - +
15E HIS* 3.0 23.2 + - - +
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Residues in contact with PHE 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E VAL* 4.7 8.0 - - + +
8E ASP 2.7 13.9 + - - +
9E THR* 3.4 8.1 - - + +
11E GLU* 1.3 75.7 - - - +
13E LEU* 1.3 81.2 + - + +
15E HIS* 3.0 17.8 + - + +
16E GLN* 3.1 46.7 + - + +
112E GLU* 3.2 29.8 - - + -
113E TYR* 3.9 10.5 - + - -
115E GLN* 4.5 4.7 - - + -
116E GLY* 3.4 28.3 - - - -
119E LEU* 3.7 16.4 - - + -
120E THR* 6.5 0.2 - - - -
132E LEU* 3.9 23.1 - - + -
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Residues in contact with LEU 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E THR* 2.8 36.5 + - + +
10E LYS 3.9 3.1 - - - +
12E PHE* 1.3 95.2 - - + +
14E ASN* 1.3 62.5 + - - +
16E GLN* 3.0 12.1 + - + +
17E VAL* 3.0 10.7 + - - +
60E VAL* 3.4 29.9 - - + +
63E ARG* 4.3 5.6 - - + -
64E LEU* 4.2 24.0 - - + +
67E ILE* 3.9 17.7 - - + -
128E THR* 3.8 24.5 - - + -
131E MET* 4.4 11.0 - - + -
132E LEU* 4.5 3.8 - - + -
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Residues in contact with ASN 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E LYS 3.0 18.1 + - - +
11E GLU* 4.0 5.8 - - - +
13E LEU* 1.3 78.0 - - - +
15E HIS* 1.3 64.3 + - - +
17E VAL* 3.1 6.9 + - - +
18E ALA 3.1 17.2 + - - -
64E LEU* 3.6 13.1 - - + +
70E SER 3.1 21.2 + - - -
71E PRO* 3.1 7.6 - - - +
72E PHE* 2.6 71.8 + - + +
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Residues in contact with HIS 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E GLU 3.0 14.3 + - - +
12E PHE* 3.0 13.5 + - + +
14E ASN* 1.3 79.0 - - - +
16E GLN* 1.3 60.9 + - - +
18E ALA* 3.1 6.2 + - - +
19E ASN* 2.9 27.9 + - - -
72E PHE* 4.3 6.4 - - - -
81E ASN* 2.8 32.0 + - + -
83E SER* 2.9 39.6 + - - -
112E GLU* 3.1 19.8 + - - -
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Residues in contact with GLN 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E PHE* 3.1 41.0 + - + +
13E LEU* 3.0 8.6 + - + +
15E HIS* 1.3 81.3 + - - +
17E VAL* 1.3 56.4 + - - +
18E ALA 3.1 1.1 - - - -
19E ASN* 3.0 24.3 + - - +
20E LEU* 2.7 48.4 + - + +
60E VAL* 4.2 12.3 - - + -
109E LEU* 3.6 5.2 - - - +
112E GLU* 2.9 35.2 + - - +
113E TYR* 3.6 25.0 - - + -
132E LEU* 5.8 0.9 - - + -
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Residues in contact with VAL 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E LEU 3.0 15.5 + - - +
14E ASN* 3.1 20.1 + - - +
16E GLN* 1.3 72.9 - - - +
18E ALA* 1.3 63.3 + - - +
20E LEU* 4.0 4.7 - - - +
21E ASN* 2.9 42.4 + - - +
57E MET* 4.4 6.1 - - - +
60E VAL* 3.7 17.7 - - + +
61E ALA* 3.9 21.5 - - + +
64E LEU* 4.9 1.6 - - + -
71E PRO* 4.6 2.7 - - + -
72E PHE* 3.9 12.1 - - + +
78E PHE* 3.8 15.5 - - + -
32G TRP* 4.4 13.0 - - + -
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Residues in contact with ALA 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E ASN 3.1 9.2 + - - +
15E HIS 3.3 9.0 - - - +
16E GLN 3.1 0.6 - - - -
17E VAL* 1.3 80.4 - - - +
19E ASN* 1.3 64.8 + - - +
21E ASN* 3.2 2.9 + - - +
22E VAL* 3.2 22.7 + - - +
72E PHE* 4.2 4.3 - - + -
78E PHE* 3.7 35.2 - - - +
81E ASN* 3.9 15.0 - - + -
82E ALA* 3.7 13.5 - - - +
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Residues in contact with ASN 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E HIS* 2.9 16.5 + - - +
16E GLN* 3.0 23.9 + - - +
18E ALA* 1.3 77.5 - - - +
20E LEU* 1.3 58.9 + - - +
22E VAL* 3.0 5.2 + - - +
23E PHE* 2.8 29.1 + - - +
82E ALA* 3.4 4.2 - - - -
83E SER* 2.6 47.8 + - - -
84E VAL* 3.1 21.1 + - + +
108E LEU* 4.0 6.1 - - - +
109E LEU* 4.1 5.6 - - + +
112E GLU* 2.9 19.6 + - - -
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Residues in contact with LEU 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E GLN* 2.7 26.8 + - + +
17E VAL 4.8 0.2 - - - +
19E ASN* 1.3 71.6 - - - +
21E ASN* 1.3 57.6 + - - +
23E PHE* 3.6 5.0 - - + +
24E THR* 2.9 32.5 + - - -
53E PHE* 4.2 24.5 - - + +
56E GLN* 4.1 9.0 - - + +
57E MET* 3.5 46.4 - - + +
60E VAL* 4.1 16.4 - - + -
109E LEU* 4.2 20.2 - - + -
113E TYR* 3.4 27.1 - - - +
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Residues in contact with ASN 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E VAL* 2.9 27.7 + - - +
18E ALA 3.2 2.7 + - - +
20E LEU* 1.3 76.3 - - - +
22E VAL* 1.3 62.2 + - - +
24E THR* 3.3 23.9 - - - +
25E VAL* 3.4 12.5 - - - +
57E MET* 3.3 38.4 - - - +
78E PHE* 3.3 49.0 - - + -
25G VAL* 4.5 9.0 - - - +
28G HIS* 5.4 1.2 - - - -
50G TYR* 5.4 1.6 + - - -
75G LEU* 4.0 3.4 - - + +
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Residues in contact with VAL 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E ALA 3.2 5.3 + - - +
19E ASN 3.0 7.1 + - - +
21E ASN* 1.3 76.8 - - - +
23E PHE* 1.3 64.0 + - - +
25E VAL* 3.2 6.2 + - - +
26E LYS* 3.0 19.8 + - - +
78E PHE 4.4 4.5 - - - +
79E LEU* 5.0 6.3 - - + -
82E ALA* 3.3 29.8 - - + -
84E VAL* 3.6 30.5 - - + +
86E GLU* 3.8 33.2 - - + +
75G LEU* 4.1 22.7 - - + -
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Residues in contact with PHE 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ASN 2.8 16.0 + - - +
20E LEU* 3.6 7.9 - - + +
22E VAL* 1.3 76.2 - - - +
24E THR* 1.3 57.8 + - - +
26E LYS* 2.9 16.8 + - + +
27E ILE* 2.8 46.2 + - + +
49E LEU* 5.3 1.1 - - + -
53E PHE* 3.7 42.4 - + + -
84E VAL* 4.3 4.7 - - + +
102E LEU* 3.4 34.5 - - + -
105E THR* 3.3 31.4 - - + -
106E LEU* 3.8 15.7 - - + -
109E LEU* 3.6 23.3 - - + -
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Residues in contact with THR 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU 2.9 14.8 + - - +
21E ASN* 3.3 24.0 - - - +
22E VAL 3.2 0.2 - - - -
23E PHE* 1.3 78.5 - - - +
25E VAL* 1.3 70.5 + - + +
27E ILE* 3.3 10.4 + - - +
28E HIS 3.3 15.1 + - - -
50E TYR* 3.3 54.9 + - + +
53E PHE* 4.8 3.9 - - - +
54E GLY* 4.3 12.6 + - - -
57E MET* 6.1 3.4 - - + -
50G TYR* 5.8 3.4 - - - +
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Residues in contact with VAL 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ASN 3.4 13.7 - - - +
22E VAL 3.2 7.9 + - - +
24E THR* 1.3 82.5 - - + +
26E LYS* 1.3 66.5 + - - +
28E HIS* 3.1 11.9 + - + +
29E GLN* 3.0 20.3 + - - +
50E TYR* 5.1 0.9 - - - +
86E GLU* 4.8 0.9 - - - +
21G ASN* 4.5 7.9 - - - +
73G SER* 3.6 23.3 - - - +
74G THR* 3.9 7.6 - - - -
75G LEU* 3.5 17.7 - - + -
78G PHE* 3.6 32.8 - - + -
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Residues in contact with LYS 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E VAL* 3.0 12.7 + - + +
23E PHE* 2.9 21.9 + - + +
25E VAL* 1.3 78.3 - - - +
27E ILE* 1.3 61.5 + - - +
29E GLN* 3.1 25.3 + - - +
30E ILE* 3.1 24.0 + - + +
84E VAL* 4.2 10.3 - - - -
85E GLU 2.8 29.4 + - - -
86E GLU* 4.0 12.6 - - + +
87E ALA 4.9 2.0 - - - +
101E ASP* 3.2 38.9 + - - +
102E LEU* 5.2 0.2 - - - -
105E THR* 3.4 25.6 - - - +
73G SER 5.3 1.3 - - - -
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Residues in contact with ILE 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E PHE* 2.8 57.4 + - + +
24E THR* 3.5 11.7 - - - +
26E LYS* 1.3 76.6 - - - +
28E HIS* 1.3 62.1 + - - +
30E ILE* 3.3 11.1 + - + +
31E HIS* 3.1 23.3 + - + +
46E MET* 3.5 37.0 - - + +
49E LEU* 4.0 31.2 - - + +
50E TYR* 3.8 13.2 - - + +
53E PHE* 4.5 3.6 - - + -
102E LEU* 4.9 6.1 - - + -
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Residues in contact with HIS 28 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E THR 3.3 4.3 + - - +
25E VAL* 3.1 14.7 + - + +
27E ILE* 1.3 79.0 - - - +
29E GLN* 1.3 63.7 + - - +
31E HIS* 3.3 10.8 + - - +
32E TRP* 2.9 50.4 + + + -
47E ASP* 4.8 8.7 + - - -
50E TYR* 3.2 50.4 - + - +
21G ASN* 5.4 1.8 - - - -
54G GLY 5.3 1.2 + - - -
57G MET* 3.4 32.3 - - + +
58G ASP* 3.7 28.3 + - + +
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Residues in contact with GLN 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E VAL 3.0 11.3 + - - +
26E LYS* 3.1 20.2 + - - +
28E HIS* 1.3 77.3 - - - +
30E ILE* 1.3 60.0 + - - +
32E TRP* 3.4 2.6 + - - -
33E TYR* 3.0 39.6 + - + +
87E ALA 3.1 28.3 + - - +
89E TYR* 3.9 21.9 + - + -
93E LYS* 4.6 13.1 - - - +
98E LEU* 5.3 3.8 - - + +
101E ASP* 4.6 8.9 + - - -
73G SER* 3.0 46.8 + - - +
74G THR* 4.1 1.2 - - - +
----------------------------------------------------------
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Residues in contact with ILE 30 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E LYS* 3.1 25.8 + - + +
27E ILE* 3.6 8.5 - - + +
28E HIS 3.3 0.2 - - - -
29E GLN* 1.3 83.1 - - + +
31E HIS* 1.3 56.4 + - - +
34E MET* 2.7 57.9 + - + +
46E MET* 3.9 10.8 - - - -
98E LEU* 3.8 46.3 - - + +
99E MET* 3.6 17.3 - - + -
101E ASP* 5.2 3.6 - - + +
102E LEU* 3.9 28.3 - - + +
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Residues in contact with HIS 31 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A FE 2.5 26.1 - - - -
27E ILE* 3.1 17.7 - - + +
28E HIS* 3.4 12.1 - - - +
30E ILE* 1.3 77.5 - - - +
32E TRP* 1.3 82.2 + + - +
34E MET* 3.8 18.5 - - - +
39E PHE* 4.5 2.1 - - - -
43E HIS* 2.8 65.2 + + - -
46E MET* 3.5 15.9 - - + +
47E ASP* 3.0 30.6 + - - -
58G ASP* 3.8 2.1 + - - -
62G GLU* 3.2 3.0 + - - -
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Residues in contact with TRP 32 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E VAL* 5.6 0.4 - - + -
28E HIS* 2.9 44.4 + + + +
29E GLN 3.8 2.2 - - - +
31E HIS* 1.3 96.1 - + - +
33E TYR* 1.3 63.2 + + + +
34E MET 3.8 2.6 + - - +
17G VAL* 4.3 5.8 - - + -
21G ASN* 5.0 1.6 - - - -
57G MET* 3.6 29.6 - - - -
58G ASP* 2.6 26.9 + - - -
61G ALA* 3.5 24.1 - - + +
62G GLU* 3.9 17.4 + - + +
65G LEU* 3.5 32.8 - - + +
71G PRO* 3.8 21.1 - - + -
72G PHE 3.5 21.1 - - - -
73G SER* 4.0 15.9 - - - -
78G PHE* 4.8 4.3 - + - -
144L TRP* 4.0 11.3 + - - -
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Residues in contact with TYR 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E GLN* 3.0 29.7 + - + +
30E ILE* 4.5 1.3 - - - +
32E TRP* 1.3 82.1 - - + +
34E MET* 1.3 67.7 + - - +
35E ARG* 3.6 12.5 + - - +
89E TYR* 3.4 70.7 + + + +
98E LEU* 4.7 2.5 - - + -
65G LEU* 4.7 5.6 - - + -
70G SER* 3.2 21.1 - - - -
71G PRO* 2.4 55.6 + - + -
73G SER* 3.5 23.6 - - - -
----------------------------------------------------------
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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