Contacts of the helix formed by residues 9 - 38 (chain E) in PDB entry 2Q7R
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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LEU* 5.5 9.2 - - + -
1E MSE 6.0 7.2 - - - -
5E THR* 3.1 22.4 - - - +
6E VAL* 3.8 10.3 - - + +
7E GLY 2.5 9.3 + - - -
8E ASN* 1.3 83.7 - - + +
10E VAL* 1.3 68.1 + - - +
11E LEU 3.2 2.7 - - - -
12E LEU* 2.8 9.6 + - + +
13E ALA* 2.8 25.5 + - + -
72E TRP* 4.1 24.0 - - + -
76E LEU* 5.2 5.4 - - + -
80E GLN* 3.3 8.9 + - - +
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Residues in contact with VAL 10 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LEU* 6.4 0.7 - - + -
130D ILE* 3.9 11.9 - - + -
133D TYR* 3.9 22.7 - - + -
134D TYR* 3.3 24.0 - - + +
6E VAL* 2.9 39.7 + - + +
7E GLY* 3.1 7.9 + - - +
9E VAL* 1.3 75.9 - - - +
11E LEU* 1.3 60.9 + - + +
13E ALA* 2.8 9.9 + - + +
14E ILE* 2.7 59.5 + - + +
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Residues in contact with LEU 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D TYR* 4.3 8.5 - - - +
7E GLY 4.0 8.3 - - - +
10E VAL* 1.3 85.3 - - + +
12E LEU* 1.3 60.8 + - - +
14E ILE* 3.2 9.9 + - + +
15E VAL* 2.9 27.0 + - - +
80E GLN* 2.8 40.8 - - + +
81E VAL* 5.1 9.9 - - + +
84E ALA* 3.4 23.0 - - + +
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Residues in contact with LEU 12 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E VAL* 2.8 14.4 + - - +
11E LEU* 1.3 74.2 - - - +
13E ALA* 1.3 56.0 - - - +
15E VAL* 3.1 4.5 - - - +
16E THR* 2.3 36.6 + - - -
71E LEU* 3.6 43.1 - - + +
72E TRP* 3.3 37.5 - - + -
75E GLY* 3.8 10.8 - - - +
76E LEU* 3.8 19.7 - - + -
80E GLN* 3.1 28.0 - - + +
83E ALA* 4.4 0.2 - - + -
84E ALA* 4.1 15.9 - - - +
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Residues in contact with ALA 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D SER* 5.8 2.2 - - - -
77D LEU* 3.8 29.8 - - + -
130D ILE* 4.5 4.3 - - + -
9E VAL* 2.8 15.8 + - + +
10E VAL* 3.1 13.5 - - - +
12E LEU* 1.3 77.3 - - - +
14E ILE* 1.3 51.3 + - - +
16E THR* 3.1 2.7 + - - -
17E LEU* 2.8 47.7 + - + +
72E TRP* 3.6 12.9 - - + -
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Residues in contact with ILE 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ILE* 3.3 24.6 - - + +
134D TYR* 4.2 9.4 - - + +
10E VAL* 2.7 53.6 + - + +
11E LEU* 3.4 13.0 - - + +
13E ALA* 1.3 71.2 - - - +
15E VAL* 1.3 67.9 + - + +
17E LEU* 2.9 10.1 + - - +
18E ILE* 2.8 41.7 + - + +
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Residues in contact with VAL 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E LEU 2.9 15.9 + - - +
12E LEU* 3.1 19.7 - - - +
14E ILE* 1.3 76.9 - - + +
16E THR* 1.3 74.5 + - - +
18E ILE* 2.9 13.5 + - - +
19E SER* 2.9 21.9 + - - -
67E PHE* 5.3 2.2 - - + -
71E LEU* 3.8 19.3 - - + -
84E ALA* 3.8 13.2 - - + +
87E GLY* 3.7 5.4 - - - -
88E LEU* 3.6 30.5 - - + +
91E LEU* 3.4 22.6 - - + +
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Residues in contact with THR 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D ALA* 4.7 14.6 - - + -
73D SER* 6.2 2.2 - - - -
12E LEU 2.3 25.7 + - - -
13E ALA* 3.4 4.9 - - - -
15E VAL* 1.3 78.7 - - - +
17E LEU* 1.3 60.6 + - + +
19E SER* 2.6 21.3 + - - -
20E VAL* 2.9 13.9 + - - +
64E TYR* 3.4 8.6 + - - +
67E PHE* 6.5 0.4 - - - -
68E LEU* 4.1 23.3 - - + -
71E LEU* 3.7 6.1 - - - +
72E TRP* 3.2 27.4 + - + +
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Residues in contact with LEU 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D VAL* 4.7 3.6 - - + -
73D SER* 4.2 25.4 - - - +
77D LEU* 5.2 1.6 - - + -
123D PHE* 3.6 40.6 - - + +
126D SER* 3.6 28.3 - - - +
127D VAL* 4.8 4.7 - - + +
130D ILE* 5.9 3.8 - - + -
13E ALA* 2.8 37.8 + - + +
14E ILE* 3.3 11.0 - - - +
16E THR* 1.3 74.0 - - + +
18E ILE* 1.3 66.1 + - + +
20E VAL* 3.0 13.8 - - + +
21E VAL* 3.0 21.3 + - - +
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Residues in contact with ILE 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E ILE* 2.8 51.7 + - + +
15E VAL* 3.0 8.7 - - - +
17E LEU* 1.3 74.6 - - + +
19E SER* 1.3 60.3 + - - +
20E VAL 3.0 0.9 - - - -
21E VAL* 2.7 29.7 + - + +
22E GLN* 2.8 16.9 + - + +
88E LEU* 5.1 11.7 - - + -
91E LEU* 3.2 26.9 - - + -
92E PHE* 6.5 0.4 - - + -
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Residues in contact with SER 19 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E VAL 2.9 8.3 + - - -
16E THR* 2.6 29.1 + - - +
18E ILE* 1.3 78.4 - - - +
20E VAL* 1.3 50.8 - - - +
22E GLN* 3.3 10.0 - - - +
23E ASN* 2.7 41.1 + - - +
64E TYR* 2.7 31.2 + - - -
67E PHE* 4.3 4.1 - - - -
68E LEU* 4.8 0.2 - - - +
91E LEU* 3.5 24.7 - - - -
94E ARG* 4.0 2.0 - - - -
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Residues in contact with VAL 20 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D THR* 3.2 47.5 - - + +
69D ALA* 3.6 20.2 - - + -
70D VAL* 4.3 10.5 - - + -
123D PHE* 3.7 24.0 - - + -
505D 3CS 4.0 12.4 - - + +
16E THR 2.9 12.1 + - - +
17E LEU* 3.0 17.5 - - + +
18E ILE 2.9 0.6 + - - -
19E SER* 1.3 78.5 + - - +
21E VAL* 1.3 63.9 + - - +
23E ASN* 3.3 11.8 - - - +
24E GLY* 3.3 6.2 + - - -
64E TYR* 3.9 4.9 - - - +
----------------------------------------------------------
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Residues in contact with VAL 21 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D PHE* 3.5 27.6 - - + -
505D 3CS 3.3 52.3 - - + +
17E LEU 3.7 3.4 - - - +
18E ILE* 2.7 18.8 + - + +
20E VAL* 1.3 73.8 - - - +
22E GLN* 1.3 70.7 + - + +
24E GLY* 2.9 11.8 + - - -
25E PHE 3.2 8.3 + - - -
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Residues in contact with GLN 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E ILE* 2.8 15.2 + - + +
19E SER* 3.3 12.3 - - - +
21E VAL* 1.3 79.7 - - + +
23E ASN* 1.3 62.3 + - - +
25E PHE* 2.7 32.2 + - + +
26E PHE* 3.0 39.1 + - + -
91E LEU* 3.6 27.6 + - - +
94E ARG* 2.4 45.7 + - - +
95E GLN* 3.4 11.5 + - - +
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Residues in contact with ASN 23 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D PRO* 5.4 0.6 - - - +
66D THR* 3.2 22.2 + - + +
505D 3CS 3.1 28.0 - - + -
19E SER 2.7 23.3 + - - +
20E VAL 3.3 9.2 - - - +
22E GLN* 1.3 73.9 - - - +
24E GLY* 1.3 59.6 + - - +
26E PHE* 3.7 9.0 + - - +
27E ALA 3.3 8.8 + - - -
61E VAL* 5.9 3.2 - - - +
64E TYR* 3.1 38.5 - - - +
94E ARG* 2.5 34.8 + - - -
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Residues in contact with GLY 24 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D THR* 5.1 0.4 - - - +
505D 3CS 3.1 43.2 - - - -
20E VAL 3.3 6.3 + - - -
21E VAL 2.9 8.8 + - - -
23E ASN* 1.3 78.5 - - - +
25E PHE* 1.3 53.2 + - - +
27E ALA 3.1 3.3 + - - -
28E HIS* 2.7 35.2 + - - +
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Residues in contact with PHE 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505D 3CS 2.9 42.5 - + + -
21E VAL 3.2 1.1 + - - +
22E GLN* 2.7 19.1 + - + +
24E GLY* 1.3 70.2 - - - +
26E PHE* 1.3 70.2 + + - +
28E HIS* 2.7 26.1 + + - +
29E LYS* 2.8 55.2 + - + -
95E GLN* 3.5 29.8 - - - -
98E PHE* 4.7 7.0 - + - -
99E VAL* 5.7 3.4 - - + -
102E LEU* 6.4 0.9 - - + -
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Residues in contact with PHE 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E GLN* 3.1 43.1 - - + -
23E ASN* 3.7 9.9 - - - +
25E PHE* 1.3 83.0 - + - +
27E ALA* 1.3 58.8 + - - +
28E HIS 2.9 5.9 + - - -
29E LYS* 3.1 11.1 + - - +
30E VAL* 3.3 14.7 + - - +
57E ASN* 3.5 19.5 - - - +
60E CYS* 3.6 28.5 - - + -
94E ARG* 3.7 16.8 - - - -
95E GLN* 3.2 23.1 - - - -
98E PHE* 3.0 56.0 - + + -
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Residues in contact with ALA 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D TYR* 3.9 21.4 - - + +
113D ILE* 6.1 1.0 - - - -
505D 3CS 3.5 57.0 - - + +
23E ASN 3.3 1.0 + - - -
24E GLY* 3.1 7.2 + - - +
26E PHE* 1.3 78.9 - - - +
28E HIS* 1.3 60.1 + - - +
30E VAL* 3.8 5.0 - - - +
31E GLU* 3.6 14.6 + - - +
57E ASN* 3.6 6.3 - - - +
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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
----------------------------------------------------------
505D 3CS 3.9 34.7 + + - -
24E GLY 2.7 12.4 + - - +
25E PHE* 2.7 22.7 + + - +
27E ALA* 1.3 77.6 - - - +
29E LYS* 1.3 84.5 + - + +
30E VAL 2.8 5.7 + - - -
31E GLU* 2.7 32.1 + - + +
32E HIS* 3.2 28.8 + + - -
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Residues in contact with LYS 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E PHE* 2.8 40.5 + - + +
26E PHE 3.8 7.6 - - - +
28E HIS* 1.3 95.2 + - + +
30E VAL* 1.3 57.7 + - - +
32E HIS* 3.9 30.3 + - + +
33E GLU* 3.7 13.7 - - - +
53E VAL* 3.3 16.1 - - + +
98E PHE* 4.0 17.3 - - + -
102E LEU* 4.9 17.7 - - + -
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Residues in contact with VAL 30 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D TYR* 3.0 40.4 - - + -
26E PHE 3.3 6.2 + - - +
27E ALA 3.8 3.8 - - - +
28E HIS 2.8 0.8 + - - -
29E LYS* 1.3 78.6 - - - +
31E GLU* 1.3 63.8 + - - +
32E HIS 3.2 0.2 - - - -
33E GLU* 3.5 4.5 + - - +
34E SER* 3.4 19.9 + - - -
42E PHE* 5.9 1.3 - - + -
50E PHE* 4.4 9.2 - - + -
53E VAL* 3.0 26.2 - - + -
54E TYR* 3.8 19.7 - - + +
57E ASN* 3.7 30.1 - - + +
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Residues in contact with GLU 31 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D GLY 3.5 9.2 - - - +
112D TYR* 3.7 11.4 - - - +
113D ILE* 3.9 21.3 + - + +
27E ALA 3.6 8.0 + - - +
28E HIS* 2.7 24.0 + - + +
30E VAL* 1.3 75.0 - - - +
32E HIS* 1.3 62.0 + - + +
34E SER* 3.2 3.6 + - - +
35E ARG* 3.0 41.9 + - - +
42E PHE* 3.0 41.1 - - - -
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Residues in contact with HIS 32 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E HIS* 3.2 25.9 + + - +
29E LYS* 3.9 37.0 + - + +
30E VAL 3.2 0.2 - - - -
31E GLU* 1.3 79.2 - - + +
33E GLU* 1.3 65.4 + - - +
35E ARG* 3.1 23.5 + - + +
36E THR* 3.1 21.0 + - + +
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Residues in contact with GLU 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E LYS 3.7 15.7 - - - +
30E VAL 3.5 3.5 + - - +
31E GLU 3.3 0.4 - - - -
32E HIS* 1.3 81.7 + - - +
34E SER* 1.3 58.7 + - - +
35E ARG 3.0 5.4 - - - -
36E THR* 2.9 28.9 + - - +
37E GLN* 3.5 15.4 + - - -
47E THR* 5.8 0.4 - - - -
49E ALA* 3.2 32.7 - - - +
50E PHE* 3.4 30.6 - - + +
53E VAL* 3.7 22.0 - - + +
102E LEU* 5.0 3.7 - - - +
----------------------------------------------------------
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Residues in contact with SER 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E VAL* 3.4 9.8 + - - -
31E GLU 3.2 5.6 + - - -
33E GLU* 1.3 77.9 - - - +
35E ARG* 1.3 73.8 + - - +
37E GLN* 3.4 17.4 - - - +
38E ASN 4.0 1.7 + - - -
39E GLY 5.1 0.7 + - - -
40E ARG 5.5 0.2 + - - -
42E PHE* 2.8 49.2 - - - +
50E PHE* 3.4 28.0 - - - -
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Residues in contact with ARG 35 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D PRO* 4.8 6.9 - - - +
113D ILE* 5.7 0.8 - - - +
31E GLU* 3.0 41.6 + - - +
32E HIS* 3.2 17.9 - - + +
33E GLU 3.0 0.4 - - - -
34E SER* 1.3 87.2 + - - +
36E THR* 1.3 55.6 + - + +
37E GLN 2.8 14.6 + - - -
38E ASN* 2.9 20.8 + - - +
39E GLY 5.4 0.6 - - - +
40E ARG* 3.8 25.7 + - - +
41E SER 4.9 0.4 - - - +
42E PHE* 3.1 29.6 - - - -
----------------------------------------------------------
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Residues in contact with THR 36 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E HIS* 3.3 14.8 - - + +
33E GLU* 2.9 34.0 + - - +
35E ARG* 1.3 75.3 - - + +
37E GLN* 1.3 69.2 + - - +
38E ASN* 4.5 2.9 - - - +
47E THR* 4.8 4.2 - - - +
----------------------------------------------------------
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Residues in contact with GLN 37 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E GLU 3.5 9.5 + - - -
34E SER* 3.4 15.9 - - - +
35E ARG 2.8 0.8 + - - -
36E THR* 1.3 83.4 + - - +
38E ASN* 1.3 71.1 + - - +
39E GLY* 3.4 5.6 + - - +
43E GLN* 6.1 0.9 - - - +
45E THR 4.3 1.2 - - - +
46E GLY* 3.9 5.0 - - - -
47E THR* 3.5 35.8 + - - +
50E PHE* 3.1 28.5 - - + -
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Residues in contact with ASN 38 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E SER 4.0 2.0 + - - -
35E ARG* 2.9 17.7 + - - +
36E THR 4.5 3.1 - - - +
37E GLN* 1.3 83.5 - - - +
39E GLY* 1.3 59.0 + - - +
40E ARG* 3.5 3.1 - - - +
----------------------------------------------------------
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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