Contacts of the helix formed by residues 3 - 34 (chain E) in PDB entry 3BVI
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 SER 3 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E LEU* 1.3 76.2 - - - +
4E LYS* 1.3 60.8 + - - +
5E ASP* 3.9 6.1 + - - +
6E ILE* 3.3 25.3 + - - +
7E ILE* 2.9 27.2 + - - +
107E HIS* 5.2 0.2 + - - -
111E SER* 4.7 10.4 + - - -
113E ASP* 5.1 3.1 + - - +
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Residues in contact with LYS 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E LEU 4.0 0.2 + - - -
3E SER* 1.3 74.7 - - - +
5E ASP* 1.3 67.1 + - - +
7E ILE* 3.4 13.1 + - + +
8E LYS* 3.0 23.4 + - - +
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Residues in contact with ASP 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E SER* 3.3 5.6 + - - +
4E LYS* 1.3 79.3 - - - +
6E ILE* 1.3 57.5 + - - +
8E LYS* 3.2 9.3 + - - +
9E LEU* 3.0 33.9 + - + +
107E HIS* 3.1 38.6 + - + +
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Residues in contact with ILE 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E LEU* 4.1 9.6 - - + -
3E SER* 3.3 20.6 + - - +
5E ASP* 1.3 72.6 - - - +
7E ILE* 1.3 59.8 + - - +
9E LEU* 3.3 3.8 + - + +
10E LEU* 2.9 52.0 + - + +
104E ILE* 4.4 14.4 - - + +
107E HIS* 3.5 30.3 - - + -
108E ALA* 4.1 22.2 - - + +
111E SER* 4.3 7.2 - - - +
113E ASP* 3.8 25.4 - - + +
116E THR* 4.0 8.7 - - + +
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Residues in contact with ILE 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0E PRO* 3.7 26.2 - - + -
2E LEU* 3.3 26.0 - - + +
3E SER 2.9 18.9 + - - +
4E LYS* 3.6 12.3 - - + +
6E ILE* 1.3 75.4 - - - +
8E LYS* 1.3 59.5 + - - +
10E LEU* 4.0 4.7 - - - +
11E ASN* 3.0 41.9 + - - +
66E VAL* 3.6 36.3 - - + +
67E PRO* 4.9 3.8 - - + +
69E GLN* 4.8 11.2 - - - +
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Residues in contact with LYS 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E LYS 3.0 14.0 + - - +
5E ASP* 3.5 11.9 - - - +
7E ILE* 1.3 79.0 - - - +
9E LEU* 1.3 60.4 + - + +
11E ASN* 3.4 4.3 + - - +
12E GLU* 2.9 64.1 + - + +
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Residues in contact with LEU 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ASP* 3.0 19.5 + - + +
6E ILE* 3.9 5.6 - - + +
8E LYS* 1.3 81.4 - - + +
10E LEU* 1.3 57.5 + - - +
12E GLU* 3.4 19.0 + - + +
13E GLN* 2.9 27.0 + - - +
103E ASN* 3.6 21.5 - - - +
104E ILE* 4.0 35.8 - - + +
107E HIS* 3.8 38.6 - - + +
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Residues in contact with LEU 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E LEU* 3.7 11.7 - - + -
6E ILE* 2.9 38.1 + - + +
7E ILE 4.1 0.9 - - - +
9E LEU* 1.3 72.8 - - - +
11E ASN* 1.3 66.7 + - - +
13E GLN* 3.1 5.8 + - + +
14E VAL* 3.0 26.5 + - - +
57E LEU* 4.7 15.3 - - + +
60E PHE* 3.9 17.3 - - + -
61E LEU* 3.6 32.8 - - + -
104E ILE* 4.0 27.4 - - + -
116E THR* 4.4 4.9 - - + -
120E LEU* 4.4 17.3 - - + -
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Residues in contact with ASN 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E ILE* 3.0 34.4 + - + +
8E LYS* 3.8 4.9 - - - +
10E LEU* 1.3 77.2 - - - +
12E GLU* 1.3 62.9 + - + +
14E VAL* 3.2 7.1 + - - +
15E ASN* 3.2 20.4 + - - +
61E LEU* 4.2 8.0 - - - +
66E VAL* 4.2 3.8 - - - +
67E PRO 3.3 14.6 - - - +
68E VAL* 3.4 18.0 - - - +
69E GLN* 2.9 48.1 + - + +
70E LEU* 5.5 2.0 - - - +
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Residues in contact with GLU 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E LYS* 2.9 60.6 + - + +
9E LEU* 3.7 23.5 - - + +
10E LEU 3.3 0.2 - - - -
11E ASN* 1.3 75.7 - - + +
13E GLN* 1.3 57.4 + - - +
15E ASN* 3.2 9.4 + - - +
16E LYS* 2.9 45.3 + - - +
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Residues in contact with GLN 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E LEU 2.9 16.4 + - - +
10E LEU* 3.1 9.4 + - + +
12E GLU* 1.3 74.7 - - - +
14E VAL* 1.3 64.3 + - - +
16E LYS* 3.3 15.3 + - - +
17E GLU* 3.1 25.3 + - - +
57E LEU* 3.8 13.9 - - + -
97E ILE* 4.2 7.3 - - - +
100E SER* 3.2 33.4 + - - -
101E ILE* 3.7 8.6 - - - +
104E ILE* 3.5 27.9 - - + +
123E TYR* 2.9 33.1 + - + +
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Residues in contact with VAL 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E LEU 3.0 18.2 + - - +
11E ASN* 3.2 8.0 + - - +
13E GLN* 1.3 76.6 - - - +
15E ASN* 1.3 64.3 + - - +
17E GLU* 3.3 4.4 + - - +
18E MET* 3.1 30.9 + - + +
54E ALA* 4.2 5.8 - - + +
57E LEU* 3.8 28.7 - - + -
58E ILE* 3.8 33.0 - - + -
61E LEU* 4.0 14.4 - - + -
68E VAL* 5.1 2.5 - - + -
70E LEU* 3.9 23.8 - - + -
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Residues in contact with ASN 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ASN 3.2 9.8 + - - +
12E GLU* 3.2 11.2 + - - +
14E VAL* 1.3 80.8 - - - +
16E LYS* 1.3 58.7 + - + +
18E MET* 3.4 3.1 + - - +
19E ASN* 2.9 32.7 + - - +
70E LEU* 5.3 4.5 - - + +
71E THR* 3.2 25.6 + - - +
72E SER 3.0 27.5 + - - +
73E ILE* 3.6 19.8 - - - +
74E SER 5.3 1.0 + - - -
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Residues in contact with LYS 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E GLU* 2.9 30.1 + - + +
13E GLN* 3.3 29.1 + - - +
15E ASN* 1.3 77.6 - - + +
17E GLU* 1.3 57.5 + - - +
19E ASN* 3.4 8.0 + - - +
20E SER* 2.9 32.3 + - - -
93E HIS* 5.3 0.7 - - - -
96E HIS* 3.6 32.7 + - + -
97E ILE* 4.3 13.1 - - + +
100E SER* 3.9 18.6 - - - +
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Residues in contact with GLU 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E GLN* 3.1 19.5 + - - +
14E VAL 3.3 4.0 + - - +
16E LYS* 1.3 73.7 - - - +
18E MET* 1.3 60.8 + - - +
20E SER* 3.3 6.0 + - - -
21E SER* 3.0 27.0 + - - -
50E GLU* 3.4 41.5 - - - +
53E HIS* 3.8 15.3 - - + -
54E ALA* 3.8 12.8 - - + +
57E LEU* 4.3 5.2 - - + -
97E ILE* 3.8 8.9 - - - +
123E TYR* 2.5 30.2 + - - +
1006E FE 2.4 29.5 - - - -
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Residues in contact with MET 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASN* 3.5 27.6 - - - +
25B MET* 4.8 4.3 - - + -
14E VAL* 3.1 29.0 + - + +
15E ASN 3.8 3.6 - - - +
17E GLU* 1.3 72.8 - - - +
19E ASN* 1.3 65.9 + - - +
21E SER* 3.5 1.6 + - - -
22E ASN* 3.3 20.6 + - - -
51E TYR* 4.5 14.6 - - + +
54E ALA* 4.0 11.9 - - + -
58E ILE* 3.9 27.4 - - + -
70E LEU* 4.2 13.2 - - + -
73E ILE* 3.8 27.4 - - + +
1009E GOL 3.4 31.7 + - - -
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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 ASN* 2.9 23.6 + - - +
16E LYS* 3.6 7.4 - - - +
18E MET* 1.3 76.8 - - - +
20E SER* 1.3 61.3 + - - +
22E ASN* 3.4 2.8 + - - +
23E LEU* 3.1 25.1 + - - +
73E ILE* 3.7 10.9 - - + +
74E SER* 3.0 43.2 + - - +
75E ALA 5.0 2.0 + - - -
76E PRO* 5.2 4.1 - - - +
93E HIS* 4.6 13.2 - - - -
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Residues in contact with SER 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LYS 2.9 17.8 + - - -
17E GLU* 3.5 11.5 + - - -
18E MET 3.3 0.2 - - - -
19E ASN* 1.3 71.6 - - - +
21E SER* 1.3 67.8 + - - +
23E LEU* 3.3 3.8 + - - +
24E TYR* 3.0 31.6 + - - -
50E GLU* 3.7 24.5 + - - -
93E HIS* 2.7 34.2 + - - -
97E ILE* 3.8 9.5 - - - +
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Residues in contact with SER 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 2.7 29.0 + - - -
17E GLU 3.0 17.1 + - - -
18E MET 3.7 5.8 - - - -
19E ASN 3.3 0.2 - - - -
20E SER* 1.3 77.0 - - - +
22E ASN* 1.3 58.5 + - - +
25E MET* 2.9 29.6 + - - +
47E ALA* 3.0 28.9 + - - +
50E GLU* 4.0 2.6 - - - +
51E TYR* 3.9 10.7 - - - +
1009E GOL 3.9 9.1 + - - -
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Residues in contact with ASN 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B MET* 3.6 19.7 - - - +
70B LEU* 3.4 26.9 - - + +
71B THR 4.8 4.9 + - - -
73B ILE* 3.8 27.7 - - - +
18E MET 3.3 8.2 + - - +
19E ASN* 3.9 4.7 - - - +
20E SER 3.3 0.2 - - - -
21E SER* 1.3 75.3 + - - +
23E LEU* 1.3 60.8 + - - +
25E MET* 3.3 1.4 + - - +
26E SER 3.0 23.2 + - - -
73E ILE* 3.8 13.5 - - + +
74E SER 5.1 2.7 + - - +
76E PRO* 3.5 18.0 - - + +
1009E GOL 2.6 27.4 + - - -
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Residues in contact with LEU 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ASN* 3.1 17.8 + - - +
20E SER* 3.3 8.5 + - - +
22E ASN* 1.3 74.6 - - - +
24E TYR* 1.3 60.2 + - + +
26E SER* 3.2 2.8 + - - -
27E MET* 2.9 60.8 + - + +
76E PRO* 3.5 21.4 - - + +
77E GLU* 4.4 17.3 - - + +
80E PHE* 4.5 4.7 - - + -
89E LYS 5.7 0.2 - - - +
93E HIS* 3.9 40.4 - - + +
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Residues in contact with TYR 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E SER* 3.0 28.6 + - - +
23E LEU* 1.3 78.1 - - + +
25E MET* 1.3 56.5 + - - +
27E MET* 3.7 16.6 - - - +
28E SER* 2.8 31.7 + - - -
43E LEU* 3.6 22.3 - - + +
46E HIS* 3.5 21.1 - + - -
47E ALA* 3.6 21.5 - - + -
50E GLU* 3.9 11.9 - - + -
90E ALA* 3.5 28.2 + - + +
93E HIS* 3.4 24.8 - + - -
94E GLU* 2.4 42.5 + - - +
134E PHE* 3.9 10.3 - + - -
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Residues in contact with MET 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B MET* 5.0 1.8 - - + -
51B TYR* 3.7 22.9 - - + +
55B LYS* 3.9 17.9 - - + -
58B ILE* 3.9 29.3 - - + +
62B ASN* 5.9 0.2 + - - -
68B VAL* 5.3 3.5 - - + +
70B LEU* 3.6 16.6 - - + -
21E SER* 2.9 23.3 + - - +
22E ASN* 3.5 11.9 - - - +
24E TYR* 1.3 76.4 - - - +
26E SER* 1.3 57.0 + - - +
28E SER* 3.5 4.1 - - - -
29E SER* 3.0 28.2 + - - -
44E PHE* 3.6 42.6 - - + +
47E ALA* 3.8 13.6 - - + +
48E ALA 5.2 0.4 - - - +
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Residues in contact with SER 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B VAL* 5.3 7.8 + - - -
70B LEU* 4.4 7.2 - - - +
22E ASN 3.0 16.4 + - - -
23E LEU 3.6 3.8 - - - -
25E MET* 1.3 73.2 - - - +
27E MET* 1.3 60.4 + - - +
29E SER* 3.5 6.6 + - - -
30E TRP* 3.1 26.3 + - - +
76E PRO* 3.8 12.9 - - - +
77E GLU 2.8 27.5 + - - -
78E HIS* 3.5 16.1 - - - +
80E PHE* 4.2 2.3 - - - -
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Residues in contact with MET 27 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E LEU* 2.9 39.9 + - + +
24E TYR* 3.7 30.5 - - - +
26E SER* 1.3 74.8 - - - +
28E SER* 1.3 64.1 + - - +
30E TRP* 3.3 5.6 + - - +
31E CYS* 3.1 26.2 + - - -
43E LEU* 3.8 14.6 - - + -
80E PHE* 3.7 29.4 - - + -
86E ILE* 3.6 36.5 - - + +
89E LYS* 4.0 13.0 - - + -
90E ALA* 3.9 16.4 - - - +
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Residues in contact with SER 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASN* 4.2 3.0 + - - -
24E TYR 2.8 21.5 + - - -
25E MET* 3.5 7.9 - - - -
27E MET* 1.3 72.9 - - - +
29E SER* 1.3 57.6 + - - +
31E CYS* 3.2 4.2 + - - +
32E TYR* 2.9 41.3 + - - -
40E GLY* 2.5 28.2 + - - -
43E LEU* 3.7 11.3 - - - +
44E PHE* 3.5 21.7 - - - +
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Residues in contact with SER 29 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 6.2 0.2 - - - -
62B ASN* 3.9 13.1 + - - -
66B VAL 4.2 1.0 + - - -
67B PRO* 3.6 8.8 - - - +
68B VAL* 3.0 47.2 + - - +
25E MET 3.0 18.4 + - - -
26E SER* 3.7 7.6 - - - -
27E MET 3.3 0.4 - - - -
28E SER* 1.3 72.8 - - - +
30E TRP* 1.3 65.1 + - - +
32E TYR* 3.3 1.5 + - - +
33E THR* 2.9 27.1 + - - +
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Residues in contact with TRP 30 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E SER 3.1 14.4 + - - +
27E MET 3.3 9.6 + - - +
29E SER* 1.3 75.5 + - - +
31E CYS* 1.3 66.4 + - - +
33E THR* 3.0 7.9 + - - -
34E HIS* 2.7 73.2 + + + -
36E LEU* 4.0 17.3 - - + -
78E HIS 3.7 20.9 - - - +
79E LYS* 5.0 0.6 - - - +
80E PHE* 3.3 45.8 + + + +
81E GLU 4.1 4.0 - - - -
82E GLY* 3.5 26.7 - - - -
86E ILE* 3.4 22.0 - - + -
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Residues in contact with CYS 31 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E MET 3.1 17.9 + - - +
28E SER 3.2 7.4 + - - +
30E TRP* 1.3 84.3 - - - +
32E TYR* 1.3 60.7 + - - +
34E HIS 3.1 7.1 + - - -
36E LEU* 2.8 50.8 + - + +
39E ALA* 3.8 19.1 - - - -
40E GLY* 3.6 7.9 - - - +
43E LEU* 3.9 10.3 - - - -
83E LEU* 4.2 11.0 - - - -
86E ILE* 3.9 20.2 - - - -
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Residues in contact with TYR 32 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASN* 3.3 58.1 - - + +
63B GLU* 5.7 0.7 - - - -
65B ASN* 3.6 17.0 + - - +
28E SER* 2.9 28.9 + - - +
29E SER 3.7 4.5 - - - +
31E CYS* 1.3 76.5 - - - +
33E THR* 1.3 62.5 + - + +
34E HIS 3.5 0.5 + - - -
35E SER* 3.8 7.4 + - - -
36E LEU 4.1 2.4 + - - -
37E ASP* 4.0 30.2 - - + +
40E GLY* 3.2 20.4 - - - -
41E LEU* 3.3 32.7 + - - +
44E PHE* 4.6 5.7 - + + +
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Residues in contact with THR 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASN* 5.8 1.1 - - - +
65B ASN* 4.0 22.8 + - - +
66B VAL 4.0 7.0 - - - +
67B PRO* 3.8 40.2 - - + +
1002B GLN 5.0 1.2 - - - +
1003B SER* 3.3 19.7 - - - -
29E SER* 2.9 17.5 + - - +
30E TRP* 3.0 16.6 + - - -
31E CYS 3.2 0.2 - - - -
32E TYR* 1.3 79.5 - - + +
34E HIS* 1.3 73.3 + - - +
35E SER 3.5 1.8 - - - -
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Residues in contact with HIS 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003B SER* 3.4 8.5 + - - +
1005B HIS* 3.4 20.0 - - + -
30E TRP* 2.7 84.6 + + + +
31E CYS* 3.1 2.4 + - - +
33E THR* 1.3 98.7 + - - +
35E SER* 1.3 69.5 + - - +
36E LEU* 3.2 11.7 + - + +
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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