Contacts of the helix formed by residues 25 - 61 (chain E) in PDB entry 3H1J
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 25 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ARG* 4.0 11.4 - - - +
236A PHE* 3.0 32.0 + - - +
258A GLU* 5.1 0.4 + - - -
17E ASP 5.2 1.8 - - - -
18E VAL* 3.8 24.0 - - - +
23E THR 2.9 7.4 + - - -
24E SER* 1.3 71.4 + - - +
26E GLN* 1.3 75.7 + - - +
28E SER* 3.0 22.0 + - - -
32E ARG* 3.1 18.6 + - - -
22G GLU* 4.2 7.6 + - - -
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Residues in contact with GLN 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A PHE* 4.1 14.1 - - - -
258A GLU* 3.2 47.2 + - + +
418A LYS* 3.1 33.5 + - - +
24E SER* 3.0 13.2 - - - +
25E SER* 1.3 82.3 + - - +
27E THR* 1.3 64.1 + - + +
29E SER* 2.7 32.1 + - - -
30E GLU* 4.2 2.6 + - - +
32E ARG* 6.0 0.2 - - - -
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Residues in contact with THR 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E THR* 5.0 7.2 - - + +
24E SER* 3.3 25.5 + - - +
26E GLN* 1.3 77.2 - - + +
28E SER* 1.3 62.4 + - - +
29E SER 3.7 0.2 + - - -
30E GLU* 4.5 4.0 + - - +
31E ASP* 3.7 9.5 - - - +
7J ARG* 4.5 12.3 + - - -
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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
----------------------------------------------------------
17E ASP* 3.4 36.4 + - - -
18E VAL* 3.3 11.8 - - - +
25E SER 3.0 9.4 + - - -
27E THR* 1.3 80.8 + - - +
29E SER* 1.3 64.4 + - - +
30E GLU 3.4 1.6 - - - -
31E ASP* 3.1 13.1 + - - +
32E ARG* 3.0 39.0 + - - +
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Residues in contact with SER 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LYS* 4.4 4.9 + - - -
25E SER 3.3 3.8 + - - -
26E GLN* 2.7 35.3 + - - -
28E SER* 1.3 76.6 - - - +
30E GLU* 1.3 71.7 + - - +
31E ASP 3.0 0.3 + - - -
32E ARG* 3.1 27.5 + - - +
33E LYS* 2.8 54.2 + - - +
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Residues in contact with GLU 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E GLN 4.9 3.4 - - - +
27E THR 4.9 2.5 - - - +
28E SER 3.4 0.6 - - - -
29E SER* 1.3 88.2 + - - +
31E ASP* 1.3 58.2 + - - +
33E LYS* 4.6 1.1 - - - +
34E GLY* 2.8 23.8 + - - -
6J LEU 3.5 2.1 - - - +
7J ARG* 3.4 58.6 + - + +
10J TYR* 3.3 38.8 - - + +
11J SER* 4.0 11.6 + - - -
15J ARG* 5.7 0.9 - - - -
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Residues in contact with ASP 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E ASP* 5.4 6.5 - - - +
27E THR 3.7 9.0 - - - +
28E SER* 3.5 15.0 - - - +
29E SER 3.0 0.4 - - - -
30E GLU* 1.3 75.6 - - - +
32E ARG* 1.3 60.4 + - + +
33E LYS 3.1 1.3 - - - -
35E PHE* 2.6 37.5 + - - +
4J ALA* 4.4 5.7 - - - +
6J LEU* 3.6 31.0 - - + +
7J ARG* 3.2 34.5 + - - +
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Residues in contact with ARG 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A CYS* 5.2 2.0 - - - -
15E ARG* 3.2 47.5 + - + +
17E ASP* 4.9 6.5 - - + +
18E VAL* 3.3 16.0 - - - +
25E SER* 3.1 29.1 + - - -
26E GLN* 6.0 0.2 - - - -
28E SER* 3.0 31.1 + - - +
29E SER* 3.2 28.0 - - - +
31E ASP* 1.3 77.5 - - + +
33E LYS* 1.3 63.4 + - - +
35E PHE* 4.9 0.2 - - - -
36E SER* 3.4 17.5 + - - -
21G PHE* 2.8 49.8 + - + +
22G GLU* 2.8 30.3 + - - -
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Residues in contact with LYS 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A TYR 5.2 0.2 + - - -
417A ASP* 2.8 32.1 + - - +
418A LYS* 4.0 21.2 - - - +
419A CYS* 4.9 5.7 - - - +
438A ARG* 3.7 12.8 - - - +
29E SER* 2.8 39.6 + - - +
30E GLU 4.4 0.4 - - - +
32E ARG* 1.3 77.2 - - + +
34E GLY* 1.3 65.0 + - - +
36E SER* 3.4 0.5 + - - -
37E TYR* 3.0 31.6 + - + -
21G PHE* 3.7 33.9 - - + -
10J TYR* 3.4 34.5 + - + +
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Residues in contact with GLY 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E GLU 2.8 23.0 + - - -
31E ASP 3.5 0.4 - - - -
33E LYS* 1.3 77.3 - - - +
35E PHE* 1.3 61.9 + - - +
38E LEU* 3.1 23.2 + - - +
6J LEU* 3.7 12.7 - - - +
10J TYR* 3.5 20.3 - - - -
14J PHE* 3.4 11.4 - - - -
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Residues in contact with PHE 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D TYR* 3.9 33.0 - + - -
15E ARG* 4.7 7.4 - - - +
31E ASP 2.6 20.2 + - - +
32E ARG* 4.0 4.3 - - - +
34E GLY* 1.3 72.8 - - - +
36E SER* 1.3 65.0 + - - +
38E LEU* 3.0 29.0 + - + +
39E VAL* 3.2 20.7 + - + +
6J LEU* 3.8 27.9 - - + +
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Residues in contact with SER 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D TYR* 2.6 37.2 + - - -
225D HIS* 3.3 11.1 - - - -
15E ARG* 3.1 19.1 + - - -
32E ARG 3.4 4.5 + - - -
33E LYS 4.1 0.2 - - - -
35E PHE* 1.3 78.2 - - - +
37E TYR* 1.3 64.2 + - - +
39E VAL* 3.2 13.2 + - - +
40E THR* 3.2 15.7 + - - -
21G PHE* 3.7 24.7 - - - -
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Residues in contact with TYR 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ASP* 2.9 41.4 + - - -
438A ARG* 3.7 4.7 + - - -
442A TYR* 4.4 6.8 - - - -
33E LYS* 3.0 29.5 + - + +
36E SER* 1.3 78.5 - - - +
38E LEU* 1.3 57.0 + - - +
40E THR* 3.4 6.6 - - - -
41E ALA* 2.8 30.0 + - - +
2005E PEE 3.2 51.7 + - - -
21G PHE* 3.5 25.5 - + - -
10J TYR* 3.7 17.5 - + - -
14J PHE* 3.6 28.9 - - + -
20J PHE* 3.8 5.7 - + + -
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Residues in contact with LEU 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E GLY 3.1 14.8 + - - +
35E PHE* 3.0 22.9 + - + +
37E TYR* 1.3 74.1 - - - +
39E VAL* 1.3 56.3 + - + +
41E ALA* 3.1 4.4 + - + +
42E THR* 2.8 48.6 + - - +
6J LEU* 4.6 15.7 - - + -
9J ALA* 5.8 1.8 - - + -
14J PHE* 3.5 26.7 - - + -
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Residues in contact with VAL 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D LEU* 3.5 42.1 - - + +
221D TYR* 3.4 43.7 - - + -
222D MET* 4.1 2.7 - - + -
35E PHE* 3.5 31.2 - - + +
36E SER 3.4 6.3 - - - +
38E LEU* 1.3 78.3 - - + +
40E THR* 1.3 51.9 + - - +
42E THR* 3.1 6.8 + - - -
43E ALA* 2.8 31.9 + - - +
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Residues in contact with THR 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D MET* 3.6 38.4 - - + +
36E SER 3.2 10.8 + - - -
37E TYR* 3.4 12.1 - - - -
39E VAL* 1.3 75.7 - - - +
41E ALA* 1.3 60.4 + - - +
43E ALA* 3.1 3.8 + - - +
44E CYS* 2.8 28.7 + - - -
2005E PEE 2.9 43.4 + - + +
20J PHE* 3.9 11.0 - - + -
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Residues in contact with ALA 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E TYR 2.8 21.3 + - - +
38E LEU* 3.4 5.4 - - + +
40E THR* 1.3 73.0 - - - +
42E THR* 1.3 57.6 + - - +
44E CYS* 3.2 7.0 + - - +
45E VAL* 2.9 33.8 + - + +
14J PHE* 3.7 25.4 - - + -
20J PHE* 3.7 19.7 - - + +
23J THR* 5.5 4.5 - - + -
24J VAL* 4.1 7.3 - - + +
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Residues in contact with THR 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D LEU* 4.4 15.5 - - + -
218D LEU* 3.2 25.8 - - + -
38E LEU* 2.8 29.9 + - - +
39E VAL* 3.3 8.4 - - - -
41E ALA* 1.3 73.8 - - - +
43E ALA* 1.3 65.3 + - - +
45E VAL* 2.9 22.6 + - + +
46E ALA* 2.9 13.3 + - - +
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Residues in contact with ALA 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D LEU* 3.6 11.7 - - + +
218D LEU* 3.4 21.7 - - + +
219D LEU* 4.4 6.1 - - + -
222D MET* 3.8 23.1 - - - -
39E VAL 2.8 16.0 + - - +
40E THR 3.3 8.3 - - - +
42E THR* 1.3 73.2 - - - +
44E CYS* 1.3 57.9 + - - +
46E ALA* 3.2 2.4 + - - +
47E THR* 2.7 33.9 + - - +
2005E PEE 5.1 3.8 - - + -
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Residues in contact with CYS 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E THR* 2.8 18.0 + - - -
41E ALA 3.3 8.7 - - - +
43E ALA* 1.3 75.3 - - - +
45E VAL* 1.3 54.0 + - - +
47E THR* 3.3 6.0 + - - -
48E ALA* 2.7 37.2 + - - +
2005E PEE 3.9 44.9 - - + -
20J PHE* 4.3 19.3 - - - -
24J VAL* 3.7 21.4 - - + +
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Residues in contact with VAL 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E ALA* 2.9 21.2 + - + +
42E THR* 2.9 13.8 + - + +
44E CYS* 1.3 76.3 - - - +
46E ALA* 1.3 56.2 + - - +
48E ALA* 3.2 8.5 + - - +
49E TYR* 2.8 27.7 + - - +
23J THR 5.1 0.7 - - - +
24J VAL* 4.2 22.4 - - - +
27J GLY* 3.8 9.4 - - - -
28J ALA* 3.4 29.8 - - - +
31J PHE* 3.8 22.2 - - + -
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Residues in contact with ALA 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D ILE* 4.7 9.8 - - + +
214D LEU* 4.6 21.1 - - + -
215D LEU* 3.6 27.4 - - + -
42E THR 2.9 10.5 + - - +
43E ALA* 3.5 8.5 - - - +
45E VAL* 1.3 76.6 - - - +
47E THR* 1.3 63.9 + - - +
49E TYR* 2.8 11.4 + - - +
50E ALA* 2.8 23.5 + - - +
31J PHE* 4.9 7.4 - - - -
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Residues in contact with THR 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D LEU* 3.7 14.3 - - - +
43E ALA 2.7 19.4 + - - -
44E CYS* 3.7 5.2 - - - -
46E ALA* 1.3 75.1 - - - +
48E ALA* 1.3 54.9 + - - +
50E ALA* 3.2 5.9 + - - +
51E ALA* 2.7 40.3 + - + +
2005E PEE 3.6 63.0 - - + +
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Residues in contact with ALA 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E CYS 2.7 23.0 + - - +
45E VAL* 3.2 10.3 - - - +
47E THR* 1.3 74.0 - - - +
49E TYR* 1.3 56.4 + - - +
51E ALA* 3.6 4.8 - - - +
52E LYS* 2.9 32.1 + - - +
2005E PEE 4.2 24.6 - - + +
24J VAL* 4.7 8.5 - - + -
28J ALA* 4.1 14.6 - - + -
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Residues in contact with TYR 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D LYS* 3.8 8.1 - - - +
211D ILE* 3.7 15.9 - - + -
45E VAL 2.8 12.9 + - - +
46E ALA 2.8 8.0 + - - +
48E ALA* 1.3 75.2 - - - +
50E ALA* 1.3 65.1 + - - +
52E LYS* 3.3 3.8 + - + +
53E ASN* 3.1 50.7 + - - -
2005E PEE 5.6 2.2 - - + -
2009E PLC 3.3 28.6 + - - -
28J ALA* 4.9 5.3 - - + +
31J PHE* 3.7 20.4 - + + -
32J GLU* 3.7 25.4 - - + -
35J PHE* 3.2 33.2 - + - -
36J ASP* 2.6 39.1 + - - -
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Residues in contact with ALA 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D ILE* 4.7 5.6 - - + -
215D LEU* 5.3 1.3 - - + -
46E ALA 2.8 14.8 + - - +
47E THR* 3.6 8.1 - - - +
49E TYR* 1.3 75.2 - - - +
51E ALA* 1.3 63.2 + - - +
53E ASN* 3.3 2.6 + - - +
54E VAL* 2.9 28.5 + - - +
2005E PEE 3.8 24.5 - - + -
2009E PLC 3.4 36.9 - - + +
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Residues in contact with ALA 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E THR* 2.7 24.7 + - + +
48E ALA* 3.6 6.1 - - - +
50E ALA* 1.3 74.6 - - - +
52E LYS* 1.3 57.4 + - - +
54E VAL* 3.1 2.3 + - - +
55E VAL* 2.8 39.5 + - + +
2005E PEE 3.7 26.2 - - + +
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Residues in contact with LYS 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ALA 2.9 17.9 + - - +
49E TYR* 3.7 4.7 - - + +
51E ALA* 1.3 75.0 - - - +
53E ASN* 1.3 69.5 + - - +
55E VAL* 3.9 5.0 - - - +
56E THR* 2.9 50.5 + - - +
2005E PEE 3.8 33.5 - - + +
32J GLU* 2.6 37.1 + - - +
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Residues in contact with ASN 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E TYR* 3.1 51.2 + - - +
50E ALA 3.7 7.0 - - - +
52E LYS* 1.3 88.8 - - - +
54E VAL* 1.3 65.4 + - - +
56E THR* 3.3 7.4 + - - +
57E GLN* 2.9 32.4 + - - +
2009E PLC 3.3 53.3 + - - +
32J GLU* 4.4 3.4 + - - -
36J ASP* 5.1 1.3 + - - +
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Residues in contact with VAL 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E ALA 2.9 21.4 + - - +
51E ALA 3.8 2.5 - - - +
53E ASN* 1.3 76.3 - - - +
55E VAL* 1.3 64.9 + - - +
57E GLN* 3.8 6.5 - - - +
58E PHE* 3.0 54.2 + - + +
2005E PEE 4.1 29.6 - - + -
2009E PLC 3.8 52.0 - - + +
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Residues in contact with VAL 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E ALA* 2.8 27.0 + - + +
52E LYS* 3.9 5.4 - - - +
54E VAL* 1.3 76.0 - - - +
56E THR* 1.3 56.1 + - - +
58E PHE* 3.9 3.5 - - - +
59E ILE* 2.6 60.3 + - + +
2005E PEE 5.0 13.5 - - + -
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Residues in contact with THR 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C TYR* 5.5 3.1 - - + +
52E LYS* 2.9 42.5 + - - +
53E ASN* 3.3 11.4 - - - +
55E VAL* 1.3 77.4 - - - +
57E GLN* 1.3 70.3 + - + +
59E ILE* 3.3 10.2 - - - +
60E SER* 2.9 25.7 + - - +
2009E PLC 6.0 1.6 - - - +
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Residues in contact with GLN 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TYR* 3.6 46.0 - - + +
79C LEU* 3.2 18.5 - - - +
204D MET* 4.2 1.6 - - - +
53E ASN* 2.9 17.3 + - - +
54E VAL* 3.8 9.2 + - - +
56E THR* 1.3 79.2 - - + +
58E PHE* 1.3 71.0 + - + +
60E SER* 2.9 18.0 + - - -
61E SER* 3.1 8.1 + - - -
2009E PLC 2.8 64.8 + - - +
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Residues in contact with PHE 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 4.6 22.2 - - + -
48C THR* 4.4 14.8 - - + -
51C LEU* 3.7 24.3 - - + +
76C TYR* 5.6 0.7 - - + -
79C LEU* 4.8 3.4 - - + -
80C ILE* 3.8 25.8 - - + -
83C LEU* 4.3 23.1 - - + -
54E VAL* 3.0 41.8 + - + +
55E VAL* 3.9 3.8 - - - +
57E GLN* 1.3 89.0 - - + +
59E ILE* 1.3 64.8 + - - +
61E SER* 2.8 26.4 + - - -
62E LEU* 3.9 4.7 + - - +
2005E PEE 6.0 2.2 - - + -
2009E PLC 4.8 12.6 - - + -
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Residues in contact with ILE 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E VAL* 2.6 40.1 + - + +
56E THR* 3.3 13.2 - - - +
58E PHE* 1.3 72.6 - - - +
60E SER* 1.3 69.2 + - - +
62E LEU* 3.3 31.1 + - + +
63E SER* 5.6 0.2 - - - +
164P TRP* 3.6 46.1 + - + +
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Residues in contact with SER 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C GLN* 3.2 32.6 + - - +
76C TYR* 3.5 21.0 - - - -
56E THR* 2.9 13.1 + - - +
57E GLN 2.9 13.4 + - - -
59E ILE* 1.3 81.0 - - - +
61E SER* 1.3 58.5 + - - +
62E LEU 2.9 6.8 + - - -
63E SER* 3.4 20.8 + - - +
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Residues in contact with SER 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 3.3 23.6 - - - +
55C HIS* 3.4 14.3 + - - -
74C VAL* 3.4 22.5 - - - +
75C GLN* 3.4 24.2 - - - -
80C ILE* 3.7 20.4 - - - +
57E GLN 3.1 7.2 + - - -
58E PHE 2.8 18.5 + - - -
60E SER* 1.3 76.4 - - - +
62E LEU* 1.3 60.9 + - - +
63E SER 4.2 2.5 - - - +
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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