Contacts of the helix formed by residues 14 - 46 (chain O) in PDB entry 2DYS
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 14 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12O ALA* 4.0 3.3 - - - +
13O THR* 1.3 78.2 - - - +
15O PRO* 1.3 71.8 - - - +
16O ILE* 3.8 5.2 + - - +
17O MET* 3.2 12.8 + - - +
18O GLU* 3.3 21.3 + - - +
168O LEU* 2.9 35.3 + - - +
185O MET* 3.2 22.9 - - - -
187O SER* 4.4 2.7 - - - -
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Residues in contact with PRO 15 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O SER* 1.3 89.0 - - - +
16O ILE* 1.3 65.0 + - + +
18O GLU* 3.2 17.0 - - + +
19O GLU* 3.0 23.3 + - - +
185O MET* 3.5 37.5 - - + +
187O SER* 4.0 7.8 - - - +
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Residues in contact with ILE 16 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14O SER* 3.2 5.3 + - - +
15O PRO* 1.3 83.0 - - + +
17O MET* 1.3 69.8 + - - +
19O GLU* 2.9 20.2 + - + +
20O LEU* 3.0 25.9 + - + +
83O ILE* 4.6 3.8 - - + -
86O MET* 4.1 34.8 - - + +
87O MET* 4.3 36.6 - - + +
168O LEU 4.7 8.7 - - - +
169O GLY 5.0 5.4 - - - +
170O LEU* 6.5 0.2 - - + -
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Residues in contact with MET 17 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366N VAL* 4.1 10.5 - - + -
9O PHE* 3.8 46.4 - - + -
10O GLN 4.7 3.6 - - - +
12O ALA* 3.8 18.4 - - + +
14O SER* 3.2 18.4 + - - +
16O ILE* 1.3 80.8 - - - +
18O GLU* 1.3 63.1 + - - +
20O LEU* 3.2 16.1 + - + +
21O LEU* 3.0 26.6 + - + +
166O PRO 3.7 18.2 - - - +
167O SER 3.6 21.5 - - - +
168O LEU 4.0 4.7 - - - -
169O GLY* 3.7 13.2 - - - -
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Residues in contact with GLU 18 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12O ALA* 3.4 13.8 - - + +
14O SER 3.3 7.1 + - - +
15O PRO* 3.2 21.5 + - - +
17O MET* 1.3 76.9 - - - +
19O GLU* 1.3 63.6 + - - +
21O LEU* 2.9 16.4 + - - +
22O HIS* 3.1 30.8 + - + +
187O SER* 5.5 2.3 + - - -
47V TYR* 3.5 47.1 - - + +
51V TYR* 4.1 17.0 - - - -
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Residues in contact with GLU 19 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15O PRO 3.0 9.7 + - - +
16O ILE* 2.9 20.5 + - + +
18O GLU* 1.3 80.8 - - - +
20O LEU* 1.3 54.9 + - - +
22O HIS* 3.4 14.2 + - - +
23O PHE 3.0 22.2 + - - -
82O ARG* 3.7 22.5 + - - +
83O ILE* 3.5 35.7 - - + +
86O MET* 4.1 17.0 - - - +
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Residues in contact with LEU 20 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362N SER* 3.8 35.2 - - - +
363N LEU* 4.2 18.2 - - + +
365N ILE* 5.7 0.4 - - + -
366N VAL* 3.9 23.3 - - + -
9O PHE* 5.6 0.4 - - - -
16O ILE* 3.0 26.1 + - + +
17O MET* 3.5 22.7 - - + +
19O GLU* 1.3 75.9 - - - +
21O LEU* 1.3 61.0 + - - +
23O PHE* 3.8 3.7 - - + +
24O HIS* 2.8 31.9 + - - +
83O ILE* 3.7 30.3 - - + -
87O MET* 5.4 4.0 - - - -
169O GLY* 4.9 3.8 - - - +
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Residues in contact with LEU 21 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O PHE* 3.4 43.5 - - + +
10O GLN 4.8 1.8 - - - +
11O ASP* 5.2 0.2 - - - -
12O ALA* 3.8 19.1 - - + +
17O MET* 3.0 15.6 + - + +
18O GLU* 2.9 10.5 + - + +
20O LEU* 1.3 76.1 - - - +
22O HIS* 1.3 62.0 + - + +
24O HIS* 3.3 5.3 + - - +
25O ASP* 2.9 34.5 + - - +
43V ARG* 4.4 25.8 - - + +
47V TYR* 3.4 39.0 - - + +
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Residues in contact with HIS 22 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O GLU* 3.1 42.4 + - + +
19O GLU* 3.7 15.5 - - - +
21O LEU* 1.3 75.8 - - + +
23O PHE* 1.3 64.4 + - - +
25O ASP* 3.2 9.1 + - - +
26O HIS* 3.1 22.2 + - - +
40V ALA* 4.8 1.6 + - - -
43V ARG* 3.2 37.4 + - + +
44V LYS* 3.7 44.7 - - + +
47V TYR* 4.9 4.3 - + - +
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Residues in contact with PHE 23 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360N ASN* 3.5 35.0 - - + -
362N SER* 5.4 0.9 - - - -
363N LEU* 3.7 37.7 - - + -
19O GLU 3.0 7.7 + - - +
20O LEU* 3.8 7.0 - - + +
21O LEU 3.3 0.2 - - - -
22O HIS* 1.3 76.7 - - - +
24O HIS* 1.3 62.0 + - - +
26O HIS* 3.2 10.3 + + - +
27O THR* 3.0 41.0 + - - -
76O ILE* 3.3 24.9 - - + -
79O PRO* 3.8 23.6 - - + -
80O SER* 3.5 11.0 - - - -
82O ARG* 5.5 1.8 - - - +
83O ILE* 3.6 28.7 - - + -
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Residues in contact with HIS 24 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357N VAL* 4.4 11.2 - - + +
363N LEU* 4.1 26.5 - - + -
367N LEU* 5.5 0.9 - - + -
372N TYR* 4.4 11.1 + - - -
433N LEU* 4.1 24.9 - - + +
9O PHE* 3.9 27.3 - + + -
20O LEU 2.8 18.0 + - - +
21O LEU* 3.8 4.2 - - - +
23O PHE* 1.3 76.2 - - - +
25O ASP* 1.3 67.5 + - - +
27O THR* 4.4 2.9 - - + -
28O LEU* 2.8 46.8 + - + +
303O TGL 3.9 28.0 + - - -
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Residues in contact with ASP 25 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O LEU* 2.9 18.3 + - - +
22O HIS* 3.2 11.8 + - - +
24O HIS* 1.3 84.1 + - - +
26O HIS* 1.3 62.4 + - - +
28O LEU* 3.3 1.8 + - - +
29O MET 3.1 18.0 + - - -
303O TGL 5.1 2.9 - - - +
35V TYR* 3.4 27.4 + - + +
39V VAL* 3.9 16.6 - - + +
40V ALA* 4.5 10.8 - - + -
43V ARG* 3.0 53.2 + - - +
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Residues in contact with HIS 26 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22O HIS 3.1 11.8 + - - +
23O PHE* 3.3 14.6 - + + +
25O ASP* 1.3 76.9 - - - +
27O THR* 1.3 71.7 + - - +
29O MET* 3.3 22.2 + - + +
30O ILE* 3.5 30.4 + - + +
75O LEU* 2.8 36.6 + - + -
76O ILE* 4.6 1.6 - - - -
79O PRO* 4.3 16.9 - - + +
36V LYS* 6.4 0.6 - - - +
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Residues in contact with THR 27 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356N ILE* 6.1 1.1 - - + -
357N VAL* 3.6 42.8 - - + -
363N LEU* 5.2 1.1 - - + -
23O PHE* 3.0 44.1 + - + -
24O HIS* 3.7 8.3 - - + +
26O HIS* 1.3 79.7 - - - +
28O LEU* 1.3 63.8 + - - +
30O ILE* 3.1 12.6 + - - +
31O VAL* 3.0 21.4 + - + +
76O ILE* 3.7 17.0 - - + +
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Residues in contact with LEU 28 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357N VAL* 6.0 1.3 - - + -
372N TYR* 5.3 1.6 - - - +
24O HIS* 2.8 35.7 + - + +
25O ASP* 3.8 4.0 - - - +
27O THR* 1.3 74.2 - - - +
29O MET* 1.3 58.2 + - - +
31O VAL* 3.8 9.0 - - + -
32O PHE* 2.9 53.2 + - + +
303O TGL 3.2 72.0 - - + +
35V TYR* 3.5 16.4 - - - +
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Residues in contact with MET 29 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25O ASP 3.1 6.4 + - - +
26O HIS* 3.6 17.5 - - + +
27O THR 3.2 0.2 - - - -
28O LEU* 1.3 77.0 - - - +
30O ILE* 1.3 72.3 + - + +
32O PHE* 3.3 6.1 + - - +
33O LEU* 2.8 45.0 + - + +
31V PHE* 4.0 12.7 - - + -
32V ALA* 4.2 25.6 - - + -
35V TYR* 3.6 42.8 + - + -
36V LYS* 4.4 19.1 - - + -
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Residues in contact with ILE 30 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353N LEU* 5.8 0.2 - - + -
605N HEA 5.3 0.9 - - + -
26O HIS* 3.6 33.2 - - + +
27O THR* 3.4 6.7 - - - +
29O MET* 1.3 84.6 - - + +
31O VAL* 1.3 63.2 + - + +
33O LEU* 3.6 6.2 - - + +
34O ILE* 2.9 53.3 + - + +
72O ILE* 3.5 24.5 - - + +
75O LEU* 5.0 5.2 - - + -
76O ILE* 3.6 35.4 - - + -
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Residues in contact with VAL 31 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353N LEU* 3.7 38.8 - - + +
354N THR* 5.0 4.5 - - + -
356N ILE* 6.1 2.0 - - + -
357N VAL* 3.8 27.8 - - + -
27O THR* 3.0 18.1 + - + +
28O LEU* 3.7 13.7 - - + +
30O ILE* 1.3 78.3 - - + +
32O PHE* 1.3 52.4 + - - +
35O SER* 2.6 37.9 + - - -
76O ILE* 6.5 1.1 - - + -
303O TGL 3.5 34.5 - - + -
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Residues in contact with PHE 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28O LEU* 2.9 51.7 + - + +
29O MET 3.5 4.3 - - - +
31O VAL* 1.3 73.2 - - - +
33O LEU* 1.3 58.3 + - - +
35O SER* 3.2 2.3 + - - -
36O SER* 2.6 36.4 + - - -
303O TGL 3.5 94.6 - - + +
31V PHE* 4.3 17.5 - + + -
35V TYR* 4.5 16.6 - + - -
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Residues in contact with LEU 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O MET* 2.8 40.5 + - + +
30O ILE* 3.6 6.7 - - - +
32O PHE* 1.3 72.2 - - - +
34O ILE* 1.3 54.5 + - + +
36O SER* 3.0 8.9 + - - +
37O LEU* 2.7 38.7 + - + +
27V VAL* 6.4 0.4 - - + -
28V SER* 4.0 40.4 - - - +
31V PHE* 3.6 34.3 - - + -
32V ALA* 4.8 3.8 - - + +
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Residues in contact with ILE 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321N PHE* 5.4 3.6 - - + -
349N THR* 4.6 0.9 - - + -
353N LEU* 3.9 20.9 - - + -
605N HEA 3.7 61.9 - - + -
30O ILE* 2.9 43.8 + - + +
31O VAL 4.1 2.2 - - - +
33O LEU* 1.3 74.6 - - + +
35O SER* 1.3 64.4 + - - +
37O LEU* 3.4 11.8 - - + +
38O VAL* 3.0 24.4 + - + +
72O ILE* 4.4 11.2 - - + -
304O PSC 5.9 4.7 - - + -
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Residues in contact with SER 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346N PHE* 3.5 13.7 - - - -
349N THR* 4.5 7.6 - - - -
350N VAL* 4.3 15.9 - - - -
353N LEU* 3.8 15.7 - - - +
31O VAL 2.6 25.0 + - - -
32O PHE* 3.2 8.3 + - - -
34O ILE* 1.3 77.3 - - - +
36O SER* 1.3 56.6 + - - +
38O VAL* 3.4 2.4 + - - +
39O LEU 3.0 21.3 + - - -
303O TGL 3.3 30.7 - - - +
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Residues in contact with SER 36 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O PHE 2.6 25.0 + - - -
33O LEU* 3.0 16.6 + - - +
35O SER* 1.3 75.3 + - - +
37O LEU* 1.3 55.3 + - - +
39O LEU* 3.3 2.7 + - - +
40O TYR* 2.8 35.7 + - - +
303O TGL 3.7 27.1 - - - +
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Residues in contact with LEU 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321N PHE* 5.0 5.8 - - + -
33O LEU* 2.7 18.8 + - + +
34O ILE* 3.4 12.6 - - + +
36O SER* 1.3 76.4 + - - +
38O VAL* 1.3 57.9 + - + +
40O TYR* 3.2 7.4 + - + +
41O ILE* 2.9 56.0 + - + +
304O PSC 4.1 31.6 - - + -
21V ILE* 6.1 1.1 - - + -
24V ALA* 4.4 22.9 - - + -
28V SER* 5.2 10.3 - - - +
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Residues in contact with VAL 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320N VAL* 4.2 13.7 - - + -
321N PHE* 4.1 24.7 - - + -
324N LEU* 4.6 4.3 - - + +
345N ILE* 4.5 14.4 - - + +
346N PHE* 4.6 6.3 - - + -
349N THR* 4.2 25.8 - - + +
605N HEA 4.4 5.4 - - + -
34O ILE* 3.0 19.9 + - + +
35O SER 3.7 5.8 - - - +
36O SER 3.3 0.2 - - - -
37O LEU* 1.3 79.1 - - + +
39O LEU* 1.3 59.8 + - - +
41O ILE* 3.4 6.8 + - - +
42O ILE* 3.0 41.1 + - + +
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Residues in contact with LEU 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346N PHE* 3.6 33.0 - - + -
607N TGL 3.7 37.4 - - + +
35O SER 3.0 9.7 + - - +
36O SER 3.3 4.2 + - - +
38O VAL* 1.3 74.2 - - - +
40O TYR* 1.3 66.2 + - - +
42O ILE* 3.4 6.7 + - + +
43O SER* 3.2 20.9 + - - -
303O TGL 3.5 44.6 - - + -
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Residues in contact with TYR 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36O SER 2.8 18.8 + - - +
37O LEU* 3.5 6.7 - - + +
39O LEU* 1.3 76.8 - - - +
41O ILE* 1.3 73.4 + - + +
43O SER* 2.7 31.4 + - - -
44O LEU* 2.9 26.3 + - + +
20V HIS* 3.1 41.9 + - + +
21V ILE* 5.7 1.1 - - + -
24V ALA* 3.8 32.9 + - + -
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Residues in contact with ILE 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321N PHE* 5.2 0.9 - - + -
324N LEU* 3.5 26.9 - - + -
37O LEU* 2.9 43.0 + - + +
38O VAL 3.8 4.3 - - - +
40O TYR* 1.3 80.8 - - + +
42O ILE* 1.3 64.0 + - - +
44O LEU* 3.1 9.9 + - + +
45O MET* 3.0 39.4 + - + +
304O PSC 3.2 40.6 - - + -
21V ILE* 4.4 18.6 - - + -
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Residues in contact with ILE 42 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324N LEU* 3.6 22.2 - - + -
327N LEU* 4.9 2.5 - - + -
342N LEU* 3.9 29.2 - - + +
345N ILE* 3.9 24.0 - - + -
346N PHE* 4.3 15.0 - - + -
607N TGL 3.4 31.2 - - + -
38O VAL* 3.0 22.1 + - + +
39O LEU* 3.5 9.6 - - - +
40O TYR 3.1 0.2 - - - -
41O ILE* 1.3 78.5 - - - +
43O SER* 1.3 60.0 + - - +
45O MET* 3.3 4.0 + - - +
46O LEU* 3.0 40.3 + - + +
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Residues in contact with SER 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607N TGL 3.8 29.2 - - - -
39O LEU* 3.2 8.2 + - - -
40O TYR* 2.7 32.2 + - - -
42O ILE* 1.3 77.6 - - - +
44O LEU* 1.3 62.7 + - - +
46O LEU 3.4 0.7 + - - +
47O THR* 2.8 35.9 + - - +
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Residues in contact with LEU 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607N TGL 5.2 2.7 - - + -
40O TYR* 2.9 29.3 + - + +
41O ILE* 3.1 12.1 + - + +
43O SER* 1.3 77.6 + - - +
45O MET* 1.3 80.9 + - + +
46O LEU 3.2 0.9 + - - -
47O THR* 3.2 13.1 + - - -
16V ARG* 3.2 49.2 + - + +
17V LEU* 4.2 17.0 - - + -
20V HIS* 3.5 45.3 - - + +
21V ILE* 4.8 9.4 - - + -
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Residues in contact with MET 45 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324N LEU* 3.6 17.5 - - + +
327N LEU* 3.9 34.5 - - + +
328N HIS* 3.5 43.3 - - + +
329N GLY 5.2 2.8 + - - +
330N GLY 5.5 1.0 + - - +
332N ILE* 4.3 6.1 - - - +
41O ILE* 3.0 29.5 + - + +
42O ILE* 3.7 6.5 - - - +
44O LEU* 1.3 101.4 - - + +
46O LEU* 1.3 61.7 + - - +
47O THR 3.8 0.3 + - - -
48O THR* 4.3 12.1 - - - +
304O PSC 4.0 11.4 - - + -
16V ARG* 5.1 3.8 - - - +
17V LEU* 4.0 13.7 - - + -
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Residues in contact with LEU 46 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327N LEU* 3.9 26.2 - - + -
332N ILE* 4.1 32.5 - - + +
334N TRP* 3.2 44.3 + - + -
342N LEU* 3.4 20.6 - - + -
607N TGL 3.9 27.5 - - + +
42O ILE* 3.0 30.2 + - + +
43O SER 4.1 3.1 - - - +
44O LEU 3.1 0.8 - - - -
45O MET* 1.3 81.2 - - + +
47O THR* 1.3 60.1 + - - +
48O THR 3.7 3.5 + - - +
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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