Contacts of the helix formed by residues 13 - 43 (chain Z) in PDB entry 5WTI
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 ASN 13 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Z GLU* 2.7 19.9 + - + +
12Z PRO* 1.3 69.8 - - - +
14Z GLU* 1.3 59.9 + - - +
15Z GLU* 2.8 22.8 + - - +
16Z VAL* 2.7 49.0 + - + +
17Z LYS* 2.8 30.2 + - - +
427Z TYR* 4.0 2.0 + - - -
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Residues in contact with GLU 14 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Z PRO 3.4 8.6 + - - +
13Z ASN* 1.3 73.6 + - - +
15Z GLU* 1.3 71.2 + - - +
17Z LYS* 3.8 24.4 + - - +
18Z LYS* 3.2 39.1 + - + +
503Z GLY 5.5 1.4 - - - +
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Residues in contact with GLU 15 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Z ASN* 2.8 13.4 + - - +
14Z GLU* 1.3 79.5 - - - +
16Z VAL* 1.3 61.3 + - - +
18Z LYS* 3.2 22.3 + - - -
19Z GLY* 2.9 23.4 + - - -
427Z TYR* 3.2 30.9 - - + +
428Z PRO* 3.4 22.5 - - + +
429Z THR 5.7 0.2 - - - +
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Residues in contact with VAL 16 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Z ILE* 4.3 9.4 - - + -
11Z GLU 4.9 2.7 - - - +
13Z ASN* 2.7 37.1 + - + +
15Z GLU* 1.3 70.6 - - - +
17Z LYS* 1.3 61.6 + - + +
19Z GLY* 2.9 1.6 + - - -
20Z LEU* 2.8 55.4 + - + +
425Z LEU* 4.9 2.1 - - + +
427Z TYR* 3.9 22.0 - - + +
440Z VAL* 5.3 0.2 - - + -
441Z ASP 4.2 18.4 - - - +
442Z ILE* 3.7 25.1 - - + -
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Residues in contact with LYS 17 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B U 5.1 4.2 + - - -
10Z ILE* 6.4 0.7 - - + -
11Z GLU 5.3 0.2 - - - +
12Z PRO* 3.8 30.9 - - + +
13Z ASN 2.8 28.4 + - - +
14Z GLU* 3.8 23.4 + - - +
16Z VAL* 1.3 73.8 - - + +
18Z LYS* 1.3 62.3 + - + +
20Z LEU* 4.1 0.9 - - + +
21Z TRP* 3.2 25.3 + - - +
503Z GLY 4.6 6.1 + - - -
504Z ASN* 5.4 2.4 + - - +
505Z VAL* 4.3 20.4 - - + +
506Z GLY 3.9 26.1 + - - +
508Z ILE* 3.9 28.1 - - + +
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Residues in contact with LYS 18 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Z GLU* 3.2 27.1 + - + +
15Z GLU* 3.2 31.1 + - - +
16Z VAL 3.2 0.4 - - - -
17Z LYS* 1.3 78.9 - - + +
19Z GLY* 1.3 58.5 + - - +
21Z TRP* 4.3 2.7 - - - +
22Z LYS* 3.1 31.2 + - - +
428Z PRO* 3.9 21.3 - - + +
429Z THR 5.4 3.0 + - - -
434Z TRP* 3.6 19.8 - - + -
503Z GLY* 6.6 0.2 - - - -
505Z VAL* 6.2 0.4 - - - -
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Residues in contact with GLY 19 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15Z GLU 2.9 14.1 + - - -
16Z VAL 2.9 3.3 + - - -
18Z LYS* 1.3 75.7 - - - +
20Z LEU* 1.3 60.1 + - - +
23Z THR* 2.8 35.2 + - - -
425Z LEU* 3.9 10.3 - - - -
426Z ILE 3.1 20.2 - - - +
427Z TYR* 4.4 0.4 - - - -
428Z PRO* 3.9 8.5 - - - +
434Z TRP* 4.6 1.8 - - - -
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Residues in contact with LEU 20 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Z ILE* 3.6 29.8 - - + -
16Z VAL* 2.8 43.6 + - + +
17Z LYS 4.1 2.5 - - - +
19Z GLY* 1.3 74.0 - - - +
21Z TRP* 1.3 57.2 + - - +
23Z THR* 3.5 1.9 + - - -
24Z HIS* 2.8 28.6 + - - +
389Z VAL* 5.7 0.2 - - - +
422Z LEU* 4.4 9.6 - - + -
425Z LEU* 4.0 27.8 - - + -
442Z ILE* 4.7 1.8 - - + -
486Z VAL* 4.1 24.8 - - + +
488Z PHE* 3.7 15.1 - - + -
508Z ILE* 3.7 20.9 - - + -
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Residues in contact with TRP 21 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Z LYS 3.2 18.0 + - - +
18Z LYS* 4.3 3.1 - - - +
20Z LEU* 1.3 77.4 - - - +
22Z LYS* 1.3 54.1 + - - +
24Z HIS* 3.1 22.9 + + - +
25Z GLU* 2.7 62.4 + - + +
382Z PRO* 3.7 26.9 - - + -
383Z ILE* 3.6 13.2 - - + -
488Z PHE* 3.5 33.8 - + + -
493Z LEU* 3.6 32.3 - - + -
500Z VAL* 3.3 28.9 + - + +
501Z GLU* 5.2 3.0 + - - +
505Z VAL* 3.8 24.5 - - + -
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Residues in contact with LYS 22 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Z LYS 3.1 20.1 + - - +
19Z GLY 4.0 2.2 - - - +
21Z TRP* 1.3 78.0 - - + +
23Z THR* 1.3 56.3 + - - +
25Z GLU* 3.1 24.4 + - - +
26Z VAL* 2.8 44.3 + - + +
197Z ILE* 4.3 11.6 - - + +
200Z GLU* 3.2 24.2 + - - -
201Z ILE* 4.5 6.5 - - + -
426Z ILE* 3.5 26.0 - - + -
434Z TRP* 3.4 42.7 - - + +
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Residues in contact with THR 23 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Z GLY 2.8 23.3 + - - -
20Z LEU 3.8 2.5 - - - -
22Z LYS* 1.3 76.1 - - - +
24Z HIS* 1.3 56.1 + - - +
26Z VAL* 3.8 7.3 - - - +
27Z LEU* 3.0 27.9 + - - +
215Z LEU* 4.4 13.4 - - + +
389Z VAL* 3.6 23.3 - - + +
391Z PHE* 5.9 0.2 - - + -
424Z ARG 5.6 0.9 - - - +
425Z LEU* 3.3 20.6 - - + +
426Z ILE* 3.1 37.3 + - + +
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Residues in contact with HIS 24 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Z LEU 2.8 16.0 + - - +
21Z TRP* 3.1 29.8 + + - +
23Z THR* 1.3 74.9 - - - +
25Z GLU* 1.3 63.9 + - - +
27Z LEU* 3.3 1.4 + - - +
28Z ASN* 2.7 44.6 + - - -
382Z PRO* 3.0 31.8 - - + +
386Z PRO* 3.8 4.3 - - + +
387Z LEU 3.1 26.8 + - - -
388Z TRP* 3.5 24.5 - + - -
389Z VAL* 4.1 11.4 - - + +
486Z VAL 4.7 1.3 - - - -
488Z PHE* 3.5 26.2 - + + -
493Z LEU* 5.1 0.7 - - + -
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Residues in contact with GLU 25 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Z TRP* 2.7 50.9 + - + +
22Z LYS* 3.5 32.8 + - - +
24Z HIS* 1.3 72.5 - - - +
26Z VAL* 1.3 63.3 + - - +
28Z ASN* 3.5 0.5 + - - +
29Z HIS* 3.1 37.1 + - - -
197Z ILE* 3.6 17.8 - - + +
382Z PRO* 4.0 21.6 - - + +
501Z GLU* 4.6 12.3 - - - +
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Residues in contact with VAL 26 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Z LYS* 2.8 31.8 + - + +
23Z THR* 3.8 8.5 - - - +
25Z GLU* 1.3 71.9 - - - +
27Z LEU* 1.3 61.6 + - - +
30Z GLY 3.0 16.8 + - - -
190Z PHE* 3.4 21.2 - - + -
191Z THR* 4.8 0.4 - - + -
197Z ILE* 4.4 16.8 - - + +
198Z VAL* 4.7 0.9 - - + -
201Z ILE* 3.6 28.9 - - + -
203Z TRP* 4.0 16.8 - - + -
215Z LEU* 3.8 23.6 - - + -
219Z MET* 3.6 2.6 - - - +
426Z ILE* 4.9 3.6 - - + -
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Residues in contact with LEU 27 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Z THR 3.0 18.8 + - - +
24Z HIS 3.6 2.5 - - - +
25Z GLU 3.2 0.4 - - - -
26Z VAL* 1.3 78.8 - - - +
28Z ASN* 1.3 58.8 + - - +
30Z GLY* 3.1 2.6 + - - -
31Z ILE* 2.8 51.6 + - + +
215Z LEU* 3.8 17.2 - - + +
218Z ASP* 3.3 27.6 - - - +
219Z MET* 3.7 25.4 - - + +
222Z GLN* 4.1 2.2 - - - +
387Z LEU 3.8 13.0 - - - +
388Z TRP 3.6 9.9 - - - +
389Z VAL* 3.6 32.8 - - + +
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Residues in contact with ASN 28 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Z HIS* 2.7 54.9 + - - +
27Z LEU* 1.3 77.4 - - - +
29Z HIS* 1.3 59.3 + - - +
31Z ILE* 3.2 8.0 + - - +
32Z ALA* 2.9 28.2 + - - +
380Z ALA* 4.1 6.8 - - - +
381Z ASP* 3.8 7.1 + - - +
382Z PRO* 3.6 29.8 - - + +
385Z HIS 4.1 1.7 - - - +
386Z PRO* 3.5 4.2 - - - +
387Z LEU* 2.6 40.9 + - - +
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Residues in contact with HIS 29 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Z GLU* 3.1 23.3 + - + +
26Z VAL 4.3 0.4 - - - +
28Z ASN* 1.3 76.3 - - - +
30Z GLY* 1.3 57.6 + - - +
32Z ALA* 3.4 8.0 + - + +
33Z TYR* 2.8 28.4 + - - +
190Z PHE* 3.9 17.5 - - + -
197Z ILE* 3.4 31.0 - - + +
380Z ALA 5.7 0.9 - - - -
381Z ASP* 5.2 3.8 - - + +
382Z PRO* 3.5 33.5 - - + +
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Residues in contact with GLY 30 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Z VAL 3.0 10.9 + - - -
27Z LEU 3.5 3.6 - - - -
29Z HIS* 1.3 75.3 - - - +
31Z ILE* 1.3 58.9 + - - +
33Z TYR* 3.1 2.3 + - - +
34Z TYR* 2.9 39.5 + - - -
190Z PHE* 3.4 31.6 - - - -
219Z MET* 3.6 7.9 - - - -
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Residues in contact with ILE 31 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Z LEU* 2.8 49.6 + - + +
28Z ASN* 3.2 6.0 + - - +
30Z GLY* 1.3 72.9 - - - +
32Z ALA* 1.3 59.0 + - - +
34Z TYR* 3.2 3.2 + - - +
35Z MET* 2.8 49.6 + - - +
219Z MET* 3.5 28.7 - - - +
222Z GLN* 3.8 14.4 - - + -
223Z ALA* 4.0 15.4 - - - +
380Z ALA* 4.0 4.0 - - + -
387Z LEU* 3.6 37.2 - - + -
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Residues in contact with ALA 32 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Z ASN 2.9 11.9 + - - +
29Z HIS* 3.7 9.2 - - + +
31Z ILE* 1.3 77.7 - - - +
33Z TYR* 1.3 59.0 + - - +
35Z MET* 3.7 10.1 - - - +
36Z ASN* 2.7 37.8 + - - +
379Z LEU* 4.4 15.7 - - + -
380Z ALA* 3.4 24.8 - - - +
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Residues in contact with TYR 33 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Z HIS 2.8 15.6 + - - +
30Z GLY 3.1 7.6 + - - +
32Z ALA* 1.3 77.9 - - - +
34Z TYR* 1.3 73.2 + + - +
36Z ASN* 3.5 6.0 + - - +
37Z ILE* 3.3 47.8 + - + +
72Z PHE* 5.5 4.8 - + - -
75Z LYS* 5.7 6.7 + - - -
187Z PHE* 4.6 0.7 - - - +
188Z ILE* 2.6 37.6 + - - +
190Z PHE* 3.4 39.7 - + + -
193Z SER* 4.1 12.2 - - - -
195Z GLU* 3.9 30.5 - - + -
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Residues in contact with TYR 34 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Z GLY 2.9 25.4 + - - +
31Z ILE 3.9 3.1 - - - +
33Z TYR* 1.3 90.1 - + - +
35Z MET* 1.3 63.0 + - - +
37Z ILE* 3.4 8.9 + - + +
38Z LEU* 3.1 28.9 + - - +
121Z LEU* 4.9 3.8 - - + +
187Z PHE* 3.5 28.3 - + - -
189Z PRO* 3.4 4.9 - - - +
190Z PHE* 2.9 16.0 + - + -
216Z ASP* 2.6 36.5 + - - +
219Z MET* 3.5 37.9 - - + -
220Z PHE* 3.5 38.3 - + + -
223Z ALA* 4.0 9.0 - - + -
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Residues in contact with MET 35 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Z ILE* 2.8 38.6 + - - +
32Z ALA 3.7 5.4 - - - +
33Z TYR 3.2 0.4 - - - -
34Z TYR* 1.3 78.5 - - - +
36Z ASN* 1.3 59.0 + - - +
38Z LEU* 4.5 0.4 - - - -
39Z LYS* 2.8 27.7 + - - +
223Z ALA* 3.9 14.4 - - + -
226Z ARG* 3.9 30.3 - - + +
227Z PHE* 3.2 21.7 - - + -
377Z PHE* 3.6 29.6 - - + -
378Z THR 3.6 20.0 - - - +
379Z LEU* 3.8 10.5 - - + -
380Z ALA 4.1 15.5 - - - -
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Residues in contact with ASN 36 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Z ALA* 2.7 22.2 + - - +
33Z TYR* 3.5 6.8 + - - +
34Z TYR 3.3 0.2 - - - -
35Z MET* 1.3 75.3 - - - +
37Z ILE* 1.3 60.0 + - + +
39Z LYS* 3.3 33.5 - - - +
40Z LEU* 2.9 38.9 + - + +
379Z LEU* 3.7 29.0 - - - +
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Residues in contact with ILE 37 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Z TYR* 3.3 43.8 + - + +
34Z TYR* 3.7 11.7 - - + +
35Z MET 3.4 0.4 - - - -
36Z ASN* 1.3 77.9 - - + +
38Z LEU* 1.3 63.6 + - + +
40Z LEU* 3.2 9.9 + - + +
41Z ILE* 3.2 33.3 + - + +
72Z PHE* 4.5 25.4 - - + -
186Z LEU* 5.5 2.7 - - + -
187Z PHE* 3.7 52.0 - - + -
220Z PHE* 6.2 1.6 - - + -
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Residues in contact with LEU 38 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Z TYR 3.1 20.5 + - - +
37Z ILE* 1.3 75.5 - - + +
39Z LYS* 1.3 66.3 + - - +
41Z ILE* 3.4 13.3 - - + +
42Z ARG* 2.9 25.5 + - - +
99Z TYR* 3.7 9.7 - - + -
102Z LEU* 3.7 33.2 - - + -
103Z VAL* 4.6 2.5 - - + -
220Z PHE* 4.9 12.3 - - + -
223Z ALA* 4.4 12.3 - - + +
224Z LEU* 4.1 24.2 - - + -
227Z PHE* 3.5 39.5 - - + -
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Residues in contact with LYS 39 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Z MET 2.8 19.8 + - - +
36Z ASN* 3.3 34.7 + - - +
38Z LEU* 1.3 76.7 - - - +
40Z LEU* 1.3 67.7 + - + +
42Z ARG* 3.5 14.5 + - - +
43Z GLN 3.8 0.2 + - - -
44Z GLU 5.1 1.3 + - - +
46Z ILE* 3.5 29.2 - - + -
48Z GLU* 3.2 25.7 + - - +
65Z ILE* 3.6 36.0 - - + +
68Z GLU* 4.3 17.2 + - - -
227Z PHE* 3.6 8.0 - - + -
377Z PHE* 4.3 14.6 - - + -
379Z LEU* 5.9 0.2 - - - -
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Residues in contact with LEU 40 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Z ASN* 2.9 27.9 + - + +
37Z ILE* 3.6 7.9 - - + +
38Z LEU 3.1 0.4 - - - -
39Z LYS* 1.3 84.0 - - + +
41Z ILE* 1.3 59.8 + - - +
42Z ARG 3.0 4.0 - - - -
43Z GLN* 2.9 28.8 + - - +
65Z ILE* 3.6 19.6 - - + +
68Z GLU* 3.7 54.7 - - + +
69Z LEU* 4.0 17.1 - - + +
72Z PHE* 4.0 24.5 - - + -
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Residues in contact with ILE 41 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Z ILE* 3.2 23.8 + - + +
38Z LEU* 3.4 24.7 - - + +
40Z LEU* 1.3 74.6 - - + +
42Z ARG* 1.3 62.0 + - - +
43Z GLN* 3.2 21.3 + - - +
69Z LEU* 3.8 18.8 - - + -
72Z PHE* 5.9 2.2 - - + -
95Z LEU* 4.0 30.1 - - + +
96Z ARG* 3.7 12.8 - - - -
98Z LEU* 4.7 9.0 - - + -
99Z TYR* 3.8 30.7 - - + +
102Z LEU* 4.4 10.1 - - + -
186Z LEU* 4.7 12.3 - - + -
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Residues in contact with ARG 42 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Z LEU 2.9 18.5 + - - +
39Z LYS* 3.5 9.0 + - - +
40Z LEU 3.0 0.4 + - - -
41Z ILE* 1.3 79.1 - - - +
43Z GLN* 1.3 67.3 + - - +
44Z GLU* 3.3 31.6 + - + +
45Z ALA 2.5 34.6 + - - -
46Z ILE* 3.8 10.1 - - - +
96Z ARG* 2.8 32.8 + - - +
99Z TYR* 3.2 32.3 - - + -
227Z PHE* 4.7 2.0 - - - -
230Z TRP* 3.4 25.0 - - - -
231Z GLU* 3.2 33.3 + - - -
234Z ASN* 3.7 9.1 - - - +
374Z GLN* 3.3 14.6 + - - +
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Residues in contact with GLN 43 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Z LYS 3.8 2.2 + - - -
40Z LEU 2.9 22.3 + - - +
41Z ILE 3.3 15.9 + - - +
42Z ARG* 1.3 78.2 - - - +
44Z GLU* 1.3 65.0 + - - +
62Z LYS* 3.4 23.0 - - - -
65Z ILE* 3.9 9.4 - - - -
66Z GLN* 3.3 31.3 + - + +
69Z LEU* 3.4 27.1 - - + +
92Z PHE* 2.9 37.0 + - - +
95Z LEU* 3.5 5.9 - - - +
96Z ARG* 3.4 17.0 - - - +
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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