Contacts of the helix formed by residues 325 - 346 (chain O) in PDB entry 2I2X
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 THR 325 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315O VAL* 3.3 30.0 - - + +
316O GLU 2.7 29.0 + - - +
317O TYR* 3.6 14.8 - - + -
318O HIS* 2.8 23.1 + - - -
320O GLU* 3.7 24.2 + - - +
323O GLY 3.6 0.8 + - - -
324O THR* 1.3 73.1 - - - +
326O VAL* 1.3 69.6 + - + +
328O CYS* 3.5 1.5 + - - +
329O TRP* 3.1 35.4 + - - -
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Residues in contact with VAL 326 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43O ILE* 3.6 11.0 - - + +
44O ASN 4.3 4.9 - - - +
45O TYR* 3.6 37.5 - - + -
65O ILE* 3.9 16.2 - - + +
68O ASP* 4.1 4.9 - - + -
69O VAL* 3.5 25.6 - - + +
315O VAL* 4.4 2.2 - - + -
317O TYR* 4.2 9.4 - - + -
324O THR* 3.3 19.1 - - + -
325O THR* 1.3 91.1 - - + +
327O GLN* 1.3 53.1 + - - +
330O SER* 2.8 36.8 + - - -
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Residues in contact with GLN 327 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68O ASP* 3.2 42.6 + - + +
69O VAL* 5.4 0.2 - - - +
71O GLU* 4.9 6.7 - - - +
72O ARG* 3.5 51.0 + - + +
323O GLY* 3.6 3.6 - - - -
324O THR* 2.7 46.2 + - + +
326O VAL* 1.3 77.0 - - - +
328O CYS* 1.3 68.1 + - - +
330O SER* 3.3 6.2 + - - -
331O GLU* 3.2 18.0 + - - +
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Residues in contact with CYS 328 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292M THR* 3.0 56.3 + - - +
293M CYS* 4.1 3.6 - - - +
329M TRP* 4.6 4.9 - - + -
72O ARG* 4.4 2.7 - - - +
320O GLU* 4.0 19.7 - - + -
322O GLY 4.1 5.2 - - - -
323O GLY 3.7 17.3 - - - -
324O THR 3.0 21.0 + - - -
325O THR 3.8 5.2 - - - +
327O GLN* 1.3 78.2 - - - +
329O TRP* 1.3 69.0 + - + +
331O GLU 3.3 6.8 + - - -
332O THR* 3.3 5.7 + - - -
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Residues in contact with TRP 329 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320M GLU* 5.4 4.2 + - + -
328M CYS* 4.7 4.9 - - + -
329M TRP* 3.3 54.9 - + - +
332M THR* 4.3 6.7 - - + -
43O ILE* 4.1 7.2 - - + -
290O THR* 3.7 40.1 - - + +
292O THR* 3.5 26.2 - - - -
293O CYS* 3.5 34.0 - - + +
312O ASN* 4.1 18.4 - - + +
315O VAL* 4.1 19.0 - - + +
320O GLU* 5.7 3.6 + - - +
325O THR* 3.1 31.3 + - - +
328O CYS* 1.3 80.1 - - + +
330O SER* 1.3 66.5 + - - +
332O THR* 3.3 4.9 + - + +
333O LEU* 3.0 26.7 + - - +
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Residues in contact with SER 330 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41O PRO* 4.7 2.4 - - - +
43O ILE* 3.8 24.7 - - - +
69O VAL* 4.5 7.7 - - - +
72O ARG* 4.4 7.3 - - - +
73O MET* 4.3 20.6 - - - +
81O ILE* 5.2 2.5 - - - -
326O VAL 2.8 26.0 + - - -
327O GLN* 3.3 10.9 + - - -
328O CYS 3.4 0.2 - - - -
329O TRP* 1.3 77.1 - - - +
331O GLU* 1.3 57.1 + - - +
333O LEU* 3.8 6.4 - - - +
334O ALA* 2.8 32.5 + - - +
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Residues in contact with GLU 331 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288M GLY 5.5 0.7 - - - +
289M LYS* 5.5 0.3 - - - -
292M THR* 3.5 23.7 - - + +
296M SER* 2.6 23.0 + - - -
297M ASP* 3.1 34.5 + - - +
72O ARG* 3.1 17.9 + - + +
73O MET* 5.5 0.2 - - - -
76O VAL* 3.5 8.5 - - - +
78O PHE* 4.1 14.4 - - + -
327O GLN 3.2 12.3 + - - +
328O CYS 3.6 9.4 - - - +
329O TRP 3.2 0.2 - - - -
330O SER* 1.3 77.2 + - - +
332O THR* 1.3 56.1 + - - +
334O ALA* 3.3 1.6 + - - +
335O TYR* 2.9 53.9 + - + -
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Residues in contact with THR 332 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289M LYS* 2.6 36.3 + - + +
290M THR* 4.3 12.3 - - + +
292M THR* 2.8 19.9 + - - -
329M TRP* 4.4 5.1 - - + -
332M THR* 4.9 6.1 - - + -
290O THR* 3.4 28.7 - - + +
328O CYS 3.3 2.3 + - - -
329O TRP* 3.3 10.2 + - + -
330O SER 3.3 0.6 - - - -
331O GLU* 1.3 74.3 - - - +
333O LEU* 1.3 66.3 + - - +
335O TYR* 3.3 4.5 + - - +
336O ASP* 3.0 30.4 + - - +
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Residues in contact with LEU 333 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41O PRO* 3.8 14.1 - - + -
42O GLU 3.8 19.1 - - - +
43O ILE* 4.2 6.3 - - + +
290O THR* 3.7 18.6 - - + +
310O TRP* 3.5 36.5 - - + +
311O SER 3.5 19.3 - - - +
312O ASN* 3.7 29.8 - - + +
329O TRP 3.0 22.8 + - - +
330O SER* 3.8 4.9 - - - +
332O THR* 1.3 74.6 - - - +
334O ALA* 1.3 58.6 + - - +
336O ASP* 3.1 5.7 + - - +
337O CYS* 3.0 31.0 + - - -
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Residues in contact with ALA 334 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41O PRO* 3.8 13.0 - - + +
73O MET* 3.6 13.5 - - + -
78O PHE* 3.5 43.7 - - + -
330O SER 2.8 23.0 + - - +
331O GLU 3.7 0.2 - - - +
333O LEU* 1.3 72.5 - - - +
335O TYR* 1.3 57.7 + - - +
337O CYS* 3.4 4.9 + - - +
338O ALA* 3.0 24.4 + - - +
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Residues in contact with TYR 335 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289M LYS* 3.7 28.5 - - + -
297M ASP 3.0 20.0 + - - -
298M VAL* 3.3 12.5 - - - -
300M GLY* 3.2 26.4 + - - -
301M ASN* 2.9 38.4 - - - +
359M SER* 4.6 0.2 - - - -
360M ASP* 3.3 23.3 - - - -
363M ARG* 3.6 11.7 - - - -
76O VAL* 3.4 10.5 - - + +
78O PHE* 3.7 10.1 - + - -
331O GLU* 2.9 53.1 + - + +
332O THR 3.7 4.0 - - - +
333O LEU 3.2 0.2 - - - -
334O ALA* 1.3 73.8 - - - +
336O ASP* 1.3 66.0 + - - +
337O CYS 3.0 1.3 - - - -
338O ALA* 2.8 12.9 + - + +
339O LEU 2.9 3.1 + - - -
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Residues in contact with ASP 336 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289M LYS* 2.8 36.4 + - - +
289O LYS* 3.9 12.9 + - - -
290O THR* 2.7 29.2 + - - +
304O MET* 4.7 5.9 - - - +
310O TRP* 2.8 25.2 + - + +
332O THR* 3.0 18.7 + - - +
333O LEU 3.4 7.6 - - - +
335O TYR* 1.3 75.6 - - - +
337O CYS* 1.3 62.3 + - - +
339O LEU* 3.3 7.2 + - - +
340O MET* 3.2 28.9 + - + +
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Residues in contact with CYS 337 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39O THR* 3.1 32.4 + - - +
40O ILE 3.6 7.2 - - - -
41O PRO* 3.6 30.5 - - + -
310O TRP* 3.8 21.8 - - - -
333O LEU 3.0 16.7 + - - -
334O ALA 3.6 8.5 - - - +
335O TYR 3.0 0.2 - - - -
336O ASP* 1.3 76.3 - - - +
338O ALA* 1.3 64.6 + - - +
340O MET* 3.3 3.5 + - - -
341O ASN* 2.9 32.1 + - - +
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Residues in contact with ALA 338 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301M ASN* 4.1 1.1 - - - +
359M SER* 3.6 17.5 - - - +
363M ARG* 3.8 20.9 - - - +
12N VAL* 4.6 12.1 - - + +
78O PHE* 5.0 1.8 - - + -
334O ALA 3.0 13.4 + - - +
335O TYR* 2.8 12.6 + - + +
337O CYS* 1.3 76.3 - - - +
339O LEU* 1.3 63.3 + - - +
341O ASN* 3.9 6.7 - - - +
342O THR* 2.8 30.5 + - - -
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Residues in contact with LEU 339 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289M LYS* 4.5 14.4 - - - +
301M ASN* 3.8 13.1 + - + +
304M MET* 5.2 2.9 - - + -
339M LEU* 4.4 22.2 - - + -
352M LEU* 4.5 9.4 - - + -
355M LEU* 3.9 13.3 - - + +
356M MET* 3.8 43.1 - - + +
359M SER* 4.6 2.0 - - - -
289O LYS* 6.1 0.4 - - - +
304O MET* 6.5 0.7 - - + -
335O TYR 2.9 9.9 + - - +
336O ASP* 3.5 10.8 - - - +
338O ALA* 1.3 78.5 - - - +
340O MET* 1.3 64.1 + - + +
342O THR* 3.3 6.5 + - - -
343O ALA* 3.1 20.3 + - - +
352O LEU* 4.4 14.8 - - + -
356O MET* 6.5 0.2 - - - -
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Residues in contact with MET 340 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19O PHE* 3.4 41.9 - - + -
39O THR* 3.8 19.1 - - + +
304O MET* 4.1 26.2 - - - +
307O CYS* 3.7 32.5 - - - -
310O TRP* 4.6 5.2 - - + -
336O ASP 3.2 22.3 + - - +
337O CYS* 3.3 22.4 + - - +
339O LEU* 1.3 81.2 - - + +
341O ASN* 1.3 57.0 + - - +
343O ALA* 3.0 6.6 + - - +
344O LEU* 2.9 24.4 + - - +
352O LEU* 4.1 10.8 - - + -
356O MET* 4.6 4.0 - - - -
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Residues in contact with ASN 341 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N LYS 5.7 1.4 + - - -
12N VAL* 4.2 21.2 + - + +
37O GLY 5.5 0.7 - - - +
38O TYR* 3.6 17.7 - - + +
39O THR* 2.8 51.4 + - - +
79O PRO* 5.7 5.9 - - - +
337O CYS* 2.9 24.1 + - - +
338O ALA* 3.9 6.0 - - - +
339O LEU 3.2 0.2 - - - -
340O MET* 1.3 73.4 - - - +
342O THR* 1.3 60.6 + - - +
344O LEU* 3.4 8.7 + - + +
345O GLU* 2.9 38.2 + - + +
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Residues in contact with THR 342 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355M LEU* 3.5 32.3 - - + +
358M LEU* 3.8 26.0 - - + -
359M SER* 3.4 17.2 - - - -
4N PHE* 3.6 23.6 - - + -
12N VAL* 4.1 3.7 - - - +
338O ALA 2.8 21.1 + - - -
339O LEU 3.5 5.8 - - - -
340O MET 3.3 0.2 - - - -
341O ASN* 1.3 76.7 - - - +
343O ALA* 1.3 54.9 + - - +
345O GLU* 3.3 0.7 + - - -
346O THR* 2.8 35.5 + - - +
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Residues in contact with ALA 343 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355M LEU* 4.0 13.2 - - + +
19O PHE* 4.2 0.7 - - + -
339O LEU 3.1 10.9 + - - +
340O MET 3.0 10.6 + - - +
342O THR* 1.3 78.4 - - - +
344O LEU* 1.3 61.2 - - - +
346O THR* 3.4 4.4 + - - -
347O LYS 3.1 4.3 + - - -
348O ASN 2.7 47.0 + - - +
349O ASP* 3.8 7.4 - - - -
352O LEU* 3.8 20.0 - - + -
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Residues in contact with LEU 344 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19O PHE* 3.4 34.3 - - + +
20O GLY* 4.1 4.0 - - - -
21O VAL* 3.8 17.5 - - + -
37O GLY* 3.5 33.7 - - - +
38O TYR* 4.0 2.2 - - - -
340O MET 2.9 12.5 + - - +
341O ASN* 3.6 25.6 - - - +
343O ALA* 1.3 75.9 - - - +
345O GLU* 1.3 64.9 + - - +
347O LYS* 3.5 17.2 + - - +
349O ASP* 3.6 29.4 - - + +
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Residues in contact with GLU 345 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA* 5.8 3.3 - - - +
4N PHE* 4.0 8.5 - - + -
7N ALA 5.2 0.2 - - - -
8N SER* 2.6 45.9 + - - +
11N LYS* 3.2 40.7 + - - +
12N VAL* 3.8 20.1 - - + +
37O GLY 4.1 7.8 - - - +
38O TYR* 5.8 0.2 - - - +
341O ASN* 2.9 25.9 + - + +
342O THR 3.9 3.6 - - - +
343O ALA 3.2 0.6 - - - -
344O LEU* 1.3 79.2 - - - +
346O THR* 1.3 58.9 + - - +
347O LYS* 3.3 16.4 + - - +
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Residues in contact with THR 346 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355M LEU* 3.5 9.7 - - - +
358M LEU* 3.6 29.6 - - + -
2N LEU* 4.4 13.7 - - + +
3N ASP 3.8 14.4 - - - +
4N PHE* 4.3 8.1 - - + -
342O THR* 2.8 21.6 + - + +
343O ALA 3.5 2.8 + - - -
345O GLU* 1.3 77.6 - - - +
347O LYS* 1.3 66.0 + - - +
348O ASN* 3.0 25.8 + - - +
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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