Contacts of the helix formed by residues 332 - 355 (chain G) in PDB entry 4E2I
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 332 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G TRP* 5.1 6.5 - - + -
330G SER* 3.2 9.9 + - - +
331G LYS* 1.3 93.9 - - - +
333G GLN* 1.3 63.1 + - - +
334G LYS 3.2 3.4 - - - +
335G THR* 3.6 28.5 + - + +
336G ILE* 3.0 29.8 + - + +
339L GLN* 3.4 1.6 - - - +
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Residues in contact with GLN 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289G LEU* 3.2 26.6 - - + +
293G LEU* 3.8 24.5 - - - +
327G PHE* 3.3 40.4 - - + +
328G ALA* 3.0 28.2 - - - +
330G SER* 3.6 13.7 - - - +
332G ASN* 1.3 77.3 - - - +
334G LYS* 1.3 59.1 + - - +
337G CYS* 3.6 9.9 + - - -
274L THR* 4.6 10.7 + - - +
339L GLN* 2.9 18.8 - - + +
343L THR* 3.2 28.3 + - - +
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Residues in contact with LYS 334 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285G VAL* 4.1 24.0 - - + +
286G LEU* 4.6 7.4 - - + -
289G LEU* 4.3 11.8 - - + +
332G ASN 3.2 0.4 - - - -
333G GLN* 1.3 78.1 - - - +
335G THR* 1.3 60.8 + - - +
337G CYS* 4.0 3.1 - - - +
338G GLN* 3.0 34.6 + - + +
338L GLN* 5.2 2.6 + - - -
339L GLN* 4.6 6.9 - - + +
342L ASP* 3.2 48.8 + - + +
512L LYS* 4.9 9.5 - - - +
514L LEU* 5.9 2.8 - - - +
516L LYS* 4.3 20.2 - - - +
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Residues in contact with THR 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G TRP* 3.6 23.6 - - + -
332G ASN* 3.1 30.8 + - + +
334G LYS* 1.3 77.9 - - - +
336G ILE* 1.3 66.1 + - - +
338G GLN* 3.1 16.0 + - + +
339G GLN* 3.2 11.4 + - - +
331H LYS 5.7 0.9 - - - +
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Residues in contact with ILE 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268G VAL* 3.9 20.4 - - + -
269G SER 4.6 0.9 - - - +
270G TRP* 3.6 46.3 - - + +
273G VAL* 3.6 33.5 - - + +
274G THR* 5.3 1.6 + - - -
327G PHE* 3.5 26.2 - - + -
330G SER* 3.3 26.2 - - - +
332G ASN* 3.0 12.9 + - + +
335G THR* 1.3 76.7 - - - +
337G CYS* 1.3 63.5 + - - +
338G GLN 3.4 0.2 + - - -
339G GLN* 3.6 4.5 + - - +
340G ALA* 3.5 16.5 + - - +
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Residues in contact with CYS 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273G VAL* 4.2 14.4 - - - -
285G VAL* 4.3 9.9 - - + +
288G LEU* 3.4 15.8 - - + +
289G LEU* 3.6 28.9 - - + -
292G TYR* 4.7 1.3 - - - -
327G PHE* 3.5 30.1 - - - -
333G GLN 3.6 9.2 + - - +
334G LYS* 4.3 3.1 - - - +
335G THR 3.3 0.4 - - - -
336G ILE* 1.3 76.8 - - - +
338G GLN* 1.3 64.8 + - - +
340G ALA* 3.3 10.1 + - - +
341G VAL* 3.0 27.6 + - - +
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Residues in contact with GLN 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285G VAL* 3.3 37.0 - - + +
334G LYS* 3.0 28.3 + - + +
335G THR* 3.1 12.3 + - + +
337G CYS* 1.3 77.6 - - - +
339G GLN* 1.3 63.6 + - - +
341G VAL* 3.1 21.0 + - - +
342G ASP* 3.0 37.7 + - - +
334H LYS* 5.3 4.3 + - - +
514L LEU* 5.2 10.5 - - - +
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Residues in contact with GLN 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G TRP* 3.1 31.0 - - + +
274G THR* 4.2 8.1 + - - +
335G THR 3.2 8.1 + - - +
336G ILE 3.9 6.7 - - - +
338G GLN* 1.3 79.2 - - - +
340G ALA* 1.3 60.9 + - - +
342G ASP* 3.2 13.4 + - + +
343G THR* 2.9 26.3 + - - +
289H LEU* 5.6 0.8 - - + +
328H ALA 5.4 0.3 - - - +
330H SER 3.1 20.4 + - - +
331H LYS 3.3 12.3 + - - -
332H ASN* 4.0 0.2 - - - +
333H GLN* 3.0 56.8 + - + +
334H LYS* 5.2 5.6 - - + +
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Residues in contact with ALA 340 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273G VAL* 4.1 3.8 - - + +
274G THR* 3.9 20.3 + - - +
277G ALA* 3.6 14.6 - - + +
288G LEU* 3.4 17.9 - - + -
336G ILE 3.5 11.1 + - - +
337G CYS* 3.3 11.4 + - - +
338G GLN 3.1 0.6 - - - -
339G GLN* 1.3 79.3 - - - +
341G VAL* 1.3 63.7 + - - +
343G THR* 3.0 11.4 + - - -
344G VAL* 2.9 27.1 + - - +
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Residues in contact with VAL 341 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282G CYS 4.3 0.9 - - - +
283G ASP* 3.4 30.5 - - - +
284G ASP 3.1 28.7 - - - +
285G VAL* 3.7 20.4 - - + -
288G LEU* 3.9 5.6 - - + -
337G CYS 3.0 17.9 - - - +
338G GLN* 3.1 10.1 + - - +
340G ALA* 1.3 76.8 - - - +
342G ASP* 1.3 57.8 + - - +
344G VAL* 3.0 11.6 + - - +
345G LEU* 2.9 38.5 + - + +
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Residues in contact with ASP 342 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338G GLN* 3.0 35.8 + - - +
339G GLN* 3.2 13.2 + - + +
341G VAL* 1.3 77.4 - - - +
343G THR* 1.3 57.5 + - - +
345G LEU* 3.8 10.8 - - - +
346G ALA* 2.8 30.2 + - - +
286H LEU* 3.7 27.0 - - + +
289H LEU* 4.2 11.9 - - + -
334H LYS* 3.8 33.4 + - + +
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Residues in contact with THR 343 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G THR* 3.5 23.7 - - + +
278G MET* 3.5 31.8 - - + +
339G GLN* 2.9 14.9 + - - +
340G ALA 3.0 9.1 + - - -
342G ASP* 1.3 76.9 - - - +
344G VAL* 1.3 61.9 + - - +
346G ALA* 3.4 7.0 - - - +
347G LYS* 3.1 16.6 + - - +
289H LEU* 4.7 1.4 - - - +
293H LEU* 3.8 23.5 - - + +
333H GLN* 3.5 18.6 + - - +
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Residues in contact with VAL 344 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G ALA* 3.7 27.6 - - + +
278G MET* 4.3 8.5 - - - +
281G LYS* 3.6 22.2 - - + +
282G CYS 3.2 24.5 - - - +
283G ASP* 4.0 4.7 - - - +
340G ALA 2.9 20.7 + - - +
341G VAL 3.0 6.7 + - - +
343G THR* 1.3 74.7 - - - +
345G LEU* 1.3 67.2 + - - +
347G LYS* 3.1 18.6 + - - +
348G LYS* 3.3 31.9 + - - +
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Residues in contact with LEU 345 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G ASP* 3.9 30.1 - - + +
341G VAL* 2.9 30.4 + - + +
342G ASP* 4.0 10.8 - - - +
344G VAL* 1.3 76.1 - - - +
346G ALA* 1.3 57.6 + - - +
348G LYS* 3.4 14.9 + - + +
349G ARG* 2.8 31.4 + - - +
466G ASP* 4.9 1.4 - - - +
511G LYS* 4.3 26.5 - - + +
286H LEU* 4.3 24.0 - - + -
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Residues in contact with ALA 346 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342G ASP 2.8 20.3 + - - +
343G THR* 3.4 11.9 - - - +
344G VAL 3.1 0.4 - - - -
345G LEU* 1.3 76.0 - - - +
347G LYS* 1.3 64.7 + - - +
349G ARG* 3.1 10.0 + - - +
350G VAL* 3.0 28.7 + - - +
286H LEU* 3.6 21.3 - - - +
289H LEU* 4.4 6.5 - - + -
290H GLY* 3.7 18.2 - - - +
293H LEU* 4.8 1.6 - - + -
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Residues in contact with LYS 347 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G MET* 3.9 26.5 - - + +
343G THR 3.1 11.9 + - - +
344G VAL* 3.1 12.1 + - + +
346G ALA* 1.3 76.3 - - - +
348G LYS* 1.3 58.0 + - + +
350G VAL* 3.0 10.4 + - + +
351G ASP* 2.7 56.9 + - - +
290H GLY* 5.7 0.9 - - - -
294H GLU* 4.6 15.6 + - - +
304H LYS* 5.6 5.5 - - - +
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Residues in contact with LYS 348 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G LYS* 3.7 23.5 + - - +
283G ASP* 4.4 12.1 - - - +
344G VAL* 3.3 35.5 + - - +
345G LEU* 3.8 17.0 - - + +
347G LYS* 1.3 79.3 - - + +
349G ARG* 1.3 63.9 + - - +
351G ASP* 4.0 8.7 - - - +
352G SER* 3.1 27.5 + - - -
466G ASP* 4.1 16.7 - - + +
467G GLN* 5.5 9.4 - - - +
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Residues in contact with ARG 349 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345G LEU* 2.8 15.1 + - - +
346G ALA* 3.1 17.0 + - - +
348G LYS* 1.3 77.1 - - - +
350G VAL* 1.3 56.4 + - - +
352G SER* 3.0 13.0 + - - -
353G LEU* 4.0 6.8 - - - +
465G ILE* 3.1 17.8 - - - +
466G ASP* 2.9 29.0 + - - -
511G LYS* 3.5 17.2 - - - +
516G LYS* 2.9 35.8 + - - +
517G ARG* 3.1 27.8 + - - +
284H ASP* 4.5 0.9 + - - -
286H LEU* 3.2 37.0 - - - +
287H LEU* 3.6 38.1 - - + +
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Residues in contact with VAL 350 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346G ALA 3.0 16.7 + - - +
347G LYS* 3.0 10.1 + - + +
349G ARG* 1.3 77.3 - - - +
351G ASP* 1.3 62.5 + - - +
352G SER 3.1 1.6 - - - -
353G LEU* 2.9 22.5 + - - +
354G GLN* 3.1 42.2 + - + +
287H LEU* 4.6 9.2 - - + +
290H GLY* 3.9 27.8 - - - +
291H MET* 3.7 20.9 - - + +
294H GLU* 4.3 10.8 - - - +
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Residues in contact with ASP 351 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347G LYS* 2.7 53.9 + - - +
348G LYS* 3.4 7.3 + - - +
350G VAL* 1.3 78.4 - - - +
352G SER* 1.3 58.3 + - - +
353G LEU 3.0 5.4 + - - -
354G GLN* 4.5 2.8 - - - +
355G LEU* 3.3 56.3 + - + +
360G MET* 4.0 8.1 - - + +
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Residues in contact with SER 352 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348G LYS 3.1 12.8 + - - -
349G ARG 3.0 19.6 + - - -
351G ASP* 1.3 75.9 - - - +
353G LEU* 1.3 63.8 + - - +
355G LEU 4.9 2.9 - - - +
360G MET* 4.2 20.3 - - - +
466G ASP* 3.1 37.7 + - - -
467G GLN 5.5 1.6 - - - -
517G ARG* 4.1 5.4 + - - -
519G GLN* 5.1 3.1 - - - -
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Residues in contact with LEU 353 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349G ARG 4.0 4.3 - - - +
350G VAL* 2.9 7.2 + - + +
352G SER* 1.3 88.1 - - - +
354G GLN* 1.3 66.7 + - + +
355G LEU 3.9 2.5 - - - +
517G ARG* 3.2 33.9 - - - +
519G GLN* 6.0 2.5 - - + -
287H LEU* 3.8 29.8 - - + -
291H MET* 6.3 1.1 - - - -
310H GLN* 5.0 7.9 + - - +
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Residues in contact with GLN 354 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350G VAL* 3.1 37.9 + - + +
351G ASP* 5.0 2.0 - - - -
353G LEU* 1.3 83.5 - - + +
355G LEU* 1.3 69.9 + - + +
356G THR* 3.5 5.7 + - - +
359G GLN* 4.6 0.9 - - - +
291H MET* 4.0 12.3 - - + +
294H GLU* 3.5 20.0 + - - -
304H LYS* 3.9 21.9 - - - +
309H GLU* 4.7 6.9 - - - +
310H GLN* 3.4 41.4 + - + +
313H HIS* 5.7 2.3 - - - +
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Residues in contact with LEU 355 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351G ASP* 3.3 48.2 + - + +
352G SER 4.9 1.0 - - - +
353G LEU 4.6 2.6 - - - +
354G GLN* 1.3 83.1 + - + +
356G THR* 1.3 70.4 + - - +
357G ARG 3.8 0.2 + - - -
359G GLN* 3.4 31.6 - - + +
360G MET* 3.8 14.3 - - + +
363G ASN* 3.6 26.7 - - - +
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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