Contacts of the helix formed by residues 332 - 355 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339J GLN* 3.5 0.7 - - - +
270K TRP* 5.1 6.3 - - + -
330K SER* 3.2 10.8 + - - +
331K LYS* 1.3 95.3 - - - +
333K GLN* 1.3 63.9 + - - +
334K LYS 3.2 3.6 - - - +
335K THR* 3.6 28.7 + - + -
336K ILE* 3.0 29.6 + - + +
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Residues in contact with GLN 333 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274J THR* 4.6 9.8 + - - +
339J GLN* 2.7 34.9 + - + +
343J THR* 3.1 27.5 + - - +
289K LEU* 3.2 26.5 - - + +
293K LEU* 3.8 24.1 - - - +
327K PHE* 3.3 39.8 - - + +
328K ALA* 3.0 28.6 - - - +
330K SER* 3.6 6.2 - - - +
332K ASN* 1.3 73.2 - - - +
334K LYS* 1.3 58.1 + - - +
337K CYS* 3.6 9.7 + - - -
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Residues in contact with LYS 334 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338J GLN* 5.1 4.0 + - - +
339J GLN* 4.5 6.3 - - + +
342J ASP* 3.4 42.3 + - + +
512J LYS* 4.7 11.1 - - - +
514J LEU* 5.9 2.8 - - - +
516J LYS* 4.5 19.5 - - - +
285K VAL* 4.2 24.5 - - + +
286K LEU* 4.6 6.7 - - + -
289K LEU* 4.6 15.5 - - + +
332K ASN* 3.2 0.8 - - - +
333K GLN* 1.3 77.4 - - - +
335K THR* 1.3 61.2 + - - +
337K CYS* 4.3 2.9 - - - +
338K GLN* 3.0 34.6 + - + +
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Residues in contact with THR 335 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270K TRP* 3.6 23.2 - - + -
332K ASN* 3.1 31.1 + - + +
334K LYS* 1.3 79.4 - - - +
336K ILE* 1.3 65.0 - - - +
338K GLN* 3.1 16.7 + - + +
339K GLN* 3.2 11.1 + - - +
331L LYS 5.6 0.9 - - - +
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Residues in contact with ILE 336 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268K VAL* 3.9 20.4 - - + -
269K SER 4.6 0.4 - - - +
270K TRP* 3.6 45.5 - - + +
273K VAL* 3.6 34.2 - - + +
274K THR* 5.3 1.6 + - - -
327K PHE* 3.5 27.1 - - + -
330K SER* 3.3 26.0 - - - +
332K ASN* 3.0 14.6 + - + +
335K THR* 1.3 77.7 - - - +
337K CYS* 1.3 60.9 + - - +
339K GLN* 3.6 4.7 + - - +
340K ALA* 3.5 16.6 + - - +
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Residues in contact with CYS 337 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273K VAL* 4.2 13.9 - - - -
285K VAL* 4.3 9.6 - - + +
288K LEU* 3.4 14.7 - - + +
289K LEU* 3.6 30.5 - - + -
292K TYR* 4.7 1.8 - - - -
327K PHE* 3.5 30.1 - - - -
333K GLN 3.6 10.5 + - - +
334K LYS* 4.3 3.4 - - - +
335K THR 3.3 0.2 - - - -
336K ILE* 1.3 76.9 - - - +
338K GLN* 1.3 64.6 + - - +
340K ALA* 3.3 9.6 + - - +
341K VAL* 3.0 28.7 + - - +
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Residues in contact with GLN 338 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514J LEU* 4.9 11.3 - - - +
285K VAL* 3.3 38.2 - - + +
334K LYS* 3.0 28.3 + - + +
335K THR* 3.1 11.6 + - + +
337K CYS* 1.3 75.1 - - - +
339K GLN* 1.3 64.5 + - - +
341K VAL* 3.1 20.6 + - - +
342K ASP* 3.0 38.4 + - - +
334L LYS* 5.0 4.9 + - - +
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Residues in contact with GLN 339 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270K TRP* 3.2 29.8 - - + +
274K THR* 4.2 8.0 + - - -
335K THR 3.2 7.7 + - - +
336K ILE 4.0 7.2 - - - +
337K CYS 3.4 0.2 - - - -
338K GLN* 1.3 78.7 + - - +
340K ALA* 1.3 62.1 + - - +
342K ASP* 3.2 14.1 + - + +
343K THR* 2.9 25.7 + - - +
289L LEU* 6.3 0.9 - - + -
330L SER 3.1 11.9 + - - +
331L LYS 3.1 23.2 + - - +
332L ASN* 3.7 0.4 - - - +
333L GLN* 2.8 54.8 - - + +
334L LYS* 4.5 6.5 - - + +
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Residues in contact with ALA 340 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273K VAL* 4.1 4.5 - - + +
274K THR* 4.0 20.5 + - - +
277K ALA* 3.6 14.2 - - + +
288K LEU* 3.4 17.7 - - + -
336K ILE 3.5 10.2 + - - +
337K CYS* 3.3 12.5 + - - +
338K GLN 3.1 0.6 - - - -
339K GLN* 1.3 78.8 - - - +
341K VAL* 1.3 62.4 + - - +
343K THR* 3.0 11.2 + - - -
344K VAL* 2.9 26.4 + - - +
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Residues in contact with VAL 341 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282K CYS 4.3 1.1 - - - +
283K ASP* 3.5 30.7 - - - +
284K ASP 3.1 28.7 - - - +
285K VAL* 3.7 21.3 - - + -
288K LEU* 3.9 5.4 - - + -
337K CYS 3.0 17.5 - - - +
338K GLN* 3.1 10.1 + - - +
340K ALA* 1.3 76.1 - - - +
342K ASP* 1.3 58.7 + - - +
344K VAL* 3.0 11.7 + - - +
345K LEU* 2.9 38.4 + - + +
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Residues in contact with ASP 342 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338K GLN* 3.0 35.4 + - - +
339K GLN* 3.2 12.3 + - + +
341K VAL* 1.3 77.4 - - - +
343K THR* 1.3 57.3 + - - +
345K LEU* 3.8 8.9 - - - +
346K ALA* 2.8 30.0 + - - +
516K LYS* 5.9 0.2 - - - -
286L LEU* 3.6 24.9 - - + +
289L LEU* 3.9 11.6 - - + +
334L LYS* 3.5 37.8 + - + +
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Residues in contact with THR 343 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274K THR* 3.6 23.2 - - + +
278K MET* 3.5 29.4 - - + +
339K GLN 2.9 14.7 + - - -
340K ALA 3.0 9.1 + - - -
342K ASP* 1.3 75.8 - - - +
344K VAL* 1.3 63.8 + - - +
346K ALA* 3.4 7.5 - - - +
347K LYS* 3.1 16.6 + - - +
289L LEU* 4.4 3.6 - - - +
293L LEU* 3.6 22.9 - - + -
333L GLN* 3.3 20.0 + - - +
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Residues in contact with VAL 344 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277K ALA* 3.7 28.0 - - + +
278K MET* 4.3 8.3 - - - +
281K LYS* 3.6 22.9 - - + +
282K CYS 3.2 23.8 - - - +
283K ASP* 3.9 4.5 - - - +
340K ALA 2.9 20.7 + - - +
341K VAL 3.0 6.3 + - - +
343K THR* 1.3 74.5 - - - +
345K LEU* 1.3 65.2 + - - +
347K LYS* 3.1 19.9 + - - +
348K LYS* 3.3 31.4 + - - +
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Residues in contact with LEU 345 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283K ASP* 3.9 30.3 - - + +
341K VAL* 2.9 30.4 + - + +
342K ASP* 4.0 10.3 - - - +
344K VAL* 1.3 76.5 - - - +
346K ALA* 1.3 52.3 + - - +
348K LYS* 3.4 15.3 + - + +
349K ARG* 2.8 36.4 + - - +
466K ASP* 4.9 1.2 - - - +
511K LYS* 4.3 24.7 - - + +
286L LEU* 4.0 24.9 - - + -
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Residues in contact with ALA 346 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342K ASP 2.8 20.6 + - - +
343K THR* 3.4 11.9 - - - +
344K VAL 3.1 0.2 - - - -
345K LEU* 1.3 74.5 - - - +
347K LYS* 1.3 64.4 + - - +
349K ARG* 3.1 5.5 + - - +
350K VAL* 3.0 29.6 + - - +
286L LEU* 3.4 26.9 - - - +
289L LEU* 4.1 7.4 - - + -
290L GLY* 3.6 17.8 - - - +
293L LEU* 4.8 0.9 - - + -
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Residues in contact with LYS 347 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278K MET* 3.9 26.9 - - + +
343K THR 3.1 11.9 + - - +
344K VAL* 3.1 12.0 + - + +
346K ALA* 1.3 75.4 - - - +
348K LYS* 1.3 57.6 + - + +
350K VAL* 3.0 10.7 + - + +
351K ASP* 2.7 55.9 + - - +
290L GLY* 4.9 1.3 - - - -
294L GLU* 4.4 18.9 + - + +
297L TYR* 5.8 2.8 + - - -
304L LYS* 5.7 4.8 - - - +
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Residues in contact with LYS 348 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281K LYS* 3.7 24.3 + - - +
283K ASP* 4.4 11.3 - - - +
344K VAL* 3.3 36.2 + - - +
345K LEU* 3.8 16.8 - - + +
347K LYS* 1.3 77.2 - - + +
349K ARG* 1.3 63.1 + - - +
351K ASP* 4.0 8.7 - - - +
352K SER* 3.1 27.4 + - - -
466K ASP* 4.1 16.2 - - + +
467K GLN* 5.5 9.4 - - - +
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Residues in contact with ARG 349 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345K LEU* 2.8 18.3 + - - +
346K ALA* 3.2 13.9 - - - +
348K LYS* 1.3 77.4 - - - +
350K VAL* 1.3 57.6 + - - +
352K SER* 3.0 13.9 + - - -
353K LEU* 4.0 5.7 - - - +
465K ILE* 3.1 17.4 - - - +
466K ASP* 3.0 29.3 + - - -
511K LYS* 3.5 16.6 - - - +
516K LYS* 2.9 36.9 + - - +
517K ARG* 3.1 27.5 + - - +
284L ASP* 4.2 1.0 + - - -
286L LEU* 3.2 36.9 - - - +
287L LEU* 3.4 40.6 - - + +
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Residues in contact with VAL 350 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346K ALA 3.0 16.0 + - - +
347K LYS* 3.0 9.8 + - + +
349K ARG* 1.3 77.1 - - + +
351K ASP* 1.3 63.7 + - - +
352K SER 3.1 1.6 - - - -
353K LEU* 2.9 22.6 + - + +
354K GLN* 3.1 42.1 + - + +
287L LEU* 4.3 9.4 - - + +
290L GLY* 3.7 7.6 - - - +
291L MET* 3.4 42.4 - - + +
294L GLU* 4.2 10.8 - - - +
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Residues in contact with ASP 351 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347K LYS* 2.7 52.1 + - - +
348K LYS* 3.9 7.3 + - - +
350K VAL* 1.3 78.5 - - - +
352K SER* 1.3 57.9 + - - +
353K LEU 3.0 4.6 + - - -
354K GLN* 4.5 3.5 - - - +
355K LEU* 3.3 56.6 + - + +
360K MET* 4.0 8.2 - - + +
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Residues in contact with SER 352 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348K LYS 3.1 12.2 + - - -
349K ARG 3.0 18.9 + - - -
351K ASP* 1.3 74.4 - - - +
353K LEU* 1.3 63.5 + - - +
355K LEU 4.9 2.9 - - - +
360K MET* 4.2 19.7 - - - +
466K ASP* 3.1 38.8 + - - -
467K GLN 5.5 1.6 - - - -
517K ARG* 4.1 5.4 + - - -
519K GLN* 5.1 3.6 - - - -
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Residues in contact with LEU 353 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349K ARG 4.0 3.6 - - - +
350K VAL 2.9 6.3 + - - +
352K SER* 1.3 88.7 - - - +
354K GLN* 1.3 67.3 + - + +
355K LEU 4.6 2.1 - - - +
517K ARG* 3.2 33.7 - - - +
519K GLN* 6.0 2.7 - - + -
287L LEU* 3.7 32.1 - - + -
291L MET* 6.2 1.3 - - - -
310L GLN* 4.9 8.0 + - - +
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Residues in contact with GLN 354 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350K VAL* 3.1 38.1 + - + +
351K ASP* 5.0 1.8 - - - -
353K LEU* 1.3 81.4 - - + +
355K LEU* 1.3 68.8 + - + +
356K THR* 3.5 5.9 + - - +
359K GLN* 4.6 1.2 - - - +
291L MET* 3.7 14.3 - - + +
294L GLU* 3.4 20.2 + - - -
304L LYS* 3.9 23.2 - - - +
309L GLU* 4.9 5.5 - - - +
310L GLN* 3.3 43.7 + - + +
313L HIS* 5.5 2.5 - - - +
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Residues in contact with LEU 355 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351K ASP* 3.3 48.5 + - + +
352K SER 4.9 0.9 - - - -
353K LEU 4.6 2.9 - - - +
354K GLN* 1.3 83.1 + - + +
356K THR* 1.3 69.6 + - - +
357K ARG 3.8 0.3 + - - -
359K GLN* 3.4 30.7 - - + +
360K MET* 3.8 16.2 - - + +
363K ASN* 3.6 26.9 - - - +
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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