Contacts of the helix formed by residues 332 - 355 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339K GLN* 3.7 0.7 - - - +
270L TRP* 5.1 6.1 - - + -
330L SER* 3.2 9.5 + - - +
331L LYS* 1.3 94.6 - - - +
333L GLN* 1.3 64.3 + - - +
334L LYS 3.2 2.9 - - - +
335L THR* 3.6 29.1 + - + +
336L ILE* 3.0 28.7 + - + +
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Residues in contact with GLN 333 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274K THR* 4.8 8.6 + - - +
339K GLN* 2.8 36.6 + - + +
343K THR* 3.3 26.3 + - - +
289L LEU* 3.2 26.9 - - + +
293L LEU* 3.8 23.6 - - - +
327L PHE* 3.3 39.4 - - + +
328L ALA* 3.0 28.2 - - - +
330L SER* 3.6 6.4 - - - +
332L ASN* 1.3 73.1 - - - +
334L LYS* 1.3 58.5 + - - +
337L CYS* 3.6 9.9 + - - -
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Residues in contact with LYS 334 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338K GLN* 5.0 4.2 + - - +
339K GLN* 4.5 6.3 - - + +
342K ASP* 3.5 40.8 + - + +
512K LYS* 4.7 13.5 - - - +
514K LEU* 5.8 3.7 - - - +
516K LYS* 4.5 17.5 - - - +
285L VAL* 4.2 23.7 - - + +
286L LEU* 4.6 6.3 - - + -
289L LEU* 4.3 16.5 - - + +
332L ASN* 3.2 0.8 - - - +
333L GLN* 1.3 77.2 - - - +
335L THR* 1.3 60.6 + - - +
336L ILE 3.5 0.2 - - - -
337L CYS* 4.0 2.9 - - - +
338L GLN* 3.0 34.5 + - + +
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Residues in contact with THR 335 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270L TRP* 3.6 22.9 - - + -
332L ASN* 3.1 30.6 + - + +
334L LYS* 1.3 77.9 - - - +
336L ILE* 1.3 66.3 + - - +
338L GLN* 3.1 16.3 + - + +
339L GLN* 3.2 11.3 + - - +
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Residues in contact with ILE 336 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268L VAL* 3.9 21.3 - - + -
269L SER 4.6 0.9 - - - +
270L TRP* 3.6 45.8 - - + +
273L VAL* 3.6 33.6 - - + +
274L THR* 5.3 1.6 + - - -
327L PHE* 3.5 25.4 - - + -
330L SER* 3.3 26.5 - - - +
332L ASN* 3.0 12.9 + - + +
335L THR* 1.3 76.3 - - - +
337L CYS* 1.3 62.3 + - - +
338L GLN 3.4 0.2 + - - -
339L GLN* 3.6 5.0 + - - +
340L ALA* 3.5 16.5 + - - +
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Residues in contact with CYS 337 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273L VAL* 4.2 13.7 - - - -
285L VAL* 4.3 9.4 - - + +
288L LEU* 3.4 15.7 - - + +
289L LEU* 3.6 30.3 - - + -
292L TYR* 4.7 1.8 - - - -
327L PHE* 3.5 29.4 - - - -
333L GLN 3.6 10.3 + - - +
334L LYS* 4.3 3.1 - - - +
335L THR 3.3 0.4 - - - -
336L ILE* 1.3 76.9 - - - +
338L GLN* 1.3 64.8 + - - +
340L ALA* 3.3 9.8 + - - +
341L VAL* 3.0 28.0 + - - +
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Residues in contact with GLN 338 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334G LYS* 5.2 2.8 + - - -
514K LEU* 4.8 13.0 - - - +
285L VAL* 3.3 38.1 - - + +
334L LYS* 3.0 27.5 + - + +
335L THR* 3.1 11.8 + - + +
337L CYS* 1.3 76.9 - - - +
339L GLN* 1.3 62.5 + - - +
341L VAL* 3.1 20.5 + - - +
342L ASP* 3.0 39.1 + - - +
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Residues in contact with GLN 339 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289G LEU* 6.6 0.2 - - + -
330G SER 3.4 11.9 + - - +
331G LYS 2.7 36.2 + - - -
332G ASN* 3.4 0.8 - - - +
333G GLN* 2.9 36.3 - - + +
334G LYS* 4.6 7.6 - - + +
270L TRP* 3.1 30.7 - - + +
274L THR* 4.2 9.6 + - - +
335L THR 3.2 8.0 + - - +
336L ILE 3.6 7.1 + - - +
338L GLN* 1.3 78.6 - - - +
340L ALA* 1.3 63.0 + - - +
342L ASP* 3.2 12.3 + - + +
343L THR* 2.9 26.7 + - - +
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Residues in contact with ALA 340 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273L VAL* 4.1 4.0 - - + +
274L THR* 4.0 21.9 + - - +
277L ALA* 3.6 13.7 - - + +
288L LEU* 3.4 17.7 - - + -
336L ILE 3.5 9.8 + - - +
337L CYS* 3.4 11.9 - - - +
339L GLN* 1.3 79.7 - - - +
341L VAL* 1.3 62.4 + - - +
343L THR* 3.0 11.6 + - - -
344L VAL* 2.9 26.3 + - - +
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Residues in contact with VAL 341 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282L CYS 4.3 0.7 - - - +
283L ASP* 3.4 30.3 - - - +
284L ASP 3.1 28.0 - - - +
285L VAL* 3.7 21.5 - - + -
288L LEU* 3.9 5.8 - - + -
337L CYS 3.0 16.8 - - - +
338L GLN* 3.1 9.4 + - - +
340L ALA* 1.3 76.5 - - - +
342L ASP* 1.3 58.2 + - - +
344L VAL* 3.0 12.1 + - - +
345L LEU* 2.9 38.5 + - + +
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Residues in contact with ASP 342 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G LEU* 3.6 18.5 - - + +
289G LEU* 3.8 8.0 - - + +
334G LYS* 3.2 47.7 + - + +
338L GLN* 3.0 36.4 + - - +
339L GLN* 3.2 12.2 + - + +
341L VAL* 1.3 77.0 - - - +
343L THR* 1.3 57.9 + - - +
345L LEU* 3.5 9.5 + - - +
346L ALA* 2.8 29.5 + - - +
516L LYS* 5.9 0.2 - - - -
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Residues in contact with THR 343 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289G LEU* 4.3 4.8 - - - +
293G LEU* 3.6 24.8 - - + +
333G GLN* 3.2 20.1 + - - +
274L THR* 3.6 23.4 - - + +
278L MET* 3.5 28.4 - - + +
339L GLN* 2.9 14.6 + - - +
340L ALA 3.0 9.9 + - - -
342L ASP* 1.3 73.8 - - - +
344L VAL* 1.3 65.2 + - - +
346L ALA* 3.4 7.2 - - - +
347L LYS* 3.1 16.6 + - - +
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Residues in contact with VAL 344 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277L ALA* 3.7 28.3 - - + +
278L MET* 4.3 9.0 - - - +
281L LYS* 3.6 22.4 - - - +
282L CYS 3.2 24.2 - - - +
283L ASP* 3.9 4.9 - - + +
340L ALA 2.9 21.1 + - - +
341L VAL 3.0 6.5 + - - +
343L THR* 1.3 75.9 - - - +
345L LEU* 1.3 65.2 + - - +
347L LYS* 3.1 19.7 + - + +
348L LYS* 3.3 32.2 + - - +
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Residues in contact with LEU 345 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G LEU* 3.9 25.4 - - + -
283L ASP* 3.9 29.2 - - + +
341L VAL* 2.9 30.2 + - + +
342L ASP* 4.0 10.1 - - - +
344L VAL* 1.3 75.0 - - - +
346L ALA* 1.3 52.3 + - - +
348L LYS* 3.4 15.6 + - + +
349L ARG* 2.8 36.0 + - - +
466L ASP* 5.0 1.6 - - - +
511L LYS* 4.3 24.7 - - + +
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Residues in contact with ALA 346 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G LEU* 3.4 25.5 - - - +
289G LEU* 3.7 18.4 - - + -
290G GLY* 3.7 10.8 - - - +
293G LEU* 4.8 1.3 - - + -
342L ASP 2.8 19.7 + - - +
343L THR* 3.4 8.1 - - - +
344L VAL 3.1 0.2 - - - -
345L LEU* 1.3 75.4 - - - +
347L LYS* 1.3 66.5 + - - +
349L ARG* 3.1 5.4 + - - +
350L VAL* 3.0 29.1 + - - +
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Residues in contact with LYS 347 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G GLY* 4.8 2.4 - - - -
294G GLU* 4.3 21.0 + - + +
297G TYR* 5.5 6.5 + - - -
304G LYS* 6.0 1.6 - - - +
278L MET* 3.9 27.4 - - + +
343L THR 3.1 11.4 + - - +
344L VAL* 3.1 11.9 + - - +
346L ALA* 1.3 76.3 - - - +
348L LYS* 1.3 58.4 + - + +
350L VAL* 3.0 10.7 + - + +
351L ASP* 2.7 56.0 + - - +
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Residues in contact with LYS 348 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281L LYS* 3.7 25.1 + - - +
283L ASP* 4.4 12.3 - - - +
344L VAL* 3.3 35.3 + - - +
345L LEU* 3.7 17.0 - - + +
347L LYS* 1.3 77.4 - - + +
349L ARG* 1.3 62.5 + - - +
351L ASP* 4.0 8.2 - - - +
352L SER* 3.1 27.4 + - - -
466L ASP* 4.1 16.8 - - + +
467L GLN* 5.5 9.4 - - - +
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Residues in contact with ARG 349 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284G ASP* 4.1 2.8 + - - -
286G LEU* 3.0 37.6 - - - +
287G LEU* 3.2 39.3 - - + +
345L LEU 2.8 13.8 + - - +
346L ALA* 3.2 17.3 - - - +
348L LYS* 1.3 75.9 - - - +
350L VAL* 1.3 56.5 + - - +
352L SER* 3.0 13.7 + - - -
353L LEU* 4.0 4.3 - - - +
465L ILE* 3.1 17.2 - - - +
466L ASP* 2.9 28.6 + - - -
511L LYS* 3.5 16.2 - - - +
516L LYS* 2.9 38.1 + - - +
517L ARG* 3.1 26.9 + - - +
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Residues in contact with VAL 350 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G LEU* 3.8 14.1 - - + +
290G GLY* 3.3 26.9 - - - -
291G MET* 3.2 20.0 - - + +
294G GLU* 4.3 11.2 - - - +
346L ALA 3.0 15.6 + - - +
347L LYS* 3.0 9.6 + - + +
349L ARG* 1.3 76.5 - - - +
351L ASP* 1.3 62.5 + - - +
352L SER 3.1 1.8 - - - -
353L LEU* 2.9 21.3 + - - +
354L GLN* 3.1 42.7 + - - +
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Residues in contact with ASP 351 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347L LYS* 2.7 53.9 + - - +
348L LYS* 3.4 8.1 + - - +
350L VAL* 1.3 76.7 - - - +
352L SER* 1.3 57.8 + - - +
353L LEU 3.0 4.7 + - - -
354L GLN* 4.0 3.5 - - - +
355L LEU* 3.3 55.5 + - + +
360L MET* 4.0 9.0 - - + +
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Residues in contact with SER 352 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348L LYS 3.1 12.2 + - - -
349L ARG 3.0 19.6 + - - -
351L ASP* 1.3 75.3 - - - +
353L LEU* 1.3 63.7 + - - +
355L LEU 4.9 2.6 - - - +
360L MET* 4.2 20.0 - - - +
466L ASP* 3.1 38.0 + - - -
467L GLN 5.5 1.6 - - - -
517L ARG* 4.1 5.2 + - - -
519L GLN* 5.1 2.7 - - - -
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Residues in contact with LEU 353 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G LEU* 3.3 37.0 - - + -
291G MET* 6.2 1.1 - - - -
310G GLN* 4.8 7.3 + - - +
349L ARG 4.0 3.8 - - - +
350L VAL* 2.9 6.8 + - + +
352L SER* 1.3 88.7 - - - +
354L GLN* 1.3 67.3 + - + +
355L LEU 3.9 2.1 - - - +
517L ARG* 3.2 33.4 - - - +
519L GLN* 6.0 2.5 - - + -
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Residues in contact with GLN 354 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G MET* 3.1 29.0 - - + +
294G GLU* 3.0 29.1 + - - +
304G LYS* 4.1 21.0 - - - +
309G GLU* 5.4 2.4 - - - +
310G GLN* 3.4 44.9 + - + +
313G HIS* 5.2 2.6 - - - +
350L VAL* 3.1 20.8 + - + +
351L ASP* 5.0 2.0 - - - +
353L LEU* 1.3 80.9 - - + +
355L LEU* 1.3 69.7 + - + +
356L THR* 3.5 5.4 + - - +
359L GLN* 4.6 1.0 - - - +
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Residues in contact with LEU 355 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304G LYS* 6.2 3.6 - - - -
351L ASP* 3.3 48.3 + - + +
352L SER 4.9 1.0 - - - -
353L LEU 4.6 2.6 - - - -
354L GLN* 1.3 83.1 + - + +
356L THR* 1.3 69.2 + - - +
357L ARG 3.8 0.2 + - - -
359L GLN* 3.4 29.8 - - + +
360L MET* 3.8 15.3 - - + +
363L 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