Contacts of the helix formed by residues 332 - 355 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A TRP* 5.1 7.2 - - + -
330A SER* 3.2 10.5 + - - +
331A LYS* 1.3 95.6 - - - +
333A GLN* 1.3 64.1 + - - +
334A LYS 3.2 3.4 - - - +
335A THR* 3.6 28.8 + - + -
336A ILE* 3.0 28.8 + - + +
339F GLN* 3.8 0.2 - - - +
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Residues in contact with GLN 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 3.2 26.1 - - + +
293A LEU* 3.8 23.8 - - - +
327A PHE* 3.3 39.6 - - + +
328A ALA* 3.0 28.6 - - - +
330A SER* 3.6 5.6 + - - +
332A ASN* 1.3 72.9 - - - +
334A LYS* 1.3 59.8 + - - +
337A CYS* 3.6 9.9 + - - -
274F THR* 4.9 7.9 + - - +
339F GLN* 2.8 37.5 - - + +
343F THR* 3.3 25.5 + - - +
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Residues in contact with LYS 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A VAL* 4.2 23.5 - - + +
286A LEU* 4.6 7.2 - - + -
289A LEU* 4.6 16.6 - - + +
332A ASN 3.2 0.6 - - - -
333A GLN* 1.3 77.3 - - - +
335A THR* 1.3 61.3 + - - +
337A CYS* 3.9 2.5 + - - +
338A GLN* 3.0 34.2 + - + +
338F GLN* 5.2 4.3 + - - +
339F GLN* 4.6 5.0 - - + +
342F ASP* 3.7 37.6 + - + +
512F LYS* 4.6 13.5 - - - +
514F LEU* 5.6 4.3 - - - +
516F LYS* 4.5 17.4 - - - +
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Residues in contact with THR 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A TRP* 3.6 23.8 - - + -
332A ASN* 3.1 32.0 + - + +
334A LYS* 1.3 78.4 - - - +
336A ILE* 1.3 64.7 + - - +
338A GLN* 3.1 16.2 + - + +
339A GLN* 3.2 11.3 + - - +
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Residues in contact with ILE 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 3.9 21.5 - - + -
269A SER 4.6 0.7 - - - +
270A TRP* 3.6 46.3 - - + +
273A VAL* 3.6 34.0 - - + +
274A THR* 5.3 1.4 + - - -
327A PHE* 3.5 25.1 - - + -
330A SER* 3.4 25.4 - - - +
332A ASN* 3.0 12.7 + - + +
335A THR* 1.3 77.3 - - - +
337A CYS* 1.3 61.6 + - - +
338A GLN 3.4 0.2 + - - -
339A GLN* 3.6 4.5 + - - +
340A ALA* 3.5 16.5 + - - +
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Residues in contact with CYS 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A VAL* 4.2 13.9 - - - -
285A VAL* 4.3 9.0 - - + +
288A LEU* 3.4 16.3 - - + +
289A LEU* 3.6 29.6 - - + -
292A TYR* 4.8 2.0 - - - -
327A PHE* 3.5 29.6 - - - -
333A GLN 3.6 10.3 + - - +
334A LYS* 4.3 3.6 - - - +
335A THR 3.3 0.2 - - - -
336A ILE* 1.3 77.2 - - - +
338A GLN* 1.3 64.4 + - - +
340A ALA* 3.3 9.7 + - - +
341A VAL* 3.0 27.7 + - - +
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Residues in contact with GLN 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A VAL* 3.3 37.0 - - + +
334A LYS* 3.0 26.6 + - + +
335A THR* 3.1 11.9 + - + +
337A CYS* 1.3 77.7 - - - +
339A GLN* 1.3 63.0 + - - +
341A VAL* 3.1 20.4 + - - +
342A ASP* 3.0 38.2 + - - +
334B LYS* 5.2 3.5 + - - +
514F LEU* 4.9 11.5 - - - +
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Residues in contact with GLN 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A TRP* 3.2 29.8 - - + +
274A THR* 4.2 9.2 + - - +
335A THR 3.2 7.8 + - - +
336A ILE 3.9 6.7 - - - +
338A GLN* 1.3 79.2 - - - +
340A ALA* 1.3 63.0 + - - +
342A ASP* 3.2 13.9 + - + +
343A THR* 2.9 24.9 + - - +
289B LEU* 6.3 0.9 - - + -
330B SER 3.4 10.8 + - - +
331B LYS 3.4 21.2 + - - -
332B ASN* 4.0 0.4 - - - +
333B GLN* 3.1 51.6 - - + +
334B LYS* 4.6 6.5 - - + +
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Residues in contact with ALA 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A VAL* 4.1 4.7 - - + +
274A THR* 3.9 20.3 + - - +
277A ALA* 3.6 14.4 - - + +
288A LEU* 3.4 17.3 - - + -
336A ILE 3.5 10.7 + - - +
337A CYS* 3.3 12.1 + - - +
338A GLN 3.2 0.4 - - - -
339A GLN* 1.3 78.8 - - - +
341A VAL* 1.3 62.2 + - - +
343A THR* 3.0 12.1 + - - -
344A VAL* 2.9 26.1 + - - +
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Residues in contact with VAL 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A CYS 4.3 0.9 - - - +
283A ASP* 3.4 30.5 - - - +
284A ASP 3.1 28.5 - - - +
285A VAL* 3.7 21.1 - - + -
288A LEU* 3.9 4.7 - - + +
337A CYS 3.0 17.9 - - - +
338A GLN* 3.1 9.8 + - - +
340A ALA* 1.3 75.9 - - - +
342A ASP* 1.3 59.4 + - - +
344A VAL* 3.0 11.6 + - - +
345A LEU* 2.9 38.9 + - + +
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Residues in contact with ASP 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLN* 3.0 36.1 + - - +
339A GLN* 3.2 12.7 + - + +
341A VAL* 1.3 76.6 - - - +
343A THR* 1.3 58.9 + - - +
345A LEU* 3.5 12.1 + - - +
346A ALA* 2.8 29.5 + - - +
516A LYS* 5.9 0.5 - - - -
286B LEU* 3.8 23.6 - - + +
289B LEU* 4.3 10.7 - - + +
334B LYS* 3.7 36.3 + - + +
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Residues in contact with THR 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A THR* 3.6 26.9 - - + +
278A MET* 3.5 31.3 - - + +
339A GLN* 2.9 14.5 + - - +
340A ALA 3.0 9.3 + - - -
342A ASP* 1.3 76.4 - - - +
344A VAL* 1.3 62.9 + - - +
346A ALA* 3.4 7.1 - - - +
347A LYS* 3.1 17.0 + - - +
289B LEU* 4.7 4.4 - - - +
293B LEU* 3.9 21.7 - - + +
333B GLN* 3.7 15.5 + - - +
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ALA* 3.7 27.8 - - + +
278A MET* 4.3 9.4 - - - +
281A LYS* 3.6 21.8 - - + +
282A CYS 3.2 24.0 - - - +
283A ASP* 3.9 4.7 - - + +
340A ALA 3.1 16.4 - - - +
341A VAL 3.0 7.2 + - - +
343A THR* 1.3 74.6 - - - +
345A LEU* 1.3 65.4 + - - +
347A LYS* 3.1 20.0 + - + +
348A LYS* 3.3 31.5 + - - +
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Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ASP* 3.9 28.3 - - + +
341A VAL* 2.9 30.7 + - + +
342A ASP* 3.9 10.8 - - - +
344A VAL* 1.3 76.2 - - - +
346A ALA* 1.3 52.5 + - - +
348A LYS* 3.4 15.3 + - + +
349A ARG* 2.8 36.0 + - - +
466A ASP* 4.9 1.4 - - - +
511A LYS* 4.3 26.7 - - + +
286B LEU* 4.2 22.4 - - + -
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Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A ASP 2.8 19.8 + - - +
343A THR* 3.4 11.7 - - - +
345A LEU* 1.3 75.7 - - - +
347A LYS* 1.3 65.1 + - - +
349A ARG* 3.1 9.3 + - - +
350A VAL* 3.0 29.9 + - - +
286B LEU* 3.6 23.0 - - + +
289B LEU* 4.4 8.1 - - + -
290B GLY* 3.9 16.2 - - - +
293B LEU* 5.0 1.8 - - + -
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Residues in contact with LYS 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A MET* 3.9 26.7 - - + +
343A THR 3.1 11.5 + - - +
344A VAL* 3.1 11.9 + - + +
346A ALA* 1.3 75.7 - - - +
348A LYS* 1.3 57.3 + - + +
350A VAL* 3.0 10.2 + - + +
351A ASP* 2.7 56.8 + - - +
290B GLY* 5.8 0.9 - - - -
294B GLU* 4.7 14.8 + - - +
304B LYS* 5.8 3.8 - - - +
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Residues in contact with LYS 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LYS* 3.7 23.6 + - - +
283A ASP* 4.4 12.4 - - - +
344A VAL* 3.3 35.5 + - - +
345A LEU* 3.7 16.4 - - + +
347A LYS* 1.3 78.7 - - + +
349A ARG* 1.3 63.2 + - - +
351A ASP* 4.0 8.5 - - - +
352A SER* 3.1 27.7 + - - -
466A ASP* 4.1 16.9 - - + +
467A GLN* 5.5 9.0 - - - +
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Residues in contact with ARG 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 2.8 14.6 + - - +
346A ALA* 3.2 17.7 - - - +
348A LYS* 1.3 75.9 - - - +
350A VAL* 1.3 57.3 + - - +
352A SER* 3.0 13.5 + - - -
353A LEU* 4.0 6.6 - - - +
465A ILE* 3.1 17.0 - - - +
466A ASP* 3.0 28.9 + - - -
511A LYS* 3.5 18.4 - - - +
516A LYS* 2.9 37.1 + - - +
517A ARG* 3.1 27.4 + - - +
284B ASP* 4.5 3.3 + - - -
286B LEU* 3.3 34.0 - - - +
287B LEU* 3.7 37.8 - - + +
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Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ALA 3.0 15.8 + - - +
347A LYS* 3.5 10.3 - - + +
349A ARG* 1.3 76.8 - - + +
351A ASP* 1.3 64.3 + - - +
352A SER 3.1 1.8 - - - -
353A LEU* 2.9 22.6 + - + +
354A GLN* 3.1 42.4 + - + +
287B LEU* 4.5 9.6 - - + +
290B GLY* 3.9 28.3 - - - -
291B MET* 3.7 19.7 - - + +
294B GLU* 4.5 9.6 - - - +
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Residues in contact with ASP 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LYS* 2.7 54.5 + - - +
348A LYS* 3.4 8.3 + - - +
350A VAL* 1.3 77.3 - - - +
352A SER* 1.3 57.6 + - - +
353A LEU 3.0 5.3 + - - -
354A GLN* 4.5 3.2 - - - +
355A LEU* 3.3 55.6 + - + +
360A MET* 4.0 9.3 - - + +
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Residues in contact with SER 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LYS 3.1 11.8 + - - -
349A ARG 3.0 19.6 + - - -
351A ASP* 1.3 75.2 - - - +
353A LEU* 1.3 64.0 + - - +
355A LEU 4.9 2.4 - - - +
360A MET* 4.2 20.6 - - - +
466A ASP* 3.1 38.0 + - - -
467A GLN 5.5 1.6 - - - -
517A ARG* 4.1 5.4 + - - -
519A GLN* 4.6 3.3 + - - -
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Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ARG 4.0 4.5 - - - +
350A VAL* 2.9 6.8 + - - +
352A SER* 1.3 88.9 - - - +
354A GLN* 1.3 66.8 + - + +
355A LEU 4.6 2.5 - - - +
517A ARG* 3.2 33.4 - - - +
519A GLN* 6.0 3.1 - - + -
287B LEU* 3.8 31.0 - - + -
291B MET* 6.4 0.4 - - - -
310B GLN* 5.1 6.9 + - - +
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Residues in contact with GLN 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A VAL* 3.1 38.1 + - + +
351A ASP* 5.0 1.6 - - - +
353A LEU* 1.3 81.9 - - + +
355A LEU* 1.3 68.9 + - + +
356A THR* 3.5 5.9 + - - +
359A GLN* 4.6 1.4 - - - +
291B MET* 3.8 13.2 - - + +
294B GLU* 3.5 20.8 + - - -
304B LYS* 4.0 22.5 - - - +
309B GLU* 4.8 4.9 - - - +
310B GLN* 3.5 41.5 + - + +
313B HIS* 5.8 2.5 - - - +
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Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ASP* 3.3 48.3 + - + +
352A SER 4.9 1.0 - - - +
353A LEU 4.6 2.6 - - - -
354A GLN* 1.3 83.8 + - + +
356A THR* 1.3 69.9 + - - +
359A GLN* 3.4 30.3 - - + +
360A MET* 3.8 15.5 - - + +
363A ASN* 3.6 26.5 - - - +
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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