Contacts of the helix formed by residues 348 - 369 (chain A) in PDB entry 4S15
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 CYS 348 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A LEU* 1.3 78.2 - - - +
349A GLN* 1.3 67.5 + - - +
350A ASN* 4.0 3.1 - - - +
351A ASP* 3.2 34.3 + - - -
352A GLN* 3.1 19.3 + - - +
437A GLN* 3.9 19.7 - - - +
438A GLU* 2.8 33.3 + - - +
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Residues in contact with GLN 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU 3.8 0.4 + - - +
348A CYS* 1.3 74.2 - - - +
350A ASN* 1.3 62.6 + - - +
352A GLN* 3.4 5.3 + - - +
353A ILE* 3.3 22.1 + - + +
501C GLN* 5.8 1.4 + - - -
506C HIS* 3.3 75.2 + - + +
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Residues in contact with ASN 350 (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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348A CYS* 3.3 3.2 - - - -
349A GLN* 1.3 79.4 - - - +
351A ASP* 1.3 78.6 + - - +
353A ILE* 3.3 9.4 + - - +
354A VAL* 3.0 34.9 + - - +
435A TRP* 3.5 12.1 + - - +
437A GLN* 3.4 37.8 - - - +
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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 LEU* 4.5 8.1 - - + -
348A CYS* 3.2 20.3 + - - +
350A ASN* 1.3 87.1 - - - +
352A GLN* 1.3 66.2 + - - +
354A VAL* 3.7 0.6 - - - +
355A LEU* 2.9 31.5 + - - +
436A LEU* 3.5 20.7 - - + +
437A GLN* 2.8 23.4 + - - +
438A GLU* 2.7 38.1 + - - +
442A ILE* 3.8 11.9 - - + +
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Residues in contact with GLN 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A PHE* 3.6 42.9 + - + +
345A MET* 3.4 41.4 + - - +
347A LEU* 3.0 24.5 + - + +
348A CYS 3.1 14.2 + - - +
349A GLN* 3.6 8.7 - - - +
351A ASP* 1.3 75.6 - - - +
353A ILE* 1.3 62.3 + - - +
355A LEU* 3.8 0.8 - - - +
356A LEU* 3.0 25.3 + - - +
504C LEU* 4.0 13.9 - - + +
506C HIS* 2.8 27.0 + - - -
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Residues in contact with ILE 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A GLN* 3.3 16.0 + - + +
350A ASN* 3.7 9.4 - - - +
351A ASP 3.2 0.4 - - - -
352A GLN* 1.3 77.4 - - - +
354A VAL* 1.3 59.5 + - + +
356A LEU* 3.2 1.7 + - - +
357A LYS* 2.8 57.7 + - + +
498C THR 5.4 1.8 - - - +
500C LEU* 3.9 17.9 - - + +
501C GLN* 3.6 37.0 - - + +
504C LEU* 4.0 9.2 - - + -
506C HIS* 4.0 13.5 - - + +
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Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ASN* 3.0 28.8 + - - +
351A ASP* 3.3 3.8 + - - +
353A ILE* 1.3 76.9 - - + +
355A LEU* 1.3 64.1 + - - +
357A LYS* 3.4 8.1 + - + +
358A ALA* 3.1 24.1 + - + +
433A ARG* 4.0 9.6 - - + -
434A SER 3.2 23.3 - - - +
435A TRP* 3.9 27.8 - - + +
436A LEU* 3.7 20.0 - - + -
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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
----------------------------------------------------------
344A PHE* 4.2 10.8 - - + -
347A LEU* 3.6 30.7 - - + -
351A ASP 2.9 19.5 + - - +
352A GLN 3.8 3.1 - - - +
354A VAL* 1.3 77.4 - - - +
356A LEU* 1.3 57.8 + - - +
358A ALA* 3.4 3.0 + - - +
359A GLY* 2.8 29.8 + - - -
428A LEU* 3.5 25.3 - - + +
429A MET* 3.7 20.9 - - + -
430A SER 3.4 27.1 - - - +
433A ARG* 3.9 12.2 + - + -
436A LEU* 4.0 13.7 - - + -
442A ILE* 4.1 7.2 - - + -
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Residues in contact with LEU 356 (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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334A VAL* 4.5 7.0 - - + -
335A VAL* 4.4 17.9 - - + -
338A ALA* 4.0 16.2 - - + -
344A PHE* 3.7 24.2 - - + -
352A GLN 3.0 16.5 + - - +
353A ILE 3.9 2.0 - - - +
355A LEU* 1.3 74.4 - - - +
357A LYS* 1.3 67.2 + - - +
360A SER* 2.6 45.4 + - - +
428A LEU* 3.9 17.7 - - + -
510A LEU* 3.9 4.3 - - + +
500C LEU* 4.3 19.3 - - + -
504C LEU* 3.8 28.5 - - + -
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Residues in contact with LYS 357 (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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353A ILE* 2.8 43.8 + - + +
354A VAL* 3.7 7.9 - - + +
356A LEU* 1.3 75.8 - - - +
358A ALA* 1.3 59.3 + - + +
360A SER 4.7 0.7 + - - -
361A LEU 5.5 0.3 + - - -
509A GLU* 3.5 33.9 + - - +
510A LEU* 3.7 37.6 - - + +
511A PHE* 4.4 14.9 - - - -
512A THR 5.8 0.9 - - - -
498C THR 6.1 0.2 - - - +
500C LEU* 4.6 4.8 - - - +
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Residues in contact with ALA 358 (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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354A VAL* 3.1 15.6 + - + +
355A LEU 4.1 0.7 - - - +
357A LYS* 1.3 78.7 - - + +
359A GLY* 1.3 59.5 + - - +
361A LEU* 5.3 1.8 + - - +
362A GLU* 3.6 19.9 + - - +
433A ARG* 3.6 36.8 + - + +
481A CYS* 5.5 3.8 - - - +
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Residues in contact with GLY 359 (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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355A LEU 2.8 16.2 + - - -
358A ALA* 1.3 79.2 - - - +
360A SER* 1.3 65.0 + - - +
361A LEU 3.3 2.2 - - - -
362A GLU* 3.1 9.6 + - - +
363A VAL* 3.1 24.1 + - - +
427A VAL* 5.0 0.2 - - - +
428A LEU* 4.4 12.8 - - - -
433A ARG* 3.6 15.9 - - - -
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Residues in contact with SER 360 (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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331A ILE* 4.3 25.5 - - - +
334A VAL* 4.0 17.8 - - - +
335A VAL* 4.9 1.7 - - - +
356A LEU* 2.6 47.5 + - - +
357A LYS 4.7 1.1 + - - -
358A ALA 3.9 0.2 - - - -
359A GLY* 1.3 76.1 - - - +
361A LEU* 1.3 63.0 + - - +
363A VAL* 3.1 6.3 + - - +
364A VAL* 3.0 25.3 + - - +
428A LEU* 4.7 0.2 - - - +
510A LEU* 4.6 7.1 - - - +
511A PHE* 5.4 1.3 - - - -
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Residues in contact with LEU 361 (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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327A ILE* 4.1 31.0 - - + -
331A ILE* 4.9 0.4 - - + -
357A LYS 5.5 0.4 + - - -
358A ALA 5.3 1.7 + - - +
359A GLY 3.3 0.8 - - - +
360A SER* 1.3 77.4 - - - +
362A GLU* 1.3 67.0 + - - +
364A VAL* 3.1 18.8 + - + +
365A PHE* 3.0 43.6 + - + -
481A CYS* 3.8 20.2 - - + +
484A HIS* 3.3 44.9 - - + +
485A THR* 6.1 0.2 - - - +
511A PHE* 3.8 24.2 - - + -
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Residues in contact with GLU 362 (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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358A ALA 3.6 9.9 + - - +
359A GLY* 3.1 7.5 + - - +
361A LEU* 1.3 77.9 - - - +
363A VAL* 1.3 62.4 + - - +
365A PHE* 3.2 3.8 + - - +
366A ILE* 3.1 27.5 + - - +
427A VAL* 3.6 24.9 - - + +
430A SER* 4.9 0.2 + - - -
433A ARG* 2.8 44.7 + - - -
474A VAL* 5.5 2.0 - - - +
477A LEU* 3.7 22.0 - - + +
478A ARG* 3.5 24.6 + - - +
481A CYS* 3.6 23.1 - - - +
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Residues in contact with VAL 363 (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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334A VAL* 3.7 32.3 - - + -
337A PHE* 4.6 7.9 - - + -
359A GLY 3.1 14.3 + - - +
360A SER 3.1 6.9 + - - +
362A GLU* 1.3 75.0 - - - +
364A VAL* 1.3 57.1 + - - +
366A ILE* 3.1 8.1 + - - +
367A ARG* 2.8 40.5 + - - +
424A SER* 3.7 43.5 - - - +
427A VAL* 4.0 6.5 - - + -
428A LEU* 4.3 11.4 - - + -
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Residues in contact with VAL 364 (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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327A ILE* 5.2 5.8 - - + +
330A ALA* 4.0 19.7 - - + -
331A ILE* 3.8 25.1 - - + -
334A VAL* 4.0 15.3 - - + -
360A SER 3.0 17.6 + - - +
361A LEU* 3.1 23.3 + - + +
363A VAL* 1.3 75.2 - - - +
365A PHE* 1.3 58.7 + - + +
367A ARG* 3.2 9.0 + - - +
368A MET* 2.9 25.8 + - - +
601A 4D8 3.7 30.3 - - + +
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Residues in contact with PHE 365 (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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327A ILE* 6.4 1.6 - - + -
361A LEU* 3.0 48.2 + - + -
362A GLU 3.2 1.1 + - - +
364A VAL* 1.3 76.4 - - + +
366A ILE* 1.3 65.9 + - - +
368A MET* 3.3 36.1 - - + +
369A CYS* 3.9 1.9 + - - +
399A PHE* 4.6 11.7 - + - -
403A VAL* 4.1 31.0 - - + -
406A PHE* 3.6 17.1 - - + -
410A LEU* 4.8 0.3 - - - +
477A LEU* 3.5 20.0 - - + -
480A LEU* 4.1 26.5 - - + -
481A CYS* 3.9 17.9 - - - -
484A HIS* 5.4 1.6 - + + -
601A 4D8 4.3 20.6 - - + -
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Residues in contact with ILE 366 (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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362A GLU 3.1 10.6 + - - +
363A VAL* 3.1 6.3 + - - +
365A PHE* 1.3 77.7 - - - +
367A ARG* 1.3 61.6 + - - +
369A CYS* 3.1 26.2 + - - +
410A LEU* 4.1 14.6 - - + -
415A LEU* 6.1 0.4 - - + -
420A ILE* 4.1 17.4 - - + +
423A PHE* 3.6 38.8 - - + +
424A SER* 3.6 20.9 - - - +
427A VAL* 3.7 25.4 - - + -
477A LEU* 3.6 30.5 - - + -
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Residues in contact with ARG 367 (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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284A HIS* 3.6 29.5 + - - +
287A THR* 2.9 45.5 + - - -
288A CYS* 4.2 3.1 - - - -
330A ALA* 4.8 1.9 + - - -
333A TYR* 3.8 18.6 - - - +
334A VAL* 4.1 15.1 - - - +
337A PHE* 3.6 18.6 - - - +
363A VAL* 2.8 32.9 + - + +
364A VAL* 3.5 6.5 - - - +
366A ILE* 1.3 77.2 - - - +
368A MET* 1.3 63.1 + - - +
370A ARG* 3.0 24.0 + - - +
371A ALA 3.9 0.5 + - - -
420A ILE* 5.1 2.2 - - + -
424A SER* 4.8 5.5 + - - +
601A 4D8 3.8 6.4 - - + +
602A GOL 3.1 47.6 + - - -
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Residues in contact with MET 368 (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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364A VAL 2.9 12.2 + - - +
365A PHE* 3.3 27.4 - - + +
366A ILE 3.1 0.2 - - - -
367A ARG* 1.3 77.4 - - - +
369A CYS* 1.3 56.0 + - - +
371A ALA* 2.8 27.2 + - - -
372A PHE* 3.3 8.9 + - + +
379A VAL* 3.7 26.2 - - + -
403A VAL* 3.5 46.7 - - + +
404A PHE* 6.3 0.2 - - - -
406A PHE* 4.3 4.9 - - + -
407A GLY* 3.7 21.3 - - - +
601A 4D8 3.6 35.4 - - + +
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Residues in contact with CYS 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ARG* 5.0 7.2 + - - -
365A PHE 3.9 1.9 + - - +
366A ILE* 3.1 21.4 + - - +
368A MET* 1.3 77.5 - - - +
370A ARG* 1.3 62.7 + - - +
371A ALA 3.2 0.6 + - - -
372A PHE* 3.7 15.0 + - - +
407A GLY* 4.4 4.9 - - - +
410A LEU* 3.9 41.5 - - + -
411A CYS* 3.7 27.2 - - - +
415A LEU* 5.4 3.1 - - - -
420A ILE* 3.7 28.5 - - - -
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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) + - + + + + + -
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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