Contacts of the helix formed by residues 320 - 341 (chain A) in PDB entry 2WTJ
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 LYS 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A ARG 4.0 1.0 + - - -
319A LEU* 1.3 74.0 - - - +
321A GLU* 1.3 66.8 + - - +
322A ALA* 4.2 9.4 - - + +
323A THR* 2.9 38.4 + - - +
324A CYS 3.0 10.2 + - - -
360A GLU* 3.1 27.7 + - - +
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Residues in contact with GLU 321 (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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319A LEU 3.6 2.2 + - - -
320A LYS* 1.3 72.6 - - - +
322A ALA* 1.3 62.5 + - - +
324A CYS* 3.2 11.7 + - - +
325A LYS* 3.0 23.9 + - - +
421A LEU* 4.3 6.7 - - + -
454A GLU 4.6 2.4 - - - +
455A VAL* 3.6 12.9 - - + +
456A SER* 2.7 52.3 + - - -
459A ALA* 4.1 5.8 - - - -
485A TRP* 2.9 28.9 + - + +
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Residues in contact with ALA 322 (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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320A LYS* 3.1 11.8 - - + +
321A GLU* 1.3 79.3 - - - +
323A THR* 1.3 60.6 + - - +
325A LYS* 3.5 10.7 + - - +
326A LEU* 3.3 21.1 + - - +
491A MET* 5.0 2.9 - - - +
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Residues in contact with THR 323 (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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319A LEU* 4.1 15.3 - - + -
320A LYS* 2.9 21.6 + - - +
322A ALA* 1.3 75.8 - - - +
324A CYS* 1.3 67.4 + - - +
325A LYS 3.0 1.7 + - - -
326A LEU* 3.1 5.3 + - - +
327A TYR* 3.0 60.6 + - + +
360A GLU* 3.2 34.3 + - + +
361A ASP* 4.6 7.1 + - - -
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Residues in contact with CYS 324 (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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319A LEU* 3.6 30.1 - - - -
320A LYS 3.0 7.8 + - - -
321A GLU 3.4 8.1 - - - +
323A THR* 1.3 77.4 - - - +
325A LYS* 1.3 52.0 + - - +
327A TYR* 3.4 3.0 + - - +
328A PHE* 2.8 37.2 + - - +
331A MET* 5.1 0.7 - - - +
417A LEU* 4.7 2.6 - - + +
420A CYS* 3.4 46.0 - - + -
421A LEU* 3.7 24.9 - - + -
485A TRP* 4.0 4.0 - - + -
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Residues in contact with LYS 325 (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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321A GLU* 3.0 14.3 + - - +
322A ALA* 3.7 10.3 - - - +
323A THR 3.0 0.4 - - - -
324A CYS* 1.3 78.3 - - - +
326A LEU* 1.3 58.1 + - - +
328A PHE* 4.1 0.3 - - - +
329A TYR* 2.9 31.7 + - - +
485A TRP* 2.9 75.4 + - + +
486A LEU* 4.6 3.9 - - + +
488A ASP* 2.9 40.7 + - + +
491A MET* 4.2 17.7 - - + +
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Residues in contact with LEU 326 (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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322A ALA 3.3 10.9 + - - +
323A THR* 3.1 9.9 + - - +
325A LYS* 1.3 79.3 - - - +
327A TYR* 1.3 69.4 + - + +
329A TYR* 3.8 1.7 - - - +
330A GLN* 3.0 42.8 + - - +
360A GLU 4.6 0.2 - - - +
361A ASP* 4.1 37.0 - - + +
362A CYS 4.1 11.0 - - - +
491A MET* 3.7 25.1 - - + +
494A LYS* 4.5 9.2 - - + -
495A PHE* 4.0 29.8 - - + +
498A LEU* 4.3 7.9 - - + -
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Residues in contact with TYR 327 (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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309A LEU* 4.0 17.5 - - + -
312A LYS* 5.5 2.0 - - + +
319A LEU* 3.9 25.1 - - + -
323A THR* 3.0 32.9 + - + +
324A CYS* 3.8 2.9 - - - +
326A LEU* 1.3 84.7 - - + +
328A PHE* 1.3 65.4 + - - +
330A GLN* 3.2 8.5 + - - +
331A MET* 3.0 38.4 + - + +
355A LEU* 4.1 15.8 - - + +
360A GLU* 2.5 41.7 + - - +
362A CYS* 3.8 29.2 - - - -
364A ILE* 4.0 20.1 - - + +
420A CYS* 6.2 1.1 - - - -
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Residues in contact with PHE 328 (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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324A CYS 2.8 22.8 + - - +
325A LYS 4.1 2.0 - - - +
327A TYR* 1.3 70.8 - - - +
329A TYR* 1.3 60.9 + - - +
331A MET* 3.1 21.6 + - + +
332A LEU* 2.8 59.6 + - + +
413A LEU* 3.2 44.9 - - + -
416A ILE* 5.4 0.2 - - + -
417A LEU* 3.6 26.9 - - + -
462A LEU* 4.0 17.9 - - + -
466A LEU* 3.7 24.0 - - + -
480A ALA* 5.1 0.2 - - + -
485A TRP* 4.2 18.2 - + + -
486A LEU* 4.6 1.1 - - + -
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Residues in contact with TYR 329 (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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325A LYS 2.9 18.6 + - - +
326A LEU 3.8 2.0 - - - +
328A PHE* 1.3 76.9 - - - +
330A GLN* 1.3 60.0 + - + +
332A LEU* 3.3 4.3 + - - +
333A LEU* 3.0 51.6 + - + +
481A LEU* 3.7 21.1 - - + -
486A LEU* 3.4 30.6 - - + +
491A MET* 3.4 24.2 - - + -
492A LYS* 3.7 40.2 - - + +
495A PHE* 3.6 34.8 - + + -
496A GLN* 5.2 4.0 + - - -
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Residues in contact with GLN 330 (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 CYS* 3.7 15.1 - - - +
326A LEU* 3.0 34.5 + - + +
327A TYR* 3.2 7.9 + - - +
329A TYR* 1.3 75.7 - - + +
331A MET* 1.3 60.9 + - - +
333A LEU* 3.3 6.5 + - - +
334A ALA* 2.9 29.3 + - - +
362A CYS 3.2 21.8 + - - -
363A LEU* 3.2 16.1 - - - +
364A ILE* 2.9 41.5 + - + +
495A PHE* 3.6 29.8 - - + -
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Residues in contact with MET 331 (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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309A LEU* 4.2 16.6 - - + -
324A CYS 5.1 0.9 - - - +
327A TYR* 3.0 42.1 + - + +
328A PHE* 3.4 27.4 - - + +
330A GLN* 1.3 75.9 - - - +
332A LEU* 1.3 57.1 + - - +
334A ALA* 3.2 5.2 + - - +
335A VAL* 2.9 35.5 + - - +
353A VAL* 4.2 19.7 - - + -
364A ILE* 3.9 16.6 - - + -
366A ILE* 4.4 8.5 - - + -
413A LEU* 3.8 21.3 - - + -
416A ILE* 4.0 24.2 - - + -
420A CYS* 5.0 5.6 - - - -
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Residues in contact with LEU 332 (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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328A PHE* 2.8 45.0 + - + +
329A TYR 3.5 7.4 - - - +
331A MET* 1.3 76.8 - - - +
333A LEU* 1.3 53.0 + - - +
335A VAL* 3.8 0.7 - - - +
336A GLN* 2.8 38.1 + - - +
410A CYS* 6.2 0.4 - - - -
413A LEU* 3.9 22.7 - - + -
466A LEU* 5.6 1.3 - - + -
477A THR* 4.2 15.5 - - + +
480A ALA* 3.6 27.8 - - + -
481A LEU* 3.8 21.5 - - + -
486A LEU* 3.6 28.9 - - + -
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Residues in contact with LEU 333 (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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282A HIS* 3.9 19.1 + - + +
284A CYS* 4.9 1.1 - - - -
329A TYR* 3.0 44.0 + - + +
330A GLN* 3.3 9.2 + - - +
332A LEU* 1.3 75.6 - - - +
334A ALA* 1.3 58.3 + - - +
336A GLN* 3.5 19.6 + - - +
337A TYR* 3.0 29.5 + - - +
481A LEU* 4.1 17.9 - - + -
495A PHE* 3.7 36.3 - - + -
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Residues in contact with ALA 334 (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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282A HIS* 4.3 8.2 - - - -
284A CYS* 3.5 27.6 - - + +
285A ILE* 3.9 10.3 - - + +
330A GLN 2.9 13.6 + - - +
331A MET 3.5 7.2 - - - +
333A LEU* 1.3 77.0 - - - +
335A VAL* 1.3 57.3 + - - +
337A TYR* 3.1 5.5 + - - +
338A LEU* 2.9 32.7 + - + +
366A ILE* 3.7 18.2 - - + -
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Residues in contact with VAL 335 (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 MET* 2.9 20.3 + - - +
334A ALA* 1.3 75.0 - - + +
336A GLN* 1.3 66.6 + - - +
338A LEU* 3.2 14.1 + - + +
339A HIS* 2.9 52.9 + - + +
348A LEU* 3.7 29.4 - - + -
366A ILE* 5.1 3.4 - - + -
409A ASP* 3.8 15.0 - - + +
413A LEU* 4.0 19.7 - - + -
477A THR* 3.8 10.5 - - + -
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Residues in contact with GLN 336 (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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332A LEU 2.8 21.6 + - - +
333A LEU* 3.7 17.8 + - - +
335A VAL* 1.3 74.5 - - - +
337A TYR* 1.3 61.7 + - - +
339A HIS* 3.3 2.7 + - - +
340A GLU* 3.0 43.3 + - - +
477A THR* 3.4 20.4 - - - +
478A GLU* 3.2 34.2 - - - +
481A LEU* 3.3 28.1 - - + +
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Residues in contact with TYR 337 (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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279A LYS 4.5 2.1 + - - -
280A LEU* 3.5 28.6 - - + +
281A ASN* 2.8 41.0 + - - +
282A HIS* 3.5 26.7 - + + +
285A ILE* 3.2 27.1 - - + -
333A LEU 3.0 18.5 + - - +
334A ALA 3.1 3.8 + - - +
336A GLN* 1.3 78.3 - - - +
338A LEU* 1.3 62.5 + - - +
340A GLU* 3.5 15.9 + - - +
341A ASN* 2.8 51.9 + - - -
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Residues in contact with LEU 338 (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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280A LEU* 3.5 32.5 - - + -
285A ILE* 3.9 11.9 - - + -
334A ALA 2.9 18.4 + - - +
335A VAL* 3.4 20.2 - - + +
337A TYR* 1.3 77.4 - - - +
339A HIS* 1.3 59.1 + - + +
341A ASN* 3.0 17.0 + - - +
342A GLY 3.2 0.2 + - - -
343A ILE* 2.9 41.7 + - + +
345A HIS* 4.0 25.6 - - + +
366A ILE* 5.3 4.0 - - + -
369A PHE* 3.6 29.6 - - + -
409A ASP* 5.0 2.0 - - - +
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Residues in contact with HIS 339 (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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335A VAL* 2.9 35.4 + - + +
336A GLN* 3.9 4.9 - - - +
338A LEU* 1.3 76.3 - - + +
340A GLU* 1.3 63.5 + - - +
342A GLY* 3.0 14.3 + - - +
343A ILE 3.3 18.8 - - - +
344A ILE* 4.0 1.3 - - + -
375A LEU* 4.4 7.2 - - - +
406A ARG* 3.3 67.9 + - + +
409A ASP* 3.0 25.8 + - + +
410A CYS* 4.4 10.9 - - - -
477A THR* 4.3 11.6 + - - +
478A GLU* 6.0 1.6 - - - +
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Residues in contact with GLU 340 (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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336A GLN* 3.0 40.3 + - + +
337A TYR* 3.7 23.9 - - - +
339A HIS* 1.3 75.5 - - - +
341A ASN* 1.3 63.1 + - - +
342A GLY 3.3 2.6 + - - -
478A GLU* 4.6 7.3 - - - +
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Residues in contact with ASN 341 (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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280A LEU* 4.2 17.6 - - + +
337A TYR* 2.8 60.4 + - - +
338A LEU 3.0 6.4 + - - +
340A GLU* 1.3 83.5 + - - +
342A GLY* 1.3 60.4 + - - -
343A ILE* 3.3 10.5 + - + +
374A ILE* 6.0 0.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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