Contacts of the helix formed by residues 358 - 380 (chain A) in PDB entry 2WWB
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 PRO 358 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A LEU 4.5 5.2 - - - +
356A GLU* 3.9 6.7 - - - +
357A ASP* 1.3 88.1 + - - +
359A VAL* 1.4 72.2 + - + +
360A HIS 3.4 2.4 + - - -
361A ALA* 3.8 10.0 + - - +
362A VAL* 3.6 16.2 - - + +
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Residues in contact with VAL 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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344A TYR* 4.6 15.7 - - + +
357A ASP 3.3 3.5 - - - +
358A PRO* 1.4 88.5 - - + +
360A HIS* 1.4 65.4 + - - +
362A VAL* 3.3 20.3 + - + +
363A VAL* 3.5 24.4 + - + +
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Residues in contact with HIS 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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343A HIS* 3.1 54.0 + + - +
344A TYR* 3.8 26.0 + - + -
346A SER 3.1 20.9 + - - -
347A PRO 3.6 6.9 - - - -
348A PRO* 3.4 35.1 - - + +
355A LEU* 6.0 0.4 - - + -
357A ASP* 3.6 24.5 - - + +
358A PRO 3.4 0.6 - - - -
359A VAL* 1.4 78.1 - - - +
361A ALA* 1.4 66.5 + - + +
363A VAL 3.7 0.5 + - - -
364A TYR* 3.5 24.3 + + - +
437A PHE* 5.6 1.8 - + - -
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Residues in contact with ALA 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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355A LEU* 4.2 31.0 - - + +
357A ASP* 4.4 5.3 + - - +
358A PRO 3.8 8.6 + - - +
359A VAL 3.4 0.4 - - - -
360A HIS* 1.4 82.2 - - - +
362A VAL* 1.4 64.4 + - + +
364A TYR* 3.4 5.9 + - - +
365A ILE* 3.4 33.6 + - + +
437A PHE* 4.7 8.7 - - + -
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Residues in contact with VAL 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 PRO* 3.6 21.3 - - + +
359A VAL* 3.3 11.6 + - + +
361A ALA* 1.4 80.4 - - + +
363A VAL* 1.4 63.7 + - + +
365A ILE* 3.7 7.0 + - - +
366A VAL* 3.5 29.7 + - + +
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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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341A LEU* 5.0 9.2 - - + -
344A TYR* 3.6 44.6 - - + -
345A LEU* 5.2 2.0 - - + -
359A VAL* 3.5 26.1 + - + +
360A HIS 4.1 2.0 - - - +
361A ALA 3.4 0.2 - - - -
362A VAL* 1.4 76.2 - - + +
364A TYR* 1.4 64.3 + - - +
365A ILE 3.5 0.2 + - - -
366A VAL* 3.6 2.6 + - - +
367A PHE* 3.2 33.5 + - + +
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Residues in contact with TYR 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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64A TRP* 3.8 9.2 + - - -
344A TYR 3.0 24.2 + - - +
345A LEU* 3.5 36.1 + - - -
346A SER 3.4 17.5 - - - -
347A PRO* 3.8 15.3 - - + +
360A HIS* 3.5 14.3 + + - +
361A ALA 3.6 9.9 - - - +
362A VAL 3.4 0.2 - - - -
363A VAL* 1.4 78.7 - - - +
365A ILE* 1.4 61.1 - - - +
367A PHE* 4.2 0.3 - - - +
368A MET* 3.1 54.8 + - + +
433A VAL* 3.7 26.0 - - + -
436A ASP* 3.0 25.5 + - - -
437A PHE* 4.2 15.3 - + - -
445A THR* 5.0 0.5 + - - -
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Residues in contact with ILE 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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361A ALA* 3.4 24.8 + - + +
362A VAL* 4.0 7.6 - - - +
363A VAL 3.4 0.4 - - - -
364A TYR* 1.4 76.4 - - - +
366A VAL* 1.4 68.5 + - + +
368A MET* 4.2 1.9 - - - +
369A LEU* 3.2 31.9 + - + +
429A GLY 4.7 2.8 - - - +
430A ALA* 4.8 12.1 - - + +
433A VAL* 3.8 25.8 - - + -
434A LEU* 4.5 15.0 - - + -
437A PHE* 4.5 13.0 - - + -
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Residues in contact with VAL 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 VAL* 3.5 22.2 - - + +
363A VAL* 3.6 3.9 + - - +
364A TYR 3.5 0.4 - - - -
365A ILE* 1.4 81.8 - - + +
367A PHE* 1.4 65.3 + - - +
369A LEU* 3.5 14.8 - - + +
370A GLY* 3.2 18.9 + - - -
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Residues in contact with PHE 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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294A GLN* 5.8 2.0 - - - -
297A LEU* 6.3 2.9 - - + -
341A LEU* 4.7 30.1 - - + -
345A LEU* 3.5 42.4 - - + -
363A VAL* 3.2 24.4 + - + +
364A TYR 4.2 0.4 - - - +
366A VAL* 1.4 77.4 - - - +
368A MET* 1.4 62.2 + - + +
370A GLY* 3.4 2.3 + - - -
371A SER* 3.0 40.8 + - - -
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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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64A TRP* 4.8 13.7 - - + -
294A GLN* 3.4 42.3 - - - +
295A SER* 5.6 1.8 - - - +
298A VAL* 4.2 12.8 - - + -
345A LEU* 4.7 11.0 - - + +
364A TYR* 3.1 47.8 + - + +
365A ILE 4.2 0.4 - - - +
367A PHE* 1.4 73.5 - - - +
369A LEU* 1.4 64.0 + - - +
371A SER* 3.4 1.1 + - - -
372A CYS* 3.1 31.6 + - - -
429A GLY* 3.9 8.1 - - - +
432A SER* 5.3 3.1 - - - -
433A VAL* 3.7 20.2 - - + -
445A THR* 4.7 18.6 - - + +
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Residues in contact with LEU 369 (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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365A ILE* 3.2 22.6 + - + +
366A VAL* 3.5 16.2 - - + +
368A MET* 1.4 78.1 - - - +
370A GLY* 1.4 62.9 + - - +
372A CYS* 3.9 2.3 + - - +
373A ALA* 3.6 20.6 + - - +
426A LEU* 3.5 40.5 - - + +
429A GLY* 4.3 11.6 + - - -
430A ALA* 4.0 25.4 - - + +
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Residues in contact with GLY 370 (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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366A VAL 3.2 11.6 + - - -
367A PHE 3.4 3.1 + - - -
368A MET 3.3 0.2 - - - -
369A LEU* 1.4 83.2 - - - +
371A SER* 1.4 59.7 + - - +
373A ALA* 3.7 5.5 + - - +
374A PHE* 3.2 26.2 + - - +
426A LEU* 5.3 0.7 - - - -
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Residues in contact with SER 371 (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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294A GLN* 3.5 27.3 + - - -
367A PHE* 3.0 35.6 + - - -
368A MET 3.4 2.4 + - - -
370A GLY* 1.4 74.7 - - - +
372A CYS* 1.4 61.6 + - - +
374A PHE* 3.4 10.7 + - - +
375A PHE* 3.1 33.4 + - - -
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Residues in contact with CYS 372 (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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290A PRO* 3.7 9.2 - - - +
291A ILE* 3.7 25.4 - - + -
294A GLN* 3.4 30.3 - - - -
368A MET 3.1 21.1 + - - +
369A LEU 4.2 2.2 - - - +
370A GLY 3.4 0.2 - - - -
371A SER* 1.4 74.8 - - - +
373A ALA* 1.4 61.5 + - - +
375A PHE* 3.3 5.6 + - - -
376A SER* 3.3 22.5 + - - -
425A GLY* 3.3 20.6 - - - +
429A GLY* 3.6 19.3 - - - -
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Residues in contact with ALA 373 (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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369A LEU 3.6 15.0 + - - +
370A GLY* 4.0 5.4 - - - +
371A SER 3.4 0.4 - - - -
372A CYS* 1.4 77.0 - - - +
374A PHE* 1.4 64.8 + - - +
376A SER* 3.3 11.3 + - - -
377A LYS* 3.2 43.6 + - - +
422A ALA 4.4 4.3 - - - +
425A GLY 4.2 4.2 + - - -
426A LEU* 3.8 26.5 - - + +
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Residues in contact with PHE 374 (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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93A LEU* 5.9 7.9 - - + -
370A GLY 3.2 15.7 + - - +
371A SER* 3.4 14.1 - - - +
372A CYS 3.3 0.4 - - - -
373A ALA* 1.4 77.0 - - - +
375A PHE* 1.4 89.9 + + - +
377A LYS* 3.4 9.3 + - + +
378A THR* 3.2 42.4 + - + +
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Residues in contact with PHE 375 (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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89A LEU* 4.4 21.8 - - + -
92A GLN* 3.5 30.6 + - + +
93A LEU* 6.2 2.7 - - + -
290A PRO* 3.6 37.9 - - + +
293A LEU* 4.8 4.3 - - + -
294A GLN* 3.9 27.8 - - + -
297A LEU* 5.2 11.0 - - + -
371A SER* 3.1 25.1 + - - -
372A CYS* 3.3 3.5 + - - +
374A PHE* 1.4 98.2 - + - +
376A SER* 1.4 59.1 + - - +
377A LYS 3.4 0.2 - - - -
378A THR* 3.3 7.1 + - - -
379A TRP* 3.1 27.4 + - - +
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Residues in contact with SER 376 (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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287A SER* 3.7 4.9 + - - -
290A PRO* 3.7 17.9 - - - +
372A CYS 3.3 15.0 + - - -
373A ALA* 3.5 11.4 - - - -
374A PHE 3.3 0.4 - - - -
375A PHE* 1.4 76.8 - - - +
377A LYS* 1.4 60.2 + - - +
379A TRP* 3.4 13.0 - - - +
380A ILE* 3.3 17.8 - - - +
421A ALA* 3.4 28.8 + - - +
422A ALA* 4.8 1.1 - - - -
425A GLY* 3.5 19.6 - - - -
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Residues in contact with LYS 377 (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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373A ALA* 3.2 29.5 + - - +
374A PHE* 3.4 9.8 + - + +
376A SER* 1.4 77.0 - - - +
378A THR* 1.4 62.7 + - + +
380A ILE* 3.5 30.2 + - + +
381A GLU* 4.1 8.7 - - - +
418A PRO 6.1 0.4 - - - +
422A ALA* 3.8 30.8 - - + +
426A LEU* 5.9 1.0 - - - +
14B PHE* 6.1 1.6 - - - -
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Residues in contact with THR 378 (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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92A GLN* 3.6 20.1 - - - +
95A ALA* 5.8 0.3 - - - +
96A GLY* 4.4 19.8 + - - +
374A PHE* 3.2 39.1 + - + +
375A PHE* 3.3 18.7 + - - -
377A LYS* 1.4 75.1 - - + +
379A TRP* 1.4 61.1 + - - +
380A ILE 3.3 1.5 + - - -
381A GLU* 3.7 30.5 + - - +
383A SER* 3.4 9.7 + - - -
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Residues in contact with TRP 379 (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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91A MET* 5.8 8.1 - - + -
92A GLN* 3.7 17.0 - - - +
286A THR* 3.3 38.3 + - - +
287A SER* 5.6 0.2 - - - -
289A ILE* 3.8 41.5 - - + -
290A PRO* 4.4 5.2 - - + -
293A LEU* 5.9 0.7 - - + -
375A PHE 3.1 18.3 + - - +
376A SER* 3.4 12.6 - - - +
377A LYS 3.3 0.2 - - - -
378A THR* 1.4 76.7 - - - +
380A ILE* 1.4 59.3 + - + +
381A GLU 3.3 0.2 - - - -
383A SER* 3.2 46.2 + - - -
384A GLY* 2.9 41.9 + - - -
385A SER* 4.0 12.1 + - - +
421A ALA* 6.6 0.4 - - + -
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Residues in contact with ILE 380 (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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376A SER 3.3 15.3 - - - +
377A LYS* 3.5 27.8 - - + +
378A THR 3.3 0.8 - - - -
379A TRP* 1.4 79.4 - - + +
381A GLU* 1.4 66.7 + - + +
382A VAL 3.7 0.3 + - - -
384A GLY 4.0 5.2 - - - +
385A SER 3.7 21.5 - - - +
386A SER* 3.6 27.5 + - - -
417A ILE* 5.0 8.5 - - + +
418A PRO* 4.4 23.8 - - + +
421A ALA* 4.1 21.8 - - + -
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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
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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