Contacts of the helix formed by residues 353 - 379 (chain A) in PDB entry 4XK8
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 SER 353 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A ILE* 3.2 16.9 + - - +
350A LEU* 5.0 0.5 - - - -
351A THR 3.9 0.4 - - - -
352A THR* 1.3 79.2 - - - +
354A TRP* 1.3 62.7 - - - +
355A HIS 3.6 0.2 + - - -
356A ALA* 3.5 18.1 + - - +
357A GLN* 3.6 16.3 + - - +
417A PHE* 3.3 26.3 - - - -
421A ASP* 2.6 33.0 + - - -
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Residues in contact with TRP 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 5.7 3.4 - - - +
71A LEU* 3.7 22.8 - - + +
74A ILE* 4.2 16.4 - - + +
75A SER* 2.9 44.3 + - - +
78A VAL* 3.5 30.3 - - + -
82A HIS* 5.2 10.3 - + - -
196A PHE* 4.7 20.0 - + + -
352A THR 4.2 0.4 + - - -
353A SER* 1.3 72.6 + - - +
355A HIS* 1.3 64.4 + - + +
357A GLN* 3.4 14.5 + - + +
358A LEU* 2.9 29.8 + - - +
421A ASP* 4.6 1.2 + - - -
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Residues in contact with HIS 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASP* 5.3 4.3 - - - -
65A ASP* 2.3 31.5 + - - -
353A SER* 3.2 1.6 + - - -
354A TRP* 1.3 81.1 - - + +
356A ALA* 1.3 60.7 + - - +
358A LEU* 3.4 5.8 + - + +
359A SER* 2.9 28.9 + - - -
413A HIS* 3.1 52.9 + + - +
416A ILE* 3.4 32.1 - - + +
417A PHE* 3.8 12.3 - - + +
420A ARG* 4.8 2.8 + - - -
421A ASP* 3.8 18.2 - - - +
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Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ILE* 4.6 7.2 - - + +
350A LEU* 3.7 21.1 - - + -
353A SER* 3.5 19.7 + - - +
354A TRP 3.3 0.2 - - - -
355A HIS* 1.3 76.9 - - - +
357A GLN* 1.3 65.9 + - - +
359A SER* 3.1 7.3 + - - -
360A ILE* 3.0 29.9 + - + +
414A ALA* 5.8 0.4 - - - +
417A PHE* 4.1 20.3 - - + +
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Residues in contact with GLN 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A VAL* 5.3 7.1 - - - +
350A LEU* 2.9 45.7 + - + +
353A SER 3.6 12.0 + - - +
354A TRP* 3.4 19.7 + - + +
356A ALA* 1.3 79.7 - - - +
358A LEU* 1.3 56.0 + - - +
360A ILE* 3.3 7.2 + - - +
361A ASN* 2.9 57.8 + - - +
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Residues in contact with LEU 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A TRP 2.9 18.1 + - - +
355A HIS* 3.7 8.7 - - + +
357A GLN* 1.3 76.5 - - - +
359A SER* 1.3 57.2 + - - +
361A ASN* 4.7 6.7 - - + +
362A LEU* 2.9 60.2 + - + +
413A HIS* 3.4 37.9 - - + +
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Residues in contact with SER 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A HIS 2.9 14.9 + - - -
356A ALA* 3.1 11.9 + - - -
358A LEU* 1.3 77.1 - - - +
360A ILE* 1.3 65.2 + - - +
363A ALA* 3.0 21.9 + - - +
410A ALA* 3.0 37.8 + - - +
413A HIS* 4.2 2.4 - - - +
414A ALA* 3.2 24.2 - - - +
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Residues in contact with ILE 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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350A LEU* 3.9 33.4 - - + -
356A ALA* 3.0 13.9 + - + +
357A GLN* 3.7 9.0 - - - +
359A SER* 1.3 75.2 - - - +
361A ASN* 1.3 67.3 + - - +
363A ALA* 3.2 7.2 + - - +
364A MET* 3.0 45.7 + - + +
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Residues in contact with ASN 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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357A GLN* 2.9 41.7 + - - +
358A LEU* 4.3 6.9 - - + +
360A ILE* 1.3 84.4 - - - +
362A LEU* 1.3 58.1 + - - +
364A MET* 4.2 4.2 - - - +
365A LEU* 2.9 35.0 + - + +
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Residues in contact with LEU 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 LEU* 2.9 50.4 + - + +
361A ASN* 1.3 74.4 - - - +
363A ALA* 1.3 67.3 + - - +
365A LEU* 4.6 5.4 - - + -
366A GLY* 2.9 22.7 + - - -
406A LEU* 3.3 56.9 - - + +
409A GLY* 3.6 28.0 - - - +
410A ALA* 3.7 6.5 - - + -
413A HIS* 3.8 8.1 - - + +
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Residues in contact with ALA 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A SER* 3.0 17.8 + - - +
360A ILE* 3.2 6.5 + - - +
362A LEU* 1.3 78.5 - - - +
364A MET* 1.3 64.9 + - + +
366A GLY* 3.9 0.5 - - - -
367A SER* 2.8 34.9 + - - +
407A ILE* 4.3 11.6 - - + +
410A ALA* 3.3 15.0 - - + +
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Residues in contact with MET 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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360A ILE* 3.0 31.6 + - + +
361A ASN* 4.2 4.0 - - - +
363A ALA* 1.3 81.1 - - + +
365A LEU* 1.3 60.0 + - - +
367A SER* 3.5 11.4 + - - -
368A LEU* 2.9 28.8 + - - +
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Residues in contact with LEU 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 ASN* 2.9 21.0 + - + +
362A LEU* 4.2 6.5 - - + +
364A MET* 1.3 74.9 - - - +
366A GLY* 1.3 57.2 + - - +
368A LEU* 3.3 22.3 + - + +
369A THR* 2.7 40.4 + - - +
406A LEU* 3.9 22.7 - - + -
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Residues in contact with GLY 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LEU 2.9 17.5 + - - -
363A ALA 3.9 0.7 - - - -
365A LEU* 1.3 74.9 - - - +
367A SER* 1.3 64.6 + - - +
369A THR 3.0 2.4 + - - -
370A ILE* 3.0 20.6 + - - +
403A GLY* 3.5 34.6 - - - -
406A LEU* 3.8 9.7 - - - +
407A ILE* 4.2 4.5 - - - -
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Residues in contact with SER 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ALA* 2.8 23.2 + - - +
364A MET* 3.7 15.7 - - - -
366A GLY* 1.3 73.9 - - - +
368A LEU* 1.3 57.7 + - - +
370A ILE* 3.1 14.7 + - - +
371A VAL* 3.0 36.1 + - - +
407A ILE* 4.3 9.6 - - - +
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Residues in contact with LEU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A MET 2.9 18.8 + - - +
365A LEU* 3.4 24.2 - - + +
366A GLY 3.2 0.2 - - - -
367A SER* 1.3 76.3 - - - +
369A THR* 1.3 57.5 + - - +
371A VAL* 3.1 23.1 - - + +
372A VAL* 2.9 42.7 + - + +
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Residues in contact with THR 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 LEU* 2.7 27.2 + - - +
366A GLY* 3.0 8.0 + - - -
368A LEU* 1.3 76.0 - - - +
370A ILE* 1.3 58.5 + - - +
372A VAL* 3.3 10.2 + - + +
373A ALA* 3.0 26.7 + - - +
399A HIS* 3.3 50.0 - - + +
402A ILE* 4.2 12.4 - - + +
403A GLY* 4.1 5.8 - - - -
406A LEU* 4.3 7.8 - - - +
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Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A GLY 3.0 13.6 + - - +
367A SER* 3.1 11.0 + - - +
369A THR* 1.3 76.8 - - - +
371A VAL* 1.3 67.3 + - + +
373A ALA* 3.0 18.3 + - - +
374A GLN* 3.1 18.7 + - + +
399A HIS 4.9 1.1 - - - -
400A MET* 3.9 34.8 - - + +
403A GLY* 4.2 14.1 - - - -
404A GLY* 4.6 2.9 - - - +
407A ILE* 3.8 28.9 - - + -
609A ILE* 5.4 5.8 - - + -
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Residues in contact with VAL 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A SER* 3.0 18.0 + - - +
368A LEU* 3.1 33.7 - - + +
370A ILE* 1.3 78.1 - - + +
372A VAL* 1.3 57.7 + - + +
374A GLN* 4.6 6.3 - - - +
375A HIS* 2.9 56.0 + - + +
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Residues in contact with VAL 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LEU* 2.9 35.8 + - + +
369A THR* 3.3 13.2 - - + +
371A VAL* 1.3 75.2 - - + +
373A ALA* 1.3 66.3 + - - +
375A HIS* 3.8 3.3 - - - -
376A MET* 2.9 49.2 + - + +
399A HIS* 4.1 19.7 - - + +
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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
----------------------------------------------------------
369A THR 3.0 13.4 + - - +
370A ILE 3.0 9.2 + - - +
372A VAL* 1.3 78.2 - - - +
374A GLN* 1.3 63.6 + - - +
376A MET* 3.8 3.6 - - - +
377A TYR* 3.0 18.4 + - - +
395A LEU 5.7 0.4 - - - -
396A PHE* 3.7 47.0 - - + +
399A HIS* 4.1 11.7 - - + -
400A MET* 4.2 12.3 - - + +
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Residues in contact with GLN 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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370A ILE* 3.1 20.3 + - + +
371A VAL* 3.9 7.0 - - - +
373A ALA* 1.3 76.1 - - - +
375A HIS* 1.3 69.8 + - + +
377A TYR* 2.9 47.1 + - + -
378A SER* 3.0 12.2 + - - -
396A PHE* 4.3 7.0 - - - -
400A MET* 3.5 24.2 - - + +
612A VAL* 5.7 0.2 - - - +
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Residues in contact with HIS 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A VAL* 2.9 40.6 + - + +
372A VAL* 4.1 3.8 - - - +
374A GLN* 1.3 81.2 - - + +
376A MET* 1.3 58.6 + - + +
378A SER* 3.8 3.4 - - - -
379A MET* 3.0 56.5 + - + +
381A PRO* 5.5 0.2 - - - +
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Residues in contact with MET 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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372A VAL* 2.9 40.7 + - + +
373A ALA* 3.9 4.0 - - - +
375A HIS* 1.3 76.0 - - + +
377A TYR* 1.3 66.0 + - - +
379A MET 4.4 3.8 - - - -
380A PRO* 3.8 13.5 - - - +
381A PRO* 4.1 19.4 - - + +
382A TYR* 3.9 29.4 - - + -
385A LEU* 4.7 2.0 - - + -
392A GLN* 3.3 18.1 + - - +
395A LEU* 4.0 31.2 - - + -
399A HIS* 4.9 11.0 - - + -
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Residues in contact with TYR 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 3.0 12.1 + - - +
374A GLN* 2.9 50.2 + - - -
376A MET* 1.3 80.7 - - - +
378A SER* 1.3 75.6 + - - +
379A MET 3.5 0.5 + - - -
380A PRO* 3.9 10.0 - - - +
392A GLN* 3.9 15.8 + - - +
396A PHE* 4.1 14.4 - + + -
514A THR* 4.5 5.9 + - + +
529A LEU* 4.2 10.7 - - + +
532A ILE* 3.9 19.7 - - + +
616A PHE* 3.5 34.1 - + + -
620A MET* 3.9 27.5 - - + +
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Residues in contact with SER 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 5.7 0.2 - - - +
374A GLN 3.0 16.4 + - - -
375A HIS* 3.8 10.4 + - - -
377A TYR* 1.3 98.2 - - - +
379A MET* 1.3 67.9 + - - +
380A PRO* 3.7 2.0 - - - -
512A SER* 2.5 33.5 + - - -
514A THR* 4.1 14.1 - - - -
529A LEU* 3.5 12.0 - - - +
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Residues in contact with MET 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 4.9 0.9 - - - -
294A LEU* 3.4 26.2 - - + +
375A HIS* 3.0 57.4 + - + +
376A MET 4.0 1.1 - - - -
378A SER* 1.3 91.5 - - - +
380A PRO* 1.3 67.2 - - - +
381A PRO* 3.0 11.0 - - - +
511A THR* 3.3 39.3 - - - +
512A SER* 3.8 6.7 - - - -
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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
------------------------------------------------------------
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