Contacts of the helix formed by residues 340 - 363 (chain A) in PDB entry 5UNJ
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 340 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A LEU* 1.3 78.6 - - - +
341A THR* 1.3 61.6 + - - +
342A PHE* 3.9 12.2 + - - +
343A GLY* 3.0 23.1 + - - -
344A LEU* 2.8 27.4 + - - +
525A ASP 5.3 2.3 + - - -
527A PRO* 5.8 0.7 - - - +
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Residues in contact with THR 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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339A LEU 3.9 0.2 + - - -
340A SER* 1.3 72.5 - - - +
342A PHE* 1.3 58.1 + - - +
344A LEU* 3.0 12.0 + - + +
345A MET* 2.9 44.5 + - + +
416A ILE* 5.3 4.3 - - + -
419A GLN* 3.5 48.1 + - - +
601A RJW 4.0 12.8 - - + -
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Residues in contact with PHE 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A SER* 3.2 9.5 + - - +
341A THR* 1.3 77.8 - - - +
343A GLY* 1.3 58.6 + - - +
345A MET* 3.1 3.8 + - - +
346A CYS* 2.9 47.4 + - - -
419A GLN 4.8 6.8 + - - +
420A ALA 5.5 2.0 - - - +
424A LEU* 4.1 15.9 - - + -
516A TYR* 4.2 8.3 - + - -
517A LEU* 3.7 18.4 - - + -
520A LYS* 3.9 31.4 - - + -
525A ASP* 3.7 24.7 - - + -
526A VAL* 4.3 2.7 - - + -
601A RJW 3.5 46.4 - + + +
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Residues in contact with GLY 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 4.2 12.3 - - - +
340A SER* 3.0 22.1 + - - -
342A PHE* 1.3 79.1 - - - +
344A LEU* 1.3 61.3 + - - +
346A CYS* 3.2 6.1 + - - +
347A LYS* 3.2 20.1 + - - +
525A ASP 5.2 0.2 - - - -
527A PRO* 4.1 27.9 - - - +
529A ASN* 5.0 0.7 + - - -
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Residues in contact with LEU 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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326A LEU* 4.2 43.4 - - + +
339A LEU* 3.9 22.3 - - + +
340A SER 2.8 15.0 + - - +
341A THR* 3.0 15.9 + - + +
343A GLY* 1.3 74.0 - - - +
345A MET* 1.3 72.2 + - + +
347A LYS* 3.2 8.5 + - + +
348A MET* 2.9 25.6 + - - +
409A GLN* 6.1 0.7 - - - +
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Residues in contact with MET 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LEU* 5.2 2.5 - - + -
341A THR* 2.9 24.3 + - + +
342A PHE 3.5 7.4 - - - +
344A LEU* 1.3 98.2 - - + +
346A CYS* 1.3 58.9 + - - +
348A MET* 3.5 37.7 - - + +
349A ALA* 2.8 31.4 + - - +
405A LEU* 4.3 17.9 - - + -
409A GLN* 6.0 0.4 - - - +
416A ILE* 4.5 7.4 - - + -
601A RJW 3.7 56.6 - - + -
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Residues in contact with CYS 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 PHE* 2.9 49.0 + - - -
343A GLY* 3.4 11.4 - - - +
345A MET* 1.3 77.2 - - - +
347A LYS* 1.3 56.7 + - - +
349A ALA 3.8 0.5 - - - -
350A ASP* 2.9 30.0 + - - +
517A LEU* 4.7 1.3 - - - -
526A VAL* 4.0 19.3 - - + -
527A PRO* 4.6 2.7 - - + -
529A ASN* 3.9 16.8 - - - +
532A LEU* 3.8 13.9 - - + +
601A RJW 3.7 17.3 - - - -
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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
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325A TYR* 5.2 9.9 - - + +
326A LEU* 3.5 23.1 - - + -
339A LEU* 5.5 4.3 - - + -
343A GLY 3.2 11.8 + - - +
344A LEU* 3.2 14.3 + - + +
346A CYS* 1.3 74.6 - - - +
348A MET* 1.3 63.9 + - - +
350A ASP* 3.3 11.1 + - + +
351A GLN* 3.0 39.1 + - + +
528A TYR* 3.7 16.1 + - - -
529A ASN* 2.5 38.4 + - - +
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Residues in contact with MET 348 (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 ILE* 4.1 7.0 - - + +
326A LEU* 3.8 27.3 - - + +
344A LEU 2.9 15.9 + - - +
345A MET* 3.3 37.4 + - - +
347A LYS* 1.3 75.4 - - - +
349A ALA* 1.3 58.8 + - - +
351A GLN* 3.3 3.7 + - - +
352A THR* 2.8 30.9 + - - -
405A LEU* 3.9 28.7 - - + -
406A VAL* 3.6 28.9 - - + +
407A THR* 4.4 2.7 - - + -
601A RJW 3.8 32.8 - - + +
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Residues in contact with ALA 349 (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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345A MET 2.8 17.2 + - - +
346A CYS 3.8 3.4 - - - +
348A MET* 1.3 73.3 - - - +
350A ASP* 1.3 66.7 + - - +
352A THR* 3.1 6.0 + - - -
353A LEU* 2.9 29.8 + - - +
386A LEU* 4.1 12.2 - - + +
532A LEU* 4.8 7.9 - - + -
601A RJW 3.7 41.9 + - + +
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Residues in contact with ASP 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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346A CYS 2.9 18.1 + - - +
347A LYS* 3.3 12.8 + - - +
349A ALA* 1.3 76.8 - - - +
351A GLN* 1.3 65.2 + - - +
353A LEU* 3.2 15.0 + - - +
354A PHE* 3.2 36.1 + - - -
529A ASN* 3.4 30.2 - - + +
530A ASN 4.8 0.7 + - - -
531A LEU* 3.4 12.8 + - - +
532A LEU* 2.8 38.5 + - + +
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Residues in contact with GLN 351 (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 LYS* 2.6 39.3 + - - -
322A ILE* 4.0 22.7 - - + -
325A TYR* 3.3 52.3 - - + -
326A LEU* 5.3 0.2 - - + -
347A LYS* 3.0 27.7 + - + +
348A MET 3.7 7.0 - - - +
349A ALA 3.2 0.2 - - - -
350A ASP* 1.3 79.3 + - - +
352A THR* 1.3 66.2 + - - +
354A PHE* 3.2 22.6 + - - +
355A SER* 3.2 21.7 + - - -
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Residues in contact with THR 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE* 4.0 6.6 - - - +
348A MET 2.8 17.2 + - - -
349A ALA* 3.1 9.2 + - - -
351A GLN* 1.3 75.8 - - - +
353A LEU* 1.3 58.1 + - - +
355A SER* 3.0 8.0 + - - +
356A ILE* 2.8 35.4 + - + +
386A LEU* 3.5 24.7 - - + -
389A ASP* 4.2 18.2 - - - +
393A ARG* 6.0 0.2 - - - +
406A VAL* 3.6 27.9 - - + +
601A RJW 4.5 3.6 + - + +
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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
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349A ALA 2.9 16.7 + - - +
350A ASP* 3.5 8.7 - - - +
351A GLN 3.2 0.2 - - - -
352A THR* 1.3 76.0 - - - +
354A PHE* 1.3 56.8 + - - +
356A ILE* 3.1 17.5 + - + +
357A VAL* 2.9 35.6 + - + +
382A TRP* 3.6 54.3 - - + +
386A LEU* 4.2 8.7 - - + -
531A LEU* 3.9 12.1 - - + -
532A LEU* 3.9 38.6 - - + +
535A MET* 4.4 11.0 - - + -
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Residues in contact with PHE 354 (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 LYS* 4.2 11.0 - - - +
350A ASP* 3.2 40.2 + - - -
351A GLN* 3.2 24.3 + - - +
353A LEU* 1.3 80.2 - - - +
355A SER* 1.3 61.9 + - - +
357A VAL* 3.3 4.4 + - - +
358A GLU* 3.1 23.2 + - - +
531A LEU* 3.8 16.6 - - + +
744C LEU* 4.0 22.2 - - + -
748C LEU* 3.8 40.2 - - + -
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Residues in contact with SER 355 (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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313A PRO* 4.9 8.5 - - - +
318A VAL* 3.9 31.1 - - - +
321A LYS* 4.0 12.6 + - - +
322A ILE* 4.4 1.9 - - - +
351A GLN 3.2 9.3 + - - -
352A THR* 3.0 13.9 + - - -
354A PHE* 1.3 78.2 - - - +
356A ILE* 1.3 59.3 + - - +
358A GLU* 3.4 5.9 + - - +
359A TRP* 2.9 28.6 + - - +
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Residues in contact with ILE 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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352A THR* 2.8 24.6 + - + +
353A LEU* 3.1 20.2 + - + +
355A SER* 1.3 74.8 - - - +
357A VAL* 1.3 68.2 + - + +
359A TRP* 3.2 15.8 + - + +
360A ALA* 3.0 21.5 + - - +
378A LEU* 4.5 9.0 - - + -
382A TRP* 4.5 4.0 - - + +
385A LEU* 3.7 35.4 - - + +
386A LEU* 4.0 42.0 - - + +
389A ASP* 5.5 4.3 - - + -
452A LYS* 6.5 1.3 - - - -
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Residues in contact with VAL 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 LEU* 2.9 23.0 + - + +
354A PHE 3.8 4.7 - - - +
356A ILE* 1.3 76.5 - - + +
358A GLU* 1.3 59.4 + - - +
360A ALA* 3.4 2.0 + - - +
361A ARG* 2.8 30.6 + - - +
378A LEU* 4.4 15.7 - - + -
531A LEU* 4.6 7.0 - - + -
535A MET* 5.9 4.0 - - + -
745C LEU* 3.9 20.9 - - + -
748C LEU* 4.0 37.9 - - + -
749C LEU* 4.1 20.3 - - + +
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Residues in contact with GLU 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 PHE 3.1 17.3 + - - +
355A SER* 3.8 6.3 - - - +
357A VAL* 1.3 74.7 - - - +
359A TRP* 1.3 57.3 + - - +
361A ARG* 3.5 27.5 + - - +
362A SER* 2.7 45.5 + - - -
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Residues in contact with TRP 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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311A CYS* 3.2 34.0 + - + +
312A GLU* 3.7 8.3 + - - -
313A PRO* 4.1 15.3 - - + -
355A SER 2.9 14.4 + - - +
356A ILE* 3.2 23.8 + - + +
358A GLU* 1.3 76.7 - - - +
360A ALA* 1.3 80.4 + - + +
362A SER* 2.7 24.6 + - - -
363A SER* 3.2 7.3 + - - -
385A LEU* 3.7 23.3 - - + -
452A LYS* 3.4 59.7 - - + +
453A PHE* 3.6 37.2 - + - -
456A LEU* 3.8 27.1 - - + -
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Residues in contact with ALA 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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356A ILE 3.0 14.9 + - - +
357A VAL 3.9 3.8 - - - +
359A TRP* 1.3 90.7 - - + +
361A ARG* 1.3 64.3 + - - +
363A SER* 2.9 22.3 + - - -
366A PHE* 3.0 36.6 - - + +
378A LEU* 4.1 14.8 - - + -
456A LEU* 4.0 13.0 - - + -
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Residues in contact with ARG 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 VAL* 2.8 23.3 + - - +
358A GLU* 3.5 28.2 + - - +
360A ALA* 1.3 74.0 - - - +
362A SER* 1.3 60.7 + - - +
363A SER 3.1 1.0 + - - -
366A PHE* 4.0 7.2 - - - -
367A ARG* 3.7 19.8 - - - +
374A GLN* 5.1 6.5 + - - +
748C LEU* 3.3 22.2 + - - -
749C LEU* 3.2 39.0 + - + +
751C ALA* 2.5 36.0 + - - +
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Residues in contact with SER 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A CYS* 3.8 24.1 + - - +
358A GLU* 2.7 29.5 + - - -
359A TRP* 2.7 14.1 + - - -
361A ARG* 1.3 72.8 - - - +
363A SER* 1.3 54.1 + - - +
367A ARG* 2.4 30.4 + - - -
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Residues in contact with SER 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A CYS* 3.6 9.6 - - - -
359A TRP* 3.5 11.2 - - - -
360A ALA* 2.9 22.6 + - - -
361A ARG 3.0 0.4 - - - -
362A SER* 1.3 77.9 + - - +
364A ILE* 1.3 85.0 + - - +
366A PHE* 3.8 7.0 - - - +
367A ARG* 3.1 29.0 + - - +
453A PHE* 2.9 31.8 - - - -
456A LEU* 5.4 0.9 - - - -
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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