Contacts of the helix formed by residues 434 - 461 (chain l) in PDB entry 6QX2
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 THR 434 (chain l).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398j ILE* 3.5 33.9 - - + +
399j ARG 4.6 0.4 - - - -
401j SER 3.6 7.0 - - - +
402j ASP 4.2 6.9 + - - -
403j THR 4.2 19.8 - - - +
404j ASP* 4.6 4.4 + - - +
407j ALA* 4.3 7.2 - - + -
426j LEU* 5.2 0.4 - - + -
431l ARG* 3.4 16.1 + - - +
432l ARG 3.4 0.9 - - - +
433l LEU* 1.3 83.5 - - - +
435l GLY* 1.3 64.1 + - - +
437l GLU* 2.7 40.4 + - - +
438l ARG* 3.7 7.8 + - - +
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Residues in contact with GLY 435 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399j ARG 4.1 6.7 + - - -
401j SER 3.2 13.3 + - - -
402j ASP* 4.1 6.1 - - - -
434l THR* 1.3 70.9 - - - +
436l LEU* 1.3 65.5 + - - +
437l GLU 3.3 0.5 + - - -
438l ARG* 3.5 14.5 + - - +
439l ASP* 3.8 14.9 + - - +
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Residues in contact with LEU 436 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402j ASP* 3.1 20.4 + - + +
403j THR* 3.9 26.7 - - + -
434l THR 3.5 0.2 - - - -
435l GLY* 1.3 75.3 - - - +
437l GLU* 1.3 67.4 + - - +
439l ASP* 3.4 14.2 + - + +
440l LYS* 3.0 36.1 + - + +
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Residues in contact with GLU 437 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402j ASP 5.0 0.2 - - - +
403j THR* 5.5 0.3 - - - -
404j ASP* 5.2 7.1 + - - +
431l ARG* 3.7 19.6 - - + +
432l ARG* 3.4 28.7 - - + +
434l THR* 2.7 30.5 + - - +
435l GLY 3.2 1.0 - - - -
436l LEU* 1.3 82.8 - - - +
438l ARG* 1.3 63.1 + - - +
440l LYS* 3.5 21.5 + - + +
441l ILE* 3.2 30.9 + - + +
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Residues in contact with ARG 438 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385l ARG* 3.7 24.4 - - - +
388l LEU* 3.8 26.8 - - + +
389l ASP* 3.1 38.9 + - - +
432l ARG 4.7 2.8 + - - +
434l THR 3.7 7.2 + - - +
435l GLY* 3.5 10.6 + - - +
436l LEU 3.4 0.4 - - - -
437l GLU* 1.3 77.4 - - - +
439l ASP* 1.3 64.9 + - - +
441l ILE* 3.5 10.0 + - - +
442l GLU* 3.2 47.1 + - - +
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Residues in contact with ASP 439 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435l GLY 3.8 11.8 + - - +
436l LEU* 3.4 17.2 + - + +
437l GLU 3.3 0.4 - - - -
438l ARG* 1.3 77.9 - - - +
440l LYS* 1.3 55.9 + - - +
442l GLU* 3.2 7.0 + - - +
443l ALA* 2.9 35.1 + - - +
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Residues in contact with LYS 440 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436l LEU* 3.0 25.8 + - + +
437l GLU* 3.6 24.9 - - + +
438l ARG 3.4 0.2 - - - -
439l ASP* 1.3 75.9 - - - +
441l ILE* 1.3 57.4 + - + +
443l ALA* 3.6 7.1 - - - +
444l GLU* 3.1 29.4 + - - +
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Residues in contact with ILE 441 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377l ARG* 6.0 1.1 - - - +
381l LEU* 4.0 26.8 - - + +
384l LEU* 4.2 28.9 - - + +
385l ARG* 3.9 26.9 - - + +
388l LEU* 5.8 4.3 - - + -
428l MET* 5.6 6.1 - - - -
432l ARG* 5.3 11.7 - - + +
437l GLU* 3.2 23.1 + - + +
438l ARG* 3.7 12.3 - - - +
439l ASP 3.2 0.4 - - - -
440l LYS* 1.3 76.1 - - + +
442l GLU* 1.3 60.1 + - - +
444l GLU* 3.5 8.8 + - - +
445l TYR* 3.0 24.8 + - - +
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Residues in contact with GLU 442 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385l ARG* 2.5 44.5 + - - -
438l ARG* 3.2 31.3 + - - +
439l ASP* 3.2 9.4 + - - +
441l ILE* 1.3 75.8 - - - +
443l ALA* 1.3 63.0 + - - +
445l TYR* 3.3 6.4 + - - +
446l ASN* 2.8 54.9 + - - +
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Residues in contact with ALA 443 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439l ASP 2.9 16.9 + - - +
440l LYS* 3.6 9.4 - - - +
442l GLU* 1.3 76.8 - - - +
444l GLU* 1.3 61.0 - - - +
446l ASN* 3.3 6.1 + - - +
447l GLU* 3.2 23.6 + - - +
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Residues in contact with GLU 444 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377l ARG* 2.8 48.8 + - - +
381l LEU* 3.7 12.0 - - + +
440l LYS 3.1 15.6 + - - +
441l ILE* 3.8 7.4 - - - +
442l GLU 3.4 0.2 - - - -
443l ALA* 1.3 78.3 - - - +
445l TYR* 1.3 56.7 + - - +
447l GLU* 3.6 6.0 + - - +
448l LEU* 3.1 30.7 + - + +
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Residues in contact with TYR 445 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378l ALA* 3.6 18.4 - - + -
381l LEU* 3.7 27.4 - - + -
382l GLU* 2.8 43.7 + - + +
385l ARG* 3.8 37.9 + - - -
441l ILE 3.0 18.0 + - - +
442l GLU* 3.6 14.1 - - - +
443l ALA 3.2 0.4 - - - -
444l GLU* 1.3 76.5 - - - +
446l ASN* 1.3 64.0 + - - +
448l LEU* 3.4 4.8 - - + +
449l LEU* 3.2 55.5 + - + +
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Residues in contact with ASN 446 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442l GLU* 2.8 50.2 + - - +
443l ALA* 3.3 6.2 + - - +
445l TYR* 1.3 76.6 - - - +
447l GLU* 1.3 63.3 + - - +
449l LEU* 3.2 25.8 + - - +
450l ASN* 3.3 19.5 + - - +
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Residues in contact with GLU 447 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443l ALA 3.2 15.9 + - - +
444l GLU* 3.9 7.2 - - - +
446l ASN* 1.3 74.5 - - - +
448l LEU* 1.3 56.5 + - - +
450l ASN* 3.3 20.5 + - - +
451l TYR* 2.9 28.2 + - - +
454l GLU* 5.7 0.9 - - - +
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Residues in contact with LEU 448 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374l ALA* 3.4 35.9 - - + +
377l ARG* 3.6 19.1 - - + -
378l ALA* 3.4 41.3 - - + +
381l LEU* 4.1 11.0 - - + -
444l GLU* 3.1 20.0 + - + +
445l TYR* 3.4 7.4 - - - +
447l GLU* 1.3 76.3 - - - +
449l LEU* 1.3 52.0 + - - +
451l TYR* 3.3 13.7 + - + +
452l ILE* 2.8 42.1 + - + +
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Residues in contact with LEU 449 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378l ALA* 5.3 2.7 - - + -
382l GLU* 5.4 0.9 - - - +
445l TYR* 3.2 56.6 + - + +
446l ASN* 3.2 17.4 + - - +
448l LEU* 1.3 74.2 - - + +
450l ASN* 1.3 63.9 - - - +
452l ILE* 3.4 17.8 + - + +
453l SER* 3.2 22.9 + - - -
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Residues in contact with ASN 450 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446l ASN* 3.3 15.3 + - - +
447l GLU* 3.3 28.1 + - - +
449l LEU* 1.3 77.4 - - - +
451l TYR* 1.3 57.5 + - - +
453l SER* 2.7 26.5 + - - -
454l GLU* 2.9 26.9 + - - +
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Residues in contact with TYR 451 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370l ASN* 3.2 33.9 + - + +
374l ALA* 4.2 18.2 - - + -
447l GLU* 2.9 17.2 + - - +
448l LEU* 3.5 16.8 - - + +
450l ASN* 1.3 73.0 - - - +
452l ILE* 1.3 64.4 + - - +
454l GLU* 3.2 21.7 + - + +
455l LEU* 2.9 62.4 + - + +
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Residues in contact with ILE 452 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371l LEU* 3.7 15.7 - - + +
374l ALA* 3.8 29.8 - - + +
375l LYS* 4.2 9.2 - - + +
378l ALA* 3.9 27.6 - - + -
448l LEU* 2.8 28.4 + - + +
449l LEU* 3.8 15.9 - - + +
450l ASN 3.3 0.2 - - - -
451l TYR* 1.3 71.3 - - - +
453l SER* 1.3 56.9 + - - +
455l LEU* 3.4 5.4 + - - +
456l GLU* 3.1 49.1 + - - +
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Residues in contact with SER 453 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449l LEU 3.2 13.3 + - - -
450l ASN* 2.7 21.5 + - - -
452l ILE* 1.3 74.9 - - - +
454l GLU* 1.3 58.2 + - - +
456l GLU* 3.3 12.9 + - - +
457l THR* 2.8 34.4 + - - -
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Residues in contact with GLU 454 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447l GLU* 5.7 0.7 - - - +
450l ASN* 2.9 24.0 + - - +
451l TYR* 3.5 28.6 + - + +
453l SER* 1.3 81.7 + - - +
455l LEU* 1.3 62.1 + - + +
457l THR* 3.5 9.7 + - - -
458l ILE* 3.4 29.3 + - + +
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Residues in contact with LEU 455 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367l THR* 3.6 29.1 - - + +
370l ASN* 3.8 9.0 - - + +
371l LEU* 3.5 40.6 - - + +
374l ALA* 4.6 1.1 - - + -
451l TYR* 2.9 65.7 + - + +
452l ILE* 3.6 8.1 - - - +
453l SER 3.3 0.2 - - - -
454l GLU* 1.3 75.5 - - + +
456l GLU* 1.3 62.9 + - - +
458l ILE* 3.2 17.6 + - + +
459l LEU* 3.2 21.2 + - - +
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Residues in contact with GLU 456 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371l LEU* 4.0 20.2 - - + +
452l ILE* 3.1 37.4 + - - +
453l SER* 3.3 13.7 + - - +
455l LEU* 1.3 74.0 - - - +
457l THR* 1.3 56.5 - - - +
459l LEU* 3.3 8.4 + - + +
460l ALA* 2.9 36.2 + - - +
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Residues in contact with THR 457 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453l SER 2.8 21.4 + - - -
454l GLU* 3.5 11.8 + - - -
456l GLU* 1.3 76.1 - - - +
458l ILE* 1.3 60.3 + - - +
460l ALA* 3.5 6.6 + - - +
461l ASP* 3.2 25.2 + - + +
464l VAL* 4.1 20.3 - - + +
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Residues in contact with ILE 458 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363l VAL* 5.3 0.4 - - + -
364l ARG* 5.2 0.7 + - - -
367l THR* 3.9 25.4 - - + +
454l GLU* 3.4 18.6 + - + +
455l LEU* 3.2 20.0 + - + +
457l THR* 1.3 74.4 - - - +
459l LEU* 1.3 64.1 + - + +
461l ASP 3.3 17.7 - - - +
462l GLU* 4.9 0.2 - - - -
464l VAL* 3.8 22.2 - - + -
465l LEU* 3.7 36.9 - - + +
468l LEU* 3.8 26.2 - - + -
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Residues in contact with LEU 459 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364l ARG* 4.1 32.7 + - + +
367l THR* 3.7 21.1 - - + -
368l GLN* 3.6 39.9 - - + +
371l LEU* 3.6 31.2 - - + -
455l LEU 3.2 16.1 + - - +
456l GLU* 3.3 6.5 + - + +
458l ILE* 1.3 78.3 - - + +
460l ALA* 1.3 61.2 + - - +
461l ASP 5.0 0.9 - - - -
462l GLU* 5.2 1.0 + - - +
465l LEU* 5.4 0.7 - - + -
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Residues in contact with ALA 460 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456l GLU 2.9 19.0 + - - +
457l THR* 3.7 7.9 - - - +
458l ILE 3.3 0.4 - - - -
459l LEU* 1.3 78.6 - - - +
461l ASP* 1.3 59.3 + - + +
462l GLU 4.1 1.5 + - - -
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Residues in contact with ASP 461 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457l THR* 3.2 8.9 + - + +
458l ILE 3.3 8.1 - - - +
460l ALA* 1.3 78.1 - - + +
462l GLU* 1.3 56.3 + - - +
463l GLU* 3.2 21.5 + - - +
464l VAL* 2.9 50.6 + - + +
465l LEU 3.3 8.1 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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