Contacts of the helix formed by residues 434 - 461 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A ARG* 3.4 20.2 + - - +
432A ARG 3.4 0.6 - - - +
433A LEU* 1.3 82.9 - - - +
435A GLY* 1.3 65.2 + - - +
436A LEU* 5.1 0.9 - - - +
437A GLU* 3.5 26.9 + - - +
438A ARG* 3.7 7.8 + - - +
398C ILE* 3.5 27.6 - - + +
399C ARG 4.7 0.7 - - - -
401C SER 3.5 13.9 - - - +
402C ASP 3.8 10.0 + - - -
403C THR* 4.2 11.2 - - - +
404C ASP* 4.0 14.3 + - - +
407C ALA* 4.7 5.6 - - + -
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Residues in contact with GLY 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A THR* 1.3 71.3 - - - +
436A LEU* 1.3 66.0 + - - +
437A GLU 3.3 0.7 + - - -
438A ARG* 3.5 14.4 + - - +
439A ASP* 3.9 13.7 + - - +
399C ARG 4.5 5.7 + - - -
401C SER 3.6 9.2 + - - -
402C ASP* 3.8 5.7 + - - -
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Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A THR* 3.5 1.3 - - - +
435A GLY* 1.3 76.1 - - - +
437A GLU* 1.3 56.3 + - + +
439A ASP* 3.3 16.1 + - + +
440A LYS* 3.1 30.8 + - + +
402C ASP* 3.5 17.1 + - + +
403C THR* 3.6 31.9 - - + -
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Residues in contact with GLU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ARG* 3.7 22.0 - - + +
432A ARG* 3.5 44.8 + - - +
434A THR* 3.7 14.2 + - - +
435A GLY 3.2 0.6 - - - -
436A LEU* 1.3 76.2 - - + +
438A ARG* 1.3 64.6 + - - +
440A LYS* 3.0 35.8 + - - +
441A ILE* 3.2 28.7 + - - +
404C ASP* 5.2 5.0 - - - +
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Residues in contact with ARG 438 (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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385A ARG* 5.2 12.4 - - - +
388A LEU* 4.1 33.8 - - + +
389A ASP* 3.7 24.0 + - - -
434A THR 3.7 6.9 + - - +
435A GLY* 3.5 11.0 + - - +
436A LEU 3.4 0.8 - - - -
437A GLU* 1.3 76.6 - - - +
439A ASP* 1.3 71.7 + - - +
441A ILE* 3.5 3.5 + - - +
442A GLU* 3.2 58.6 + - - +
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Residues in contact with ASP 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A GLY 3.9 11.8 + - - +
436A LEU* 3.3 19.3 + - + +
437A GLU 3.3 0.4 - - - -
438A ARG* 1.3 86.9 + - - +
440A LYS* 1.3 56.2 + - - +
442A GLU* 3.2 4.1 + - - +
443A ALA* 2.9 35.1 + - - +
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Residues in contact with LYS 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A LEU* 3.1 19.6 + - + +
437A GLU* 3.0 38.2 + - - +
439A ASP* 1.3 75.9 - - - +
441A ILE* 1.3 60.8 + - + +
443A ALA* 3.6 8.6 - - + +
444A GLU* 3.2 23.6 + - - +
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Residues in contact with ILE 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LEU* 4.0 23.3 - - + +
384A LEU* 4.2 12.6 - - + -
385A ARG* 3.9 26.2 - - + +
388A LEU* 3.5 28.7 - - + -
428A MET* 5.4 1.3 - - - -
432A ARG* 3.9 36.6 - - + +
437A GLU* 3.2 22.0 + - - +
438A ARG* 3.7 6.7 - - - +
439A ASP 3.2 0.4 - - - -
440A LYS* 1.3 74.4 - - - +
442A GLU* 1.3 59.6 + - - +
444A GLU* 3.5 8.9 + - - +
445A TYR* 3.1 25.8 + - - +
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Residues in contact with GLU 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ARG* 3.3 35.5 + - - +
438A ARG* 3.2 43.4 + - - +
439A ASP* 3.2 4.7 + - - +
441A ILE* 1.3 78.2 - - + +
443A ALA* 1.3 62.5 + - - +
445A TYR* 3.3 5.2 + - + +
446A ASN* 2.8 48.9 + - - +
468d ARG* 3.7 18.6 - - - +
469d LEU 5.1 0.9 + - - -
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Residues in contact with ALA 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ASP 2.9 17.0 + - - +
440A LYS* 3.6 10.1 - - - +
442A GLU* 1.3 76.9 - - - +
444A GLU* 1.3 62.5 + - - +
446A ASN* 3.3 5.7 + - - +
447A GLU* 3.2 23.8 + - - +
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Residues in contact with GLU 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ARG* 2.9 47.1 + - - +
381A LEU* 3.7 12.0 - - + +
440A LYS 3.2 11.6 + - - +
441A ILE* 3.8 10.2 - - - +
443A ALA* 1.3 78.8 - - - +
445A TYR* 1.3 56.8 + - - +
447A GLU* 3.6 5.7 + - - +
448A LEU* 3.1 33.0 + - + +
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Residues in contact with TYR 445 (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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378A ALA* 3.6 29.8 - - + -
381A LEU* 3.6 27.6 - - + -
382A GLU* 2.8 33.6 + - + +
385A ARG* 3.8 38.7 + - - -
441A ILE 3.1 17.6 + - - +
442A GLU* 3.6 9.0 - - + +
443A ALA 3.2 0.4 - - - -
444A GLU* 1.3 78.1 - - - +
446A ASN* 1.3 67.5 + - - +
448A LEU* 3.4 4.1 - - + +
449A LEU* 3.2 54.5 + - + +
470d ASP* 4.9 5.4 + - + -
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Residues in contact with ASN 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A GLU* 2.8 43.1 + - - +
443A ALA* 3.3 5.8 + - - +
445A TYR* 1.3 77.9 - - - +
447A GLU* 1.3 63.0 + - - +
449A LEU* 3.2 16.8 + - - +
450A ASN* 3.3 20.5 + - - +
468d ARG* 4.9 1.7 - - - +
469d LEU* 3.4 42.8 + - + +
470d ASP* 3.0 31.3 + - - +
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Residues in contact with GLU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ALA 3.2 15.7 + - - +
444A GLU* 3.9 7.2 - - - +
446A ASN* 1.3 75.8 - - - +
448A LEU* 1.3 56.6 + - - +
450A ASN* 3.3 13.9 + - - +
451A TYR* 3.0 28.9 + - - +
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Residues in contact with LEU 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ALA* 3.5 37.7 - - + +
377A ARG* 3.4 31.2 - - + -
378A ALA* 3.7 20.0 - - + +
381A LEU* 3.8 18.2 - - + -
444A GLU* 3.1 21.1 + - + +
445A TYR* 3.4 6.7 - - - +
446A ASN 3.2 0.2 - - - -
447A GLU* 1.3 76.8 - - - +
449A LEU* 1.3 56.7 + - - +
451A TYR* 3.3 13.5 + - + +
452A ILE* 2.8 37.9 + - + +
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Residues in contact with LEU 449 (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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378A ALA* 5.1 2.5 - - + -
382A GLU* 5.3 1.1 - - - +
445A TYR* 3.2 50.2 + - + +
446A ASN* 3.2 10.8 + - - +
448A LEU* 1.3 74.7 - - + +
450A ASN* 1.3 65.7 + - - +
452A ILE* 3.4 20.2 + - + +
453A SER* 3.2 22.3 + - - -
470d ASP* 2.8 54.7 - - + +
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Residues in contact with ASN 450 (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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446A ASN 3.3 14.4 + - - +
447A GLU* 3.3 12.6 + - - +
449A LEU* 1.3 76.6 - - - +
451A TYR* 1.3 56.8 + - - +
453A SER* 3.2 9.0 + - - -
454A GLU* 3.0 41.9 + - - +
469d LEU* 6.1 2.0 - - - +
470d ASP* 5.6 2.3 - - - +
473d LEU* 4.4 21.4 - - - +
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Residues in contact with TYR 451 (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 ASN* 3.2 39.3 + - + +
374A ALA* 4.2 14.1 - - + -
447A GLU 3.0 14.0 + - - +
448A LEU* 3.3 15.5 + - + +
450A ASN* 1.3 72.8 - - - +
452A ILE* 1.3 64.3 - - - +
454A GLU* 3.2 21.3 + - + +
455A LEU* 2.9 62.2 + - + +
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Residues in contact with ILE 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LEU* 3.7 15.9 - - + +
374A ALA* 3.8 29.4 - - + +
375A LYS* 4.2 16.6 - - + +
378A ALA* 4.0 26.9 - - + -
448A LEU 2.8 29.3 + - - +
449A LEU* 3.8 16.4 - - + +
450A ASN 3.3 0.2 - - - -
451A TYR* 1.3 70.3 - - - +
453A SER* 1.3 57.5 + - - +
455A LEU* 3.4 6.3 + - - +
456A GLU* 3.1 49.3 + - - +
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Residues in contact with SER 453 (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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449A LEU 3.2 13.1 + - - -
450A ASN* 3.2 12.3 + - - -
452A ILE* 1.3 73.7 - - - +
454A GLU* 1.3 58.0 + - - +
456A GLU* 3.3 13.0 + - - +
457A THR* 2.8 34.5 + - - -
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Residues in contact with GLU 454 (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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450A ASN* 3.0 31.5 + - - +
451A TYR* 3.2 24.1 + - + +
453A SER* 1.3 74.8 - - - +
455A LEU* 1.3 63.3 + - + +
457A THR* 3.5 11.1 + - - -
458A ILE* 3.4 27.8 + - + +
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Residues in contact with LEU 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A THR* 3.6 30.1 - - + +
370A ASN* 3.7 9.6 - - + +
371A LEU* 3.5 41.3 - - + +
374A ALA* 4.7 0.9 - - + -
451A TYR* 2.9 66.2 + - + +
452A ILE* 3.6 8.1 - - - +
454A GLU* 1.3 76.1 - - + +
456A GLU* 1.3 61.8 + - - +
458A ILE* 3.2 16.1 + - + +
459A LEU* 3.2 21.4 + - - +
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Residues in contact with GLU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LEU* 4.0 15.5 - - + -
375A LYS* 3.6 22.3 + - - -
452A ILE* 3.1 34.4 + - - +
453A SER* 3.3 14.3 + - - +
455A LEU* 1.3 73.1 - - - +
457A THR* 1.3 56.2 + - - +
459A LEU* 3.3 8.6 + - + +
460A ALA* 2.9 35.3 + - - +
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Residues in contact with THR 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A SER* 2.8 20.4 + - - -
454A GLU* 3.5 12.0 + - - -
456A GLU* 1.3 76.8 - - - +
458A ILE* 1.3 60.3 + - + +
460A ALA* 3.5 6.3 + - - +
461A ASP* 3.2 19.6 + - + +
464A VAL* 3.7 24.8 - - + +
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Residues in contact with ILE 458 (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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363A VAL* 5.5 1.6 - - + -
367A THR* 4.0 25.1 - - + +
454A GLU* 3.4 18.6 + - + +
455A LEU* 3.2 21.6 + - + +
457A THR* 1.3 77.7 - - - +
459A LEU* 1.3 60.4 + - + +
461A ASP 3.3 14.6 + - - +
464A VAL* 4.7 12.3 - - + -
465A LEU* 2.8 56.2 - - + +
468A LEU* 4.4 23.1 - - + -
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Residues in contact with LEU 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ARG* 4.0 21.7 - - + +
367A THR* 3.7 20.9 - - + -
368A GLN* 3.6 36.8 - - + +
371A LEU* 3.6 31.2 - - + -
455A LEU 3.2 15.8 + - - +
456A GLU* 3.3 6.7 + - + +
458A ILE* 1.3 78.1 - - + +
460A ALA* 1.3 60.7 + - - +
461A ASP 3.8 1.0 + - - -
462A GLU* 5.1 3.3 + - - +
465A LEU* 4.8 1.8 - - + -
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Residues in contact with ALA 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A GLU 2.9 18.3 + - - +
457A THR* 3.7 7.6 - - - +
458A ILE 3.3 0.4 - - - -
459A LEU* 1.3 79.1 - - - +
461A ASP* 1.3 58.3 + - + +
462A GLU 4.1 1.3 + - - -
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Residues in contact with ASP 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A THR* 3.2 5.9 + - + +
458A ILE 3.3 12.0 - - - +
459A LEU 3.5 0.4 - - - -
460A ALA* 1.3 78.2 - - + +
462A GLU* 1.3 56.5 + - - +
463A GLU* 3.2 19.4 + - - +
464A VAL* 2.9 54.6 + - + +
465A LEU 3.6 1.6 + - - -
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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