Contacts of the helix formed by residues 453 - 478 (chain A) in PDB entry 4YOZ
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 HIS 453 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A TYR* 3.5 5.0 - - - -
452A SER* 1.3 76.9 - - - +
454A ILE* 1.3 75.8 + - + +
455A ASP* 3.1 52.3 + - - +
456A PHE* 3.2 30.4 + + + +
457A ALA 3.4 7.8 + - - -
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Residues in contact with ILE 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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439A CYS* 3.7 34.5 - - + +
443A THR* 3.7 25.8 - - + +
452A SER 3.6 1.4 + - - -
453A HIS* 1.3 84.8 + - + +
455A ASP* 1.3 70.4 + - - +
457A ALA* 3.2 2.7 + - + -
458A VAL* 2.9 38.6 + - + +
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Residues in contact with ASP 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A HIS* 3.1 29.6 + - - +
454A ILE* 1.3 83.9 - - - +
456A PHE* 1.3 65.1 + - + +
458A VAL* 3.7 6.8 + - - +
459A ASN* 3.2 22.2 + - - +
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Residues in contact with PHE 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A TYR* 3.4 18.6 - - + +
452A SER* 5.9 1.3 - - - -
453A HIS* 3.2 27.7 + + + +
454A ILE 3.2 0.6 - - - -
455A ASP* 1.3 81.1 - - + +
457A ALA* 1.3 58.8 + - - +
459A ASN* 3.2 8.2 + - + +
460A ARG* 2.8 57.4 + - - +
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Residues in contact with ALA 457 (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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438A PHE* 3.3 18.1 - - + -
439A CYS* 4.0 10.5 - - - -
442A TYR* 3.3 37.8 - - + -
453A HIS 3.4 2.8 + - - +
454A ILE* 3.2 26.0 + - + +
456A PHE* 1.3 78.4 - - - +
458A VAL* 1.3 51.1 + - - +
460A ARG* 3.2 1.8 + - - -
461A LEU* 2.8 31.7 + - - +
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Residues in contact with VAL 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A CYS* 4.4 7.6 - - - -
454A ILE* 2.9 38.3 + - + +
455A ASP* 4.0 7.0 - - - +
457A ALA* 1.3 74.1 - - - +
459A ASN* 1.3 53.4 + - - +
461A LEU* 3.5 10.8 - - + +
462A LYS* 2.7 42.5 + - + +
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Residues in contact with ASN 459 (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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455A ASP 3.2 12.9 + - - +
456A PHE* 3.2 12.3 + - + +
458A VAL* 1.3 77.9 - - - +
460A ARG* 1.3 87.3 + - - +
462A LYS* 3.8 6.5 - - - +
463A LEU* 3.1 32.3 + - - +
513A TYR* 4.0 13.8 + - - -
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Residues in contact with ARG 460 (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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438A PHE* 4.0 13.7 - - + -
442A TYR* 4.4 23.3 + - + +
456A PHE* 2.8 48.4 + - - +
457A ALA* 3.4 9.2 - - - +
459A ASN* 1.3 95.1 + - - +
461A LEU* 1.3 64.0 + - - +
463A LEU* 3.3 3.2 + - - +
464A ALA* 3.0 22.7 + - - +
506A LEU* 4.4 4.2 - - + +
509A VAL* 3.7 28.6 - - + +
510A LEU* 4.5 15.1 - - + +
513A TYR* 3.6 48.4 - - - +
515A SER* 5.8 1.6 - - - -
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Residues in contact with LEU 461 (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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431A LEU 5.3 0.2 - - - +
435A GLY* 3.5 40.6 - - - +
438A PHE* 4.3 8.3 - - + -
439A CYS* 4.5 9.2 - - - -
457A ALA 2.8 21.0 + - - +
458A VAL* 3.5 9.9 - - + +
460A ARG* 1.3 73.1 - - - +
462A LYS* 1.3 58.1 + - - +
464A ALA* 3.0 4.3 + - - +
465A GLU* 2.9 49.6 + - + +
502A MET* 3.6 29.2 - - + -
506A LEU* 4.2 15.5 - - + -
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Residues in contact with LYS 462 (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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406A ASN* 3.8 33.2 + - + +
458A VAL* 2.7 28.5 + - + +
459A ASN* 3.8 8.1 - - - +
461A LEU* 1.3 73.7 - - - +
463A LEU* 1.3 63.4 + - + +
465A GLU* 3.3 13.0 + - - +
466A ILE* 3.0 41.3 + - + +
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Residues in contact with LEU 463 (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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394A VAL* 6.0 0.7 - - + -
397A LEU* 3.7 34.8 - - + -
398A GLN* 5.8 7.2 - - + -
401A VAL* 4.2 26.2 - - + +
459A ASN* 3.1 25.2 + - - +
460A ARG 3.6 4.7 - - - +
462A LYS* 1.3 79.7 - - + +
464A ALA* 1.3 61.7 + - - +
466A ILE* 3.3 13.5 + - + +
467A LEU* 3.1 24.3 + - - +
509A VAL* 4.1 8.7 - - + -
513A TYR* 3.9 24.9 - - + +
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Residues in contact with ALA 464 (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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460A ARG 3.0 9.1 + - - +
461A LEU 3.0 7.2 + - - +
463A LEU* 1.3 77.6 - - - +
465A GLU* 1.3 58.5 + - - +
467A LEU* 3.3 3.9 + - - +
468A TYR* 2.8 28.4 + - - +
502A MET* 3.6 10.5 - - + -
505A CYS* 3.5 10.3 - - - +
506A LEU* 3.6 45.5 - - + +
509A VAL* 3.9 7.8 - - + +
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Residues in contact with GLU 465 (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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406A ASN* 3.5 36.6 + - + +
431A LEU* 3.9 37.5 - - + +
432A LYS* 5.6 0.3 - - - -
461A LEU* 2.9 32.4 + - + +
462A LYS* 3.6 13.3 - - - +
463A LEU 3.3 0.2 - - - -
464A ALA* 1.3 75.2 - - - +
466A ILE* 1.3 64.8 + - - +
468A TYR* 3.3 7.3 + - - +
469A TYR* 3.2 29.5 + - - -
502A MET* 3.8 15.3 - - + -
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Residues in contact with ILE 466 (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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401A VAL* 3.7 34.1 - - + +
404A LEU* 3.7 40.2 - - + +
405A LYS 3.7 10.0 - - - +
406A ASN* 3.7 19.5 - - + +
462A LYS* 3.0 32.2 + - + +
463A LEU* 3.6 17.7 - - + +
464A ALA 3.3 0.2 - - - -
465A GLU* 1.3 75.4 - - - +
467A LEU* 1.3 63.2 + - - +
469A TYR* 3.6 2.1 + - - +
470A LYS* 3.2 21.2 + - + +
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Residues in contact with LEU 467 (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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397A LEU* 3.8 24.5 - - + -
400A ILE* 3.7 31.2 - - + -
401A VAL* 4.3 10.7 - - + +
463A LEU 3.1 11.0 + - - +
464A ALA 3.5 8.1 - - - +
466A ILE* 1.3 77.6 - - - +
468A TYR* 1.3 62.4 + - - +
470A LYS* 3.3 6.4 + - + +
471A ILE* 2.9 45.1 + - + +
505A CYS* 3.8 14.8 - - + +
508A ILE* 3.9 22.9 - - + -
509A VAL* 4.3 12.6 - - + -
544A GLU* 4.9 5.2 - - + +
547A LEU* 5.4 2.7 - - + -
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Residues in contact with TYR 468 (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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427A ILE* 3.2 29.6 - - + +
431A LEU* 3.8 25.6 - - + -
464A ALA 2.8 17.8 + - - +
465A GLU 3.5 4.7 - - - +
466A ILE 3.3 0.2 - - - -
467A LEU* 1.3 76.8 - - - +
469A TYR* 1.3 71.3 - + - +
471A ILE* 3.9 0.5 - - - -
472A LEU* 2.8 48.9 + - + +
498A HIS* 2.6 51.0 + - - +
501A LEU* 3.6 32.2 - - + +
502A MET* 3.8 24.0 - - + -
505A CYS* 3.6 9.6 - - - -
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Residues in contact with TYR 469 (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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405A LYS 4.6 2.9 - - - +
406A ASN 3.0 34.1 - - - -
407A ALA* 3.7 14.4 - - - +
408A PRO* 3.5 36.5 - - + +
409A SER 5.3 1.3 + - - +
412A LEU* 3.9 14.3 - - + +
416A PHE* 5.0 1.8 - + - -
427A ILE* 4.1 12.1 - - + +
428A MET* 4.0 22.7 - - - +
431A LEU* 3.4 30.9 - - + +
465A GLU 3.2 21.4 + - - +
466A ILE 4.3 2.5 - - - +
468A TYR* 1.3 95.4 - + - +
470A LYS* 1.3 61.3 + - - +
472A LEU* 4.3 4.5 - - + -
473A GLU* 3.1 26.9 + - - +
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Residues in contact with LYS 470 (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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400A ILE* 3.3 34.5 - - + +
401A VAL* 5.4 1.1 - - + -
404A LEU* 3.7 26.7 - - + -
466A ILE 3.2 18.9 + - - +
467A LEU* 3.5 8.5 - - + +
468A TYR 3.2 0.6 - - - -
469A TYR* 1.3 77.1 - - - +
471A ILE* 1.3 62.3 + - - +
473A GLU* 3.4 7.7 + - - +
474A THR* 3.1 32.3 + - - +
543A SER 5.7 0.2 + - - -
544A GLU* 2.7 34.5 + - - +
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Residues in contact with ILE 471 (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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467A LEU* 2.9 36.7 + - + +
468A TYR 4.0 2.2 - - - +
470A LYS* 1.3 74.0 - - - +
472A LEU* 1.3 61.7 + - - +
474A THR* 3.2 7.8 + - - -
475A VAL* 2.8 40.1 + - + +
501A LEU* 3.8 21.8 - - + -
505A CYS* 4.0 19.5 - - - -
508A ILE* 6.3 1.6 - - + -
539A VAL* 5.5 0.7 - - + -
540A VAL* 4.3 28.3 - - + -
543A SER* 3.9 20.4 - - - -
544A GLU* 4.3 22.0 - - + +
547A LEU* 6.1 0.9 - - + -
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Residues in contact with LEU 472 (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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412A LEU* 3.9 9.0 - - + -
416A PHE* 3.9 26.9 - - + -
427A ILE* 4.2 6.1 - - + -
468A TYR* 2.8 47.3 + - + +
469A TYR* 4.0 3.8 - - + +
471A ILE* 1.3 78.0 - - - +
473A GLU* 1.3 57.8 + - - +
475A VAL* 3.3 3.7 + - + +
476A MET* 2.9 62.2 + - + +
492A LEU* 4.3 1.6 - - + -
497A PHE* 4.1 12.6 - - + -
498A HIS* 4.0 16.8 - - + +
501A LEU* 4.0 10.7 - - + +
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Residues in contact with GLU 473 (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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409A SER* 2.4 34.1 + - - +
411A GLN* 3.3 31.1 + - - +
412A LEU* 3.9 25.8 - - + +
415A ILE* 5.8 0.2 - - + -
469A TYR 3.1 20.8 + - - +
470A LYS* 3.6 6.7 - - - +
471A ILE 3.2 0.2 - - - -
472A LEU* 1.3 76.2 - - - +
474A THR* 1.3 64.0 + - - +
476A MET* 3.3 0.7 + - - +
477A VAL* 3.0 40.7 + - + +
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Residues in contact with THR 474 (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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470A LYS* 3.1 22.8 + - - +
471A ILE* 3.2 8.9 + - - -
473A GLU* 1.3 77.4 - - - +
475A VAL* 1.3 61.1 + - - +
477A VAL* 4.0 4.1 - - - +
478A GLN* 3.3 48.9 + - - +
543A SER* 3.3 35.7 + - - +
544A GLU* 5.6 0.2 + - - -
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Residues in contact with VAL 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ILE* 2.8 30.6 + - + +
472A LEU* 3.7 7.0 - - - +
474A THR* 1.3 74.5 - - - +
476A MET* 1.3 80.5 + - + +
478A GLN* 3.5 4.3 + - - +
479A GLU* 3.2 29.0 + - - +
497A PHE* 4.2 18.6 - - + -
539A VAL* 3.8 20.0 - - + -
542A ARG* 6.1 2.5 - - - +
543A SER* 3.3 25.6 - - - +
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Residues in contact with MET 476 (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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412A LEU* 4.2 12.6 - - + -
415A ILE* 4.0 21.8 - - + -
472A LEU* 2.9 39.8 + - + +
473A GLU 3.9 3.1 - - - +
475A VAL* 1.3 106.2 - - + +
477A VAL* 1.3 63.1 + - - +
479A GLU* 3.3 16.2 + - - +
482A ARG* 3.4 14.6 - - - +
488A MET* 4.1 7.4 - - - +
491A LEU* 3.9 28.0 - - + +
492A LEU* 3.6 35.9 - - + -
497A PHE* 4.8 7.2 - - + -
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Residues in contact with VAL 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A GLN* 3.9 21.8 - - + +
415A ILE* 4.1 15.9 - - + -
473A GLU* 3.0 29.6 + - + +
474A THR* 4.0 5.2 - - - +
476A MET* 1.3 77.0 - - - +
478A GLN* 1.3 65.6 + - + +
479A GLU 3.2 3.0 + - - +
482A ARG* 3.0 46.2 + - - +
483A LEU* 4.2 1.7 - - - +
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Residues in contact with GLN 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A THR* 3.3 38.4 + - + +
475A VAL* 3.5 4.5 + - - +
477A VAL* 1.3 81.9 - - + +
479A GLU* 1.3 64.9 + - - +
480A THR* 3.6 1.9 + - - -
483A LEU* 3.8 14.0 - - - +
542A ARG* 5.1 11.6 + - - +
543A SER* 4.8 8.7 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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