Contacts of the helix formed by residues 457 - 494 (chain A) in PDB entry 4BEJ
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 PHE 457 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A GLU* 4.6 19.1 - - + -
326A VAL* 4.6 15.7 - - + -
332A THR* 4.5 10.1 - - + -
336A LEU* 3.5 26.2 - - + -
454A LEU 5.3 1.6 - - - -
455A LEU* 3.2 18.9 - - + +
456A ARG* 1.3 90.9 - - + +
458A PRO* 1.3 58.3 - - - +
459A LYS 3.4 3.1 - - - -
460A LEU* 3.2 11.9 + - + -
461A HIS* 2.7 38.9 + - - +
673A LEU 4.0 0.9 - - - +
674A LEU* 3.2 57.0 - - + -
675A THR 4.3 4.3 - - - -
676A GLU* 3.8 17.9 - - + -
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Residues in contact with PRO 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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455A LEU 6.0 0.2 - - - -
456A ARG* 3.6 10.8 - - - +
457A PHE* 1.3 87.1 - - - +
459A LYS* 1.3 64.4 + - + +
461A HIS* 4.5 4.9 - - + +
462A ASP* 2.9 37.4 + - - +
675A THR 4.4 10.5 - - - +
677A SER* 4.1 27.1 - - - +
680A MET* 5.1 1.8 - - - -
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Residues in contact with LYS 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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457A PHE 3.4 0.4 - - - -
458A PRO* 1.3 79.9 - - + +
460A LEU* 1.3 62.3 - - - +
462A ASP* 4.0 3.0 - - - +
463A ALA* 3.3 21.8 + - - +
672A ASP* 3.2 47.6 - - - +
673A LEU* 4.0 10.1 - - + +
675A THR* 4.0 29.0 + - - +
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Residues in contact with LEU 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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333A LEU* 3.2 35.2 - - + -
336A LEU* 3.5 33.0 - - + -
337A ILE* 5.1 3.8 - - + -
455A LEU* 3.7 5.8 - - + -
457A PHE* 3.2 9.5 + - + +
459A LYS* 1.3 78.4 - - - +
461A HIS* 1.3 65.4 + - - +
463A ALA* 3.2 4.9 + - - +
464A ILE* 3.1 42.5 + - + +
664A LEU* 5.2 0.2 - - - +
673A LEU* 3.1 41.2 + - + +
674A LEU* 3.6 17.0 - - + -
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Residues in contact with HIS 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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340A PHE* 6.5 1.1 - + - -
444A GLN* 4.9 4.7 - - - -
446A CYS 5.3 1.6 - - - -
447A SER* 2.8 47.1 + - - -
455A LEU* 3.5 30.5 - - + -
457A PHE 2.7 23.3 + - - +
458A PRO* 4.4 4.0 - - + +
460A LEU* 1.3 75.7 - - - +
462A ASP* 1.3 74.8 + - - +
464A ILE* 3.3 11.2 + - + +
465A VAL* 3.3 31.0 + - + +
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Residues in contact with ASP 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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458A PRO* 2.9 24.6 + - - +
459A LYS* 4.0 4.3 - - - +
460A LEU 3.3 0.4 - - - -
461A HIS* 1.3 91.7 + - - +
463A ALA* 1.3 62.2 + - - +
465A VAL* 3.4 8.0 + - - +
466A GLU* 3.3 21.0 + - - +
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Residues in contact with ALA 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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459A LYS 3.3 12.7 + - - +
460A LEU 3.2 10.0 + - - +
462A ASP* 1.3 79.1 - - - +
464A ILE* 1.3 55.5 - - - +
466A GLU* 3.1 14.8 + - - +
467A VAL* 2.9 32.5 + - + +
664A LEU* 4.6 12.8 - - + -
673A LEU* 4.1 17.3 - - + -
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Residues in contact with ILE 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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336A LEU* 4.3 8.5 - - + -
337A ILE* 3.9 18.6 - - + -
340A PHE* 3.2 41.5 - - + -
455A LEU* 5.2 0.9 - - + -
460A LEU* 3.1 38.2 + - + +
461A HIS* 3.3 12.8 + - + +
463A ALA* 1.3 73.4 - - - +
465A VAL* 1.3 60.6 + - + +
467A VAL* 3.1 9.3 + - - +
468A VAL* 2.9 29.0 + - + +
660A LEU* 3.8 11.7 - - + -
664A LEU* 3.5 18.6 - - + -
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Residues in contact with VAL 465 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A PHE* 5.7 1.1 - - + -
443A ILE* 3.8 26.9 - - + -
444A GLN* 4.7 12.6 - - - +
447A SER* 3.9 16.4 - - - +
461A HIS* 3.3 22.1 + - + +
462A ASP* 3.7 9.2 - - - +
464A ILE* 1.3 77.5 - - + +
466A GLU* 1.3 55.5 + - - +
468A VAL* 3.2 0.3 + - - +
469A THR* 2.7 53.4 + - - +
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Residues in contact with GLU 466 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A ASP 3.3 9.5 + - - +
463A ALA* 3.1 15.3 + - - +
465A VAL* 1.3 81.9 - - - +
467A VAL* 1.3 57.0 + - + +
469A THR* 4.3 3.8 - - - -
470A CYS* 3.0 38.2 + - + +
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Residues in contact with VAL 467 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A ALA* 2.9 23.3 + - + +
464A ILE* 3.1 8.3 + - - +
466A GLU* 1.3 79.6 - - + +
468A VAL* 1.3 60.0 + - + +
470A CYS* 4.3 2.6 - - - +
471A LEU* 3.3 24.5 + - + +
659A GLU 4.5 4.5 - - - +
660A LEU* 3.5 37.7 - - + +
663A GLN* 4.5 23.5 + - + +
664A LEU* 4.0 23.3 - - + -
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Residues in contact with VAL 468 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A PHE* 4.1 21.5 - - + -
344A TYR* 5.6 7.4 - - + -
443A ILE* 3.5 27.6 - - + -
464A ILE* 2.9 23.3 + - + +
465A VAL 4.0 1.1 - - - +
467A VAL* 1.3 75.5 - - - +
469A THR* 1.3 58.6 + - - +
470A CYS 3.0 1.6 - - - -
471A LEU* 2.7 32.1 + - + +
472A LEU* 3.2 17.2 + - + +
652A VAL* 5.6 2.5 - - + -
656A LEU* 3.4 35.0 - - + -
660A LEU* 4.4 4.5 - - + -
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Residues in contact with THR 469 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A HIS* 4.8 0.9 + - - -
440A GLN* 3.8 24.2 + - + +
443A ILE* 3.5 19.6 - - - +
465A VAL* 2.7 40.8 + - - +
466A GLU* 4.3 3.4 - - - -
468A VAL* 1.3 73.1 - - - +
470A CYS* 1.3 58.0 + - - +
472A LEU* 3.7 10.7 + - - +
473A ARG* 3.5 24.2 + - + +
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Residues in contact with CYS 470 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A GLU* 3.0 23.9 + - + +
467A VAL* 4.3 2.9 - - - +
468A VAL 3.0 0.8 - - - -
469A THR* 1.3 74.9 - - - +
471A LEU* 1.3 66.0 + - - +
472A LEU 3.2 0.4 - - - -
473A ARG* 3.0 29.1 + - - +
474A LYS* 3.3 7.6 + - - +
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Residues in contact with LEU 471 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A VAL* 3.3 16.9 + - + +
468A VAL* 2.7 18.2 + - + +
470A CYS* 1.3 73.7 - - - +
472A LEU* 1.3 60.1 + - + +
474A LYS* 3.1 29.2 + - - +
475A ARG* 3.7 9.8 + - + +
651A HIS* 5.8 0.2 - - + -
652A VAL* 3.5 35.4 - - + -
655A THR* 3.6 32.1 - - + -
656A LEU* 4.0 30.5 - - + -
659A GLU* 4.6 15.5 - - + +
660A LEU 5.5 1.8 - - - +
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Residues in contact with LEU 472 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A TYR* 4.8 0.4 - - + +
436A HIS* 3.7 20.4 - - + +
439A MET* 3.8 23.1 - - + -
440A GLN* 3.6 43.1 - - + +
443A ILE* 4.4 5.6 - - + -
468A VAL* 3.6 16.2 - - + +
469A THR* 3.7 8.7 - - - +
470A CYS 3.2 0.4 - - - -
471A LEU* 1.3 75.7 - - + +
473A ARG* 1.3 63.6 + - - +
474A LYS 3.2 0.2 + - - -
475A ARG* 3.3 4.1 + - - +
476A LEU* 3.2 27.8 + - - +
648A LEU* 4.4 11.7 - - + +
652A VAL* 3.7 31.6 - - + -
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Residues in contact with ARG 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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436A HIS* 3.5 27.6 + - - -
440A GLN* 4.1 14.8 + - - +
469A THR* 3.5 17.7 + - + +
470A CYS* 3.0 20.1 + - - +
472A LEU* 1.3 76.7 - - - +
474A LYS* 1.3 59.2 + - - +
476A LEU* 3.9 19.3 + - - +
477A PRO* 3.3 16.6 - - - +
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Residues in contact with LYS 474 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470A CYS* 3.3 4.5 + - - +
471A LEU* 3.1 24.0 + - - +
472A LEU 3.1 0.2 - - - -
473A ARG* 1.3 79.4 - - - +
475A ARG* 1.3 64.4 + - - +
477A PRO* 3.1 20.0 - - - +
478A VAL* 4.3 5.9 - - - +
659A GLU* 3.4 29.7 + - - -
663A GLN* 5.4 6.1 - - - +
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Residues in contact with ARG 475 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A LEU* 3.7 11.6 + - + +
472A LEU 3.3 7.2 + - - +
474A LYS* 1.3 82.6 - - + +
476A LEU* 1.3 65.5 + - - +
477A PRO* 3.2 3.4 - - - -
478A VAL* 3.1 24.2 + - - +
479A THR* 3.0 26.3 + - - +
646A HIS* 4.9 0.6 + - - -
647A PHE* 3.0 56.8 + - - +
648A LEU* 4.4 11.4 - - + -
651A HIS* 3.1 53.6 + - + +
652A VAL* 4.6 11.0 - - + -
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Residues in contact with LEU 476 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A VAL* 3.9 27.1 - - + -
433A GLU* 5.1 2.7 - - + -
436A HIS* 3.3 51.6 - - + +
472A LEU 3.2 18.0 + - - +
473A ARG* 3.9 22.9 - - - +
475A ARG* 1.3 76.5 - - - +
477A PRO* 1.3 66.6 - - + +
479A THR* 3.5 7.0 - - + -
480A ASN* 2.6 40.0 + - - +
648A LEU* 5.0 7.3 - - + +
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Residues in contact with PRO 477 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A ARG 3.3 14.1 - - - +
474A LYS* 3.1 22.4 - - - +
475A ARG 3.3 0.2 - - - -
476A LEU* 1.3 92.8 - - + +
478A VAL* 1.3 68.8 + - + +
480A ASN* 3.6 3.6 - - + +
481A GLU* 2.9 26.0 + - - +
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Residues in contact with VAL 478 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A LYS 4.3 12.6 - - - +
475A ARG* 3.1 30.0 + - - +
477A PRO* 1.3 78.9 - - + +
479A THR* 1.3 64.6 + - - +
481A GLU* 3.0 37.7 - - + +
482A MET* 3.1 5.8 + - + +
647A PHE* 3.6 31.0 - - + -
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Residues in contact with THR 479 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A VAL* 3.5 31.1 - - + +
475A ARG 3.0 17.0 + - - +
476A LEU* 3.5 15.9 - - + +
478A VAL* 1.3 77.4 - - - +
480A ASN* 1.3 69.3 + - - +
482A MET* 3.0 6.1 + - - +
483A VAL* 2.9 23.6 + - - +
643A ALA* 4.8 1.2 + - - +
644A VAL* 4.1 13.7 + - - -
647A PHE* 3.7 28.8 - - - +
648A LEU* 4.4 15.6 - - + +
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Residues in contact with ASN 480 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A LEU* 3.8 26.8 - - + +
432A VAL* 3.4 23.5 - - - +
476A LEU* 2.6 41.0 + - - +
477A PRO* 3.3 5.0 + - + +
479A THR* 1.3 82.5 - - - +
481A GLU* 1.3 60.4 + - - +
483A VAL* 3.5 7.2 + - - +
484A HIS* 3.2 22.0 + - - +
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Residues in contact with GLU 481 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477A PRO 2.9 12.3 + - - +
478A VAL* 3.0 27.4 + - + +
480A ASN* 1.3 74.7 - - - +
482A MET* 1.3 64.8 + - + +
484A HIS* 3.2 8.2 + - - +
485A ASN* 2.7 43.9 + - - +
481B GLU* 5.7 2.4 - - - +
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Residues in contact with MET 482 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A VAL* 3.1 5.4 + - + +
479A THR 3.0 8.6 + - - +
481A GLU* 1.3 83.7 - - + +
483A VAL* 1.3 61.5 + - - +
485A ASN* 3.2 11.2 + - - +
486A LEU* 3.1 48.2 + - + +
643A ALA* 4.2 6.5 - - + -
647A PHE* 3.4 35.4 - - + -
482B MET* 3.5 38.8 - - + +
485B ASN* 3.9 14.8 - - + +
486B LEU 4.6 0.4 - - - +
489B ILE* 3.6 31.0 - - + -
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Residues in contact with VAL 483 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A GLU* 4.7 0.7 - - + +
428A SER* 3.7 28.3 - - - -
429A LEU* 3.6 24.2 - - + +
432A VAL* 3.6 26.9 - - + -
479A THR* 2.9 17.7 + - - +
480A ASN* 3.6 8.5 - - - +
481A GLU 3.2 0.2 - - - -
482A MET* 1.3 73.8 - - - +
484A HIS* 1.3 67.6 + - - +
486A LEU* 3.3 11.8 + - - +
487A VAL* 3.3 22.0 + - + +
640A VAL* 4.3 15.7 - - + +
643A ALA* 4.6 11.2 - - + -
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Residues in contact with HIS 484 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A GLU* 2.9 38.0 + - - +
429A LEU* 4.6 3.1 - - + +
480A ASN 3.2 10.0 + - - +
481A GLU* 3.5 10.5 - - - +
483A VAL* 1.3 80.3 - - - +
485A ASN* 1.3 70.5 + - - +
487A VAL* 3.2 4.3 + - - +
488A ALA* 2.9 39.0 + - + +
646B HIS* 6.1 1.0 + + - -
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Residues in contact with ASN 485 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A GLU* 2.7 30.7 + - - +
482A MET* 3.2 15.5 - - - +
484A HIS* 1.3 87.3 - - - +
486A LEU* 1.3 54.5 + - - +
488A ALA* 2.9 8.4 + - - +
489A ILE* 2.5 39.6 + - - +
482B MET* 4.1 21.2 - - + +
646B HIS* 5.1 4.7 - - - -
647B PHE* 4.2 25.7 - - + -
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Residues in contact with LEU 486 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A MET* 3.1 43.8 + - + +
483A VAL* 3.3 10.1 + - - +
485A ASN* 1.3 78.9 - - - +
487A VAL* 1.3 66.2 + - + +
489A ILE* 3.6 10.1 + - + +
490A GLU* 3.4 22.9 - - - +
636A ILE* 4.3 10.2 - - + +
639A SER* 3.9 28.3 - - - +
640A VAL* 4.7 9.6 - - + +
643A ALA* 3.6 30.1 - - + -
482B MET* 4.4 1.1 - - + +
486B LEU* 4.5 12.3 - - + -
489B ILE* 4.2 9.6 - - + -
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Residues in contact with VAL 487 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A ILE* 3.6 26.0 - - + +
422A LYS* 4.8 1.8 - - - -
424A LEU* 4.4 1.8 - - + -
425A GLU* 3.7 45.3 - - + +
428A SER* 4.3 9.9 - - - +
483A VAL 3.3 10.9 + - - +
484A HIS 3.2 6.6 + - - +
485A ASN 3.1 1.0 - - - -
486A LEU* 1.3 76.5 - - + +
488A ALA* 1.3 59.5 + - - +
490A GLU* 2.9 28.4 + - - +
491A LEU* 3.0 19.5 - - + +
636A ILE* 4.1 21.5 - - + -
640A VAL* 5.7 0.4 - - + -
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Residues in contact with ALA 488 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A HIS* 2.9 34.7 + - + +
485A ASN* 3.4 7.6 - - - +
487A VAL* 1.3 76.6 - - - +
489A ILE* 1.3 61.8 - - - +
490A GLU 3.3 0.2 - - - -
491A LEU* 3.4 23.4 + - - +
492A ALA* 3.5 12.0 + - - +
646B HIS* 4.1 24.2 - - + +
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Residues in contact with ILE 489 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ASN 2.5 21.6 + - - +
486A LEU* 3.6 5.2 - - - +
487A VAL 3.0 0.4 + - - -
488A ALA* 1.3 72.4 - - - +
490A GLU* 1.3 79.1 + - - +
492A ALA* 3.0 21.4 + - - +
493A TYR 3.8 3.3 + - - -
482B MET* 3.3 45.3 - - + -
486B LEU* 4.3 7.4 - - + -
639B SER* 4.0 6.7 - - - +
642B LYS* 3.4 26.8 - - + +
643B ALA* 3.8 23.3 - - + +
646B HIS* 4.5 5.6 - - + +
647B PHE* 4.5 9.9 - - + -
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Residues in contact with GLU 490 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ILE* 3.7 18.6 - - + -
486A LEU 3.4 12.7 - - - +
487A VAL 2.9 13.7 + - - +
489A ILE* 1.3 92.4 - - - +
491A LEU* 1.3 57.6 + - - +
492A ALA 2.8 6.9 + - - -
493A TYR 3.5 4.2 + - - -
494A ILE* 3.5 8.7 + - - +
628A TYR* 5.6 1.4 - - + -
632A VAL* 3.6 23.5 - - + +
635A ASN* 3.2 32.1 + - - +
636A ILE* 3.8 12.6 - - + -
638B ASP* 4.6 0.2 - - - +
639B SER* 5.4 3.9 + - - -
642B LYS* 2.8 37.5 + - - +
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Residues in contact with LEU 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LYS* 3.3 58.1 - - + +
421A ILE* 3.8 19.5 - - + +
422A LYS* 3.3 24.5 - - + +
487A VAL* 3.0 49.4 - - + +
488A ALA* 3.6 12.8 - - + +
489A ILE 3.3 0.6 - - - -
490A GLU* 1.3 76.0 - - - +
492A ALA* 1.3 57.9 + - - +
494A ILE* 5.3 0.4 - - - -
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Residues in contact with ALA 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LYS* 5.1 7.3 + - - -
488A ALA 3.5 8.9 + - - +
489A ILE 3.0 11.6 + - - +
490A GLU 2.8 1.4 + - - -
491A LEU* 1.3 80.7 - - - +
493A TYR* 1.3 62.1 + - - +
642B LYS 4.2 1.8 - - - +
645B MET* 4.1 1.6 - - - +
646B HIS* 3.8 38.4 - - + +
650B ASN* 3.1 27.5 + - + +
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Residues in contact with TYR 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ILE 3.8 1.6 + - - -
490A GLU 3.5 2.0 + - - -
491A LEU 3.8 0.2 - - - -
492A ALA* 1.3 80.1 - - - +
494A ILE* 1.3 78.2 + - - +
495A ASN* 3.4 34.2 - - + +
367B CYS* 3.7 30.5 - - - +
370B PHE* 4.7 10.5 - + - -
371B HIS* 3.9 23.1 + + - -
641B PRO* 4.9 3.6 - - + -
642B LYS* 3.7 30.5 - - + -
645B MET* 3.4 39.9 - - + -
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Residues in contact with ILE 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A PHE* 3.6 28.9 - - + -
414A GLU* 4.1 32.5 - - + +
417A VAL* 3.8 23.8 - - + -
418A LYS* 4.0 29.2 - - + +
421A ILE* 6.0 0.4 - - + -
490A GLU 3.5 6.2 + - - +
491A LEU* 5.9 0.2 - - - -
493A TYR* 1.3 87.6 - - - +
495A ASN* 1.3 65.1 + - - +
496A THR* 3.7 8.9 + - + +
628A TYR* 3.2 33.7 - - + -
642B LYS* 3.2 12.3 - - - +
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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