Contacts of the helix formed by residues 459 - 491 (chain A) in PDB entry 5DO7
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 GLN 459 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A SER* 3.6 5.8 - - - +
458A TYR* 1.3 73.4 - - - +
460A LYS* 1.3 58.9 + - - +
461A TRP* 3.0 42.9 - - + -
462A GLN* 2.7 50.7 + - + +
643A LYS* 3.7 17.5 + - - +
646A ASP* 3.7 21.0 + - - +
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Residues in contact with LYS 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A SER* 4.0 14.8 - - - +
450A ASP* 3.5 41.8 + - - +
453A SER* 3.8 25.5 + - - +
454A GLN* 5.2 6.4 - - - +
458A TYR* 3.6 2.8 + - - -
459A GLN* 1.3 72.0 - - - +
461A TRP* 1.3 60.9 + - - +
462A GLN 3.6 0.2 + - - -
463A MET* 3.7 16.2 + - - +
464A MET 3.9 0.7 + - - -
642A PHE* 3.7 32.7 - - + +
645A ARG* 4.6 7.1 + - - +
646A ASP* 3.3 51.6 + - + +
649A ILE* 4.5 14.8 + - - +
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Residues in contact with TRP 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A VAL* 4.7 10.1 - - + +
368A LEU* 5.0 0.4 - - - +
459A GLN* 2.9 48.7 + - + -
460A LYS* 1.3 73.5 - - - +
462A GLN* 1.3 116.6 - - - +
463A MET 2.8 4.1 + - - -
464A MET* 2.8 13.5 + - - +
465A LEU* 2.8 26.7 + - + +
639A ILE* 3.4 44.6 - - + +
642A PHE* 3.7 11.7 - - + +
643A LYS* 3.1 48.0 - - + +
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Residues in contact with GLN 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A VAL* 3.4 32.4 + - - +
367A LYS* 4.2 14.4 + - + +
368A LEU* 3.8 26.7 - - + +
371A LEU* 3.8 20.0 - - + -
458A TYR* 3.7 9.0 - - + -
459A GLN* 2.7 47.4 + - + +
461A TRP* 1.3 108.3 - - - +
463A MET* 1.3 60.0 + - - +
465A LEU* 3.1 5.5 - - - +
466A ALA* 3.0 19.4 + - - +
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Residues in contact with MET 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 5.6 1.8 - - + -
371A LEU* 3.9 12.8 - - + +
374A ARG* 4.4 8.7 - - - +
375A VAL* 3.9 12.6 - - + -
442A PHE* 4.5 7.2 - - + -
445A LEU* 3.3 50.9 - - + +
448A VAL* 3.7 10.8 - - + -
449A SER* 2.8 35.0 - - - +
458A TYR* 3.5 28.0 - - + +
459A GLN 4.2 0.2 + - - -
460A LYS 3.7 7.1 + - - +
461A TRP 2.8 3.6 + - - -
462A GLN* 1.3 75.4 - - - +
464A MET* 1.3 68.3 + - - +
466A ALA* 2.8 14.8 + - - +
467A TYR* 2.8 13.3 + - - -
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Residues in contact with MET 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A PHE* 4.1 11.6 - - + -
460A LYS 3.9 1.0 + - - -
461A TRP 2.8 9.6 + - - +
463A MET* 1.3 72.2 - - - +
465A LEU* 1.3 73.7 + - - +
467A TYR* 3.9 0.3 - - - +
468A ALA* 3.1 15.8 + - - +
518A LEU* 3.4 27.8 - - + +
519A VAL* 5.6 0.2 - - + -
635A VAL* 3.6 11.4 - - - +
638A GLY* 2.7 49.6 - - - +
639A ILE* 2.8 24.7 - - + +
642A PHE* 3.3 41.7 - - + -
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Residues in contact with LEU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LEU* 3.7 19.7 - - + -
461A TRP* 2.8 21.0 + - + +
462A GLN 3.1 11.7 - - - +
464A MET* 1.3 86.7 - - - +
466A ALA* 1.3 60.4 + - - +
468A ALA* 2.8 11.9 + - - +
469A LEU* 2.7 44.5 + - + +
635A VAL* 3.9 15.5 - - + -
639A ILE* 3.8 27.6 - - + -
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Residues in contact with ALA 466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LEU* 4.8 4.7 - - + +
371A LEU* 4.2 10.3 - - + -
372A LEU* 4.0 33.5 - - + +
375A VAL* 4.3 8.3 - - + -
462A GLN 3.0 8.3 + - - +
463A MET* 2.8 18.0 + - - +
465A LEU* 1.3 74.7 - - - +
467A TYR* 1.3 68.3 + - - +
469A LEU* 2.8 20.6 + - - +
470A HIS* 3.0 13.0 + - - -
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Residues in contact with TYR 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A VAL* 4.6 7.3 - - + +
379A LEU* 4.5 1.6 - - + -
389A ARG* 3.4 13.4 + - - -
437A ASN 3.9 0.9 + - - -
438A ALA* 3.2 19.9 - - + -
441A LEU* 4.3 12.7 - - + +
442A PHE* 3.4 33.2 - + + -
445A LEU* 4.8 9.6 - - + -
463A MET 2.8 11.2 + - - +
464A MET 3.9 2.9 - - - +
466A ALA* 1.3 74.5 - - - +
468A ALA* 1.3 67.2 + - - +
470A HIS* 2.8 62.2 + + - -
471A VAL* 3.3 6.6 + - + +
514A GLU* 2.3 43.6 + - + -
518A LEU* 3.1 34.8 - - + -
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Residues in contact with ALA 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A MET 3.1 9.7 + - - +
465A LEU 2.8 12.2 + - - +
467A TYR* 1.3 82.5 - - - +
469A LEU* 1.3 60.0 + - + +
471A VAL* 2.9 22.7 - - - +
472A LEU* 3.7 3.6 - - - +
515A PHE* 3.4 37.5 - - + -
518A LEU* 3.8 7.6 - - + -
635A VAL* 4.0 18.4 - - + -
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Residues in contact with LEU 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LEU* 4.7 12.6 - - + -
372A LEU* 3.6 16.6 - - + -
465A LEU* 2.7 63.1 + - + +
466A ALA* 2.8 12.1 + - - +
468A ALA* 1.3 78.7 - - + +
470A HIS* 1.3 62.9 + - - +
472A LEU* 2.9 33.8 + - + +
473A PRO* 4.0 2.3 - - - +
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Residues in contact with HIS 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LEU* 4.0 10.5 - - + +
375A VAL* 3.2 28.9 - - + +
376A THR* 3.3 30.7 - - + -
379A LEU* 2.8 36.5 - - + +
389A ARG* 4.3 3.8 - - - -
466A ALA 3.0 6.7 + - - +
467A TYR* 2.8 56.1 + + - -
469A LEU* 1.3 71.3 - - - +
471A VAL* 1.3 87.7 + - - +
472A LEU 2.8 1.6 + - - -
473A PRO* 2.9 22.5 - - - +
474A PHE* 3.5 12.3 - - + -
----------------------------------------------------------
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Residues in contact with VAL 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ARG* 3.0 26.7 - - - +
467A TYR* 3.9 4.7 - - + +
468A ALA* 2.9 31.9 - - - +
470A HIS* 1.3 90.2 + - + +
472A LEU* 1.3 68.0 - - - +
474A PHE* 2.8 14.9 + - - -
475A SER* 2.8 41.5 + - - +
511A LEU* 4.1 3.8 - - + -
514A GLU* 3.8 17.0 - - + +
515A PHE* 3.5 24.0 - - + -
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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
----------------------------------------------------------
468A ALA 3.7 9.2 - - - +
469A LEU* 2.9 33.7 - - + +
470A HIS 2.8 1.2 + - - -
471A VAL* 1.3 80.9 - - + +
473A PRO* 1.3 75.1 - - + +
476A VAL* 2.8 27.5 + - - +
507A LEU* 5.2 1.2 - - + +
511A LEU* 4.4 27.1 - - + -
515A PHE* 4.9 6.1 - - + -
631A ILE* 5.6 4.5 - - + -
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Residues in contact with PRO 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A THR* 6.0 2.2 - - + -
469A LEU 4.0 2.7 - - - +
470A HIS* 2.9 24.5 - - + +
472A LEU* 1.3 87.1 - - + +
474A PHE* 1.3 69.9 + - + +
476A VAL* 2.8 12.4 - - + +
477A VAL* 2.8 31.1 + - - +
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Residues in contact with PHE 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A THR* 4.5 17.3 - - + -
379A LEU* 3.9 20.2 - - + -
380A VAL* 5.1 15.7 - - + -
386A VAL* 4.0 20.6 - - + -
389A ARG* 3.9 30.1 - - + +
390A LEU* 3.8 21.5 - - + +
470A HIS* 3.5 32.1 - - - -
471A VAL 2.8 10.1 + - - +
473A PRO* 1.3 80.2 - - + +
475A SER* 1.3 68.3 + - - +
477A VAL* 2.7 27.6 - - - +
478A ALA* 2.8 7.7 + - - +
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Residues in contact with SER 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ARG* 5.1 1.3 + - - +
437A ASN* 3.7 5.8 + - - +
471A VAL* 2.8 40.6 + - - +
472A LEU 4.1 0.2 - - - -
474A PHE* 1.3 72.2 - - - +
476A VAL* 1.3 52.3 + - - -
478A ALA* 2.8 24.9 + - - +
479A THR* 2.7 24.9 + - - -
507A LEU* 3.9 3.6 - - - -
510A HIS* 2.9 33.8 + - - -
511A LEU* 4.0 15.3 - - - -
514A GLU* 3.8 0.7 + - - -
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Residues in contact with VAL 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A LEU 2.8 21.8 + - - +
473A PRO* 2.8 26.5 - - + +
475A SER* 1.3 70.3 - - - +
477A VAL* 1.3 67.9 + - + +
479A THR* 3.7 2.2 + - - -
480A MET* 3.2 34.1 + - + +
507A LEU* 3.6 35.6 - - + +
----------------------------------------------------------
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Residues in contact with VAL 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU* 3.2 26.5 - - + -
473A PRO 2.8 21.8 + - - +
474A PHE* 2.7 23.3 - - - +
476A VAL* 1.3 74.2 - - + +
478A ALA* 1.3 50.8 + - - +
480A MET* 2.8 28.1 + - + +
481A ILE* 2.8 38.7 + - + +
----------------------------------------------------------
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Residues in contact with ALA 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ARG 3.2 20.4 - - - +
390A LEU* 3.1 30.2 - - - +
393A ASN* 4.2 11.8 - - + +
474A PHE 2.8 9.1 + - - +
475A SER* 2.8 12.5 + - - +
477A VAL* 1.3 75.8 - - - +
479A THR* 1.3 54.1 + - - +
481A ILE* 3.2 4.1 + - - +
482A PHE* 2.8 37.5 + - - +
510A HIS* 4.6 4.5 - - + -
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Residues in contact with THR 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ASN* 4.0 13.1 + - - +
475A SER 2.7 15.1 + - - -
476A VAL* 3.8 6.3 - - - -
477A VAL 3.2 0.2 - - - -
478A ALA* 1.3 77.3 - - - +
480A MET* 1.3 58.5 + - - +
482A PHE* 3.5 4.4 - - + +
483A SER* 2.8 32.2 + - - -
503A SER* 3.4 27.1 - - - +
506A LEU* 3.3 34.9 + - + +
507A LEU* 3.3 21.5 - - - +
510A HIS* 4.7 2.3 - - - +
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Residues in contact with MET 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A VAL* 3.2 26.0 + - + +
477A VAL* 2.8 13.2 + - + +
479A THR* 1.3 76.1 - - - +
481A ILE* 1.3 52.8 - - - +
483A SER* 2.9 3.2 + - - -
484A SER* 2.1 44.6 + - - -
499A PHE* 4.8 8.7 - - + -
500A GLY* 5.7 1.8 - - - +
503A SER* 3.8 34.8 - - - +
----------------------------------------------------------
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Residues in contact with ILE 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU* 3.6 33.9 - - + +
391A LEU* 4.2 14.6 - - + -
394A LEU* 3.3 31.2 - - + -
477A VAL* 2.8 39.3 + - + +
478A ALA* 3.4 5.6 - - - +
480A MET* 1.3 70.6 - - - +
482A PHE* 1.3 66.2 + - - +
484A SER* 3.1 12.9 + - - -
485A VAL* 3.3 17.8 + - + +
----------------------------------------------------------
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Residues in contact with PHE 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ASN* 3.0 45.8 - - + -
394A LEU* 3.6 22.9 - - - +
396A MET* 4.4 2.0 - - + -
397A GLY* 3.7 14.4 - - - -
426A PHE* 3.1 48.2 - + + -
430A THR* 5.2 2.0 - - + -
478A ALA 2.8 20.3 + - - +
479A THR* 3.5 9.6 - - + +
481A ILE* 1.3 76.1 - - - +
483A SER* 1.3 68.9 + - - +
486A CYS* 2.8 44.0 + - + +
502A PHE* 4.1 10.5 - + - -
506A LEU* 3.6 25.8 - - + -
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Residues in contact with SER 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A THR 2.8 18.7 + - - -
480A MET* 2.9 14.8 + - - -
482A PHE* 1.3 82.1 - - - +
484A SER* 1.3 72.0 + - - +
487A TYR* 2.8 35.5 + - - +
499A PHE* 3.2 11.6 - - - -
502A PHE* 4.2 13.5 - - - -
503A SER* 2.7 32.5 + - - -
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Residues in contact with SER 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A MET* 2.1 29.8 + - - -
481A ILE* 3.1 12.6 + - - -
483A SER* 1.3 77.5 + - - +
485A VAL* 1.3 64.5 + - - +
488A TRP* 3.4 20.2 - - - +
499A PHE* 3.4 19.3 - - - -
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Residues in contact with VAL 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LEU* 3.7 16.2 - - + -
398A LEU* 3.8 28.5 - - + -
401A LEU* 5.0 4.0 - - + -
481A ILE* 3.3 18.7 + - + +
482A PHE 3.6 1.8 - - - +
483A SER 3.3 0.4 - - - -
484A SER* 1.3 85.4 + - - +
486A CYS* 1.3 62.7 + - - +
488A TRP* 4.6 0.9 - - - +
489A THR* 2.5 31.6 + - - +
----------------------------------------------------------
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Residues in contact with CYS 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LEU* 4.4 1.8 - - - -
397A GLY* 3.5 38.8 - - - -
398A LEU* 4.0 5.4 - - - -
401A LEU* 4.9 2.2 - - + -
426A PHE* 5.0 4.5 - - + -
482A PHE* 2.8 43.8 + - + +
483A SER* 5.1 0.2 - - - -
485A VAL* 1.3 86.2 - - - +
487A TYR* 1.3 67.9 + - - +
489A THR* 2.8 20.4 + - - -
490A LEU* 2.8 30.9 + - + +
502A PHE* 6.3 0.2 - - + -
----------------------------------------------------------
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Residues in contact with TYR 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A SER* 2.8 23.7 + - - +
486A CYS* 1.3 73.3 - - - +
488A TRP* 1.3 60.1 + + - +
490A LEU* 3.4 7.9 - - - +
491A GLY* 2.5 31.5 + - - -
492A LEU* 2.4 50.0 + - + +
493A HIS* 2.4 29.3 + - - -
494A PRO* 4.0 12.8 - - + -
498A ARG* 4.0 10.3 + - - +
499A PHE* 3.6 42.1 + + + -
502A PHE* 3.6 43.6 - + + -
578A ASN* 4.5 4.8 + - - -
579A GLU* 4.6 2.1 - - + +
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Residues in contact with TRP 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ARG* 4.2 7.6 + - - -
484A SER* 3.4 22.4 - - - +
485A VAL 4.1 0.6 + - - +
486A CYS 3.2 0.8 - - - -
487A TYR* 1.3 76.1 - + - +
489A THR* 1.3 63.6 + - - +
490A LEU 3.1 1.8 - - - -
491A GLY* 2.8 22.0 + - - +
494A PRO* 3.4 44.9 - - + -
495A GLU 4.9 0.2 - - - -
496A VAL* 4.1 34.5 - - + -
499A PHE* 3.3 36.8 - + + -
----------------------------------------------------------
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Residues in contact with THR 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A LEU* 3.8 30.3 - - + +
406A ARG* 3.2 27.9 + - - +
485A VAL* 2.5 31.8 + - - +
486A CYS* 2.8 7.9 + - - -
488A TRP* 1.3 74.1 - - - +
490A LEU* 1.3 65.4 + - - +
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Residues in contact with LEU 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A GLY 5.4 2.0 - - - +
400A LEU* 5.9 0.4 - - + -
401A LEU* 3.3 43.3 - - + +
404A VAL* 4.7 2.9 - - + -
405A LEU 4.1 6.7 - - - +
406A ARG* 3.6 8.3 - - - +
407A VAL* 2.8 38.3 + - + +
422A LEU* 3.4 43.3 - - + -
426A PHE* 4.3 13.5 - - + -
486A CYS* 2.8 27.6 + - + +
487A TYR* 3.8 4.7 - - - +
489A THR* 1.3 77.7 - - - +
491A GLY* 1.3 58.9 + - - +
492A LEU* 3.3 12.2 + - + +
----------------------------------------------------------
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Residues in contact with GLY 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ARG* 4.0 18.9 + - - -
407A VAL* 4.1 7.2 - - - +
487A TYR 2.5 16.4 + - - -
488A TRP* 2.8 18.2 + - - -
490A LEU* 1.3 74.6 - - - +
492A LEU* 1.3 59.5 + - - -
493A HIS* 3.7 2.1 + - - -
494A PRO* 4.0 19.0 - - - +
----------------------------------------------------------
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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