Contacts of the helix formed by residues 474 - 498 (chain A) in PDB entry 2FY5
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 PRO 474 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472A ALA 3.2 7.2 - - - +
473A VAL* 1.3 94.6 - - + +
475A ALA* 1.3 66.0 + - - +
476A SER* 4.1 15.3 - - - +
477A GLU* 3.0 15.3 + - + +
478A LYS* 3.0 18.4 + - - +
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Residues in contact with ALA 475 (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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473A VAL 3.6 2.0 + - - -
474A PRO* 1.3 72.0 - - - +
476A SER* 1.3 57.6 + - - +
478A LYS* 3.1 15.6 + - + +
479A LEU* 3.0 27.7 + - - +
603A LEU* 4.2 9.6 - - + +
606A LEU* 3.7 26.3 - - + +
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Residues in contact with SER 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A PRO* 4.1 10.4 - - - +
475A ALA* 1.3 79.2 - - - +
477A GLU* 1.3 63.1 + - - +
479A LEU* 3.5 9.2 + - - +
480A LEU* 3.3 25.8 + - - +
606A LEU* 4.1 10.2 - - - +
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Residues in contact with GLU 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A VAL* 3.6 19.7 - - + -
474A PRO* 3.0 22.9 + - + +
476A SER* 1.3 80.3 + - - +
478A LYS* 1.3 65.3 + - - +
480A LEU* 3.1 23.9 + - - +
481A LEU* 3.0 44.1 + - + +
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Residues in contact with LYS 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A PHE* 3.7 4.1 - - - -
465A ALA* 3.3 30.0 + - + +
466A VAL* 3.9 31.1 + - + +
473A VAL* 3.3 31.9 + - + +
474A PRO 3.0 13.8 + - - +
475A ALA* 3.4 15.4 - - + +
477A GLU* 1.3 77.0 - - - +
479A LEU* 1.3 55.4 + - - +
481A LEU* 3.2 11.3 + - - +
482A LEU* 2.8 30.0 + - - +
603A LEU* 4.0 23.1 - - + -
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Residues in contact with LEU 479 (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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475A ALA 3.0 12.2 + - - +
476A SER* 3.6 12.3 - - - +
477A GLU 3.2 0.2 - - - -
478A LYS* 1.3 77.6 - - - +
480A LEU* 1.3 66.4 + - + +
482A LEU* 3.0 14.0 + - + +
483A LYS* 2.9 50.0 + - + +
603A LEU* 3.5 37.2 - - + +
604A CYS* 4.3 8.3 - - - +
606A LEU* 4.9 10.5 - - + -
607A LEU 5.9 1.1 - - - +
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Residues in contact with LEU 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A SER 3.4 14.4 - - - +
477A GLU* 3.1 31.5 + - - +
479A LEU* 1.3 82.0 - - + +
481A LEU* 1.3 59.4 + - + +
483A LYS* 3.0 9.8 + - + +
484A ASP* 2.8 29.4 + - - +
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Residues in contact with LEU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A GLU 4.3 3.6 - - - +
461A ALA* 3.6 24.5 - - + +
462A PHE* 3.9 16.9 - - + +
465A ALA* 3.5 31.4 - - + -
473A VAL* 4.9 0.9 - - + -
477A GLU* 3.0 41.0 + - + +
478A LYS 3.6 6.1 - - - +
480A LEU* 1.3 76.4 - - + +
482A LEU* 1.3 56.8 + - - +
484A ASP* 3.8 12.5 - - + +
485A ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 482 (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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416A PHE* 5.1 0.7 - - + -
419A VAL* 5.1 0.2 - - + -
462A PHE* 3.6 26.9 - - + -
478A LYS 2.8 13.6 + - - +
479A LEU* 3.2 12.6 - - + +
481A LEU* 1.3 77.8 - - - +
483A LYS* 1.3 63.6 + - + +
485A ALA* 3.2 4.6 + - - +
486A ILE* 2.9 51.7 + - + +
600A MET* 3.7 32.8 - - + +
603A LEU* 3.7 33.9 - - + -
604A CYS* 4.2 10.8 - - - -
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Residues in contact with LYS 483 (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 GLN* 3.5 22.7 + - - +
410A LYS 5.7 0.4 - - - +
411A CYS* 3.7 30.5 - - - -
479A LEU* 2.9 31.8 + - + +
480A LEU* 3.6 8.7 - - + +
482A LEU* 1.3 81.0 - - + +
484A ASP* 1.3 61.1 + - - +
486A ILE* 3.2 3.5 + - - +
487A ARG* 2.8 28.1 + - - +
604A CYS* 4.1 23.3 - - - +
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Residues in contact with ASP 484 (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 GLU* 3.3 25.2 - - + +
480A LEU 2.8 15.6 + - - +
481A LEU* 3.8 15.0 - - + +
483A LYS* 1.3 76.9 - - - +
485A ALA* 1.3 63.7 + - - +
487A ARG* 2.6 50.4 + - - +
488A ALA* 3.0 10.0 + - - +
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Residues in contact with ALA 485 (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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419A VAL* 4.2 21.1 - - + +
456A THR* 5.1 2.1 + - - -
458A GLU* 3.7 27.1 - - - +
459A ALA* 4.3 5.8 - - + +
462A PHE* 4.2 9.2 - - + -
481A LEU 2.9 18.9 + - - +
482A LEU 3.4 5.2 - - - +
483A LYS 3.2 0.2 - - - -
484A ASP* 1.3 77.4 - - - +
486A ILE* 1.3 62.4 + - - +
487A ARG 3.1 0.3 + - - -
488A ALA* 3.1 3.3 + - - +
489A GLN* 3.1 22.5 + - - +
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Residues in contact with ILE 486 (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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411A CYS* 3.6 39.7 - - + -
412A SER 4.5 2.5 - - - +
415A ALA* 3.8 18.1 - - + +
416A PHE* 3.6 27.1 - - + +
419A VAL* 3.8 21.3 - - + -
482A LEU* 2.9 42.5 + - + +
483A LYS* 3.8 5.6 - - + +
485A ALA* 1.3 76.3 - - - +
487A ARG* 1.3 61.2 + - - +
489A GLN* 4.5 2.2 - - - -
490A THR* 3.2 24.1 + - - +
600A MET* 4.4 1.3 - - + -
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Residues in contact with ARG 487 (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 GLU* 4.0 16.4 + - - +
483A LYS 2.8 13.3 + - - +
484A ASP* 2.6 59.7 + - - +
485A ALA 3.0 0.4 - - - -
486A ILE* 1.3 79.5 - - - +
488A ALA* 1.3 69.5 + - - +
490A THR* 3.5 5.6 + - - -
491A ALA* 3.0 32.3 + - + +
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Residues in contact with ALA 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A THR* 4.4 12.4 - - + +
458A GLU* 3.4 40.2 - - + +
484A ASP 3.0 10.3 + - - +
485A ALA 3.8 5.2 - - - +
487A ARG* 1.3 81.4 - - - +
489A GLN* 1.3 66.3 + - - +
491A ALA* 3.3 7.4 + - - +
492A TYR* 3.0 24.4 + - - +
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Residues in contact with GLN 489 (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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414A ASP* 5.3 0.4 + - - +
415A ALA* 3.7 29.8 - - + +
418A GLN* 3.5 12.4 - - + +
419A VAL* 4.5 5.3 - - + +
437A GLU* 3.0 19.8 + - - -
452A ILE* 3.4 15.1 - - - +
453A ARG 4.7 0.2 - - - +
454A SER* 2.7 49.2 + - - +
456A THR* 4.3 7.7 - - + +
485A ALA 3.1 14.0 + - - +
486A ILE* 4.0 5.8 - - - +
487A ARG 3.3 0.2 - - - -
488A ALA* 1.3 75.3 - - - +
490A THR* 1.3 58.2 + - - +
492A TYR* 3.2 5.7 + - - +
493A THR* 2.8 36.3 + - - +
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Residues in contact with THR 490 (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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144A GLN* 3.6 23.1 - - - +
412A SER* 3.6 11.3 - - - -
415A ALA* 3.3 17.8 - - - +
486A ILE* 3.2 18.7 + - - +
487A ARG* 3.8 5.4 - - - -
488A ALA 3.3 0.2 - - - -
489A GLN* 1.3 78.6 - - - +
491A ALA* 1.3 57.4 + - - +
493A THR* 3.6 6.4 - - - -
494A VAL* 3.0 35.7 + - + +
2000A SOP 6.2 0.4 - - - +
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Residues in contact with ALA 491 (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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487A ARG* 3.0 25.5 + - + +
488A ALA* 3.6 9.0 - - - +
489A GLN 3.2 0.2 - - - -
490A THR* 1.3 78.7 - - - +
492A TYR* 1.3 61.2 + - - +
494A VAL* 3.6 6.4 + - - +
495A MET* 3.1 22.6 + - - +
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Residues in contact with TYR 492 (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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27A THR* 4.3 3.5 - - + +
31A CYS* 4.0 20.0 - - - -
451A ASN 3.5 16.7 + - - -
452A ILE* 3.6 20.4 - - + -
453A ARG* 3.3 50.7 - - + +
456A THR* 5.1 7.9 - - + -
488A ALA 3.0 16.7 + - - +
489A GLN* 3.7 6.5 - - - +
491A ALA* 1.3 73.9 - - - +
493A THR* 1.3 56.6 + - - +
495A MET* 3.1 34.4 + - + +
496A ALA* 2.7 32.7 + - + +
501A ALA* 4.4 5.8 - - + -
502A ILE* 4.0 20.8 + - - +
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Residues in contact with THR 493 (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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144A GLN* 4.3 21.8 - - + +
414A ASP* 4.9 3.9 + - - +
415A ALA* 5.8 1.2 - - - +
437A GLU* 4.7 0.9 + - - -
452A ILE* 3.6 22.8 - - + +
489A GLN* 2.8 30.3 + - - +
490A THR* 3.6 8.7 - - - -
492A TYR* 1.3 75.3 - - - +
494A VAL* 1.3 66.0 + - - +
496A ALA* 2.9 12.6 + - - +
497A ILE* 2.9 20.9 + - + +
2000A SOP 3.5 31.9 - - + +
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Residues in contact with VAL 494 (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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144A GLN* 3.7 22.2 - - - +
145A LEU* 4.1 22.0 - - + -
490A THR* 3.0 25.3 + - + +
491A ALA* 3.8 6.5 - - - +
493A THR* 1.3 75.2 - - - +
495A MET* 1.3 64.7 + - - +
497A ILE* 3.3 13.2 - - - +
498A THR* 2.9 25.9 + - + +
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Residues in contact with MET 495 (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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23A GLN* 5.0 4.9 - - - +
27A THR* 4.4 21.5 - - + -
491A ALA 3.1 11.8 + - - +
492A TYR* 3.1 61.8 + - + +
494A VAL* 1.3 81.0 - - - +
496A ALA* 1.3 59.1 + - - +
498A THR* 3.2 9.4 + - - -
500A MET* 3.0 57.8 + - + +
501A ALA* 3.9 5.6 - - - +
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Residues in contact with ALA 496 (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 ALA* 3.8 9.6 - - + -
441A ILE* 3.7 9.7 - - - +
450A ASP* 4.4 6.2 - - + +
451A ASN 4.1 4.7 - - - +
452A ILE* 3.4 33.0 - - + -
492A TYR* 2.7 14.7 + - + +
493A THR 2.9 5.9 + - - +
495A MET* 1.3 72.1 - - - +
497A ILE* 1.3 57.9 + - - +
499A GLY* 3.0 20.4 + - - -
501A ALA* 3.7 22.8 - - + +
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Residues in contact with ILE 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLN* 2.9 31.9 - - + +
145A LEU* 4.2 4.9 - - + -
439A ALA* 4.1 12.8 - - + -
440A SER 3.7 25.1 - - - +
441A ILE* 4.4 4.7 - - - +
443A ARG* 2.8 45.6 + - - +
444A PHE* 4.0 10.9 - - - -
493A THR* 2.9 17.5 + - + +
494A VAL* 3.3 17.7 - - - +
496A ALA* 1.3 71.2 - - - +
498A THR* 1.3 57.0 + - + +
499A GLY 3.3 2.0 + - - -
2000A SOP 3.8 29.4 - - + +
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Residues in contact with THR 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PRO* 3.4 12.1 - - - +
145A LEU* 3.6 16.4 - - + -
443A ARG* 3.2 26.2 - - - +
444A PHE* 3.7 15.7 - - - -
494A VAL* 2.9 23.4 + - + +
495A MET* 3.2 10.4 + - - -
496A ALA 3.1 0.4 + - - -
497A ILE* 1.3 77.7 - - + +
499A GLY* 1.3 60.2 + - - +
500A MET* 3.5 15.1 + - - +
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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) + - + + + + + -
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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