Contacts of the helix formed by residues 469 - 498 (chain A) in PDB entry 5MKF
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 469 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ILE* 4.2 20.6 - - + -
239A TYR* 5.6 8.7 - + - -
240A GLY* 4.0 27.8 - - - -
466A VAL* 3.6 4.3 + - + +
468A THR* 1.3 84.5 - - + +
470A ASP* 1.3 64.8 + - - +
471A PHE 3.5 0.9 - - - -
472A PHE* 3.2 32.3 + + + +
473A LEU* 3.2 32.6 + - + -
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Residues in contact with ASP 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A LYS* 5.3 1.7 + - - -
464A ARG* 2.9 28.4 + - - +
465A TYR* 3.0 21.5 - - - -
466A VAL* 3.2 30.0 + - + +
469A PHE* 1.3 75.2 - - - +
471A PHE* 1.3 57.5 + - + +
472A PHE 2.9 4.9 - - - -
473A LEU* 2.5 26.0 + - - +
474A ALA* 2.4 54.8 + - - +
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Residues in contact with PHE 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A TYR* 5.4 17.9 - + + -
466A VAL 4.2 2.7 - - - -
467A THR* 3.3 52.0 - - + -
468A THR 4.8 3.1 - - - +
469A PHE 3.5 0.4 - - - -
470A ASP* 1.3 77.3 - - + +
472A PHE* 1.3 65.2 + - + +
474A ALA* 4.6 3.1 - - + +
475A ALA* 3.1 28.2 - - - +
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Residues in contact with PHE 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A THR 4.8 8.5 - - - -
469A PHE* 3.2 36.6 + + + +
470A ASP 2.9 0.6 - - - -
471A PHE* 1.3 84.5 - - + +
473A LEU* 1.3 60.1 + - - +
475A ALA* 4.2 1.7 - - - +
476A CYS* 3.0 28.6 + - - +
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Residues in contact with LEU 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ILE* 4.4 17.9 - - + -
237A LEU* 4.1 34.3 - - + -
240A GLY 4.4 4.9 - - - +
241A MET* 3.8 30.5 - - + +
461A LYS* 4.1 11.0 - - - +
464A ARG* 6.2 1.8 - - - +
469A PHE* 3.2 23.3 + - + +
470A ASP* 2.5 26.4 + - - +
472A PHE* 1.3 73.4 - - - +
474A ALA* 1.3 52.8 + - - +
476A CYS* 2.9 8.8 + - + +
477A GLU* 2.4 38.5 + - + +
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Residues in contact with ALA 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ARG* 5.3 3.6 - - + +
465A TYR* 4.2 15.3 - - + -
470A ASP* 2.4 48.8 + - - +
471A PHE* 4.9 3.1 - - + -
473A LEU* 1.3 71.2 - - - +
475A ALA* 1.3 60.3 + - - +
477A GLU* 3.0 25.6 + - + +
478A ILE* 3.0 14.4 + - - +
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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
----------------------------------------------------------
471A PHE* 3.1 24.6 + - - +
472A PHE* 4.2 2.0 - - - +
473A LEU 3.3 0.6 - - - -
474A ALA* 1.3 77.5 - - - +
476A CYS* 1.3 57.1 + - - +
478A ILE* 3.1 26.4 - - + +
479A ILE* 3.1 16.1 - - + +
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Residues in contact with CYS 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A VAL* 3.7 33.2 - - - -
236A ILE* 5.2 12.6 - - + -
237A LEU* 5.3 5.1 - - - +
472A PHE 3.0 18.5 + - - +
473A LEU* 2.9 11.4 + - + +
475A ALA* 1.3 74.2 - - - +
477A GLU* 1.3 58.5 + - - +
478A ILE 3.4 0.2 - - - -
479A ILE* 3.2 19.8 + - + +
480A PHE* 2.9 26.0 + - - +
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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
----------------------------------------------------------
237A LEU* 6.0 6.3 - - + -
464A ARG* 4.2 22.9 + - - +
473A LEU* 2.4 29.7 + - + +
474A ALA* 3.1 19.9 - - - +
476A CYS* 1.3 69.0 - - - +
478A ILE* 1.3 78.2 + - - +
480A PHE* 2.9 31.0 + - + +
481A CYS* 3.2 15.8 + - - +
525A ASN* 5.1 6.6 + - - +
526A ILE* 3.8 25.0 - - - +
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Residues in contact with ILE 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ALA 3.0 7.0 + - - +
475A ALA* 3.1 24.5 - - - +
477A GLU* 1.3 90.3 + - - +
479A ILE* 1.3 65.1 + - + +
481A CYS* 3.2 23.5 - - - -
482A PHE* 3.0 23.4 + - + +
526A ILE* 5.8 5.6 - - + -
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Residues in contact with ILE 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A VAL* 5.9 4.9 - - + -
475A ALA* 3.1 20.2 - - + +
476A CYS* 3.2 25.5 + - + +
477A GLU 3.1 0.2 - - - -
478A ILE* 1.3 82.5 - - + +
480A PHE* 1.3 52.0 + - - +
482A PHE* 3.2 11.8 + - + +
483A PHE* 2.6 41.2 + - + +
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Residues in contact with PHE 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PHE* 3.4 23.1 - + - -
233A VAL* 4.5 15.3 - - + -
234A LEU* 3.4 35.0 - - + -
237A LEU* 5.3 9.9 - - + -
476A CYS 2.9 11.9 + - - +
477A GLU* 2.9 16.5 + - + +
479A ILE* 1.3 77.0 - - - +
481A CYS* 1.3 62.2 + - + +
483A PHE* 2.7 25.0 + - - +
484A ILE* 3.0 44.3 + - + +
518A SER* 5.4 8.7 - - - -
522A ILE* 5.0 14.1 - - + -
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Residues in contact with CYS 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A GLU* 3.2 13.4 + - - +
478A ILE* 3.2 46.7 - - - -
480A PHE* 1.3 86.8 - - + +
482A PHE* 1.3 59.3 + - - +
484A ILE* 4.2 5.3 - - - +
485A PHE* 3.3 21.3 + - - +
522A ILE* 4.6 26.0 - - + +
526A ILE* 5.8 3.8 - - - -
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Residues in contact with PHE 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A ILE* 3.0 20.5 + - + +
479A ILE* 3.4 12.3 - - + +
481A CYS* 1.3 77.1 - - - +
483A PHE* 1.3 71.8 + + + +
485A PHE* 3.0 32.9 + + - +
486A TYR* 3.1 19.7 + + + +
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Residues in contact with PHE 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A THR* 3.5 44.0 - - + -
227A TYR* 4.2 4.0 - + - -
229A LEU* 6.1 3.8 - - + -
230A PHE* 3.3 50.7 - + + -
233A VAL* 6.4 1.3 - - + -
479A ILE* 2.6 28.3 + - + +
480A PHE* 2.7 13.0 + - - +
482A PHE* 1.3 78.8 - + + +
484A ILE* 1.3 65.7 + - + +
486A TYR* 3.0 25.1 - + + +
487A TYR* 3.6 20.0 + + - -
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Residues in contact with ILE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PHE* 3.8 17.5 - - + -
480A PHE* 3.0 70.4 + - + +
481A CYS* 4.4 3.4 - - - +
483A PHE* 1.3 73.7 - - + +
485A PHE* 1.3 56.4 + - - +
486A TYR 3.0 2.0 - - - -
487A TYR* 2.8 8.9 + - + +
488A VAL* 2.5 52.6 + - + +
515A VAL* 5.1 10.5 - - + -
518A SER* 4.3 21.3 - - - +
519A VAL* 5.2 0.7 - - + -
522A ILE* 4.4 14.8 - - + -
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Residues in contact with PHE 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A CYS 3.3 14.4 + - - +
482A PHE* 3.0 30.8 + + - +
484A ILE* 1.3 77.0 - - - +
486A TYR* 1.3 67.0 + - - +
488A VAL* 3.4 28.0 + - + +
489A VAL* 3.6 22.4 + - + +
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Residues in contact with TYR 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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222A ARG* 5.2 13.6 + - - +
223A GLU* 6.2 0.3 - - - +
226A THR* 5.0 8.4 - - + +
482A PHE* 3.1 17.8 + + + +
483A PHE* 3.0 19.3 - + + +
484A ILE 2.9 0.4 + - - -
485A PHE* 1.3 82.6 - - - +
487A TYR* 1.3 104.6 - + - +
488A VAL 3.0 1.0 + - - -
489A VAL* 3.2 1.6 + - - +
490A GLU* 3.0 46.8 + - + +
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Residues in contact with TYR 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A GLU* 3.4 24.8 + - + +
226A THR* 2.6 36.7 + - - +
227A TYR* 3.3 31.4 - + - +
483A PHE* 3.6 21.9 + + - +
484A ILE* 2.8 12.9 + - + +
486A TYR* 1.3 108.7 - + - +
488A VAL* 1.3 66.1 + - - +
490A GLU* 3.9 17.9 - - - -
491A GLU* 2.7 64.1 - - + +
515A VAL* 5.6 2.2 - - + -
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Residues in contact with VAL 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ILE* 2.5 44.5 + - + +
485A PHE* 3.4 21.5 - - + +
486A TYR 3.0 0.4 + - - -
487A TYR* 1.3 75.7 - - - +
489A VAL* 1.3 68.7 + - + +
491A GLU* 4.3 0.8 - - - +
492A ILE* 3.1 37.9 + - + +
515A VAL* 4.8 16.1 - - + +
519A VAL* 5.0 9.4 - - + -
522A ILE* 5.9 1.1 - - + -
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Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A PHE* 4.2 25.1 - - + +
486A TYR 3.2 4.8 + - - +
488A VAL* 1.3 82.5 - - + +
490A GLU* 1.3 68.1 + - - +
491A GLU 3.1 2.2 - - - -
492A ILE* 3.0 20.8 + - + +
493A LEU* 3.2 27.6 + - + +
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Residues in contact with GLU 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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223A GLU* 4.9 10.0 - - - +
486A TYR* 3.0 46.7 + - + +
487A TYR* 3.9 17.6 - - + -
489A VAL* 1.3 77.4 - - - +
491A GLU* 1.3 72.8 + - - +
493A LEU* 3.7 26.1 + - + +
494A GLU* 4.3 12.9 + - - +
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Residues in contact with GLU 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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227A TYR* 2.9 26.9 + - - -
487A TYR* 2.7 42.6 + - + +
488A VAL 4.3 0.9 - - - +
489A VAL 3.1 0.8 - - - -
490A GLU* 1.3 78.1 - - - +
492A ILE* 1.3 66.2 + - + +
493A LEU 3.2 2.4 + - - -
494A GLU* 3.5 9.9 + - - +
495A ILE* 3.2 23.0 + - + +
511A ASP 5.1 4.3 - - - +
515A VAL* 3.3 28.5 - - - +
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Residues in contact with ILE 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A VAL* 3.1 31.4 - - + +
489A VAL* 3.0 12.8 + - + +
491A GLU* 1.3 76.6 - - + +
493A LEU* 1.3 56.9 + - + +
495A ILE* 2.8 18.2 + - + +
496A ARG* 2.7 46.8 + - + +
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Residues in contact with LEU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A VAL* 3.2 27.4 + - + +
490A GLU* 3.7 22.0 - - + +
491A GLU 3.2 0.6 - - - -
492A ILE* 1.3 76.5 - - + +
494A GLU* 1.3 60.7 + - + +
496A ARG* 3.1 41.3 - - - +
497A ILE* 2.9 38.6 + - + +
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Residues in contact with GLU 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A GLU* 5.1 12.4 - - - +
491A GLU* 3.5 11.1 + - - +
492A ILE 3.3 0.2 - - - -
493A LEU* 1.3 76.8 - - + +
495A ILE* 1.3 63.9 + - + +
497A ILE* 4.5 1.6 - - - +
498A HIS* 2.8 52.4 + - + +
501A HIS* 6.2 3.8 - - + -
502A TYR* 4.2 2.2 - - + -
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Residues in contact with ILE 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A GLU* 3.2 18.6 - - + +
492A ILE* 2.8 22.4 + - + +
494A GLU* 1.3 79.5 - - + +
496A ARG* 1.3 60.9 + - - +
498A HIS 3.2 11.6 - - - +
499A LYS* 4.2 2.8 - - - +
502A TYR* 3.5 49.8 + - + +
508A ASN* 5.3 4.7 - - - +
512A VAL* 5.0 16.8 - - + -
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Residues in contact with ARG 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ILE* 2.7 24.7 + - + +
493A LEU* 3.1 42.3 - - - +
495A ILE* 1.3 76.4 - - - +
497A ILE* 1.3 102.2 + - - +
498A HIS 4.5 1.4 - - - -
499A LYS* 4.6 3.8 + - - +
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Residues in contact with ILE 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A LEU* 2.9 26.4 + - + +
494A GLU* 4.6 0.7 - - + -
496A ARG* 1.3 118.5 - - - +
498A HIS* 1.3 79.9 + - + +
499A LYS* 3.6 3.1 + - - +
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Residues in contact with HIS 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A GLU* 2.8 42.3 + - + +
495A ILE 3.2 2.4 - - - +
497A ILE* 1.3 91.9 - - + +
499A LYS* 1.3 61.4 + - - +
500A LEU 3.6 0.4 - - - +
501A HIS* 3.4 44.9 - + + -
502A TYR* 3.0 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