Contacts of the helix formed by residues 464 - 495 (chain A) in PDB entry 4S15
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 ASP 464 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A GLN* 4.6 18.7 - - - +
462A ARG 4.4 4.5 - - - +
463A GLU* 1.3 73.8 - - - +
465A GLY* 1.3 56.4 + - - +
466A ILE* 3.1 6.2 + - - +
467A LEU* 3.9 11.2 + - - +
468A THR* 4.1 7.1 + - - +
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Residues in contact with GLY 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A GLU* 3.0 12.9 - - - +
464A ASP* 1.3 77.1 - - - +
466A ILE* 1.3 63.3 + - - +
467A LEU 3.4 0.7 - - - -
468A THR* 3.3 19.2 + - - -
469A LYS* 3.3 14.9 + - - +
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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
----------------------------------------------------------
413A MET* 3.6 29.6 - - + +
415A LEU* 4.5 4.0 - - + -
457A LEU* 3.8 34.8 - - + -
462A ARG* 3.6 42.4 - - + +
463A GLU* 3.0 42.6 + - - +
464A ASP* 4.6 2.5 - - - -
465A GLY* 1.3 78.8 - - - +
467A LEU* 1.3 73.8 + - + +
469A LYS* 3.2 8.2 + - - +
470A LEU* 3.1 22.1 + - + +
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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
----------------------------------------------------------
450A GLN* 4.4 18.6 - - + +
453A LEU* 3.8 30.1 - - + -
454A GLN* 4.1 33.7 - - + +
457A LEU* 3.9 16.4 - - + -
464A ASP 3.9 6.8 + - - +
466A ILE* 1.3 84.4 - - + +
468A THR* 1.3 58.7 + - + +
470A LEU* 3.1 8.6 + - + +
471A ILE* 2.9 45.7 + - + +
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Residues in contact with THR 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ASP 4.1 4.2 + - - +
465A GLY* 3.3 23.6 + - - -
467A LEU* 1.3 73.7 - - + +
469A LYS* 1.3 62.4 + - - +
471A ILE* 3.8 15.9 - - + +
472A CYS* 3.1 30.5 + - - -
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Residues in contact with LYS 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A SER* 4.0 7.9 + - - -
412A SER* 5.9 0.2 + - - -
413A MET* 3.6 27.8 - - + +
465A GLY 3.3 13.0 + - - +
466A ILE* 3.2 11.8 + - - +
467A LEU 3.2 0.2 - - - -
468A THR* 1.3 79.5 - - - +
470A LEU* 1.3 60.5 + - - +
472A CYS* 3.4 11.4 + - + +
473A LYS* 3.2 50.1 + - - +
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Residues in contact with LEU 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A LEU* 3.8 29.6 - - + -
413A MET* 3.9 15.3 - - + -
415A LEU* 3.9 22.2 - - + -
419A GLU* 5.6 0.4 - - + +
423A PHE* 3.5 36.7 - - + -
453A LEU* 4.2 18.2 - - + -
457A LEU* 4.2 26.7 - - + -
466A ILE* 3.1 13.7 + - + +
467A LEU* 3.1 12.7 + - + +
469A LYS* 1.3 74.5 - - - +
471A ILE* 1.3 60.4 + - - +
473A LYS* 2.9 25.9 + - + +
474A VAL* 3.4 4.3 + - - +
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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
----------------------------------------------------------
423A PHE* 5.3 0.2 - - - -
426A PHE* 5.1 7.9 - - + -
450A GLN* 3.5 30.5 - - - +
467A LEU* 2.9 39.8 + - + +
468A THR* 3.8 17.0 - - + +
470A LEU* 1.3 74.7 - - - +
472A CYS* 1.3 64.5 + - - +
474A VAL* 3.1 27.6 + - + +
475A SER* 4.1 1.7 + - - -
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Residues in contact with CYS 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A THR* 3.1 24.2 + - - -
469A LYS* 3.5 15.0 - - + +
470A LEU 3.2 0.2 - - - -
471A ILE* 1.3 78.0 - - - +
473A LYS* 1.3 62.1 + - + +
474A VAL 3.2 0.5 + - - -
475A SER* 2.8 28.3 + - - -
476A THR* 3.8 3.7 + - - -
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Residues in contact with LYS 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A PHE* 3.9 23.2 - - + -
409A SER* 3.0 33.4 + - - +
410A LEU* 4.2 7.1 - - + +
413A MET* 3.4 27.9 - - - -
423A PHE* 4.3 9.6 - - + -
469A LYS* 3.2 35.1 - - - +
470A LEU* 2.9 20.0 + - + +
472A CYS* 1.3 77.7 - - + +
474A VAL* 1.3 57.8 + - - +
475A SER 3.2 0.2 - - - -
476A THR* 3.1 14.5 + - - +
477A LEU* 2.9 31.2 + - - +
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Residues in contact with VAL 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLU* 5.5 1.8 - - - +
423A PHE* 4.0 18.6 - - + -
426A PHE* 4.1 17.9 - - + -
427A VAL* 4.3 14.4 - - + -
430A SER* 5.9 1.6 - - - +
470A LEU 3.7 9.9 - - - +
471A ILE* 3.3 20.9 - - + +
472A CYS 3.1 0.4 - - - -
473A LYS* 1.3 77.4 - - - +
475A SER* 1.3 62.6 + - - +
477A LEU* 3.2 10.0 + - + +
478A ARG* 3.0 47.3 + - + +
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Residues in contact with SER 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ILE 4.1 1.5 + - - -
472A CYS* 2.8 22.1 + - - -
474A VAL* 1.3 80.6 - - - +
476A THR* 1.3 64.4 + - - +
478A ARG* 3.3 8.5 + - - +
479A ALA* 3.1 22.7 + - - +
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Residues in contact with THR 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A PHE* 3.6 30.5 - - + -
406A PHE* 3.8 26.0 - - + -
472A CYS 3.9 9.2 + - - -
473A LYS* 3.1 16.8 + - + +
475A SER* 1.3 80.6 + - - +
477A LEU* 1.3 57.4 + - - +
479A ALA* 3.2 7.2 + - - +
480A LEU* 2.9 29.3 + - + +
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Residues in contact with LEU 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLU* 3.7 25.6 - - + +
365A PHE* 3.5 30.5 - - + -
366A ILE* 3.6 31.9 - - + -
406A PHE* 3.4 30.9 - - + -
423A PHE* 4.5 6.7 - - + -
427A VAL* 4.2 14.8 - - + -
473A LYS 2.9 10.9 + - - +
474A VAL* 3.2 11.9 + - + +
476A THR* 1.3 75.9 - - - +
478A ARG* 1.3 56.4 + - + +
480A LEU* 3.2 8.0 + - + +
481A CYS* 3.0 33.6 + - - -
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Residues in contact with ARG 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLU* 3.5 20.3 + - - +
430A SER* 3.2 24.2 + - - -
432A ASP* 3.1 41.2 + - - -
433A ARG* 3.6 19.4 - - - +
474A VAL* 3.0 33.6 + - + +
475A SER* 3.8 7.4 - - - +
477A LEU* 1.3 75.9 - - - +
479A ALA* 1.3 52.8 + - - +
481A CYS* 3.4 4.1 + - - +
482A GLY* 2.7 31.7 + - - -
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Residues in contact with ALA 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A PHE* 4.2 15.7 - - + -
475A SER 3.1 13.8 + - - +
476A THR* 3.2 11.9 + - - +
478A ARG* 1.3 72.5 - - - +
480A LEU* 1.3 60.1 + - - +
482A GLY* 3.3 2.3 + - - -
483A ARG* 3.0 34.2 + - - +
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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
----------------------------------------------------------
365A PHE* 4.1 26.5 - - + -
399A PHE* 3.6 17.7 - - + -
402A PHE* 3.5 34.1 - - + +
403A VAL* 3.7 29.8 - - + +
406A PHE* 3.7 41.7 - - + -
476A THR* 2.9 14.9 + - + +
477A LEU* 3.2 11.4 + - + +
479A ALA* 1.3 73.9 - - - +
481A CYS* 1.3 65.2 + - - +
483A ARG* 3.2 5.9 + - - +
484A HIS* 3.1 18.7 + - - +
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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
----------------------------------------------------------
358A ALA 5.5 3.1 - - - +
361A LEU* 3.8 28.4 - - + +
362A GLU* 3.6 45.8 - - + +
365A PHE* 3.9 9.9 - - - -
477A LEU 3.0 15.0 + - - +
478A ARG* 3.9 6.1 - - - +
480A LEU* 1.3 76.6 - - - +
482A GLY* 1.3 62.8 + - - +
484A HIS* 3.2 3.0 + - - +
485A THR* 2.9 28.2 + - - +
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Residues in contact with GLY 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A ARG 2.7 21.6 + - - -
479A ALA* 3.6 3.4 - - - -
480A LEU 3.2 0.2 - - - -
481A CYS* 1.3 73.3 - - - +
483A ARG* 1.3 60.5 + - - +
485A THR* 3.4 6.9 + - - -
486A GLU* 3.1 29.3 + - - +
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Residues in contact with ARG 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A CYS* 5.2 2.6 - - - +
398A ASP* 3.1 33.5 + - - +
399A PHE* 3.6 42.5 - - + +
402A PHE* 5.1 11.5 - - + +
479A ALA* 3.0 21.2 + - + +
480A LEU* 3.2 8.0 + - - +
482A GLY* 1.3 70.5 - - - +
484A HIS* 1.3 61.9 + - - +
486A GLU* 3.3 6.5 + - - +
487A LYS* 2.9 49.1 + - + +
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Residues in contact with HIS 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TRP* 5.5 2.2 - + - -
327A ILE* 4.4 6.6 - - + +
361A LEU* 3.3 30.1 - - + +
365A PHE* 5.4 2.7 - + + -
399A PHE* 4.1 15.0 - + + -
480A LEU 3.1 12.8 + - - +
481A CYS 3.2 7.3 + - - +
483A ARG* 1.3 76.5 - - - +
485A THR* 1.3 61.4 + - - +
487A LYS* 3.7 6.3 - - + +
488A LEU* 2.9 35.3 + - + +
507A TYR* 2.7 34.7 + + - -
511A PHE* 3.9 32.5 - + + -
601A 4D8 4.3 22.7 - - + -
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Residues in contact with THR 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A CYS* 2.9 20.1 + - - +
482A GLY* 3.6 7.4 - - - +
484A HIS* 1.3 82.7 + - - +
486A GLU* 1.3 62.5 + - + +
488A LEU* 3.3 4.6 + - - +
489A MET* 2.9 42.7 + - + +
511A PHE* 4.8 20.5 + - - +
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Residues in contact with GLU 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A GLY 3.1 21.1 + - - +
483A ARG* 4.0 6.3 - - - +
485A THR* 1.3 81.2 - - + +
487A LYS* 1.3 62.5 + - - +
489A MET* 4.0 5.8 - - - +
490A ALA* 3.1 24.6 + - - +
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Residues in contact with LYS 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TRP* 3.5 25.0 - - + -
394A LEU* 4.9 3.6 + - - +
396A CYS* 3.1 41.2 - - - +
399A PHE* 3.8 27.1 - - + -
483A ARG* 2.9 39.2 + - - +
484A HIS* 3.7 5.6 - - + +
486A GLU* 1.3 76.8 - - + +
488A LEU* 1.3 62.9 + - - +
490A ALA* 3.3 5.8 + - - +
491A PHE* 3.0 18.2 + - - +
601A 4D8 3.9 16.4 - - - +
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Residues in contact with LEU 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TRP* 3.9 16.6 - - + -
484A HIS* 2.9 20.9 + - + +
485A THR* 3.8 4.3 - - - +
487A LYS* 1.3 76.7 - - - +
489A MET* 1.3 58.5 + - + +
491A PHE* 3.1 8.4 + - + +
492A LYS* 2.8 27.6 + - - +
499A VAL* 4.9 4.7 - - + -
503A PHE* 4.0 18.2 - - + -
507A TYR* 3.5 41.5 - - + +
511A PHE* 3.6 30.7 - - + +
512A THR* 3.6 22.9 - - + -
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Residues in contact with MET 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A THR* 2.9 34.6 + - + +
486A GLU* 4.1 4.7 - - - +
488A LEU* 1.3 76.6 - - + +
490A ALA* 1.3 57.9 + - - +
492A LYS* 3.4 19.9 + - + +
493A ALA* 3.0 27.5 + - - +
511A PHE 3.9 5.2 - - - +
512A THR* 3.9 36.1 - - - -
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Residues in contact with ALA 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A GLU 3.1 18.1 + - - +
487A LYS* 3.7 5.8 - - - +
489A MET* 1.3 73.1 - - - +
491A PHE* 1.3 66.4 + - - +
493A ALA* 3.2 15.5 + - - +
494A ILE* 3.3 20.1 + - - +
----------------------------------------------------------
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Residues in contact with PHE 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ARG* 3.6 28.7 - - - +
317A GLU* 3.7 31.0 - - + -
320A TRP* 3.5 35.2 - + + -
487A LYS 3.0 13.9 + - - +
488A LEU* 3.4 9.6 - - + +
490A ALA* 1.3 76.7 - - - +
492A LYS* 1.3 56.5 + - - +
494A ILE 3.3 1.0 + - - -
495A TYR* 2.8 49.1 + + + +
498A ILE* 4.0 16.8 - - + -
499A VAL* 3.5 22.0 - - + -
503A PHE* 3.4 34.3 - + - -
----------------------------------------------------------
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Residues in contact with LYS 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A LEU 2.8 15.9 + - - +
489A MET* 3.7 20.5 - - + +
491A PHE* 1.3 77.7 - - - +
493A ALA* 1.3 62.8 + - - +
495A TYR 4.4 0.2 - - - -
496A PRO* 3.2 29.8 - - + +
499A VAL* 3.7 31.6 - - + -
512A THR* 3.9 42.8 + - + -
----------------------------------------------------------
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Residues in contact with ALA 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A MET 3.0 17.7 + - - +
490A ALA* 3.5 9.6 - - - +
491A PHE 3.2 0.2 - - - -
492A LYS* 1.3 79.2 - - - +
494A ILE* 1.3 68.0 + - + +
496A PRO* 4.0 6.9 - - - +
----------------------------------------------------------
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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
----------------------------------------------------------
490A ALA 3.3 14.1 + - - +
491A PHE 3.3 2.0 + - - -
493A ALA* 1.3 84.7 - - + +
495A TYR* 1.3 94.2 + - + +
496A PRO* 3.3 9.5 - - - +
----------------------------------------------------------
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Residues in contact with TYR 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ARG* 3.3 28.4 + - - -
317A GLU* 4.0 16.1 + - + -
491A PHE* 2.8 31.5 + + + +
492A LYS 3.6 2.7 - - - -
494A ILE* 1.3 103.1 - - + +
496A PRO* 1.3 63.8 - - - +
497A ASP 3.3 2.5 - - - -
498A ILE* 3.3 35.3 + - + -
499A VAL* 3.2 22.3 + - - +
----------------------------------------------------------
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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