Contacts of the helix formed by residues 473 - 501 (chain A) in PDB entry 3DYQ
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 473 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A THR* 3.2 16.4 - - + +
470A LYS 5.2 2.5 - - - +
471A LEU 3.7 7.4 - - - +
472A PHE* 1.3 83.3 - - - +
474A MET* 1.3 73.1 + - + +
475A VAL 2.9 6.3 - - - -
476A GLU* 2.9 22.9 + - - +
477A GLU* 4.3 1.0 + - - +
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Residues in contact with MET 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 3.3 43.1 - - + +
271A CYS* 4.5 5.6 - - - -
272A SER* 5.4 5.8 - - - +
472A PHE* 3.6 31.0 - - + -
473A PRO* 1.3 86.0 - - + +
475A VAL* 1.3 63.5 + - - +
476A GLU 3.2 0.5 + - - -
477A GLU* 3.6 6.6 + - - +
478A ILE* 3.5 24.8 + - + +
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Residues in contact with VAL 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A MET* 4.8 2.5 - - + -
270A LEU* 3.9 15.5 - - + -
271A CYS* 3.7 29.8 - - - -
465A PHE* 4.1 30.1 - - + +
468A VAL* 4.0 11.9 - - + -
469A THR* 3.3 17.3 - - - +
472A PHE* 3.0 20.5 + - + +
473A PRO 2.9 1.4 - - - -
474A MET* 1.3 80.8 - - - +
476A GLU* 1.3 62.8 + - - +
479A MET* 3.0 27.9 + - + -
480A LEU* 3.3 3.1 + - + +
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Residues in contact with GLU 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A THR* 3.8 17.4 + - + +
473A PRO 2.9 13.8 + - - +
475A VAL* 1.3 78.4 - - - +
477A GLU* 1.3 64.2 + - - +
480A LEU* 3.1 38.6 + - + +
481A GLN* 3.2 12.6 + - - +
484A TRP* 3.3 30.8 - - + -
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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 PRO 4.3 1.0 + - - +
474A MET* 3.6 7.4 + - - +
475A VAL 3.3 0.2 - - - -
476A GLU* 1.3 80.8 - - + +
478A ILE* 1.3 80.0 + - + +
481A GLN* 3.4 46.0 + - - +
482A PRO* 4.0 0.9 - - - +
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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
----------------------------------------------------------
199A PRO* 3.6 33.1 - - + +
270A LEU* 3.7 26.7 - - + -
407A VAL* 4.6 2.3 - - - +
474A MET* 3.5 16.1 + - + +
475A VAL 3.5 1.4 + - - -
476A GLU 3.3 0.2 - - - -
477A GLU* 1.3 101.5 - - + +
479A MET* 1.3 70.7 + - + +
482A PRO* 3.2 19.0 - - - +
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Residues in contact with MET 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A PRO* 5.2 1.8 - - + -
263A MET* 3.7 26.9 - - + +
267A MET* 3.5 23.8 - - - +
270A LEU* 3.7 25.8 - - - -
400A CYS* 6.0 0.2 - - + -
407A VAL* 3.7 25.3 - - + +
465A PHE* 3.5 34.5 - - + -
475A VAL* 3.0 20.5 + - + +
477A GLU 3.4 0.2 - - - -
478A ILE* 1.3 92.3 - - + +
480A LEU* 1.3 66.6 + - - +
481A GLN 3.3 1.3 - - - -
482A PRO* 3.5 4.3 - - - +
483A LEU* 3.2 28.3 + - - +
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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
----------------------------------------------------------
462A ILE* 3.9 19.1 - - + +
465A PHE* 3.4 33.4 - - + +
466A GLU* 4.1 19.1 - - + -
469A THR* 3.5 26.7 - - + +
475A VAL 3.3 2.6 + - - +
476A GLU* 3.1 29.3 + - + +
479A MET* 1.3 75.7 - - - +
481A GLN* 1.3 59.4 + - - +
483A LEU* 3.1 14.0 + - + +
484A TRP* 2.8 57.0 + - + +
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Residues in contact with GLN 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A GLU* 3.2 9.0 + - - +
477A GLU* 3.4 42.0 + - - +
480A LEU* 1.3 76.1 - - - +
482A PRO* 1.3 72.0 - - + +
484A TRP* 3.0 32.7 + - + +
485A GLU* 2.9 36.4 + - + +
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Residues in contact with PRO 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLU 4.3 3.9 - - - +
407A VAL 3.3 29.4 - - - +
408A ARG 4.7 4.7 - - - +
409A PRO* 6.1 0.9 - - + -
477A GLU 4.0 0.7 - - - +
478A ILE 3.2 28.3 - - - +
479A MET* 3.5 8.3 - - - +
481A GLN* 1.3 95.3 - - + +
483A LEU* 1.3 55.7 + - - +
485A GLU* 3.2 13.9 + - + +
486A SER* 2.8 30.5 + - - -
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Residues in contact with LEU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLU* 3.6 38.8 - - + +
407A VAL* 3.9 8.5 - - + +
457A ILE* 3.7 11.6 - - + +
461A LEU* 3.9 29.2 - - + -
462A ILE* 4.1 13.0 - - + +
465A PHE* 3.9 27.8 - - + -
479A MET 3.2 16.8 + - - +
480A LEU* 3.1 21.7 + - + +
481A GLN 3.1 0.6 - - - -
482A PRO* 1.3 72.8 - - - +
484A TRP* 1.3 67.0 + - - +
486A SER* 3.8 2.6 - - - -
487A ARG* 2.9 25.6 + - - +
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Residues in contact with TRP 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A ILE* 3.6 29.2 - - + +
466A GLU* 5.2 3.8 + - + -
476A GLU* 3.3 32.3 - - + -
480A LEU* 2.8 39.9 + - + +
481A GLN* 3.0 36.8 + - + +
483A LEU* 1.3 75.7 - - - +
485A GLU* 1.3 64.8 + - + +
487A ARG* 3.4 29.3 + - - +
488A ASP* 3.1 29.5 + - - +
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Residues in contact with GLU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A GLN* 2.9 28.9 + - + +
482A PRO* 3.5 13.2 - - + +
484A TRP* 1.3 79.2 - - + +
486A SER* 1.3 57.5 + - - +
488A ASP* 3.4 7.4 + - - +
489A ARG* 3.0 28.6 + - - +
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Residues in contact with SER 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLU* 2.5 33.5 + - - -
410A MET* 5.9 4.5 - - - +
457A ILE* 3.8 9.0 - - - -
482A PRO 2.8 20.2 + - - -
483A LEU* 3.8 5.4 - - - -
485A GLU* 1.3 68.9 - - - +
487A ARG* 1.3 70.5 + - - +
489A ARG* 3.1 8.9 + - - +
490A TYR* 2.9 41.2 + - - -
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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
----------------------------------------------------------
454A ILE* 4.4 5.7 - - + +
457A ILE* 3.7 20.7 - - + +
458A LYS* 4.0 37.5 - - + +
462A ILE* 4.0 10.3 - - + +
483A LEU 2.9 18.3 + - - +
484A TRP* 3.4 44.6 + - - +
486A SER* 1.3 76.8 - - - +
488A ASP* 1.3 89.2 + - - +
490A TYR* 3.3 3.4 + - - +
491A GLU* 3.0 41.2 + - - +
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Residues in contact with ASP 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A TRP* 3.1 14.4 + - - +
485A GLU* 3.7 6.9 - - - +
486A SER 3.1 0.4 - - - -
487A ARG* 1.3 116.2 + - - +
489A ARG* 1.3 58.0 + - - +
491A GLU* 3.4 16.3 + - - +
492A GLU* 3.1 36.3 + - - +
495A ARG* 5.4 0.2 + - - -
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Residues in contact with ARG 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A MET* 3.8 43.6 - - - +
414A GLU* 3.8 26.9 + - - +
485A GLU 3.0 17.7 + - - +
486A SER* 3.7 7.4 + - - +
488A ASP* 1.3 74.9 - - - +
490A TYR* 1.3 97.8 + - + +
492A GLU* 3.2 14.2 + - + +
493A LEU* 2.9 35.4 + - + +
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Residues in contact with TYR 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLU* 3.6 21.6 + - - -
414A GLU* 3.6 25.8 + - - +
417A VAL* 3.6 10.7 - - - +
449A LYS* 4.5 11.1 + - + -
450A ALA* 3.7 18.4 - - - +
453A GLN* 3.6 26.5 - - + -
454A ILE* 3.6 24.3 - - + +
457A ILE* 4.1 4.0 - - + -
486A SER* 2.9 43.3 + - - +
487A ARG* 3.9 1.8 - - - +
489A ARG* 1.3 96.4 + - - +
491A GLU* 1.3 57.4 + - - +
493A LEU* 3.5 19.6 - - + +
494A LYS* 2.9 31.7 + - - +
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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
----------------------------------------------------------
454A ILE* 3.9 20.9 - - + +
458A LYS* 3.4 33.3 + - - +
487A ARG* 3.0 20.9 + - - +
488A ASP* 3.6 25.9 - - - +
490A TYR* 1.3 77.5 - - - +
492A GLU* 1.3 61.4 + - - +
494A LYS* 3.5 5.1 + - + +
495A ARG* 3.2 35.2 + - - +
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Residues in contact with GLU 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ASP* 3.1 26.7 + - - +
489A ARG* 3.4 14.5 - - + +
491A GLU* 1.3 77.1 - - - +
493A LEU* 1.3 63.8 + - - +
495A ARG* 3.0 44.4 + - - +
496A ILE* 3.3 10.2 + - - +
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Residues in contact with LEU 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A GLU* 5.5 2.2 - - - +
449A LYS* 4.8 11.7 - - + -
450A ALA* 4.3 9.9 - - + +
489A ARG* 2.9 24.9 + - + +
490A TYR* 3.5 34.1 - - + +
492A GLU* 1.3 75.9 - - - +
494A LYS* 1.3 52.7 + - - +
496A ILE* 3.1 14.5 + - + -
497A ASP* 2.8 50.3 + - - +
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Residues in contact with LYS 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ALA* 3.9 15.9 - - + +
451A THR* 3.9 23.6 - - + -
454A ILE* 4.1 17.5 - - + -
490A TYR 2.9 16.6 + - - +
491A GLU* 3.6 7.0 - - + +
493A LEU* 1.3 73.7 - - - +
495A ARG* 1.3 67.1 + - - +
496A ILE 3.0 0.2 - - - -
497A ASP* 3.8 5.6 - - + +
498A ASP* 2.5 63.9 + - - +
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Residues in contact with ARG 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ASP 5.4 0.4 + - - -
491A GLU* 3.2 30.2 + - - +
492A GLU* 3.0 42.1 + - - +
494A LYS* 1.3 80.4 - - - +
496A ILE* 1.3 63.4 + - + +
498A ASP* 3.7 6.8 + - - +
499A ALA* 3.2 22.7 + - - +
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Residues in contact with ILE 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A GLU 3.3 8.1 + - - +
493A LEU* 3.1 19.5 + - + +
494A LYS 3.0 0.6 - - - -
495A ARG* 1.3 85.6 - - + +
497A ASP* 1.3 64.2 + - - +
498A ASP 3.2 1.3 - - - -
499A ALA* 3.4 9.4 + - + +
500A MET* 2.9 42.2 + - + +
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Residues in contact with ASP 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A THR* 4.1 21.5 - - + +
449A LYS* 5.4 0.5 + - - +
450A ALA* 4.2 7.1 + - - +
493A LEU* 2.8 41.9 + - - +
494A LYS* 3.8 7.2 - - + +
496A ILE* 1.3 75.8 - - - +
498A ASP* 1.3 61.1 - - - +
500A MET* 3.2 7.0 + - - +
501A LYS* 3.1 47.8 + - - +
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Residues in contact with ASP 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A THR* 5.8 1.2 - - - +
494A LYS* 2.5 55.5 + - - +
495A ARG* 3.7 6.8 - - - +
497A ASP* 1.3 75.7 - - - +
499A ALA* 1.3 66.9 + - - +
501A LYS* 3.1 20.5 + - - +
502A GLU* 3.1 21.5 + - - +
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Residues in contact with ALA 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ARG 3.2 12.5 + - - +
496A ILE* 3.5 16.2 - - + +
498A ASP* 1.3 77.9 - - - +
500A MET* 1.3 64.5 + - + +
502A GLU* 2.7 37.8 + - - +
503A LEU* 3.4 7.9 + - - +
----------------------------------------------------------
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Residues in contact with MET 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A ILE* 2.9 33.7 + - + +
497A ASP* 3.5 9.4 - - - +
498A ASP 3.1 0.4 - - - -
499A ALA* 1.3 82.7 - - + +
501A LYS* 1.3 59.8 + - + +
502A GLU 3.2 4.0 + - - -
503A LEU* 3.3 37.1 - - + +
504A GLN* 3.5 20.0 + - - +
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Residues in contact with LYS 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A THR* 3.6 28.8 - - - +
497A ASP* 3.1 26.8 + - - +
498A ASP* 3.1 14.3 + - - +
500A MET* 1.3 73.7 - - + +
502A GLU* 1.3 50.5 + - - +
503A LEU 2.4 19.2 - - - +
504A GLN* 3.7 21.1 - - - +
505A LYS* 3.9 18.7 - - + +
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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