Contacts of the helix formed by residues 453 - 476 (chain A) in PDB entry 6QNW
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 CYS 453 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A ALA 3.4 20.9 - - - -
415A CYS 4.2 0.4 - - - -
416A GLU 3.8 8.3 - - - -
417A LEU* 4.4 3.9 - - - +
418A THR* 4.1 1.8 + - - -
422A TRP* 4.3 2.3 - - - -
450A VAL 3.0 17.3 + - - +
451A SER 3.0 3.7 + - - +
452A HIS* 1.3 80.2 - - - +
454A ARG* 1.3 74.0 + - - +
455A ALA* 3.2 13.5 - - - -
456A THR* 3.1 20.8 + - - +
457A GLU 3.5 3.8 + - - -
638A ARG* 3.7 42.6 - - + -
641A LEU* 4.3 5.8 - - + -
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Residues in contact with ARG 454 (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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284A LEU 5.4 1.3 - - - -
285A MET* 6.3 1.1 - - - +
289A LYS* 3.4 20.6 - - - +
413A LYS* 3.8 36.6 + - + +
414A ALA 3.9 3.4 - - - +
416A GLU* 3.2 21.7 + - - +
417A LEU 4.9 4.6 + - - -
418A THR* 3.5 26.6 - - + +
453A CYS* 1.3 73.6 - - - +
455A ALA* 1.3 60.8 + - - +
457A GLU* 3.0 35.3 + - - +
458A TYR* 2.9 55.0 + - + +
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Residues in contact with ALA 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ALA 3.5 4.9 + - - +
453A CYS* 3.2 5.6 - - - -
454A ARG* 1.3 77.2 - - - +
456A THR* 1.3 57.4 + - - +
458A TYR* 3.2 15.3 + - + +
459A ILE* 2.9 32.9 + - - +
641A LEU* 3.6 23.6 - - + -
642A ALA* 3.8 31.4 - - + -
645A VAL* 4.0 7.5 - - + +
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Residues in contact with THR 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A TRP* 3.6 16.8 - - + +
423A ILE* 3.5 32.3 - - + -
450A VAL* 2.9 26.6 + - + +
451A SER 3.4 8.3 - - - +
453A CYS 3.1 10.1 + - - -
455A ALA* 1.3 75.5 - - - +
457A GLU* 1.3 65.1 + - - +
459A ILE* 3.2 11.4 + - + +
460A MET* 3.0 27.0 + - + +
585A LEU* 4.9 7.7 - - + +
641A LEU* 3.7 9.8 - - - +
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Residues in contact with GLU 457 (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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284A LEU 5.7 0.5 - - - +
289A LYS* 3.8 10.3 + - - -
418A THR* 4.5 1.0 - - - +
422A TRP* 3.2 50.8 + - + +
453A CYS 3.5 2.6 + - - -
454A ARG* 3.0 43.9 + - - +
456A THR* 1.3 77.9 - - - +
458A TYR* 1.3 65.5 + - + +
460A MET* 3.5 1.0 + - - +
461A LYS* 2.9 33.7 + - + +
501A TYR* 2.4 42.2 + - + +
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Residues in contact with TYR 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE* 4.2 12.8 - + + -
284A LEU* 3.1 52.8 + - + +
285A MET* 3.6 11.4 + - - +
410A GLU* 4.6 1.7 + - - -
413A LYS* 4.6 2.8 - - - +
414A ALA* 3.8 28.3 + - + +
454A ARG* 2.9 43.6 + - + +
455A ALA* 3.2 16.8 + - + +
457A GLU* 1.3 83.8 - - + +
459A ILE* 1.3 62.5 + - - +
461A LYS* 3.4 7.8 + - + +
462A GLY* 2.9 21.8 + - - -
581A MET* 4.4 2.9 - - - +
645A VAL* 4.1 14.6 - - + -
646A PHE* 4.1 22.7 - + - -
649A LEU* 5.3 4.0 - - + -
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Residues in contact with ILE 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ALA 2.9 18.2 + - - +
456A THR* 3.6 12.6 - - + +
458A TYR* 1.3 77.5 - - - +
460A MET* 1.3 65.9 + - - +
462A GLY* 3.3 0.7 + - - -
463A VAL* 2.9 36.8 + - + +
581A MET* 3.7 28.9 - - + +
582A ARG* 3.6 30.3 - - + +
584A CYS* 4.0 6.5 - - + -
585A LEU* 4.2 17.7 - - + -
641A LEU* 4.0 13.2 - - + -
645A VAL* 3.5 29.8 - - + -
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Residues in contact with MET 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A TRP* 3.3 40.6 - - + +
423A ILE* 5.6 3.6 - - - -
424A GLU* 4.4 12.1 - - - +
456A THR* 3.0 21.8 + - + +
457A GLU 4.0 2.9 - - - +
459A ILE* 1.3 83.4 - - - +
461A LYS* 1.3 58.1 + - - +
463A VAL* 3.6 2.7 - - + +
464A TYR* 2.9 58.6 + - + +
487A SER* 5.4 3.4 - - - -
488A LYS 5.3 7.6 - - - +
582A ARG* 4.1 28.0 - - - +
553B LYS* 4.2 14.6 - - - +
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Residues in contact with LYS 461 (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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282A PHE* 3.4 25.3 - - + -
283A LEU 2.8 27.3 + - - +
284A LEU 5.0 1.8 + - - -
287A ALA* 3.3 22.0 - - - +
457A GLU* 2.9 22.8 + - + +
458A TYR* 3.6 9.2 - - + +
460A MET* 1.3 77.4 - - - +
462A GLY* 1.3 64.0 + - - +
464A TYR* 3.9 1.4 - - - -
465A ILE* 2.9 37.9 + - + +
485A MET* 4.1 9.6 - - - -
487A SER* 4.8 9.5 - - - -
501A TYR* 3.4 51.5 - - + +
524A GLU* 4.5 3.2 + - - -
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Residues in contact with GLY 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE* 3.8 24.1 - - - -
458A TYR 2.9 12.9 + - - -
459A ILE 3.8 2.7 - - - -
461A LYS* 1.3 76.4 - - - +
463A VAL* 1.3 62.8 + - - +
465A ILE* 4.0 2.2 - - - +
466A ASN* 2.9 34.9 + - - -
578A GLY 3.4 5.8 - - - -
581A MET* 4.2 7.9 - - - -
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Residues in contact with VAL 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ILE* 2.9 25.9 + - + +
460A MET* 3.6 6.3 - - + +
462A GLY* 1.3 76.1 - - - +
464A TYR* 1.3 69.5 + - + +
466A ASN* 4.0 0.7 - - - +
467A THR* 2.6 40.9 + - - +
578A GLY 3.3 13.0 + - - +
579A MET* 3.4 26.4 - - - +
581A MET* 4.2 11.0 - - + +
582A ARG* 3.3 34.3 - - - +
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Residues in contact with TYR 464 (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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298A GLU* 4.5 13.7 + - - -
424A GLU* 4.6 8.8 + - - -
460A MET* 2.9 38.9 + - + +
461A LYS* 3.9 3.1 - - - +
463A VAL* 1.3 85.7 - - + +
465A ILE* 1.3 65.3 + - + +
467A THR* 3.4 7.6 + - + -
468A ALA* 2.9 25.6 + - - +
486A ILE* 3.2 30.7 - - + +
487A SER* 3.6 9.0 - - - -
488A LYS* 3.8 41.1 + - + +
582A ARG* 5.6 0.7 - - - -
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Residues in contact with ILE 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE* 5.5 8.7 - - + -
461A LYS* 2.9 32.9 + - + +
462A GLY* 4.0 4.7 - - - +
464A TYR* 1.3 79.6 - - - +
466A ASN* 1.3 62.5 + - - +
468A ALA* 3.8 4.0 - - + +
469A LEU* 2.9 34.2 + - + +
483A ILE* 5.3 3.1 - - + +
484A PRO 4.4 3.4 - - - +
485A MET* 3.4 54.7 - - + -
486A ILE 3.9 9.0 - - - +
501A TYR* 5.8 0.2 - - + -
504A ILE* 4.1 25.4 - - + -
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Residues in contact with ASN 466 (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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282A PHE* 5.6 3.0 - - - -
462A GLY* 2.9 29.2 + - - +
465A ILE* 1.3 78.9 - - - +
467A THR* 1.3 57.8 + - - +
469A LEU* 4.0 7.4 - - - +
470A LEU* 2.9 33.8 + - - +
570A THR* 5.2 1.6 + - - -
574A LYS 4.3 2.7 + - - +
575A MET* 3.3 41.6 - - - +
577A TRP 4.8 1.0 + - - -
578A GLY* 3.5 22.4 + - - -
579A MET* 3.6 9.6 - - + -
581A MET* 4.9 4.0 - - - +
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Residues in contact with THR 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A VAL* 2.6 32.8 + - - +
464A TYR* 3.7 8.1 - - + -
466A ASN* 1.3 76.7 - - - +
468A ALA* 1.3 56.9 + - - +
470A LEU* 4.0 0.9 - - - +
471A ASN* 2.9 39.2 + - + +
579A MET* 3.4 31.8 - - + +
557B TYR* 4.7 14.6 - - - +
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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
----------------------------------------------------------
303A PRO* 6.3 3.6 - - + -
464A TYR 2.9 17.2 + - - +
465A ILE* 3.8 4.7 - - + +
467A THR* 1.3 76.2 - - - +
469A LEU* 1.3 58.3 + - - +
471A ASN* 3.4 5.1 + - - +
472A ALA* 2.9 30.8 + - - +
483A ILE* 3.7 22.2 - - + +
484A PRO* 4.8 7.0 - - + +
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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
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465A ILE* 2.9 21.0 + - + +
466A ASN* 4.0 7.0 - - - +
467A THR 3.3 0.2 - - - -
468A ALA* 1.3 78.1 - - - +
470A LEU* 1.3 57.3 + - - +
472A ALA* 3.3 2.8 + - - +
473A SER* 2.9 45.3 + - - +
483A ILE* 4.0 21.9 - - + +
504A ILE* 4.5 24.9 - - + -
506A LYS* 4.4 13.5 - - + -
518A VAL* 4.5 6.1 - - + -
520A PHE* 4.6 15.3 - - + -
570A THR* 4.2 22.7 - - + -
575A MET* 3.6 17.3 - - + -
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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
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466A ASN 2.9 17.5 + - - +
467A THR 4.1 1.8 - - - +
469A LEU* 1.3 76.9 - - - +
471A ASN* 1.3 62.3 + - - +
473A SER* 3.3 16.1 + - - -
474A CYS* 3.7 8.5 + - - +
511A LEU* 5.3 1.8 - - + -
572A LYS* 3.9 32.5 - - + +
575A MET* 3.6 36.5 - - + -
576A LYS* 5.1 7.9 - - + +
579A MET* 3.7 25.8 - - + -
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Residues in contact with ASN 471 (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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467A THR* 2.9 25.4 + - + +
468A ALA* 3.8 5.4 - - - +
470A LEU* 1.3 76.1 - - - +
472A ALA* 1.3 60.6 + - - +
474A CYS* 3.5 17.4 + - - +
475A ALA* 3.9 8.0 + - - +
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Residues in contact with ALA 472 (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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468A ALA 2.9 17.4 + - - +
469A LEU 3.7 4.0 - - - +
470A LEU 3.3 0.2 - - - -
471A ASN* 1.3 72.7 - - - +
473A SER* 1.3 55.5 + - - +
474A CYS 3.0 5.7 + - - -
475A ALA* 5.7 1.3 - - - -
476A ALA* 2.9 36.4 + - - +
481A GLN* 3.5 34.3 - - - +
483A ILE* 4.0 16.4 - - + -
506A LYS* 3.7 6.2 - - - -
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Residues in contact with SER 473 (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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469A LEU* 2.9 32.3 + - - +
470A LEU* 3.3 15.0 + - - -
472A ALA* 1.3 73.0 - - - +
474A CYS* 1.3 57.0 + - - +
477A MET* 4.5 3.5 - - - +
506A LYS* 3.5 13.8 - - - +
509A SER* 3.1 41.0 + - - +
511A LEU* 3.9 23.7 - - - +
518A VAL* 4.3 2.3 - - - +
575A MET* 4.4 1.6 - - - +
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Residues in contact with CYS 474 (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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470A LEU 3.7 6.5 + - - +
471A ASN* 3.5 12.5 + - - +
472A ALA 3.0 0.8 - - - -
473A SER* 1.3 78.8 - - - +
475A ALA* 1.3 65.6 + - + +
476A ALA 3.5 0.2 - - - -
477A MET* 3.9 19.8 - - - +
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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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471A ASN 3.9 7.1 + - - +
472A ALA* 3.6 2.1 + - - -
474A CYS* 1.3 77.3 - - + +
476A ALA* 1.3 57.2 + - - +
477A MET* 3.3 8.0 + - - +
479A ASP* 4.9 0.7 - - - +
481A GLN* 6.0 0.4 - - - +
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Residues in contact with ALA 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ASN* 5.2 0.7 - - - +
472A ALA* 2.9 15.7 + - - +
475A ALA* 1.3 75.5 - - - +
477A MET* 1.3 54.6 + - - +
478A ASP 3.0 11.6 + - - -
479A ASP* 3.3 19.8 - - - +
481A GLN* 3.2 32.5 - - + +
506A LYS* 2.7 37.0 + - - +
509A SER* 3.7 4.0 - - - -
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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