Contacts of the helix formed by residues 499 - 522 (chain A) in PDB entry 6R4F
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 MET 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A GLU* 3.9 15.9 - - - +
391A LEU* 4.1 20.4 - - + +
393A GLU* 3.7 22.2 - - + +
493A CYS* 3.7 33.9 - - + +
496A ARG* 3.1 40.7 + - + +
497A ILE 2.9 1.4 + - - -
498A SER* 1.3 85.7 - - - +
500A GLN* 1.3 66.1 + - - +
501A GLU 3.3 2.9 - - - -
502A ARG* 3.2 13.4 + - + +
503A ARG* 3.0 25.5 + - + +
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Residues in contact with GLN 500 (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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494A ASP 5.9 3.1 - - - +
496A ARG 3.5 9.8 + - - +
497A ILE* 3.1 39.2 + - - +
498A SER 3.6 0.2 - - - -
499A MET* 1.3 77.1 - - - +
501A GLU* 1.3 65.0 + - + +
503A ARG* 3.3 12.3 + - - +
504A LYS* 3.0 24.0 + - - +
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Residues in contact with GLU 501 (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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497A ILE 4.9 0.6 + - - -
498A SER 5.0 4.1 + - - +
499A MET 3.3 0.4 - - - -
500A GLN* 1.3 78.9 - - + +
502A ARG* 1.3 57.9 + - - +
504A LYS* 3.3 21.1 + - - +
505A GLU* 2.9 28.8 + - - +
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Residues in contact with ARG 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A GLU* 2.7 43.4 + - - +
391A LEU* 4.1 11.0 - - + -
498A SER 5.5 0.6 + - - +
499A MET* 3.2 17.6 + - + +
501A GLU* 1.3 77.4 - - - +
503A ARG* 1.3 64.1 + - - +
505A GLU* 2.9 30.1 + - - +
506A ILE* 3.0 47.5 + - + +
547A TYR* 3.5 9.7 + - - -
641A VAL* 3.6 9.3 - - - +
642A ASP* 3.0 36.7 + - - -
643A CYS* 3.8 9.3 - - - +
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Residues in contact with ARG 503 (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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349A TYR* 3.1 26.5 + - - +
350A THR* 4.4 0.8 - - - +
351A VAL* 4.2 13.9 - - - +
391A LEU* 5.4 1.8 - - + -
490A LEU* 3.0 49.7 + - + +
491A MET* 5.1 0.4 - - - +
493A CYS* 3.4 38.4 - - - -
494A ASP* 3.6 22.2 + - - +
496A ARG 5.5 0.2 - - - -
499A MET* 3.0 21.9 + - + +
500A GLN* 3.7 9.5 + - - +
502A ARG* 1.3 76.8 - - + +
504A LYS* 1.3 62.0 + - - +
506A ILE* 3.2 3.0 + - - +
507A MET* 2.9 53.4 + - + +
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Residues in contact with LYS 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A TYR* 3.4 58.2 - - + +
500A GLN 3.0 14.4 + - - +
501A GLU* 3.3 22.1 + - - +
503A ARG* 1.3 75.9 - - - +
505A GLU* 1.3 62.5 + - - +
507A MET* 3.2 1.8 + - - +
508A LEU* 2.9 40.1 + - + +
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Residues in contact with GLU 505 (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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501A GLU 2.9 13.5 + - - +
502A ARG* 2.9 41.6 + - - +
504A LYS* 1.3 77.5 - - - +
506A ILE* 1.3 65.3 + - - +
508A LEU* 3.5 7.5 + - - +
509A GLY 3.1 16.5 + - - -
641A VAL* 3.2 30.6 - - + +
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Residues in contact with ILE 506 (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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387A VAL* 4.3 4.0 - - + -
391A LEU* 4.0 24.0 - - + -
486A VAL* 3.8 28.3 - - + -
490A LEU* 4.2 13.7 - - + -
502A ARG* 3.0 42.4 + - + +
503A ARG 3.7 3.8 - - - +
505A GLU* 1.3 75.9 - - - +
507A MET* 1.3 59.0 + - - +
509A GLY* 2.9 15.8 + - - -
510A LEU* 2.9 14.6 + - + +
641A VAL* 4.1 10.8 - - + -
643A CYS* 3.6 31.0 - - - -
644A LEU* 3.6 7.4 - - + +
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Residues in contact with MET 507 (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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344A VAL* 4.4 11.7 - - + -
345A ASN 4.8 0.4 - - - +
346A PHE* 3.1 16.7 - - + -
349A TYR* 3.3 47.8 - - + +
350A THR 3.9 3.8 - - - +
351A VAL* 3.8 19.1 - - + -
490A LEU* 3.8 19.1 - - + -
503A ARG* 2.9 63.9 + - + +
504A LYS 3.9 2.9 - - - +
506A ILE* 1.3 73.2 - - - +
508A LEU* 1.3 60.3 + - - +
509A GLY 3.0 1.1 - - - -
510A LEU* 3.0 10.1 + - + +
511A LYS 2.8 23.9 + - - -
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Residues in contact with LEU 508 (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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346A PHE* 5.6 1.8 - - + -
349A TYR* 3.6 33.0 - - + +
504A LYS* 2.9 35.2 + - + +
505A GLU* 3.9 7.0 - - - +
507A MET* 1.3 76.1 - - - +
509A GLY* 1.3 60.2 + - - +
511A LYS* 3.5 24.6 + - + +
512A ARG* 3.2 35.3 + - - +
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Residues in contact with GLY 509 (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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505A GLU 3.1 6.7 + - - -
506A ILE 2.9 10.2 + - - -
508A LEU* 1.3 75.2 - - - +
510A LEU* 1.3 58.9 + - - +
512A ARG* 3.2 10.7 + - - +
513A LEU* 2.9 28.9 + - - +
640A SER* 4.5 8.7 + - - -
641A VAL* 3.9 13.2 - - - +
644A LEU* 3.6 15.0 - - - +
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Residues in contact with LEU 510 (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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340A MET* 3.6 27.7 - - - +
344A VAL* 5.1 5.4 - - + -
346A PHE* 4.2 5.2 - - + -
483A VAL* 4.1 22.4 - - + -
486A VAL* 4.4 8.7 - - + -
487A MET* 4.7 11.2 - - + -
490A LEU* 3.9 28.0 - - + -
506A ILE* 2.9 16.9 + - + +
507A MET* 3.5 13.0 - - + +
509A GLY* 1.3 72.4 - - - +
511A LYS* 1.3 67.6 + - - +
513A LEU* 3.3 22.2 + - + +
514A PRO* 3.4 10.6 - - - +
644A LEU* 3.7 27.4 - - + -
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Residues in contact with LYS 511 (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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340A MET* 5.5 0.4 - - - -
346A PHE* 3.6 47.8 - - + +
347A ASP* 5.7 2.6 + - - -
507A MET 2.8 12.3 + - - +
508A LEU* 3.5 29.2 - - + +
510A LEU* 1.3 79.0 - - - +
512A ARG* 1.3 63.9 + - + +
514A PRO* 3.4 10.6 - - - +
515A ASP* 6.0 0.9 - - - -
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Residues in contact with ARG 512 (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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508A LEU* 3.2 23.3 + - + +
509A GLY* 3.2 8.5 + - - +
511A LYS* 1.3 82.0 - - + +
513A LEU* 1.3 64.7 + - - +
514A PRO* 3.4 1.3 - - - -
515A ASP* 3.2 10.7 + - - +
516A LEU* 3.1 52.6 + - + +
639A HIS 3.7 19.8 + - - -
640A SER* 4.1 10.5 + - - +
641A VAL* 5.2 1.4 - - - +
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Residues in contact with LEU 513 (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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336A VAL* 4.0 19.1 - - + -
483A VAL* 4.2 6.5 - - + -
509A GLY 2.9 16.2 + - - +
510A LEU* 3.5 18.8 - - + +
512A ARG* 1.3 77.6 - - - +
514A PRO* 1.3 70.5 - - + +
516A LEU* 3.0 9.6 + - + +
517A ILE* 2.9 33.2 + - + +
640A SER* 4.8 5.2 - - - +
644A LEU* 4.7 10.5 - - + +
647A ILE* 3.7 39.5 - - + -
648A LEU* 4.0 29.2 - - + -
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Residues in contact with PRO 514 (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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333A PRO* 3.8 19.6 - - + +
336A VAL* 4.4 7.4 - - + -
337A VAL* 3.5 33.4 - - + -
340A MET* 4.4 4.3 - - + -
510A LEU 3.4 14.4 - - - +
511A LYS 3.4 11.9 - - - +
512A ARG 3.5 1.1 - - - -
513A LEU* 1.3 91.8 - - + +
515A ASP* 1.3 64.9 + - - +
517A ILE* 3.5 7.6 + - + +
518A LYS* 3.2 29.1 + - - +
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Residues in contact with ASP 515 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511A LYS 6.0 0.9 - - - -
512A ARG* 3.2 11.7 + - + +
514A PRO* 1.3 79.1 - - - +
516A LEU* 1.3 65.1 + - + +
518A LYS* 3.4 27.9 + - - +
519A GLU* 3.0 27.4 + - - +
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Residues in contact with LEU 516 (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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509A GLY 5.0 0.2 - - - +
512A ARG* 3.1 59.8 + - + +
513A LEU* 3.0 11.7 + - + +
515A ASP* 1.3 75.5 - - + +
517A ILE* 1.3 64.9 + - - +
519A GLU* 3.0 17.2 + - - +
520A VAL* 2.9 25.1 + - - +
638A PRO* 3.8 20.5 - - + +
639A HIS 4.1 1.8 - - - +
640A SER* 3.6 26.2 - - - +
648A LEU* 3.7 21.5 - - + -
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Residues in contact with ILE 517 (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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332A GLN* 4.0 12.3 - - + +
333A PRO* 3.5 28.5 - - + -
336A VAL* 3.7 31.9 - - + -
479A THR* 5.9 0.2 - - - -
513A LEU* 2.9 25.4 + - + +
514A PRO 3.7 6.7 - - - +
516A LEU* 1.3 75.1 - - - +
518A LYS* 1.3 62.9 + - - +
520A VAL* 3.0 7.1 + - - +
521A LEU* 2.9 27.6 + - + +
647A ILE* 4.1 15.3 - - + -
648A LEU* 3.9 17.7 - - + -
651A ILE* 3.7 24.0 - - + -
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Residues in contact with LYS 518 (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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333A PRO* 3.7 25.8 - - + -
514A PRO* 3.2 11.5 + - - +
515A ASP* 3.5 29.9 + - - +
516A LEU 3.3 0.2 - - - -
517A ILE* 1.3 76.7 - - - +
519A GLU* 1.3 62.5 + - - +
521A LEU* 3.3 11.2 + - + +
522A SER* 3.0 23.0 + - - -
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Residues in contact with GLU 519 (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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515A ASP 3.0 14.7 + - - +
516A LEU* 3.0 23.3 + - - +
518A LYS* 1.3 76.6 - - - +
520A VAL* 1.3 60.7 - - - +
522A SER* 2.6 28.4 + - - +
523A MET* 3.7 8.4 + - - +
638A PRO* 3.6 28.8 - - + +
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Residues in contact with VAL 520 (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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516A LEU 2.9 13.8 + - - +
517A ILE* 3.0 7.2 + - - +
519A GLU* 1.3 74.6 - - - +
521A LEU* 1.3 59.4 + - - +
523A MET* 2.9 38.9 + - + +
527A ILE* 5.8 0.7 - - - +
637A VAL* 4.3 4.3 - - + -
638A PRO* 3.5 22.2 - - + -
648A LEU* 4.0 26.0 - - + +
651A ILE* 3.9 17.0 - - + -
652A PRO* 3.9 34.5 - - + -
655A LEU* 5.0 4.2 - - + +
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Residues in contact with LEU 521 (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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329A ILE* 4.2 14.6 - - + +
330A PHE* 3.4 56.5 - - + +
333A PRO* 3.9 22.7 - - + -
517A ILE* 2.9 19.4 + - + +
518A LYS* 3.3 10.5 + - + +
520A VAL* 1.3 76.1 - - - +
522A SER* 1.3 60.0 + - - +
523A MET 3.1 0.4 - - - -
524A ASP* 3.1 23.1 + - - +
651A ILE* 3.9 24.9 - - + -
655A LEU* 4.2 13.7 - - + -
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Residues in contact with SER 522 (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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518A LYS 3.0 12.6 + - - -
519A GLU* 2.6 25.0 + - - +
521A LEU* 1.3 76.4 - - - +
523A MET* 1.3 59.0 + - - +
524A ASP 3.3 3.6 + - - -
525A ASP* 4.8 4.5 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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