Contacts of the helix formed by residues 504 - 525 (chain A) in PDB entry 4ASQ
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 TYR 504 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A PHE* 3.3 33.2 - + - -
444A PHE* 3.4 24.0 - + - -
445A ALA* 3.7 20.3 - - + +
448A MET* 3.7 19.3 - - + -
449A ASP* 3.1 20.1 + - - +
452A ARG* 3.2 8.3 - - - +
495A LYS* 3.9 7.2 - - + -
497A HIS* 3.5 42.8 - + + -
498A ILE* 6.3 0.4 - - + -
503A GLU* 1.3 71.7 - - - +
505A LEU* 1.3 60.7 + - - +
506A ARG 3.1 2.9 - - - -
507A TYR* 2.9 39.5 + + - +
508A LEU 3.9 1.6 + - - -
3P PRO 2.5 25.6 + - - -
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Residues in contact with LEU 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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205A LEU* 3.8 11.4 - - + -
208A TYR* 3.5 22.9 - - + -
213A PHE* 4.0 4.3 - - + -
217A LEU* 3.7 32.1 - - + -
445A ALA 5.2 1.6 - - - -
446A PHE* 4.3 10.3 - - + -
449A ASP* 2.8 19.2 + - + +
453A TRP* 3.7 35.9 - - + -
503A GLU* 3.3 11.8 + - - +
504A TYR* 1.3 76.3 - - - +
506A ARG* 1.3 63.7 + - - +
508A LEU* 3.0 22.2 + - + +
509A VAL* 3.0 22.9 + - + +
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Residues in contact with ARG 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A TYR* 3.0 9.7 + - - -
391A PRO* 3.7 38.3 - - + +
392A GLY* 3.3 11.3 - - - -
395A GLU* 3.7 29.5 + - + +
502A VAL* 3.7 17.3 - - - +
503A GLU* 3.0 55.3 + - - +
505A LEU* 1.3 76.0 - - - +
507A TYR* 1.3 76.3 + - + +
509A VAL* 3.9 0.9 - - - -
510A SER* 2.8 29.2 + - - -
1624A FLC 4.9 14.8 + - - -
1P ARG* 5.7 2.0 - - - +
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Residues in contact with TYR 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A HIS* 4.6 1.6 - + - -
395A GLU* 3.3 30.3 + - + -
441A PHE* 3.6 23.1 - + + -
497A HIS* 3.0 39.8 + + - -
502A VAL* 4.7 1.4 - - - +
503A GLU 4.2 1.3 - - - -
504A TYR* 2.9 41.5 + + + +
506A ARG* 1.3 92.1 + - + +
508A LEU* 1.3 60.5 + - - +
510A SER* 4.0 3.1 - - - -
511A PHE* 2.9 41.1 + + + +
1P ARG* 2.7 36.8 + - - +
3P PRO* 3.7 22.4 - - + -
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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
----------------------------------------------------------
217A LEU* 4.0 24.2 - - + +
221A PHE* 5.3 7.0 - - + -
441A PHE* 5.0 0.4 - - - -
442A LEU* 3.8 40.6 - - + +
445A ALA* 4.0 15.2 - - + +
446A PHE* 3.6 46.9 - - + +
504A TYR 3.9 1.2 + - - -
505A LEU* 3.0 20.6 + - + +
507A TYR* 1.3 75.2 - - - +
509A VAL* 1.3 66.2 + - - +
511A PHE* 3.4 3.2 + - - +
512A ILE* 3.3 35.9 + - + +
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Residues in contact with VAL 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A TYR* 3.9 9.4 - - + -
213A PHE* 3.6 34.1 - - + -
217A LEU* 4.4 7.0 - - + -
390A ASN* 4.1 12.8 - - - +
392A GLY* 3.9 16.4 - - - -
505A LEU* 3.0 24.4 + - + +
506A ARG 3.7 4.7 - - - +
508A LEU* 1.3 75.5 - - - +
510A SER* 1.3 56.9 + - - +
512A ILE* 3.2 9.6 + - - +
513A ILE* 2.9 43.2 + - + +
577A MET* 4.1 16.6 - - - -
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Residues in contact with SER 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLY* 3.6 18.8 - - - -
395A GLU* 3.4 15.8 + - - +
396A ALA* 3.3 15.8 + - - -
399A ASP* 4.2 1.0 + - - -
506A ARG 2.8 22.1 + - - -
507A TYR* 3.6 8.0 - - - -
508A LEU 3.3 0.4 - - - -
509A VAL* 1.3 74.8 - - - +
511A PHE* 1.3 59.4 + - - +
513A ILE* 3.7 4.0 - - - +
514A GLN* 2.8 52.5 + - - +
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Residues in contact with PHE 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLN* 3.9 15.0 - - - -
399A ASP* 3.7 16.4 - - - -
437A ASP 3.4 20.2 - - - -
438A LYS* 3.6 43.7 - - + +
441A PHE* 3.4 35.9 - + + -
442A LEU* 3.7 18.4 - - + -
507A TYR* 2.9 30.6 + + + +
508A LEU 3.4 0.9 + - - +
509A VAL 3.4 0.2 - - - -
510A SER* 1.3 79.6 - - - +
512A ILE* 1.3 57.3 + - - +
514A GLN* 3.6 11.9 - - - +
515A PHE* 3.0 30.1 - - - -
582A ILE* 3.7 5.9 - - - +
3P PRO* 4.4 14.1 - - + -
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Residues in contact with ILE 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 3.7 27.6 - - + +
220A ILE* 3.7 26.5 - - + -
221A PHE* 5.8 0.4 - - - +
224A ILE* 6.4 0.4 - - + -
442A LEU* 4.7 9.4 - - + -
508A LEU* 3.3 28.6 + - + +
509A VAL* 3.2 6.6 + - - +
510A SER 3.2 0.2 - - - -
511A PHE* 1.3 77.4 - - - +
513A ILE* 1.3 66.4 + - + +
515A PHE* 3.3 15.6 + - - +
516A GLN* 3.7 9.2 + - - +
577A MET* 4.2 15.3 - - + -
578A SER 3.4 29.8 - - - +
579A GLY* 4.3 6.7 - - - +
582A ILE* 4.8 11.6 + - + +
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Residues in contact with ILE 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLY 3.8 19.1 - - - +
393A PHE* 3.6 36.8 - - + -
396A ALA* 4.0 1.3 - - + -
509A VAL* 2.9 32.7 + - + +
510A SER* 3.7 6.1 - - - +
512A ILE* 1.3 67.2 - - - +
514A GLN* 1.3 61.1 + - - +
515A PHE 3.1 2.9 - - - -
516A GLN* 2.9 31.6 + - + +
517A PHE* 2.9 52.2 + - + -
564A TRP* 5.9 2.7 - - + -
568A LEU* 6.0 4.3 - - + -
577A MET* 3.8 20.4 - - + -
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Residues in contact with GLN 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ALA* 4.1 12.1 - - + +
399A ASP* 3.1 32.2 + - + +
400A VAL* 3.7 15.0 - - + +
403A LEU* 3.9 13.1 - - + +
438A LYS* 2.8 32.0 + - - +
510A SER* 2.8 39.1 + - - +
511A PHE* 3.6 25.1 - - - +
513A ILE* 1.3 73.1 - - - +
515A PHE* 1.3 66.1 + - + +
517A PHE* 3.9 10.1 - - - -
518A TYR* 2.9 29.0 + - - +
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Residues in contact with PHE 515 (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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403A LEU* 4.1 18.4 - - + -
438A LYS* 3.8 29.8 - - + -
511A PHE* 3.0 28.0 - - - -
512A ILE 3.3 5.6 + - - +
513A ILE 3.1 1.0 - - - -
514A GLN* 1.3 89.9 - - + +
516A GLN* 1.3 60.1 + - - +
518A TYR* 4.0 5.2 - + - +
519A LYS* 3.0 31.4 + - - +
537A LEU* 5.6 1.2 - - + +
581A ALA* 3.3 5.0 - - - +
582A ILE* 3.6 37.7 - - + +
585A TYR* 3.6 51.1 - + + -
586A PHE* 3.8 11.9 - + - -
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Residues in contact with GLN 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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512A ILE* 4.1 3.3 - - - +
513A ILE* 2.9 39.5 + - + +
515A PHE* 1.3 78.6 - - - +
517A PHE* 1.3 64.9 + - + +
519A LYS* 4.0 2.5 - - - +
520A SER* 3.2 28.1 + - - -
568A LEU* 4.1 12.1 - - + +
572A ASN* 4.0 9.6 + - - +
574A GLU* 3.7 15.0 - - - +
576A ILE 3.1 18.7 - - - +
577A MET* 3.6 4.2 - - - +
578A SER* 3.0 45.8 + - - +
581A ALA* 3.8 13.2 - - + +
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Residues in contact with PHE 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A PHE* 3.7 22.0 - + - -
396A ALA* 3.9 19.7 - - + -
397A VAL* 5.4 1.1 - - + -
400A VAL* 3.6 21.1 - - + -
513A ILE* 2.9 44.1 + - + -
514A GLN* 3.8 2.7 - - - +
516A GLN* 1.3 74.8 - - - +
518A TYR* 1.3 54.8 + - - +
520A SER 3.4 0.5 + - - -
521A ALA* 2.8 37.4 + - - +
552A PHE* 4.8 2.7 - + + -
555A MET* 3.6 38.1 - - + -
568A LEU* 3.6 26.0 - - + -
571A PHE* 3.4 32.6 - + + -
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Residues in contact with TYR 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A VAL* 3.6 26.9 - - + +
403A LEU* 3.7 24.2 - - + -
404A SER* 3.7 23.6 - - - -
407A THR* 3.7 10.2 - - - +
514A GLN 2.9 19.5 + - - +
515A PHE* 4.0 5.6 - + - +
516A GLN 3.4 0.2 - - - -
517A PHE* 1.3 74.4 - - - +
519A LYS* 1.3 60.6 + - - +
521A ALA* 3.8 1.4 - - - +
522A CYS* 2.8 55.3 + - - -
537A LEU* 3.3 37.6 + - + -
538A ASP 4.8 0.2 - - - -
540A CYS* 2.7 26.5 + - - +
542A ILE* 5.2 4.3 - - + -
585A TYR* 3.7 22.6 + + - -
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Residues in contact with LYS 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A PHE 3.0 19.5 + - - +
516A GLN* 4.0 3.4 - - - +
518A TYR* 1.3 75.9 - - - +
520A SER* 1.3 60.5 + - - +
522A CYS* 3.4 2.3 + - - +
523A ILE* 3.0 54.3 + - + +
528A TYR* 4.1 12.5 - - + -
537A LEU* 3.9 20.2 - - + -
580A LYS* 4.4 18.2 - - - +
581A ALA* 4.1 17.0 - - + +
584A GLU* 2.8 39.7 + - - +
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Residues in contact with SER 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A GLN 3.2 12.7 + - - -
519A LYS* 1.3 76.8 - - - +
521A ALA* 1.3 60.6 + - - +
523A ILE* 3.3 9.7 + - - +
524A LYS* 2.9 39.5 + - - +
571A PHE* 3.8 10.1 - - - -
572A ASN* 2.9 42.4 + - - +
574A GLU* 5.4 1.0 + - - -
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Residues in contact with ALA 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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400A VAL* 4.9 0.4 - - + -
517A PHE 2.8 22.4 + - - +
518A TYR* 3.8 4.7 - - - +
520A SER* 1.3 72.9 - - - +
522A CYS* 1.3 57.7 + - - +
524A LYS* 3.3 10.2 + - - +
525A ALA* 2.9 29.6 + - - +
542A ILE* 4.0 19.3 - - + -
548A ALA* 3.9 23.7 - - + +
552A PHE* 4.5 4.7 - - + -
571A PHE* 4.1 13.8 - - + -
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Residues in contact with CYS 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A TYR* 2.8 47.1 + - - +
519A LYS 3.6 4.7 - - - +
521A ALA* 1.3 74.5 - - - +
523A ILE* 1.3 61.9 + - - +
525A ALA* 3.3 1.5 + - - -
526A GLY 3.2 3.1 + - - -
527A GLN* 2.8 30.5 + - - +
528A TYR* 3.3 17.4 + - + -
537A LEU* 4.1 3.4 - - + -
540A CYS* 2.0 50.5 - - - -
542A ILE* 4.0 5.2 - - - -
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Residues in contact with ILE 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A LYS* 3.0 47.9 + - + +
520A SER* 3.3 8.9 + - - +
522A CYS* 1.3 74.5 - - - +
524A LYS* 1.3 66.5 + - + +
526A GLY* 3.1 13.2 + - - -
528A TYR* 3.7 34.8 - - + +
530A PRO* 5.9 3.1 - - + -
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Residues in contact with LYS 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A SER* 2.9 36.4 + - - +
521A ALA* 3.6 7.9 - - - +
523A ILE* 1.3 77.9 - - + +
525A ALA* 1.3 58.6 + - - +
526A GLY 3.2 1.2 + - - -
547A ALA* 3.4 38.9 - - + +
548A ALA* 4.8 0.4 - - - -
551A ALA* 3.8 22.4 - - + +
571A PHE* 3.3 28.3 + - - -
572A ASN* 4.4 7.2 - - - +
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Residues in contact with ALA 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A ALA 2.9 16.5 + - - +
522A CYS 3.7 6.1 - - - +
523A ILE 3.2 0.4 - - - -
524A LYS* 1.3 76.9 - - - +
526A GLY* 1.3 61.0 + - - +
527A GLN* 3.9 20.6 - - + +
542A ILE* 4.2 10.5 - - + -
545A SER* 3.4 32.0 + - - +
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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