Contacts of the helix formed by residues 501 - 523 (chain A) in PDB entry 5UNJ
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 LEU 501 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A GLY 3.0 22.7 + - - +
498A GLN* 3.7 35.7 - - - +
499A LEU 3.1 0.4 - - - -
500A LEU* 1.3 76.6 - - - +
502A ARG* 1.3 76.7 + - - +
504A PRO* 3.3 15.9 - - + +
505A GLU* 3.6 14.4 - - - +
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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
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434A LEU* 4.7 10.1 - - + -
437A LYS* 4.6 26.8 - - - +
438A LEU* 4.0 33.7 - - + -
441A LEU* 4.4 9.2 - - - +
451A LEU* 5.7 2.7 - - + -
498A GLN* 3.0 45.0 + - - +
499A LEU 3.0 15.2 + - - +
501A LEU* 1.3 93.9 - - - +
503A LEU* 1.3 61.0 + - + +
504A PRO 3.5 0.2 - - - -
505A GLU* 2.9 45.5 + - - +
506A ILE* 2.8 43.6 + - + +
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Residues in contact with LEU 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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384A GLU* 3.2 14.7 - - - +
388A LEU* 4.9 2.2 - - + -
451A LEU* 4.3 30.1 - - + -
454A LEU* 4.3 25.1 - - + -
455A VAL* 3.5 29.2 - - + +
499A LEU 4.6 2.2 - - - +
500A LEU* 3.1 25.4 + - + +
502A ARG* 1.3 78.1 - - - +
504A PRO* 1.3 70.2 - - + +
505A GLU 3.3 0.2 + - - -
506A ILE* 3.3 12.9 + - + +
507A ARG* 2.9 20.5 + - - +
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Residues in contact with PRO 504 (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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500A LEU 3.2 14.8 - - - +
501A LEU* 3.3 13.9 - - + +
503A LEU* 1.3 92.2 - - + +
505A GLU* 1.3 60.7 + - + +
507A ARG* 3.4 7.4 + - + +
508A ALA* 3.0 24.8 + - - +
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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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430A HIS* 4.8 10.9 + - + +
434A LEU* 3.7 27.8 - - + +
437A LYS* 5.3 3.5 - - - +
501A LEU* 3.6 12.2 - - - +
502A ARG* 2.9 50.3 + - - +
504A PRO* 1.3 75.7 - - + +
506A ILE* 1.3 66.4 + - - +
508A ALA* 3.3 6.7 + - - +
509A ILE* 3.1 27.7 + - - +
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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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384A GLU* 3.8 28.7 - - + +
387A ILE* 3.8 21.3 - - + +
388A LEU* 3.7 31.0 - - + +
391A ILE* 3.8 15.5 - - + -
434A LEU* 3.5 20.4 - - + -
438A LEU* 5.5 3.1 - - + -
451A LEU* 5.9 1.6 - - + -
502A ARG* 2.8 34.0 + - + +
503A LEU* 3.8 11.9 - - + +
505A GLU* 1.3 71.0 - - - +
507A ARG* 1.3 58.8 + - - +
509A ILE* 3.2 8.3 + - - +
510A SER* 2.9 25.8 + - - -
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Residues in contact with ARG 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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380A ASN* 3.1 52.1 + - - +
381A CYS* 4.6 1.4 - - - +
384A GLU* 3.0 33.6 + - - +
458A SER* 6.1 0.2 - - - -
460A ASP* 4.5 18.1 + - - -
503A LEU 2.9 17.4 + - - +
504A PRO* 3.7 8.5 - - + +
505A GLU 3.2 0.2 - - - -
506A ILE* 1.3 78.3 - - - +
508A ALA* 1.3 56.2 + - - +
510A SER* 2.8 23.6 + - - +
511A MET* 2.9 35.4 + - + +
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Residues in contact with ALA 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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430A HIS* 6.0 2.0 - - + +
504A PRO 3.0 16.7 + - - +
505A GLU* 3.7 7.0 - - - +
506A ILE 3.3 0.2 - - - -
507A ARG* 1.3 76.7 - - - +
509A ILE* 1.3 63.6 + - + +
511A MET* 3.3 18.7 + - + +
512A GLN* 3.1 32.2 + - - +
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Residues in contact with ILE 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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387A ILE* 4.3 13.9 - - + -
427A LEU* 4.2 15.0 - - + +
430A HIS* 3.4 48.7 - - + +
431A ALA* 4.1 12.6 - - + +
434A LEU* 4.2 16.2 - - + -
505A GLU 3.1 15.7 + - - +
506A ILE* 3.2 8.9 + - - +
508A ALA* 1.3 76.8 - - + +
510A SER* 1.3 56.8 + - - +
512A GLN* 3.3 12.3 + - - +
513A ALA* 2.9 26.0 + - - +
601A RJW 4.2 25.4 - - + -
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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
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383A SER* 3.4 41.8 + - - -
384A GLU* 3.6 9.7 + - - +
387A ILE* 4.0 7.0 - - - -
506A ILE 2.9 12.6 + - - -
507A ARG* 2.8 29.3 + - - +
509A ILE* 1.3 73.4 - - - +
511A MET* 1.3 60.3 + - - +
513A ALA* 3.6 7.7 - - - +
514A GLU* 2.9 34.0 + - - +
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Residues in contact with MET 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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507A ARG* 2.9 36.3 + - + +
508A ALA* 3.7 22.0 - - + +
510A SER* 1.3 79.2 + - - +
512A GLN* 1.3 62.1 + - + +
514A GLU* 3.4 9.6 + - - +
515A GLU* 3.1 30.0 + - + +
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Residues in contact with GLN 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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426A ASN* 5.3 5.5 - - - +
427A LEU* 3.4 32.1 - - + +
430A HIS* 5.1 5.5 - - - -
508A ALA* 3.1 22.6 + - - +
509A ILE* 3.6 12.8 - - - +
511A MET* 1.3 76.8 - - + +
513A ALA* 1.3 63.0 + - - +
515A GLU* 3.4 7.5 + - - +
516A TYR* 3.1 23.0 + - - +
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Residues in contact with ALA 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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383A SER* 5.8 2.0 - - - -
387A ILE* 4.8 7.4 - - + -
424A LEU* 5.4 3.3 - - + +
427A LEU* 3.7 16.5 - - + +
509A ILE 2.9 15.7 + - - +
510A SER* 3.6 9.4 - - - +
511A MET 3.3 0.2 - - - -
512A GLN* 1.3 77.2 - - - +
514A GLU* 1.3 56.9 + - + +
516A TYR* 3.2 5.0 + - - +
517A LEU* 2.9 37.0 + - + +
601A RJW 4.4 26.2 - - + -
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Residues in contact with GLU 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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379A GLN 5.5 0.5 - - - +
380A ASN 5.6 1.9 - - - +
382A TRP* 3.4 42.1 + - + -
383A SER* 2.5 28.5 + - - +
510A SER 2.9 19.0 + - - +
511A MET* 3.7 9.4 - - - +
513A ALA* 1.3 77.6 - - - +
515A GLU* 1.3 53.2 + - + +
517A LEU* 3.3 3.5 + - + +
518A TYR* 2.7 37.4 + - - +
535A MET 4.7 3.1 - - - +
536A LEU* 3.7 17.2 - - + +
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Residues in contact with GLU 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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511A MET* 3.1 22.3 + - + +
512A GLN* 3.8 7.6 - - - +
513A ALA 3.3 0.2 - - - -
514A GLU* 1.3 76.7 - - + +
516A TYR* 1.3 56.4 + - - +
518A TYR* 3.5 10.0 + - - +
519A TYR* 2.9 28.4 + - - +
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Residues in contact with TYR 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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342A PHE* 4.2 7.0 - + - -
420A ALA 4.2 10.6 + - - -
421A GLY* 5.5 1.7 - - - -
423A THR* 3.6 40.2 + - + -
424A LEU* 3.6 37.9 - - + -
427A LEU* 5.1 2.5 - - + -
512A GLN 3.1 17.5 + - - +
513A ALA* 3.6 5.6 - - - +
514A GLU 3.2 0.2 - - - -
515A GLU* 1.3 78.1 - - - +
517A LEU* 1.3 64.1 + - + +
519A TYR* 3.2 14.4 + + + +
520A LYS* 2.9 72.5 + - + +
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Residues in contact with LEU 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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342A PHE* 3.7 20.2 - - + -
346A CYS* 4.7 2.7 - - - -
382A TRP* 5.0 6.1 - - + -
386A LEU* 6.0 0.2 - - + -
424A LEU* 5.4 1.8 - - + -
513A ALA* 2.9 24.1 + - + +
514A GLU* 3.9 6.3 - - - +
516A TYR* 1.3 82.7 - - + +
518A TYR* 1.3 56.9 + - - +
520A LYS* 3.3 5.0 + - - +
521A HIS* 2.9 29.3 + - - +
526A VAL* 3.7 6.2 - - + +
532A LEU* 4.7 18.8 - - + -
536A LEU* 4.2 15.7 - - + +
601A RJW 3.6 59.0 - - + -
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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
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514A GLU 2.7 22.8 + - - +
515A GLU* 3.8 11.2 - - - +
517A LEU* 1.3 74.3 - - - +
519A TYR* 1.3 63.4 + - - +
521A HIS* 3.3 6.8 + + - +
522A LEU* 3.0 59.7 + - + +
536A LEU* 3.6 45.7 - - + +
537A HIS* 3.9 33.4 + + - -
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Residues in contact with TYR 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 GLU 2.9 14.8 + - - +
516A TYR* 3.4 18.2 - + + +
518A TYR* 1.3 78.0 - - - +
520A LYS* 1.3 75.7 + - + +
522A LEU* 3.3 11.6 + - + +
523A ASN* 2.8 54.3 + - + +
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Residues in contact with LYS 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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342A PHE* 3.9 22.7 - - + -
516A TYR* 2.9 59.2 + - + +
517A LEU* 3.7 4.9 - - - +
519A TYR* 1.3 92.5 - - + +
521A HIS* 1.3 54.7 + - - +
523A ASN* 3.2 6.3 + - - +
524A GLY 3.0 8.1 + - - -
525A ASP* 2.7 55.6 + - + -
526A VAL* 3.7 13.2 - - + -
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Residues in contact with HIS 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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517A LEU 2.9 17.2 + - - +
518A TYR* 3.6 11.0 - + - +
520A LYS* 1.3 72.8 - - - +
522A LEU* 1.3 71.8 + - + +
524A GLY* 2.8 20.8 + - - -
526A VAL* 3.3 25.9 + - + +
533A ILE* 3.4 46.1 - - + +
536A LEU* 4.8 3.6 - - + -
537A HIS* 3.8 24.3 - + - -
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Residues in contact with LEU 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 TYR* 3.0 56.2 + - + +
519A TYR* 3.7 10.1 - - + +
521A HIS* 1.3 84.3 - - + +
523A ASN* 1.3 59.6 + - - +
524A GLY* 3.4 1.0 + - - -
537A HIS* 5.7 2.9 - - - +
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Residues in contact with ASN 523 (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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519A TYR* 2.8 43.2 + - + +
520A LYS* 3.4 11.1 - - - +
521A HIS 3.1 0.2 - - - -
522A LEU* 1.3 76.4 - - - +
524A GLY* 1.3 59.7 + - - +
525A ASP* 3.2 24.7 + - - +
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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
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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