Contacts of the helix formed by residues 499 - 512 (chain A) in PDB entry 5Y41
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 ASP 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453A TYR* 3.3 2.9 + - - -
497A ASN 3.5 4.2 + - - -
498A ILE* 1.3 76.6 - - - +
500A ILE* 1.3 57.7 + - - +
501A SER 3.3 0.5 + - - -
502A ALA* 2.8 36.3 + - - +
503A PHE 2.9 25.3 + - - -
538A HIS* 2.8 25.6 - - - -
542A ASN* 4.4 3.6 - - - +
602A PGE 3.5 6.3 - - - +
362B VAL* 3.9 14.1 - - + +
366B SER* 2.6 40.5 + - - +
370B ARG* 5.7 0.9 - - - +
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Residues in contact with ILE 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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369A VAL* 4.1 23.8 - - + -
372A HIS* 4.2 17.7 - - + +
373A VAL* 4.4 5.6 - - + -
453A TYR* 3.6 9.2 - - + +
499A ASP* 1.3 74.3 - - - +
501A SER* 1.3 56.3 + - - +
503A PHE* 3.4 3.6 + - - +
504A SER* 2.8 38.8 + - - +
602A PGE 3.7 8.3 + - - +
369B VAL* 4.6 3.8 - - + -
370B ARG* 3.7 67.5 - - + +
373B VAL* 3.9 24.7 - - + -
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Residues in contact with SER 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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365A ILE* 3.9 15.2 - - - +
369A VAL* 3.6 21.3 - - - +
499A ASP 3.3 0.4 - - - -
500A ILE* 1.3 76.6 - - - +
502A ALA* 1.3 61.5 + - - +
504A SER* 3.3 4.3 + - - -
505A CYS* 3.3 25.3 + - - -
538A HIS* 3.4 29.7 - - - -
602A PGE 3.1 25.7 + - - -
369B VAL* 5.5 1.2 - - - +
501B SER* 5.1 1.2 + - - -
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Residues in contact with ALA 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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498A ILE* 3.8 17.3 - - + -
499A ASP* 2.8 24.0 + - - +
501A SER* 1.3 72.4 - - - +
503A PHE* 1.3 63.1 + - - +
505A CYS* 3.2 5.5 + - - +
506A ILE* 3.0 25.3 + - - +
535A LEU* 3.7 25.4 - - + +
538A HIS* 4.0 8.2 - - - +
539A VAL* 5.0 3.4 - - + -
551A TYR* 5.9 2.0 - - + +
555A LEU* 4.5 8.5 - - + -
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Residues in contact with PHE 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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372A HIS* 3.4 40.6 - + - -
449A LEU* 3.5 47.1 - - + -
450A ARG* 4.1 12.6 - - + -
453A TYR* 3.5 57.7 - + + -
493A LEU* 4.5 5.6 - - + -
498A ILE* 3.5 11.3 - - + +
499A ASP 2.9 17.3 + - - +
500A ILE 3.7 2.9 - - - +
502A ALA* 1.3 73.8 - - - +
504A SER* 1.3 61.9 + - - +
506A ILE* 3.2 8.2 + - + +
507A ALA* 2.9 36.3 + - + +
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Residues in contact with SER 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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368A LEU* 3.4 34.6 - - - +
369A VAL* 3.4 14.8 - - - +
372A HIS* 3.3 24.8 - - - +
420A TRP* 4.9 3.7 + - - +
500A ILE* 2.8 22.6 + - - +
501A SER 3.6 6.1 - - - -
503A PHE* 1.3 80.5 - - - +
505A CYS* 1.3 60.4 + - - +
507A ALA* 3.9 3.7 - - - +
508A ALA* 3.3 21.3 + - - +
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Residues in contact with CYS 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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365A ILE* 3.8 23.1 - - - -
368A LEU* 4.1 13.9 - - - -
501A SER 3.3 13.7 + - - -
502A ALA 3.2 8.2 + - - +
503A PHE 3.1 0.6 - - - -
504A SER* 1.3 76.4 - - - +
506A ILE* 1.3 59.4 + - - +
508A ALA* 3.2 4.5 + - - +
509A LEU* 2.9 33.1 + - - +
531A ILE* 3.5 13.0 - - + +
534A CYS* 4.1 18.6 - - - -
535A LEU* 3.9 27.8 - - + -
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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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449A LEU* 4.2 21.1 - - + -
493A LEU* 6.1 1.8 - - + -
498A ILE* 5.2 2.0 - - + -
502A ALA 3.0 17.6 + - - +
503A PHE* 3.2 14.1 + - + +
505A CYS* 1.3 73.4 - - - +
507A ALA* 1.3 65.6 + - - +
509A LEU* 3.1 7.5 + - - +
510A ALA 3.0 18.4 + - - -
535A LEU* 3.7 23.1 - - + -
555A LEU* 3.8 42.0 - - + +
556A LEU* 3.8 19.1 - - + -
558A LYS* 5.5 4.5 - - + -
559A LEU* 3.8 19.7 - - + +
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Residues in contact with ALA 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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372A HIS* 5.4 1.8 - - - +
420A TRP* 3.3 31.1 - - + +
446A LEU* 3.5 7.9 - - + +
449A LEU* 3.7 16.5 - - + +
450A ARG* 5.2 3.6 - - + +
503A PHE* 2.9 35.1 + - + +
504A SER* 3.9 4.9 - - - +
506A ILE* 1.3 76.0 - - - +
508A ALA* 1.3 62.8 + - - +
510A ALA* 3.1 16.8 + - - +
511A MET 3.5 1.2 + - - -
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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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368A LEU* 3.9 17.9 - - + -
420A TRP* 3.5 16.0 - - + -
424A ILE* 4.5 7.6 - - + -
504A SER 3.3 12.4 + - - +
505A CYS 3.2 9.9 + - - +
507A ALA* 1.3 77.7 - - - +
509A LEU* 1.3 52.3 + - - +
511A MET* 3.0 4.7 + - - +
512A VAL* 2.7 38.4 + - - +
531A ILE* 3.9 21.8 - - + -
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Residues in contact with LEU 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 CYS 2.9 19.3 + - - +
506A ILE* 3.1 8.9 + - - +
508A ALA* 1.3 71.8 - - - +
510A ALA* 1.3 64.2 + - - +
511A MET 3.4 0.3 + - - -
512A VAL 3.7 14.0 - - - +
513A THR* 3.7 10.9 + - - +
528A GLN* 3.6 47.5 + - + +
531A ILE* 3.8 18.2 - - + -
532A VAL* 3.8 17.0 - - + -
535A LEU* 4.3 13.0 - - + -
556A LEU* 3.8 26.9 - - + -
559A LEU* 4.0 16.8 - - + +
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Residues in contact with ALA 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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442A ALA* 3.6 12.0 - - - +
445A GLU* 4.9 8.1 - - - +
446A LEU* 3.6 18.8 - - + -
449A LEU* 4.7 0.9 - - + -
506A ILE 3.0 7.5 + - - +
507A ALA* 3.1 12.3 + - - +
509A LEU* 1.3 77.1 - - - +
511A MET* 1.3 60.0 + - - +
513A THR* 3.8 4.8 - - - +
515A ARG* 3.7 12.5 + - - -
559A LEU* 3.6 24.5 - - + -
562A LEU* 4.2 14.6 - - + -
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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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417A ILE* 6.0 0.4 - - - -
420A TRP* 3.7 18.2 - - + -
421A ALA* 3.6 18.6 - - + -
424A ILE* 3.3 33.9 - - + -
427A PHE* 3.5 37.0 - - + -
438A LEU* 3.5 38.0 - - + +
439A PHE* 4.1 14.1 - - - -
442A ALA* 3.9 11.2 - - + +
446A LEU* 4.2 2.0 - - + -
507A ALA 3.5 0.8 + - - -
508A ALA 3.0 5.5 + - - +
510A ALA* 1.3 81.7 - - - +
512A VAL* 1.3 63.7 + - + +
513A THR* 3.0 12.5 + - - +
515A ARG* 5.0 0.5 + - - -
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Residues in contact with VAL 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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424A ILE* 4.4 8.5 - - + -
427A PHE* 4.9 6.3 - - + -
430A LEU* 6.2 0.4 - - + -
438A LEU* 4.7 5.4 - - + -
508A ALA 2.7 21.7 + - - +
509A LEU* 3.7 9.3 - - - +
511A MET* 1.3 84.0 - - + +
513A THR* 1.3 61.2 + - - +
524A VAL* 3.6 32.3 - - + +
527A LEU* 3.8 28.5 - - + -
528A GLN* 3.4 30.5 + - - +
531A ILE* 4.2 13.0 - - + -
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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
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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