Contacts of the helix formed by residues 452 - 466 (chain A) in PDB entry 4AY6
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 PHE 452 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A ALA* 4.1 11.2 - - + -
420A ASP* 3.6 34.3 - - + -
423A SER* 3.7 31.9 - - - -
445A ALA* 4.8 5.8 - - + -
446A LEU* 3.6 10.5 - - + +
449A LYS* 3.6 31.6 + - - +
450A PRO 3.7 3.0 + - - -
451A ASP* 1.3 76.2 + - - +
453A PRO* 1.3 75.2 - - + +
454A ASP* 3.8 29.2 - - + -
455A ALA* 3.7 11.7 - - + -
456A TYR* 2.9 23.7 + - - +
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Residues in contact with PRO 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ASP* 3.4 16.6 - - - +
452A PHE* 1.3 87.5 - - + +
454A ASP* 1.3 69.2 + - - +
456A TYR* 2.8 19.2 + - + +
457A CYS* 2.8 14.8 + - - -
482A ILE* 3.9 30.7 - - + -
486A GLN* 3.9 14.8 - - + +
494A SER* 3.4 13.9 - - - +
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Residues in contact with ASP 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A SER* 5.0 3.6 - - - +
452A PHE* 3.5 22.4 - - + -
453A PRO* 1.3 77.3 - - - +
455A ALA* 1.3 56.9 + - - +
457A CYS* 3.6 1.4 + - - +
458A ASN* 2.9 44.5 + - - +
486A GLN* 5.2 1.1 + - - -
492A LEU 5.3 1.7 - - - +
494A SER* 2.5 34.3 + - - +
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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
----------------------------------------------------------
423A SER* 4.0 12.8 + - - +
442A TYR* 3.9 23.4 - - + +
445A ALA* 4.6 4.7 - - + -
446A LEU* 3.8 18.4 - - + -
452A PHE* 3.6 29.0 + - + -
453A PRO 3.1 0.6 - - - -
454A ASP* 1.3 76.5 - - - +
456A TYR* 1.3 65.7 + - - +
459A LEU* 3.0 26.4 + - - +
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Residues in contact with TYR 456 (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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446A LEU* 3.9 24.6 - - + +
452A PHE 2.9 18.2 + - - +
453A PRO* 2.8 13.7 + - + +
455A ALA* 1.3 73.2 - - - +
457A CYS* 1.3 58.8 + - - +
459A LEU* 3.5 5.3 - - + +
460A ALA* 3.0 25.5 + - + +
474A GLU* 4.7 3.8 + - - -
475A ARG* 3.4 42.3 - - + +
478A LYS* 3.6 42.5 - - + +
479A LEU* 3.9 19.3 - - + -
482A ILE* 3.8 17.3 - - + -
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Residues in contact with CYS 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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453A PRO 2.8 15.3 + - - +
454A ASP 4.0 1.1 - - - +
456A TYR* 1.3 72.0 - - - +
458A ASN* 1.3 65.5 + - - +
460A ALA* 3.2 4.3 + - - +
461A HIS* 3.1 20.3 + - - +
479A LEU* 3.6 28.0 - - + +
482A ILE* 4.5 17.5 - - - -
483A VAL* 5.5 1.1 - - - -
494A SER* 3.3 44.0 - - - +
495A VAL* 4.1 14.8 - - + +
503A TYR* 4.5 3.3 + - - -
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Residues in contact with ASN 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A SER* 5.1 1.4 + - - -
427A SER* 4.3 5.9 + - - -
430A LYS* 3.7 12.6 - - - +
442A TYR* 3.2 35.1 + - + +
454A ASP* 2.9 33.5 + - - +
457A CYS* 1.3 73.0 - - - +
459A LEU* 1.3 67.0 + - - +
461A HIS* 3.1 16.8 + - - +
462A CYS* 3.1 19.1 + - - -
494A SER 4.7 9.1 + - - +
499A HIS* 5.9 2.4 - - - -
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Residues in contact with LEU 459 (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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439A ILE* 3.9 31.6 - - + +
442A TYR* 4.1 25.2 - - + -
443A ARG* 4.5 20.0 - - + +
446A LEU* 3.6 28.5 - - + -
455A ALA 3.0 17.9 + - - +
456A TYR* 3.5 6.1 - - + +
458A ASN* 1.3 77.1 - - - +
460A ALA* 1.3 64.5 + - - +
462A CYS* 2.7 16.9 + - - +
463A LEU* 2.9 39.4 + - + +
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Residues in contact with ALA 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A TYR* 3.0 15.7 + - + +
457A CYS* 3.2 13.7 + - - +
459A LEU* 1.3 76.0 - - - +
461A HIS* 1.3 57.1 + - - +
463A LEU* 3.6 6.8 + - - +
464A GLN* 3.0 25.8 + - - +
475A ARG* 3.9 32.2 + - + +
476A MET* 5.5 0.2 - - + -
479A LEU* 4.3 23.3 - - + -
503A TYR* 4.2 6.1 + - + +
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Residues in contact with HIS 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LYS* 2.7 31.0 + - - +
457A CYS 3.1 8.9 + - - +
458A ASN* 3.1 11.3 + - - +
459A LEU 3.0 0.8 - - - -
460A ALA* 1.3 75.6 - - - +
462A CYS* 1.3 62.2 + - - +
464A GLN* 3.1 13.5 - - + +
465A ILE* 3.0 40.0 - - + +
499A HIS* 3.3 50.6 - + + +
502A LEU* 4.2 16.5 - - + +
503A TYR* 3.7 17.2 + - - +
841A TYR* 5.2 6.1 - - - -
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Residues in contact with CYS 462 (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 LYS* 3.7 25.4 - - - -
435A ILE* 3.8 12.1 - - + -
438A ALA* 4.6 4.5 - - - -
439A ILE* 3.6 24.5 - - + -
442A TYR* 4.0 20.6 - - - -
458A ASN 3.1 19.7 + - - -
459A LEU* 2.7 13.4 + - - +
461A HIS* 1.3 67.1 - - - +
463A LEU* 1.3 58.3 + - - +
464A GLN 2.9 1.1 - - - -
465A ILE* 2.6 35.2 + - - +
466A VAL* 3.0 15.6 + - - +
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Residues in contact with LEU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ILE* 3.9 16.8 - - + -
443A ARG* 4.0 18.4 - - - +
459A LEU* 2.9 42.6 + - + +
460A ALA* 3.8 5.4 - - - +
462A CYS* 1.3 75.9 - - - +
464A GLN* 1.3 61.1 + - - +
466A VAL* 3.5 5.1 - - - +
467A CYS* 3.1 2.9 + - - -
468A ASP* 2.8 71.2 + - + +
470A THR 5.9 0.2 - - - +
475A ARG* 3.7 25.1 - - + +
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Residues in contact with GLN 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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460A ALA 3.0 13.0 + - - +
461A HIS* 3.1 19.5 - - + +
462A CYS 2.9 0.4 + - - -
463A LEU* 1.3 78.7 - - - +
465A ILE* 1.3 56.5 + - - +
467A CYS* 3.5 12.2 + - - +
468A ASP 5.0 0.2 - - - -
469A TRP* 4.6 7.0 + - - +
472A TYR* 4.0 21.6 + - - -
475A ARG* 4.2 7.5 + - - +
476A MET* 4.6 0.7 - - - +
502A LEU* 4.2 26.2 - - + +
503A TYR* 4.4 15.1 - - + +
841A TYR* 3.0 43.2 + - + +
843A ILE 3.5 14.2 + - - +
844A ASP* 4.8 4.2 - - - +
916A LEU* 4.4 11.1 - - - +
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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
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430A LYS* 3.8 8.3 - - - +
435A ILE* 4.5 20.0 - - + -
461A HIS* 3.0 48.5 - - + +
462A CYS* 2.6 22.1 + - - +
464A GLN* 1.3 73.0 - - - +
466A VAL* 1.3 60.7 + - + +
467A CYS* 3.3 4.4 + - - -
839A GLN* 5.8 2.7 - - - +
840A LEU* 4.5 0.5 - - - +
841A TYR* 3.8 28.1 + - + +
869A PRO* 3.4 34.4 - - + +
872A GLY* 5.1 0.2 - - - -
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Residues in contact with VAL 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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435A ILE* 3.9 25.6 - - + -
436A PRO* 5.9 1.8 - - + -
439A ILE* 4.4 10.1 - - + -
462A CYS 3.0 13.1 + - - +
463A LEU* 3.5 14.8 - - - +
465A ILE* 1.3 80.1 - - + +
467A CYS* 1.3 66.3 + - - +
468A ASP* 3.7 14.1 - - + +
869A PRO* 4.8 2.7 - - + -
871A VAL* 3.4 31.6 - - + +
872A GLY* 3.5 16.0 - - - -
875A ASN* 2.8 27.7 + - - +
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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
------------------------------------------------------------
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