Contacts of the helix formed by residues 497 - 508 (chain A) in PDB entry 4OE4
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 497 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A HIS* 3.9 16.2 - - + +
329A SER* 3.0 18.8 + - - +
495A ALA* 3.7 0.9 - - - +
496A LYS* 1.3 76.0 - - - +
498A ARG* 1.3 57.1 + - - +
499A LYS* 2.8 25.1 + - - +
500A ALA* 3.1 13.2 + - + +
501A ILE* 3.0 27.6 + - - +
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Residues in contact with ARG 498 (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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496A LYS* 3.2 12.0 + - - +
497A ASP* 1.3 70.3 + - - +
499A LYS* 1.3 60.6 + - - +
501A ILE* 3.5 41.0 - - - +
502A GLU* 2.8 31.2 + - - +
517A ILE* 4.7 2.0 - - - +
518A ASN* 5.1 1.6 - - - +
193B TRP* 6.1 0.6 - - - -
560B GLU* 2.4 45.3 + - - -
562B PHE* 5.2 0.8 - - - -
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Residues in contact with LYS 499 (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 ASP* 2.8 10.8 + - - +
498A ARG* 1.3 76.9 - - - +
500A ALA* 1.3 59.6 + - - +
502A GLU* 3.3 11.0 + - - +
503A TYR* 2.9 30.6 + - - +
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Residues in contact with ALA 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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327A HIS* 3.4 44.4 - - + +
474A PHE* 3.7 15.8 - - + -
475A ASN* 5.8 0.4 - - - -
493A ILE* 4.4 2.2 - - - -
495A ALA* 5.1 1.3 - - + -
497A ASP* 3.1 16.1 + - - +
499A LYS* 1.3 74.0 - - - +
501A ILE* 1.3 64.8 + - - +
503A TYR* 3.4 4.1 + - - +
504A ALA* 2.9 26.7 + - - +
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Residues in contact with ILE 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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493A ILE* 4.2 12.8 - - + -
495A ALA* 3.7 34.5 - - + +
496A LYS 4.2 3.6 - - - +
497A ASP 3.0 18.6 + - - +
498A ARG* 3.5 48.9 - - - +
499A LYS 3.3 0.2 - - - -
500A ALA* 1.3 77.4 - - - +
502A GLU* 1.3 58.2 + - - +
504A ALA* 3.8 1.0 - - - +
505A ASP* 2.8 30.6 + - + +
515A PHE* 4.9 1.2 - - - -
517A ILE* 3.7 43.1 - - + -
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Residues in contact with GLU 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 ARG 2.8 18.8 + - - +
499A LYS* 3.7 8.3 - - - +
501A ILE* 1.3 79.2 - - - +
503A TYR* 1.3 61.5 + - - +
505A ASP* 3.3 8.2 + - + +
506A GLU* 3.0 25.8 + - + +
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Residues in contact with TYR 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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474A PHE* 4.7 1.3 - + - -
475A ASN* 3.6 56.9 + - + +
478A CYS* 4.1 17.9 - - + -
479A ASP* 3.4 20.4 + - - -
499A LYS 2.9 18.7 + - - +
500A ALA* 3.7 6.3 - - - +
502A GLU* 1.3 77.1 - - - +
504A ALA* 1.3 60.1 + - - +
506A GLU* 3.8 3.6 - - - +
507A LYS* 2.8 41.7 + - + +
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Residues in contact with ALA 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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325A LEU* 4.5 0.4 - - + -
474A PHE* 4.2 0.4 - - + -
478A CYS* 4.0 25.6 - - - -
493A ILE* 3.6 24.2 - - + -
500A ALA 2.9 16.8 + - - +
501A ILE 3.8 1.3 - - - +
503A TYR* 1.3 74.1 - - - +
505A ASP* 1.3 67.7 + - - +
507A LYS* 4.5 0.7 - - - +
508A LEU* 2.9 42.9 + - + +
515A PHE* 4.2 4.9 - - + -
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Residues in contact with ASP 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 ILE* 2.8 24.4 + - + +
502A GLU* 3.4 10.0 - - + +
504A ALA* 1.3 74.0 - - - +
506A GLU* 1.3 59.1 + - - +
509A LYS* 3.5 4.0 + - - -
515A PHE* 3.5 17.5 - - + -
517A ILE* 4.5 6.0 - - - +
195B LYS* 2.7 31.8 + - - -
556B ARG* 2.6 66.0 + - - +
558B THR* 3.4 11.3 + - - +
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Residues in contact with GLU 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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502A GLU* 3.0 18.1 + - + +
503A TYR* 4.0 3.4 - - - +
505A ASP* 1.3 74.1 - - - +
507A LYS* 1.3 64.1 + - - +
508A LEU 3.2 1.6 - - - -
509A LYS* 3.2 29.0 + - + +
117B TYR* 5.6 0.9 + - - -
556B ARG* 5.3 0.4 - - - +
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Residues in contact with LYS 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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478A CYS* 4.2 21.1 - - + +
479A ASP* 3.2 28.3 - - - +
482A ASP* 3.4 33.1 - - + +
503A TYR* 2.8 41.9 + - + +
504A ALA 4.3 1.3 - - - +
506A GLU* 1.3 73.4 - - - +
508A LEU* 1.3 59.6 + - - +
509A LYS* 3.3 2.1 + - - +
510A PHE* 4.8 0.9 + - - -
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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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323A PHE* 3.9 17.5 - - + -
325A LEU* 4.2 14.1 - - + -
478A CYS* 3.3 31.6 - - + +
481A ILE* 3.8 24.0 - - + -
482A ASP 4.1 0.9 - - - +
504A ALA* 2.9 34.6 + - + +
505A ASP 3.9 2.9 - - - +
507A LYS* 1.3 77.2 - - - +
509A LYS* 1.3 64.2 + - - +
510A PHE 3.2 3.4 - - - -
511A SER* 2.9 28.2 + - - +
512A ALA* 3.8 6.6 + - - +
515A PHE* 3.8 27.2 - - + -
556B ARG* 3.9 5.0 + - - -
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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