Contacts of the helix formed by residues 499 - 503 (chain A) in PDB entry 2OK5
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 ALA 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498A THR* 1.3 80.9 + - - +
500A ALA* 1.3 63.3 + - - +
501A HIS* 3.5 34.0 + - + +
502A CYS* 3.8 8.7 + - - -
503A PHE* 3.6 20.6 - - - -
551A ASP* 3.4 14.8 - - - +
553A ALA 4.1 2.5 - - - -
675A GLY* 3.7 17.9 - - - -
691A VAL* 4.0 2.2 - - + -
692A ILE 4.0 4.5 - - - +
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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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499A ALA* 1.3 68.1 - - - +
501A HIS* 1.3 54.5 + - - +
502A CYS 3.1 5.4 - - - -
503A PHE* 3.0 29.5 + - - +
530A PHE* 3.8 16.9 - - + -
534A TYR* 3.6 35.5 + - + -
551A ASP* 2.8 17.6 + - - +
552A VAL 3.8 18.4 - - - +
553A ALA* 3.9 8.3 - - + -
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Residues in contact with HIS 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A ARG* 5.4 0.7 + - - -
484A GLU* 4.1 6.5 - - - +
499A ALA* 3.5 17.3 - - + +
500A ALA* 1.3 71.1 - - - +
502A CYS* 1.3 67.0 + - - +
503A PHE 3.2 4.3 + - - +
504A THR* 5.8 1.2 - - - +
534A TYR* 3.4 17.3 - - - +
536A ILE* 4.7 3.1 - - + -
548A TYR* 4.1 20.1 - + + -
551A ASP* 2.7 35.2 + - - +
671A ARG* 4.2 13.5 + - - -
674A SER* 2.7 27.2 + - - -
675A GLY 4.6 0.2 - - - -
692A ILE 4.1 0.2 - - - -
693A SER* 3.0 28.8 + - - -
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Residues in contact with CYS 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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474A ILE* 5.4 0.9 - - + -
476A VAL* 3.8 1.0 - - - +
478A ARG* 2.9 20.4 + - - -
484A GLU* 3.5 16.5 - - + +
486A CYS* 2.1 53.8 - - + -
498A THR* 4.2 5.6 - - - -
499A ALA* 3.8 28.0 - - - +
500A ALA 3.1 0.8 - - - -
501A HIS* 1.3 82.7 - - - +
503A PHE* 1.3 76.7 + - + +
674A SER 4.5 1.8 - - - -
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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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474A ILE* 3.9 9.9 - - + -
476A VAL* 3.8 15.5 - - + -
478A ARG* 3.8 0.9 - - - +
498A THR* 3.6 13.9 - - + -
499A ALA 3.6 22.9 - - - -
500A ALA* 3.0 18.9 + - - +
501A HIS* 3.2 3.6 - - - +
502A CYS* 1.3 90.2 - - + +
504A THR* 1.3 69.1 + - - +
507A ASP* 3.5 7.9 - - + +
512A ILE* 3.7 42.8 - - + -
528A VAL* 4.0 22.2 - - + -
530A PHE* 3.8 22.8 - + + -
534A TYR* 5.0 4.3 + - - -
553A ALA* 4.6 1.1 - - + -
555A ILE* 3.7 26.5 - - + -
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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