Contacts of the strand formed by residues 498 - 502 (chain A) in PDB entry 1OH7
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 498 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476A GLN* 3.6 35.7 - - + +
477A ILE 3.4 10.1 - - - +
478A SER* 4.8 0.7 - - - -
479A ARG* 3.6 10.3 + - - +
495A LEU* 3.1 43.4 + - + +
497A ASN* 1.3 80.2 - - - +
499A GLU* 1.3 64.8 + - - +
500A ARG 4.3 0.2 - - - -
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Residues in contact with GLU 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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475A ILE 3.5 0.2 - - - +
477A ILE 3.0 25.3 + - - -
479A ARG* 3.7 14.0 + - - +
482A SER* 3.9 20.7 + - - +
491A ARG* 3.3 22.8 - - + +
493A GLN 3.9 2.1 - - - +
494A THR* 2.5 44.2 + - - +
498A ALA* 1.3 75.0 - - - +
500A ARG* 1.3 62.5 + - - +
501A TYR* 3.1 42.1 - - + +
491B ARG* 4.0 1.7 + - - +
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Residues in contact with ARG 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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468A ASN* 4.4 0.8 - - - +
474A TYR* 3.0 57.4 + - + -
475A ILE 3.2 3.6 - - - -
476A GLN* 2.9 33.2 + - + -
491A ARG* 4.0 1.4 - - - -
492A ARG* 3.1 22.7 + - - -
493A GLN* 2.9 47.1 + - + +
495A LEU* 3.5 27.3 - - + +
499A GLU* 1.3 78.7 - - - +
501A TYR* 1.3 64.8 + - - +
28F G 3.1 41.6 + - - -
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Residues in contact with TYR 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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474A TYR* 3.2 10.9 - - - -
475A ILE* 2.8 44.3 + - + +
477A ILE* 4.4 18.4 - - + -
482A SER* 3.7 18.5 + - - -
485A ALA* 4.4 8.1 - - + -
486A PRO 5.7 0.4 - - - -
489A TYR* 3.6 46.0 - + + -
490A MET 3.1 25.6 - - - +
491A ARG* 3.7 16.8 - - + +
492A ARG* 4.2 3.6 - - - -
499A GLU* 3.1 43.7 - - + +
500A ARG* 1.3 75.0 - - - +
502A ILE* 1.3 62.4 + - - +
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Residues in contact with ILE 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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473A TYR 3.7 12.6 - - - +
490A MET* 2.8 57.9 + - + +
491A ARG 5.1 1.1 - - - +
492A ARG* 3.5 50.9 - - + +
501A TYR* 1.3 76.1 - - - +
503A ILE* 1.3 67.7 + - - +
506A LEU* 3.8 17.5 - - + -
507A LYS* 3.8 34.8 - - + +
510A GLU* 4.8 0.9 - - - +
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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