Contacts of the strand formed by residues 461 - 466 (chain A) in PDB entry 2OR4
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 THR 461 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A TYR* 1.3 98.6 - - + +
462A LEU* 1.3 76.6 + - - +
485A ASP* 4.6 1.8 + - - -
493A LEU* 5.9 0.3 - - - +
496A SER* 4.3 0.3 + - - -
497A TRP* 3.4 27.0 + - - -
500A LYS* 3.7 22.1 - - + +
501A SER* 4.1 14.6 - - - -
537A TYR* 3.4 17.9 + - - -
538A THR* 2.8 37.9 + - + +
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Residues in contact with LEU 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A THR* 1.3 89.4 + - - +
463A ARG* 1.3 60.6 + - - +
464A VAL* 3.6 24.0 - - + -
478A THR* 4.0 17.7 - - + -
493A LEU* 4.1 13.5 - - + -
497A TRP* 3.3 50.1 + - + -
501A SER* 4.7 2.4 + - - -
535A ALA* 4.5 3.4 - - + -
536A ARG 3.5 22.0 - - - +
537A TYR* 4.0 24.1 - - + -
538A THR* 4.3 0.7 - - - +
575A THR* 5.2 0.2 - - + -
576A VAL* 4.7 5.8 - - + -
579A VAL* 4.4 18.8 - - + -
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Residues in contact with ARG 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A GLU* 2.6 43.8 + - - -
462A LEU* 1.3 75.5 - - - +
464A VAL* 1.3 63.1 + - - +
465A ASP* 4.1 8.6 + - - +
497A TRP* 4.8 0.7 - - - +
513A SER* 6.0 0.9 - - - +
535A ALA* 3.2 1.7 - - - -
536A ARG* 2.7 75.6 + - + +
538A THR* 3.7 21.1 + - + -
539A LYS* 5.3 1.0 - - - +
545A LYS* 3.1 64.0 + - - +
546A PHE* 4.3 8.5 - - - -
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Residues in contact with VAL 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LEU* 3.6 28.9 - - + -
463A ARG* 1.3 79.6 - - - +
465A ASP* 1.3 70.2 + - - +
466A CYS* 4.2 23.6 - - + -
474A VAL* 4.2 21.8 - - + -
497A TRP* 3.6 25.6 - - + -
511A ARG 4.3 2.1 + - - +
512A ILE* 3.4 10.8 - - + -
513A SER* 3.1 17.2 + - - -
534A ARG 3.3 11.2 - - - +
535A ALA* 3.9 11.7 - - + -
579A VAL* 5.4 1.1 - - + -
583A MET* 5.7 2.2 - - + -
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Residues in contact with ASP 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ARG* 4.1 12.2 + - - +
464A VAL* 1.3 81.4 - - - +
466A CYS* 1.4 62.5 + - - +
513A SER* 3.2 30.5 + - - +
514A LYS 4.1 8.9 - - - +
515A LEU* 3.6 19.4 - - + +
533A GLY* 3.4 1.4 - - - -
534A ARG* 2.9 43.0 + - + +
536A ARG* 3.0 29.8 + - - +
545A LYS* 5.6 0.9 - - - -
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Residues in contact with CYS 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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464A VAL* 4.2 13.2 - - + -
465A ASP* 1.4 76.3 - - - +
467A THR* 1.3 78.9 + - - +
468A PRO* 3.7 2.3 - - - +
470A MET* 3.9 20.4 - - + -
471A TYR* 3.8 16.2 + - - -
474A VAL* 4.4 6.1 - - - -
512A ILE* 3.7 21.2 - - - +
513A SER 3.2 13.4 + - - +
514A LYS* 5.0 3.5 - - - -
515A LEU* 4.0 11.5 - - - +
532A SER 3.4 13.5 - - - +
533A GLY* 3.6 8.1 - - - -
583A MET* 5.3 1.3 - - + -
692A TYR* 5.3 1.7 + - - -
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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
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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