Contacts of the strand formed by residues 476 - 478 (chain A) in PDB entry 1WXR
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 ILE 476 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447A VAL* 4.2 25.4 - - + -
450A ASN 4.9 0.7 - - - +
452A LEU* 3.5 8.3 - - + +
454A PHE* 3.8 24.7 - - + -
466A LEU* 4.0 24.7 - - + -
475A THR* 1.3 76.4 - - - +
477A THR* 1.3 61.5 + - - +
478A LEU* 3.7 26.5 + - + -
566A LEU* 5.6 1.6 - - + -
570A LEU* 3.8 32.3 - - + -
571A ASN 2.9 12.7 + - - +
572A VAL* 3.4 12.1 - - + +
573A ASP 2.9 26.2 + - - -
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Residues in contact with THR 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LEU 2.7 10.7 + - - -
453A THR* 3.2 28.5 - - + +
454A PHE 2.8 29.6 + - - +
475A THR* 3.6 13.8 + - - +
476A ILE* 1.3 71.6 - - - +
478A LEU* 1.3 71.1 + - - +
479A ASP* 4.8 4.3 - - + -
573A ASP* 3.8 15.6 + - + +
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Residues in contact with LEU 478 (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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454A PHE* 3.5 8.5 - - + +
457A LEU* 3.7 30.5 - - + -
466A LEU* 5.8 0.2 - - + -
476A ILE* 3.7 25.4 - - + -
477A THR* 1.3 77.3 - - - +
479A ASP* 1.3 59.8 - - - +
480A TYR* 3.9 11.7 - - + -
560A TYR* 5.9 1.6 - - + -
562A PHE* 6.4 0.2 - - + -
566A LEU* 6.3 1.8 - - + -
572A VAL* 4.6 14.1 - - + -
573A ASP 2.8 20.1 + - - +
574A ASN* 3.8 25.2 - - + +
575A ARG 4.5 5.7 + - - +
584A LEU* 3.9 33.9 - - + -
586A MET* 6.3 0.4 - - - -
596A PHE* 5.4 0.7 - - + -
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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