Contacts of the strand formed by residues 435 - 440 (chain A) in PDB entry 2WXF
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 GLY 435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A THR* 1.3 67.2 + - - -
436A GLU* 1.3 65.1 + - - +
437A ARG* 3.5 7.5 + - - +
474A TYR* 3.5 16.1 - - - -
475A LEU* 2.7 51.6 + - - +
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Residues in contact with GLU 436 (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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328A ILE* 3.6 21.8 - - + +
435A GLY* 1.3 74.4 + - - +
437A ARG* 1.3 84.0 + - - +
438A CYS* 6.0 0.5 - - - +
472A VAL* 4.5 14.0 - - + +
473A ILE 3.3 13.5 - - - +
474A TYR* 3.5 20.6 - - + -
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Residues in contact with ARG 437 (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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423A LEU* 4.6 14.4 - - + -
427A ASP* 5.9 2.4 - - - +
433A LYS* 4.0 37.5 - - - +
434A THR 2.7 37.9 + - - +
435A GLY 3.5 7.8 + - - +
436A GLU* 1.3 89.6 + - - +
438A CYS* 1.3 64.4 + - - +
439A LEU* 4.0 10.3 - - + -
471A LEU 3.8 0.5 - - - +
472A VAL* 3.2 4.7 - - - +
473A ILE* 2.8 49.8 + - + +
475A LEU* 5.8 3.6 - - + -
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Residues in contact with CYS 438 (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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331A ARG* 4.5 7.4 - - - -
436A GLU* 6.0 0.4 - - - +
437A ARG* 1.3 75.7 - - - +
439A LEU* 1.3 67.6 + - - +
440A TYR* 3.6 47.3 + - + +
470A ALA* 4.1 13.5 - - - -
471A LEU 3.6 2.2 - - - -
472A VAL* 3.8 21.5 - - + -
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Residues in contact with LEU 439 (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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392A PHE* 3.8 34.5 - - + -
421A ALA* 4.2 18.2 - - + +
422A ASN 5.0 4.7 - - - +
423A LEU* 3.9 29.4 - - + -
437A ARG* 4.7 7.9 - - + -
438A CYS* 1.3 77.5 - - - +
440A TYR* 1.3 64.6 + - - +
441A MET* 3.3 5.1 + - - +
470A ALA* 3.3 3.7 - - - -
471A LEU* 2.6 48.9 + - + +
473A ILE* 3.8 24.9 - - + -
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Residues in contact with TYR 440 (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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331A ARG* 5.9 1.1 - - - -
421A ALA* 4.7 3.7 - - - +
438A CYS* 3.6 37.5 + - + -
439A LEU* 1.3 69.0 - - - +
441A MET* 1.3 61.6 + - - +
442A TRP* 4.6 2.3 - - - -
461A GLY* 3.6 11.5 - - - -
462A ASN* 2.9 45.4 + - + +
465A THR* 3.7 48.9 - - + -
468A ALA* 4.4 8.7 - - + -
469A ALA 3.8 2.5 - - - -
470A ALA* 4.0 15.7 - - + -
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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