Contacts of the strand formed by residues 428 - 432 (chain A) in PDB entry 4WXS
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 ASN 428 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A THR* 5.1 1.6 + - - -
371A TYR* 3.6 24.2 - - - -
373A TRP* 4.6 2.8 - - - +
377A THR* 5.5 0.6 - - - +
380A ASP* 3.1 5.6 - - - +
426A VAL* 3.4 6.2 - - - +
427A ALA* 1.3 80.0 + - + +
429A ALA* 1.3 69.9 + - - +
438A THR* 3.6 1.9 - - - -
439A VAL* 2.9 31.0 + - + +
474A SER 5.7 0.2 + - - -
475A SER 4.0 7.5 + - - -
476A MET* 3.9 12.1 - - - +
477A ILE* 3.3 41.0 - - + +
601A CA 2.5 29.9 - - - -
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Residues in contact with ALA 429 (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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371A TYR* 3.5 19.4 + - + +
380A ASP* 3.2 3.3 - - - +
391A ILE* 4.2 7.9 - - + +
401A ILE* 4.7 1.6 - - + -
428A ASN* 1.3 83.3 + - - +
430A PHE* 1.3 68.9 + - - +
436A LEU* 4.0 16.8 - - + -
437A TYR 3.2 13.9 - - - +
438A THR* 4.3 9.9 - - + +
477A ILE 3.3 1.0 - - - +
601A CA 2.4 31.0 - - - -
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Residues in contact with PHE 430 (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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248A LEU* 4.1 12.3 - - + -
382A ALA* 5.1 4.9 - - + -
391A ILE* 4.4 5.6 - - - -
429A ALA* 1.3 82.6 - - - +
431A ILE* 1.3 66.3 - - - +
432A ILE* 3.8 30.5 - - + -
436A LEU* 3.6 4.1 - - - +
437A TYR* 2.8 53.5 + - + +
439A VAL* 3.6 28.7 - - + -
449A VAL* 4.4 4.0 - - + -
477A ILE* 4.0 26.0 - - + +
478A ASP* 4.3 2.0 - - - +
479A TYR* 3.9 20.2 - - + +
486A LEU* 3.9 29.6 - - + -
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Residues in contact with ILE 431 (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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382A ALA* 4.1 15.6 - - + +
383A VAL 4.1 1.9 - - - +
384A ASP* 3.4 32.2 - - + +
389A TRP* 3.4 48.9 - - + -
391A ILE* 4.3 11.7 - - + -
403A LEU* 4.3 11.2 - - + -
430A PHE* 1.3 80.4 - - - +
432A ILE* 1.3 66.3 + - - +
434A GLY* 3.9 4.9 - - - +
435A THR 3.3 21.3 - - - +
436A LEU* 4.2 16.8 - - + -
479A TYR* 3.1 22.7 - - - +
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Residues in contact with ILE 432 (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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246A GLY 4.2 4.9 - - - +
248A LEU* 4.3 15.0 - - + -
430A PHE* 3.8 27.6 - - + -
431A ILE* 1.3 79.2 - - - +
433A CYS* 1.3 82.5 + - - +
434A GLY 3.2 1.3 - - - -
435A THR* 2.9 26.7 + - - -
437A TYR* 3.7 17.5 + - + -
479A TYR* 3.6 46.0 - - + +
486A LEU* 4.8 0.9 - - + -
499A ILE* 4.2 11.7 - - + -
501A LEU* 3.9 18.2 - - + -
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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