Contacts of the strand formed by residues 467 - 474 (chain A) in PDB entry 2WIN
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 TYR 467 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A HIS* 2.8 39.9 + + - +
26A ASP* 4.9 5.3 + - - -
59A ASN* 5.7 3.6 - - - +
465A ILE* 3.8 5.0 - - - +
466A ARG* 1.3 95.2 + - + +
468A TYR* 1.3 66.8 + - - +
469A THR* 4.2 6.7 + - - -
483A ARG* 3.2 54.9 + - + +
484A GLN 3.3 14.1 - - - +
485A VAL* 4.7 3.1 - - + -
486A ARG* 4.4 0.4 - - - +
513A TYR* 4.0 17.2 - - - +
514A THR* 4.9 9.2 + - + +
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Residues in contact with TYR 468 (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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434A LEU* 3.8 21.1 - - + -
453A PHE* 3.9 38.4 + + + -
455A LEU* 3.5 26.0 + - - +
465A ILE* 4.4 2.9 - - + -
467A TYR* 1.3 74.6 - - - +
469A THR* 1.3 63.7 + - - +
470A TYR* 3.8 1.7 + - - -
483A ARG* 3.3 10.4 - - - -
484A GLN* 3.0 45.9 + - + +
486A ARG* 3.3 38.6 + - + -
490A GLN 5.0 0.2 + - - -
491A ASP 5.3 0.5 + - - -
493A VAL* 4.0 16.3 - - + +
511A ALA* 5.0 1.8 - - + -
512A TYR 3.8 4.3 - - - +
513A TYR* 3.5 38.6 - + + -
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Residues in contact with THR 469 (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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7A ILE* 5.1 0.2 - - + -
21A VAL* 5.5 2.7 - - + -
23A GLU* 2.9 34.2 + - - +
25A HIS* 4.7 1.6 - - - -
61A MET* 4.6 4.7 - - - -
467A TYR* 4.2 6.8 - - - -
468A TYR* 1.3 69.5 - - - +
470A TYR* 1.3 61.3 + - - +
471A LEU* 3.7 12.1 - - + +
481A ALA* 6.0 1.3 - - + -
482A GLY 3.8 9.0 - - - +
483A ARG* 3.0 17.5 + - - +
510A VAL 3.7 0.9 - - - +
511A ALA* 3.6 1.4 - - - -
512A TYR* 3.0 63.3 + - + -
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Residues in contact with TYR 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A PHE* 4.6 6.5 - + + -
468A TYR 4.3 2.5 - - - -
469A THR* 1.3 72.9 - - - +
471A LEU* 1.3 67.1 + - - +
472A ILE* 4.7 10.3 - - + -
480A LYS* 4.2 22.0 + - + -
481A ALA* 3.3 10.7 - - - +
482A GLY* 3.2 55.9 + - - +
483A ARG* 3.4 19.3 + - - -
484A GLN* 4.2 5.2 - - + -
495A LEU* 3.7 37.5 - - + +
497A LEU* 5.2 7.8 - - + +
509A LEU* 3.8 21.3 - - + -
510A VAL 3.0 11.0 - - - +
511A ALA* 4.2 10.3 - - + +
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Residues in contact with LEU 471 (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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7A ILE* 3.6 48.5 - - + -
21A VAL* 3.9 22.2 - - + -
469A THR* 3.7 21.8 - - + +
470A TYR* 1.3 82.1 - - - +
472A ILE* 1.3 63.3 + - - +
473A MET* 4.1 1.0 + - - +
478A LEU* 4.0 20.2 - - + -
480A LYS 3.5 6.7 - - - +
481A ALA* 4.0 8.5 - - + -
508A ARG 3.8 0.3 - - - +
509A LEU* 3.3 8.6 - - - +
510A VAL* 2.8 48.6 + - + +
512A TYR* 4.4 2.7 - - + -
622A LEU* 4.4 3.6 - - + -
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Residues in contact with ILE 472 (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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470A TYR* 4.7 8.5 - - + -
471A LEU* 1.3 74.0 - - - +
473A MET* 1.3 70.8 + - - +
478A LEU* 3.4 10.4 - - - +
479A LEU* 2.9 52.6 + - + -
480A LYS* 2.7 37.9 + - + +
497A LEU* 3.9 27.6 - - + -
503A PHE* 4.2 11.4 - - + -
507A PHE* 4.4 7.9 - - + -
508A ARG 3.5 9.6 - - - +
509A LEU* 3.5 26.9 - - + -
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Residues in contact with MET 473 (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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9A PRO* 5.5 1.8 - - + -
471A LEU 4.1 1.8 + - - +
472A ILE* 1.3 73.8 - - - +
474A ASN* 1.3 63.0 + - - +
476A GLY* 3.8 33.0 - - - +
477A ARG 3.7 4.9 - - - +
478A LEU* 3.5 28.5 - - - -
507A PHE* 3.1 11.4 - - - +
508A ARG* 3.0 51.5 + - + +
510A VAL* 5.4 2.2 - - + -
602A ASP* 5.5 1.8 - - - +
603A ILE* 3.9 21.8 - - + -
620A ALA* 3.7 18.6 - - + +
621A GLY 4.0 3.6 - - - +
622A LEU* 3.8 22.9 - - + -
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Residues in contact with ASN 474 (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 MET* 1.3 76.4 - - - +
475A LYS* 1.3 89.6 + - - +
476A GLY 2.9 10.7 + - - +
477A ARG* 2.9 56.5 + - - +
479A LEU* 4.1 20.2 - - + +
502A ASP 2.6 28.6 + - - +
503A PHE* 3.7 10.7 + - - -
504A ILE 3.5 7.7 + - - -
505A PRO* 4.5 0.2 - - - +
506A SER 3.8 9.1 + - - -
507A PHE* 4.7 2.7 - - + -
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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