Contacts of the strand formed by residues 484 - 490 (chain B) in PDB entry 2WNT
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 HIS 484 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431B GLU* 5.6 3.2 + - - -
448B VAL* 3.7 19.5 - - + +
449B ILE 3.4 17.5 - - - +
450B ASP* 3.6 23.3 - - + +
451B LYS* 4.8 2.0 - - - -
480B ASP* 3.5 8.7 - - - +
481B ASP* 3.0 27.8 + - - +
483B LYS* 1.3 91.6 - - + +
485B VAL* 1.3 60.4 + - - +
486B TYR* 3.6 30.9 + - + +
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Residues in contact with VAL 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447B LYS 3.4 2.3 - - - +
448B VAL* 3.7 1.4 - - - +
449B ILE* 2.8 67.6 + - + +
451B LYS* 4.5 9.2 - - + +
456B PRO* 3.5 20.9 - - + -
460B ILE* 4.0 26.9 - - + -
478B VAL* 4.4 3.8 - - + -
479B TYR 3.3 10.3 - - - +
480B ASP* 4.4 11.7 - - + +
484B HIS* 1.3 74.3 - - - +
486B TYR* 1.3 64.8 + - - +
487B LEU* 4.2 11.2 - - + -
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Residues in contact with TYR 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B SER* 5.9 9.9 - - - -
446B VAL* 4.0 13.2 - - + -
447B LYS 3.6 3.1 - - - -
448B VAL* 3.7 37.2 - - + -
477B ASP 3.6 1.0 - - - +
478B VAL* 3.4 7.3 - - - +
479B TYR* 2.7 63.9 + - + +
481B ASP* 2.8 33.1 + - + -
484B HIS* 3.6 28.3 + - + +
485B VAL* 1.3 72.7 - - - +
487B LEU* 1.3 63.3 + - - +
488B VAL* 3.7 1.3 + - + -
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Residues in contact with LEU 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B ALA 3.5 2.1 - - - +
446B VAL* 3.2 4.0 - - - -
447B LYS* 2.8 57.2 + - + +
449B ILE* 3.9 25.1 - - + -
456B PRO* 5.3 0.2 - - + -
459B GLU* 4.0 25.1 - - + +
460B ILE* 3.6 35.2 - - + -
463B LEU* 4.6 10.8 - - + -
475B LEU* 4.3 12.1 - - + -
477B ASP 3.9 2.0 - - - -
478B VAL* 4.1 12.6 - - + -
485B VAL* 4.2 4.0 - - + -
486B TYR* 1.3 74.6 - - - +
488B VAL* 1.3 62.1 + - - +
489B THR* 3.8 7.0 + - + +
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Residues in contact with VAL 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B TYR* 3.7 42.4 - - + +
435B CYS* 4.8 2.9 - - - -
444B TYR* 4.0 21.3 - - + -
445B ALA 3.5 4.3 - - - +
446B VAL* 4.4 12.8 - - + +
475B LEU* 3.1 7.1 - - - +
476B LYS* 2.7 32.8 + - + -
477B ASP* 2.7 37.6 + - + +
479B TYR* 4.2 11.2 - - + -
486B TYR* 4.5 1.8 - - + +
487B LEU* 1.3 75.0 - - - +
489B THR* 1.3 57.2 + - - +
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Residues in contact with THR 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444B TYR* 3.4 14.5 - - - +
445B ALA* 2.9 32.9 + - - +
447B LYS* 5.9 2.2 - - + +
463B LEU* 5.3 5.6 - - + -
473B ILE* 3.2 33.4 - - + +
474B THR 3.2 15.0 - - - +
475B LEU* 3.8 17.0 - - + -
476B LYS* 4.2 3.8 - - - +
487B LEU* 4.1 13.5 - - + +
488B VAL* 1.3 81.2 - - - +
490B GLU* 1.3 69.2 + - - +
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Residues in contact with GLU 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444B TYR* 4.3 4.5 - - - -
445B ALA* 3.9 3.9 - - - +
473B ILE* 3.8 5.9 - - + +
474B THR* 2.8 48.3 + - - +
476B LYS* 4.0 20.2 + - - +
489B THR* 1.3 84.2 + - - +
491B LEU* 1.3 63.8 + - - +
492B MET* 3.4 26.5 + - + +
544B VAL* 3.9 14.0 - - + +
554B ARG* 3.0 36.9 + - - -
1710B NA 3.9 0.3 - - - -
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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