Contacts of the strand formed by residues 2361 - 2368 (chain B) in PDB entry 1WUF
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 THR2361 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2009B ILE* 3.6 18.8 - - + +
2010B HIS 3.4 4.3 - - - +
2011B ALA* 4.1 1.8 - - - -
2357B LEU* 2.8 36.2 + - - +
2358B LYS* 3.4 17.4 + - - +
2359B LYS 5.2 0.7 - - - -
2360B TYR* 1.3 79.3 - - - +
2362B LYS* 1.3 63.5 + - - +
2363B SER* 3.5 24.5 - - - +
2364B THR* 3.9 8.5 - - - +
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Residues in contact with LYS2362 (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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2010B HIS* 2.6 48.0 + - + +
2011B ALA 4.4 0.4 - - - -
2012B GLU* 2.6 37.7 + - + +
2030B ASP* 2.9 27.3 + - - -
2360B TYR 4.0 8.7 - - - +
2361B THR* 1.3 76.6 - - - +
2363B SER* 1.3 63.3 + - - +
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Residues in contact with SER2363 (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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2008B LEU 5.2 1.0 + - - -
2009B ILE* 3.8 0.5 - - - -
2010B HIS* 3.1 44.9 + - - +
2032B TYR* 5.1 3.3 + - - -
2361B THR* 3.5 7.9 - - - +
2362B LYS* 1.3 81.8 - - - +
2364B THR* 1.3 67.3 + - - +
2365B GLU* 6.1 0.5 - - - +
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Residues in contact with THR2364 (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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2007B ARG* 4.5 18.6 - - + -
2008B LEU 3.7 4.3 - - - +
2009B ILE* 4.3 8.7 - - + +
2361B THR* 3.9 12.3 - - - +
2363B SER* 1.3 79.5 + - - +
2365B GLU* 1.3 69.9 + - - +
2366B GLU* 4.8 7.9 - - + +
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Residues in contact with GLU2365 (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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2006B ALA 3.8 0.5 - - - +
2007B ARG* 3.4 1.9 - - - -
2008B LEU* 2.8 50.2 + - + +
2069B LYS* 3.4 35.3 + - - +
2363B SER* 6.1 0.7 - - - +
2364B THR* 1.3 79.2 - - - +
2366B GLU* 1.3 68.7 + - - +
2367B ILE* 4.0 20.1 + - + +
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Residues in contact with GLU2366 (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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2005B LYS* 3.1 36.6 + - + +
2006B ALA 3.3 5.2 - - - +
2007B ARG* 3.7 30.9 + - + +
2364B THR* 4.8 8.0 - - + +
2365B GLU* 1.3 77.7 - - - +
2367B ILE* 1.3 67.8 + - - +
2368B LEU* 4.2 5.5 + - + +
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Residues in contact with ILE2367 (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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2005B LYS* 3.3 3.1 - - - +
2006B ALA* 2.6 41.1 + - + +
2008B LEU* 3.6 33.7 - - + -
2069B LYS* 4.2 12.3 - - + -
2073B LEU* 3.8 19.1 - - + -
2365B GLU* 4.0 14.6 - - + +
2366B GLU* 1.3 80.6 - - - +
2368B LEU* 1.3 71.6 + - - +
2369B LEU* 3.3 19.8 + - + +
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Residues in contact with LEU2368 (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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2004B GLN* 4.2 4.5 - - + +
2005B LYS* 4.5 22.7 - - + +
2077B ALA* 5.6 0.2 - - - +
2366B GLU* 4.3 4.9 + - + -
2367B ILE* 1.3 79.7 - - - +
2369B LEU* 1.3 57.1 + - - +
2370B ASN* 3.0 26.1 + - + +
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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