Contacts of the strand formed by residues 325 - 327 (chain K) in PDB entry 1UW9
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 325 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158K GLU* 2.4 43.5 + - - -
169K LEU* 5.0 0.2 - - - +
199K PHE* 4.0 10.8 - + - -
239K TYR* 3.5 19.7 + + - -
264K ILE* 3.9 18.6 - - + +
291K LEU 3.3 2.8 + - - -
292K HIS* 3.1 38.3 + - - +
293K ILE* 2.9 30.9 + - - +
318K LEU* 4.4 0.2 - - - +
324K ASP* 1.3 83.6 + - + +
326K LEU* 1.3 60.3 + - - +
374K VAL* 3.6 4.5 - - - +
375K MET* 3.2 15.8 - - + +
377K VAL* 3.7 12.4 - - + +
399K CYS* 4.8 7.0 - - + -
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Residues in contact with LEU 326 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269K TYR* 3.7 29.6 - - + +
293K ILE* 3.5 18.6 - - + +
295K ARG* 4.1 9.4 - - + -
311K PHE* 3.8 19.3 - - + -
315K ALA* 3.8 26.9 - - + +
318K LEU* 4.0 15.9 - - + -
325K HIS* 1.3 75.0 - - - +
327K HIS* 1.3 78.2 + - - +
349K MET* 3.6 13.2 - - + +
374K VAL* 3.5 13.8 - - + +
375K MET 2.9 7.5 + - - -
376K PRO* 3.3 7.1 - - - +
377K VAL* 2.8 22.8 + - - -
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Residues in contact with HIS 327 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201K KCX 3.3 23.8 + - - -
292K HIS* 2.9 39.4 + + - -
293K ILE 3.4 10.7 + - - -
294K HIS* 3.6 18.2 - + - -
295K ARG* 3.4 25.3 - - + +
311K PHE* 3.4 13.0 - - - -
326K LEU* 1.3 76.1 - - - +
328K SER* 1.3 59.4 + - - +
329K GLY 3.7 0.4 - - - -
349K MET* 5.0 0.3 - - - +
377K VAL* 3.2 10.1 - - + +
379K SER* 3.8 13.1 - - - -
401K GLN* 3.7 13.7 + - - -
1478R CAP 2.8 39.5 + - - +
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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
------------------------------------------------------------
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