Contacts of the strand formed by residues 258 - 261 (chain F) in PDB entry 4BQ7
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 LEU 258 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220F PHE* 3.7 53.8 - - + -
226F CYS 5.1 1.6 + - - -
227F THR* 3.6 26.5 - - + +
230F LYS* 3.8 11.0 - - + -
243F PHE* 3.8 24.9 - - + -
249F SER* 3.1 7.6 - - - -
250F GLY* 2.9 30.7 + - - +
255F ALA 5.1 0.4 + - - -
256F LYS* 4.2 3.3 - - - +
257F SER* 1.3 78.5 - - - +
259F ARG* 1.3 64.3 + - - +
271F MET* 5.1 0.4 - - + -
272F HIS 3.4 13.0 - - - +
273F ALA* 3.8 9.6 - - + -
275F TYR* 4.0 9.2 - - + -
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Residues in contact with ARG 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243F PHE* 4.8 1.6 - - - -
248F THR 3.4 10.5 - - - +
249F SER* 4.3 5.6 - - - +
256F LYS* 4.1 24.9 - - + +
258F LEU* 1.3 77.9 - - - +
260F ILE* 1.4 63.5 - - - +
261F VAL* 3.5 31.1 - - + +
270F GLU 3.8 0.3 - - - +
271F MET* 3.4 4.5 - - - +
272F HIS* 2.9 62.8 + - + +
274F ARG* 3.2 32.7 - - + +
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Residues in contact with ILE 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232F TYR* 4.9 3.8 - - + -
241F ALA* 3.9 23.0 - - - +
242F ALA* 3.4 31.0 - - - +
243F PHE* 3.4 49.4 - - + +
248F THR* 3.0 26.3 + - - +
259F ARG* 1.4 73.9 - - - +
261F VAL* 1.3 71.2 + - - +
269F VAL* 4.0 22.4 - - + -
270F GLU 3.2 10.8 - - - +
271F MET* 3.9 10.3 - - + -
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Residues in contact with VAL 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F ALA* 5.2 1.1 - - - -
259F ARG* 3.5 27.6 - - + +
260F ILE* 1.3 80.8 - - - +
262F GLU* 1.3 63.4 + - - +
269F VAL* 3.4 3.3 - - - +
270F GLU* 2.8 59.7 + - + +
272F HIS* 3.7 20.4 - - + +
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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