Contacts of the strand formed by residues 211 - 213 (chain C) in PDB entry 2X86
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 PHE 211 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C ASN* 3.4 24.2 - - + -
171C TYR* 3.7 19.6 + + + -
183C SER* 6.5 0.4 - - - -
184C VAL* 5.5 6.5 - - + -
209C ARG* 3.2 28.6 + - + -
210C ASP* 1.3 70.2 + - - +
212C VAL* 1.3 59.2 + - - +
237C THR* 3.1 18.9 + - - +
239C ARG 4.5 1.8 + - - +
241C GLU* 3.2 25.8 - - + +
242C SER 4.1 4.9 - - - -
243C PHE* 3.8 35.7 - + - -
246C VAL* 3.7 30.5 - - + -
293C LYS 4.6 2.1 - - - +
295C VAL* 3.6 28.3 + - + +
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Residues in contact with VAL 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C PHE 4.6 0.2 - - - +
169C ASN 2.9 20.5 + - - +
170C VAL* 3.4 21.1 - - + -
171C TYR* 3.2 27.3 + - - -
210C ASP 4.4 2.7 - - - +
211C PHE* 1.3 73.8 - - - +
213C TYR* 1.3 72.4 + - - +
216C ASP* 4.4 1.8 - - + +
217C VAL* 4.2 11.4 - - + -
235C LEU* 3.9 19.7 - - + +
236C GLY* 3.9 20.0 - - - -
237C THR* 4.0 6.3 - - + -
292C PHE* 4.1 26.2 - - + -
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Residues in contact with TYR 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C TYR* 3.6 36.7 + + - +
172C GLY* 4.0 16.8 - - - -
173C PRO* 3.4 26.0 - - + +
212C VAL* 1.3 76.0 - - - +
214C VAL* 1.3 65.7 + - + +
215C GLY* 3.3 32.8 - - - -
216C ASP* 2.9 29.4 + - - +
217C VAL* 3.2 10.2 + - - +
293C LYS* 4.2 28.5 + - + -
298C GLY* 3.7 22.7 - - - -
301C GLU* 3.3 35.0 + - - +
302C TYR* 4.1 6.6 + - + -
305C TRP* 5.7 0.5 - - - +
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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