Contacts of the strand formed by residues 211 - 213 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G ASN* 3.4 23.6 - - + -
171G TYR* 3.7 20.2 + + + -
183G SER* 6.5 0.9 - - - -
184G VAL* 5.6 6.7 - - + -
209G ARG* 3.2 29.1 + - + -
210G ASP* 1.3 71.6 + - - +
212G VAL* 1.3 58.3 - - - +
237G THR* 3.1 18.9 + - - +
239G ARG 4.5 1.8 + - - +
241G GLU* 3.2 25.8 - - + +
242G SER 4.1 4.7 - - - -
243G PHE* 3.8 35.0 - + - -
246G VAL* 3.7 31.0 - - + -
293G LYS 4.6 2.3 - - - +
295G VAL* 3.6 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G ASN 2.9 19.4 + - - +
170G VAL* 3.3 21.0 - - + -
171G TYR* 3.2 28.0 + - - -
210G ASP 4.4 3.1 - - - +
211G PHE* 1.3 74.3 - - - +
213G TYR* 1.3 72.8 + - - +
216G ASP* 4.4 2.2 - - + +
217G VAL* 4.2 11.0 - - + -
235G LEU* 3.9 20.4 - - + +
236G GLY* 3.9 18.8 - - - -
237G THR* 4.0 6.3 - - + -
292G PHE* 4.1 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 213 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171G TYR* 3.6 36.4 + + - +
172G GLY* 4.0 16.6 - - - -
173G PRO* 3.4 25.9 - - + +
212G VAL* 1.3 75.5 - - - +
214G VAL* 1.3 68.5 + - + +
215G GLY* 3.3 32.5 - - - -
216G ASP* 2.9 29.6 + - - +
217G VAL* 3.2 9.5 + - - +
293G LYS* 4.3 28.3 + - + -
298G GLY* 3.7 21.5 - - - -
301G GLU* 3.3 34.7 + - - +
302G TYR* 4.1 7.6 + - + -
305G TRP* 5.7 0.5 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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