Contacts of the strand formed by residues 249 - 253 (chain B) in PDB entry 1XR2
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 ARG 249 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LYS* 4.8 4.9 - - - +
4B TYR* 4.0 9.6 - - + +
194B LYS 4.9 0.8 + - - -
195B GLU* 3.3 30.5 + - - +
225B PHE 4.7 1.0 + - - -
226B PRO* 3.4 27.9 + - - +
227B LEU 3.0 25.9 + - - +
228B THR* 2.8 45.6 + - + +
229B VAL 3.2 20.4 + - - -
247B VAL* 3.6 9.8 - - - +
248B LYS* 1.3 105.6 - - - +
250B LEU* 1.3 60.8 + - - +
274B LYS* 3.5 19.5 - - + +
276B VAL* 5.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B VAL* 3.7 33.0 - - + +
231B THR* 5.1 2.2 - - + -
242B CYS* 3.8 34.3 - - - +
243B VAL* 4.0 13.7 - - + -
245B LEU* 5.6 2.9 - - + -
247B VAL* 4.5 11.2 - - + -
248B LYS 4.4 0.2 + - - -
249B ARG* 1.3 76.0 - - - +
251B HIS* 1.3 64.1 + - - +
252B PHE* 3.5 33.7 - - + -
269B PHE* 4.5 4.9 - - + -
273B LYS* 4.5 16.2 - - + -
274B LYS 3.2 5.7 + - - -
275B LEU* 3.6 10.0 - - - +
276B VAL* 3.1 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 4.0 2.0 - + - -
228B THR* 5.2 0.2 - - + -
229B VAL 2.9 13.8 + - - +
230B PHE* 3.3 32.0 - + + -
231B THR* 3.0 54.2 + - - -
232B TYR* 4.2 2.6 - - - -
250B LEU* 1.3 79.4 - - - +
252B PHE* 1.3 71.2 + - - +
276B VAL* 3.3 24.2 + - + +
278B GLY* 3.7 11.7 - - - -
306B SER* 3.3 16.3 + - - -
307B ASN 3.3 26.0 - - - -
308B SER 3.4 14.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B THR* 3.9 7.6 - - - -
236B VAL* 3.6 31.6 - - + -
239B TYR* 4.1 15.5 - + - -
242B CYS* 4.3 6.3 - - - -
243B VAL* 3.9 13.9 - - + -
250B LEU* 3.5 35.2 - - + -
251B HIS* 1.3 85.8 - - - +
253B ASP* 1.3 61.4 + - - +
254B PHE* 3.4 26.9 + + + -
260B ASN* 3.8 24.7 - - + +
264B LEU* 5.4 0.9 - - + -
269B PHE* 3.9 15.7 - + - -
275B LEU* 3.5 21.3 - - + -
276B VAL 3.4 4.9 + - - -
278B GLY* 2.9 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B THR* 3.5 19.3 + - - +
232B TYR* 3.6 8.2 - - - +
233B TYR* 2.9 17.7 + - - -
234B ASP 4.3 6.1 - - - +
251B HIS* 4.3 0.2 - - - -
252B PHE* 1.3 72.5 - - - +
254B PHE* 1.3 56.8 + - - +
255B VAL 2.8 17.7 + - - -
256B SER* 2.5 33.8 + - - -
257B ASN* 2.9 25.2 + - - -
260B ASN* 3.0 12.5 + - - +
278B GLY 4.2 2.0 - - - -
308B SER* 3.3 26.3 - - - +
309B CYS* 4.8 2.8 - - - +
----------------------------------------------------------
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