Contacts of the strand formed by residues 250 - 255 (chain B) in PDB entry 1YXJ
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 ALA 250 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ARG* 3.8 24.9 - - - +
246B ILE* 3.3 1.8 - - - -
247B GLN 2.8 29.5 + - - +
248B ARG 3.3 3.7 - - - +
249B GLY* 1.3 78.9 - - - +
251B VAL* 1.3 63.1 + - - +
252B TYR* 3.4 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 5.0 3.6 - - + -
204B MSE 3.7 28.0 - - + -
228B PHE* 3.6 51.8 - - + +
229B ARG 3.4 8.4 + - - +
230B VAL* 4.5 7.2 - - + -
231B ARG* 2.9 29.6 + - - +
244B ALA* 4.1 16.8 - - + -
245B TYR 3.4 9.2 - - - +
246B ILE* 4.6 9.4 - - + -
249B GLY 5.2 0.7 - - - +
250B ALA* 1.3 77.3 - - - +
252B TYR* 1.3 65.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B VAL* 4.2 4.9 - - - -
231B ARG* 3.4 35.0 + - + +
232B GLY* 4.0 11.0 - - - -
244B ALA* 3.1 4.7 - - - +
245B TYR* 2.9 72.2 + + + +
247B GLN* 3.6 19.4 + - + -
248B ARG* 5.8 1.2 - - - +
250B ALA* 3.4 41.9 - - + +
251B VAL* 1.3 72.9 - - - +
253B ALA* 1.3 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TRP* 3.5 33.0 - - + -
230B VAL* 3.6 7.9 - - + -
231B ARG 2.8 15.5 + - - +
232B GLY* 4.0 1.9 - - - -
233B ALA* 3.1 24.5 + - - +
234B VAL* 3.7 8.7 - - + -
242B THR* 3.8 6.3 - - + -
243B CYS 3.4 5.4 - - - -
244B ALA* 4.4 0.2 - - - +
245B TYR* 4.4 1.9 + - - -
252B TYR* 1.3 75.6 - - - +
254B GLU* 1.3 66.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PRO* 5.7 0.7 - - - +
203B TRP* 3.2 32.1 - - + -
233B ALA* 4.5 9.0 - - + -
242B THR* 3.4 9.1 - - - +
243B CYS* 2.9 30.8 + - - +
245B TYR* 3.4 34.1 + - + +
253B ALA* 1.3 77.5 - - - +
255B ASN* 1.3 68.3 + - - +
256B CYS* 4.1 0.2 - - - -
258B LEU* 3.4 29.8 - - + +
259B ALA 4.5 7.1 - - - +
260B ALA* 4.5 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B TRP* 3.8 0.9 - - - -
238B TYR* 3.4 57.9 - - + +
239B PRO* 4.9 4.3 - - - +
240B SER* 4.9 3.2 - - - +
241B GLY 4.0 1.2 + - - -
254B GLU* 1.3 77.4 - - - +
256B CYS* 1.3 68.1 + - - +
257B ILE* 3.1 43.4 + - - +
258B LEU* 3.2 33.2 + - + +
----------------------------------------------------------
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