Contacts of the strand formed by residues 250 - 259 (chain B) in PDB entry 2Y7Q
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 THR 250 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B SER* 3.9 3.1 + - - -
248B PRO* 3.1 15.3 - - - +
249B PRO* 1.3 91.3 + - - +
251B ILE* 1.3 61.7 + - - +
252B GLN* 3.8 2.8 + - + +
298B THR* 3.1 32.1 - - + -
299B LEU 3.1 21.1 + - - +
300B SER* 4.9 2.6 - - - -
301B GLN 4.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLN* 4.7 4.5 - - + +
239B SER* 3.7 12.6 - - - +
247B PHE* 4.7 7.0 - - + -
248B PRO* 4.3 18.8 - - + -
250B THR* 1.3 73.5 - - - +
252B GLN* 1.3 73.3 + - - +
253B LEU* 3.6 12.5 + - + +
297B LEU 3.9 0.2 - - - +
298B THR* 3.6 3.3 - - - -
299B LEU* 2.9 38.8 + - + +
301B GLN* 4.1 21.8 - - + -
304B TRP* 2.9 65.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU 3.9 0.3 - - - +
238B GLN* 3.3 8.3 - - - +
239B SER* 2.8 41.7 + - - +
250B THR* 3.8 2.3 + - + +
251B ILE* 1.3 73.4 - - - +
253B LEU* 1.3 66.7 + - + +
296B GLU* 4.4 23.0 - - - +
297B LEU 3.7 2.2 - - - +
298B THR* 3.5 30.2 + - + +
235D LYS* 6.0 2.4 - - - +
237D LEU* 5.7 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B LYS 3.5 1.4 - - - +
236B ILE* 3.0 21.0 - - + +
237B LEU* 2.7 50.0 + - + +
238B GLN* 3.9 20.0 - - + +
251B ILE* 4.3 3.6 - - + +
252B GLN* 1.3 87.0 - - + +
254B CYS* 1.3 64.2 + - - +
255B LEU* 3.6 23.5 + - + +
268B TRP* 4.0 19.2 - - + -
294B GLN* 4.1 29.4 - - + -
295B SER 4.0 3.4 - - - +
296B GLU* 3.2 25.1 - - + +
297B LEU* 2.6 54.4 + - + +
299B LEU* 3.5 29.4 - - + -
304B TRP* 4.2 21.3 - - + -
310B TYR* 3.9 24.2 - - + -
325B THR* 4.5 7.2 - - + -
237D LEU* 3.4 28.7 - - + -
253D LEU* 6.2 1.1 - - - +
255D LEU* 5.4 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B VAL* 3.7 16.6 - - - -
235B LYS 3.6 3.6 - - - -
236B ILE* 4.6 1.3 - - - +
253B LEU* 1.3 72.2 + - - +
255B LEU* 1.3 62.0 + - - +
256B VAL* 3.6 13.9 + - - +
266B ILE* 4.2 4.3 - - + -
268B TRP* 3.5 9.9 - - + -
294B GLN* 3.2 8.8 - - - -
295B SER 3.1 41.6 + - - +
312B CYS* 2.0 46.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B THR 3.1 7.3 - - - +
234B VAL* 3.4 1.0 - - - -
235B LYS* 2.7 54.6 + - + +
237B LEU* 3.5 35.0 - - + -
253B LEU* 3.6 31.4 - - + +
254B CYS* 1.3 70.5 - - - +
256B VAL* 1.3 62.1 + - - +
257B SER* 3.9 6.2 - - - -
293B THR 4.1 1.8 - - - -
294B GLN* 4.0 20.6 - - + -
253D LEU* 5.2 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PRO* 3.4 30.3 - - + -
233B THR 3.5 3.8 - - - +
234B VAL* 4.4 2.5 - - + -
254B CYS* 3.8 8.5 - - - -
255B LEU* 1.3 74.8 - - - +
257B SER* 1.3 59.6 + - - +
259B TYR* 4.7 9.9 - - + -
264B ILE* 5.5 4.3 - - + -
266B ILE* 3.6 26.0 - - + -
292B SER* 3.3 3.2 - - - -
293B THR* 2.7 46.6 + - - +
314B VAL* 3.4 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B THR* 3.0 40.6 + - - -
255B LEU* 4.9 7.0 - - - -
256B VAL* 1.3 79.8 - - - +
258B GLY* 1.3 58.6 + - - +
259B TYR* 3.7 3.1 - - - -
292B SER* 3.6 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B THR* 4.4 2.8 - - - +
231B PRO 3.3 17.0 - - - +
233B THR* 5.2 0.9 + - - -
257B SER* 1.3 75.4 - - - +
259B TYR* 1.3 60.5 + - - +
290B LEU* 5.1 10.5 - - - -
291B ALA 3.0 13.9 + - - -
292B SER* 4.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B THR* 3.5 14.4 - - - +
232B PRO* 3.7 26.9 - - + -
256B VAL* 4.2 7.0 - - + -
257B SER 4.3 3.1 - - - -
258B GLY* 1.3 82.2 - - - +
260B THR* 1.3 75.6 + - - +
261B PRO* 3.2 2.6 - - + -
262B GLY 4.2 15.8 + - - -
264B ILE* 4.2 23.4 - - + +
280B SER 5.6 1.9 + - - -
290B LEU* 3.2 6.9 - - - -
291B ALA* 3.1 36.6 + - + +
292B SER* 3.2 44.6 + - - -
293B THR* 4.0 11.2 - - - -
316B TYR* 3.7 16.2 - + + -
----------------------------------------------------------
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