Contacts of the strand formed by residues 310 - 316 (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 TYR 310 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ILE* 4.5 0.5 - - - +
253B LEU* 3.9 19.5 - - + -
268B TRP* 4.6 7.2 - - + -
269B LEU 3.4 2.5 - - - +
270B GLU* 2.8 48.4 + - + -
275B MET* 5.6 0.7 - - + -
297B LEU* 4.1 14.4 - - + -
299B LEU* 3.2 34.3 - - + +
303B HIS* 2.9 31.1 + - - -
304B TRP* 4.3 15.3 - + - -
308B ARG* 3.3 33.0 - - + +
309B THR* 1.3 72.5 - - - +
311B THR* 1.3 61.0 + - - +
312B CYS 4.3 0.3 + - - -
324B SER* 3.2 3.9 - - - -
325B THR* 2.8 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B THR 3.5 1.7 - - - +
268B TRP* 3.4 10.7 - - - -
269B LEU* 2.8 62.2 + - + +
272B GLY* 5.2 2.6 + - - -
309B THR* 4.1 7.3 + - - +
310B TYR* 1.3 74.8 - - - +
312B CYS* 1.3 62.5 + - - +
313B GLN 3.7 0.6 + - - +
322B GLU* 3.5 31.0 - - + +
323B ASP 3.6 4.3 - - - +
324B SER* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B VAL* 4.0 7.1 - - + +
236B ILE* 4.1 8.7 - - + +
254B CYS* 2.0 49.8 - - - -
266B ILE* 3.5 17.3 - - - -
267B THR 3.8 2.7 - - - -
268B TRP* 3.9 20.1 - - + -
310B TYR 4.3 0.4 + - - -
311B THR* 1.3 70.7 - - - +
313B GLN* 1.3 58.1 + - - +
314B VAL* 3.7 3.4 + - - -
322B GLU* 3.2 24.9 - - - -
323B ASP 2.9 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B GLN 3.4 2.8 - - - +
266B ILE* 4.4 0.7 - - - -
267B THR* 2.7 61.1 + - - +
269B LEU* 3.2 33.8 - - + +
311B THR* 4.9 0.4 - - + -
312B CYS* 1.3 72.8 - - - +
314B VAL* 1.3 60.3 + - - +
315B THR* 3.6 5.9 + - - +
320B THR* 4.7 22.2 - - + +
321B PHE 3.6 6.7 - - - +
322B GLU* 4.0 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PRO* 4.7 4.0 - - + -
234B VAL* 3.5 25.8 - - + -
256B VAL* 3.4 44.4 - - + -
264B ILE* 4.5 10.5 - - + -
265B GLN 3.5 9.6 - - - +
266B ILE* 4.4 7.6 - - + +
312B CYS* 3.7 4.2 + - - -
313B GLN* 1.3 71.1 - - - +
315B THR* 1.3 63.6 + - - +
316B TYR* 4.0 18.4 - - + -
319B HIS 3.8 1.0 - - - +
320B THR* 3.4 2.6 - - - -
321B PHE* 2.7 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B THR 3.9 3.1 - - - +
264B ILE* 3.8 1.7 - - - -
265B GLN* 3.0 56.5 + - - +
267B THR* 4.2 2.9 + - - -
313B GLN* 3.9 9.3 + - - +
314B VAL* 1.3 72.2 - - - +
316B TYR* 1.3 58.9 + - - +
318B GLY* 5.2 2.0 - - - -
319B HIS* 3.9 5.8 - - - +
320B THR* 3.3 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PHE* 4.1 11.5 - - + +
230B THR 3.5 21.9 + - - -
231B PRO* 4.6 1.3 - - + -
232B PRO* 3.7 31.6 - - + -
259B TYR* 3.7 17.9 - + - -
260B THR* 2.7 49.0 + - - +
262B GLY* 4.3 10.3 - - - -
263B THR 4.1 15.0 - - - -
264B ILE* 4.5 4.7 - - + -
314B VAL* 4.0 8.7 - - + -
315B THR* 1.3 74.1 - - - +
317B GLN* 1.3 95.0 + - + +
318B GLY 2.9 3.6 + - - -
319B HIS* 2.9 24.0 + - - +
321B PHE* 4.2 9.3 - + + -
----------------------------------------------------------
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