Contacts of the strand formed by residues 290 - 295 (chain F) in PDB entry 2Y1M
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 SER 290 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281F LEU* 4.9 5.4 - - - -
284F PHE* 3.4 28.4 - - - +
287F LYS* 3.4 32.5 + - - +
288F PRO 3.7 0.2 - - - -
289F GLY* 1.3 82.4 - - - +
291F TYR* 1.3 60.5 + - - +
307F TYR* 3.3 2.9 - - - +
308F VAL* 2.8 31.2 + - - +
339F PHE* 3.4 12.5 - - - +
342F GLY* 3.7 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 291 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265F HIS* 3.1 19.2 + - - -
267F GLY* 4.5 0.9 - - - -
281F LEU* 4.3 3.8 - - - -
289F GLY 4.5 0.2 - - - +
290F SER* 1.3 75.9 - - - +
292F ILE* 1.3 71.3 + - - +
293F PHE* 3.9 28.0 - + - -
305F ILE* 4.9 1.6 - - + -
306F GLY 3.2 15.7 - - - +
307F TYR* 3.9 9.0 - - + +
328F LEU* 4.3 15.0 - - + +
337F TYR* 3.3 48.5 - + + -
338F LEU 3.4 6.1 - - - -
339F PHE 3.3 6.7 + - - -
340F PRO* 3.5 19.4 - - + +
341F ASP* 2.9 26.0 + - - -
346F ASN* 2.5 33.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 292 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267F GLY 3.5 10.8 - - - +
269F MET* 3.1 42.0 - - + -
272F LEU* 4.5 0.4 - - + -
277F VAL* 4.0 35.2 - - + -
280F ARG* 3.7 19.7 - - + -
281F LEU* 3.8 25.1 - - + +
291F TYR* 1.3 84.2 - - - +
293F PHE* 1.3 67.3 + - - +
305F ILE* 3.5 3.1 - - - +
306F GLY 2.8 30.3 + - - +
341F ASP* 3.8 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 293 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F LEU* 3.5 21.1 - - + -
265F HIS* 3.9 13.9 - + - -
267F GLY* 2.9 24.3 + - - -
268F TYR* 3.5 27.7 - + + -
269F MET* 2.9 27.9 + - - -
270F ALA 4.1 0.5 + - - -
291F TYR* 3.9 17.7 - + - -
292F ILE* 1.3 78.7 - - - +
294F ARG* 1.3 59.3 + - - +
303F TRP* 3.7 20.6 - + + -
304F ALA 3.1 16.4 - - - +
305F ILE* 3.9 12.3 - - + +
306F GLY 4.6 0.4 - - - +
324F LEU* 3.9 14.8 - - + -
328F LEU* 3.7 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 294 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269F MET* 4.2 5.2 - - + -
270F ALA 2.9 17.3 - - - +
272F LEU* 2.8 35.3 + - + +
273F THR* 3.8 6.8 - - - +
274F TYR* 3.6 27.7 - - - +
277F VAL* 3.5 22.2 - - + +
293F PHE* 1.3 75.0 - - - +
295F LEU* 1.3 76.9 + - - +
296F SER* 3.9 19.7 + - - -
302F GLN 4.1 0.2 - - - +
303F TRP* 3.7 8.4 - - - -
304F ALA* 3.0 46.1 + - + +
316F GLN* 3.2 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 295 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227F THR* 5.6 8.1 - - + +
230F LEU* 6.3 1.1 - - + -
247F LEU* 3.5 37.2 - - + -
248F PHE* 5.8 0.7 - - + -
268F TYR* 4.1 17.7 - - + +
270F ALA* 2.6 18.0 + - + +
271F PHE* 3.1 42.0 - - + +
272F LEU 3.3 10.0 + - - +
294F ARG* 1.3 88.3 - - - +
296F SER* 1.3 57.8 + - - +
302F GLN 4.2 4.5 - - - +
303F TRP* 3.3 38.4 - - + -
304F ALA* 6.2 0.2 - - - -
----------------------------------------------------------
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