Contacts of the strand formed by residues 272 - 280 (chain F) in PDB entry 2W3S
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 PHE 272 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F LEU* 4.8 3.8 - - - -
167F GLU* 3.7 4.1 - - - +
168F ILE* 2.8 60.1 + - + +
270F HIS* 3.2 40.6 - - + -
271F ASP* 1.3 76.1 - - - +
273F ARG* 1.3 58.4 + - - +
274F ILE* 4.1 14.8 - - + -
293F HIS* 4.0 31.0 - + + -
294F LEU 3.3 11.0 - - - -
295F ALA* 3.6 19.5 - - + -
307F VAL* 5.2 2.2 - - + -
308F CYS* 4.2 12.8 - - + -
311F ALA* 3.9 24.2 - - + -
328F SER* 5.7 0.9 - - - -
348F GLN* 3.5 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 273 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F LEU* 3.9 20.5 - - + +
130F ASP* 2.8 45.4 + - - +
133F LEU* 5.8 1.2 - - - +
165F CYS* 4.9 14.6 - - - -
166F PHE 3.8 8.7 - - - +
167F GLU* 3.0 30.5 + - - +
272F PHE* 1.3 72.3 - - - +
274F ILE* 1.3 73.1 + - - +
275F ARG* 4.2 4.0 - - + +
292F VAL 3.3 3.2 - - - +
294F LEU* 2.7 69.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 274 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F CYS* 3.0 5.4 - - - -
166F PHE* 3.0 45.5 + - + +
168F ILE* 3.7 19.3 - - + -
272F PHE* 4.2 11.4 - - + -
273F ARG* 1.3 83.0 - - - +
275F ARG* 1.3 62.4 + - - +
276F TYR* 4.2 4.6 - - + -
291F PHE* 4.2 17.3 - - + -
292F VAL 3.2 6.1 - - - +
293F HIS* 3.7 29.2 - - + +
348F GLN 3.4 28.5 - - - +
352F GLY* 3.9 21.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 275 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F LEU* 5.5 4.0 - - - +
164F GLY 4.0 2.2 - - - +
165F CYS* 3.5 23.6 - - + -
273F ARG* 4.2 5.0 - - + +
274F ILE* 1.3 73.8 - - - +
276F TYR* 1.3 63.7 + - - +
290F ASP 3.8 0.6 - - - +
291F PHE* 3.4 3.1 - - - -
292F VAL* 2.7 74.2 + - + +
294F LEU* 4.7 14.6 - - - +
329F HIS* 5.7 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 276 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162F ALA 4.1 8.5 - - - -
163F GLU* 3.3 5.3 - - - +
164F GLY* 2.9 54.5 + - - +
165F CYS* 3.6 8.7 - - - -
166F PHE* 4.5 7.0 - + - -
274F ILE* 4.2 8.7 - - + -
275F ARG* 1.3 77.2 - - - +
277F ARG* 1.3 67.4 + - - +
278F ILE* 4.6 0.7 - - + -
290F ASP 3.2 5.4 - - - -
291F PHE* 3.8 25.6 - - + -
352F GLY 4.9 2.9 - - - -
355F ARG* 3.4 35.8 + - + -
356F ALA* 3.6 35.7 - - + -
359F HIS* 3.0 37.6 - + + -
754F TRP* 4.2 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 277 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F GLU* 3.0 29.9 + - - -
155F LEU* 3.5 35.7 - - + +
161F LEU* 4.6 3.2 - - + +
162F ALA 3.2 3.8 - - - +
163F GLU* 3.2 44.1 + - + +
276F TYR* 1.3 79.4 - - - +
278F ILE* 1.3 62.4 + - - +
289F ALA* 3.3 2.3 - - - -
290F ASP* 2.7 70.8 + - - +
325F ARG* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 278 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F LEU* 3.7 4.5 - - - +
161F LEU* 3.2 5.0 - - - +
162F ALA* 2.8 48.2 + - + +
276F TYR* 4.6 0.9 - - + -
277F ARG* 1.3 76.4 - - - +
279F GLY* 1.3 61.8 + - - +
286F LEU* 3.5 31.4 - - + -
288F GLY 3.5 8.5 - - - +
289F ALA* 4.2 9.6 - - + -
291F PHE* 5.9 0.2 - - + -
321F VAL* 6.4 0.2 - - + -
353F MET* 4.0 25.8 - - - -
356F ALA* 3.6 39.9 - - + +
357F ILE* 4.3 9.0 - - + +
360F LEU* 3.6 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 279 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F LEU* 3.5 10.5 - - - +
158F ALA* 4.1 6.5 - - - -
160F HIS 3.0 12.3 - - - -
278F ILE* 1.3 76.6 - - - +
280F ALA* 1.3 56.3 + - - +
286F LEU* 3.5 7.1 - - - +
287F LEU* 2.8 31.7 + - - -
288F GLY 3.0 15.7 + - - +
360F LEU* 4.4 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 280 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158F ALA* 4.4 0.8 - - - +
159F ALA 3.4 8.3 + - - -
160F HIS* 3.0 27.7 + - - -
279F GLY* 1.3 74.0 - - - +
281F ASP* 1.3 70.9 + - - +
284F GLY* 4.0 12.1 - - - +
285F LYS 3.2 19.1 - - - +
286F LEU* 4.2 2.7 - - + +
287F LEU* 3.7 8.6 - - - +
360F LEU* 4.0 19.5 - - + +
364F MET* 4.4 9.2 - - + -
371F LEU* 5.5 0.7 - - + -
----------------------------------------------------------
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