Contacts of the strand formed by residues 313 - 318 (chain F) in PDB entry 2W8B
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 GLN 313 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305F THR* 3.6 3.8 - - - -
306F SER 3.0 29.2 + - - +
309F ALA* 4.8 4.9 - - + -
311F ARG* 3.4 8.9 + - - +
312F PRO* 1.3 76.6 + - - +
314F VAL* 1.3 60.9 + - - +
315F TYR* 3.6 18.6 - - + -
326F ARG* 3.5 37.0 - - - +
328F THR* 2.6 34.5 - - + +
331F GLY 3.5 7.9 + - - +
332F SER 3.2 34.1 - - - +
333F GLN* 3.6 1.6 - - - +
334F ASN* 2.8 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 314 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F ALA* 3.9 13.0 - - + -
304F PHE 3.3 18.4 - - - +
313F GLN* 1.3 72.6 - - - +
315F TYR* 1.3 66.7 + - - +
326F ARG* 3.7 1.2 - - - +
327F ILE* 2.8 37.5 + - + +
328F THR* 2.9 29.7 + - - +
334F ASN* 3.8 17.3 - - + +
335F GLN* 3.9 18.4 - - - +
336F ASP 4.8 0.4 - - - +
337F ALA* 4.1 16.8 - - + -
346F MET* 4.1 11.0 - - + -
348F MET* 4.3 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 315 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F ALA* 3.0 6.9 - - - +
304F PHE* 2.7 56.5 + - + -
306F SER* 3.7 26.0 - - - -
308F GLN* 3.2 30.9 + - + -
309F ALA* 3.3 32.0 + - - +
313F GLN* 3.6 28.3 - - + -
314F VAL* 1.3 77.9 - - - +
316F LYS* 1.3 59.5 + - - +
324F PRO* 4.1 9.6 - - + -
325F GLN 3.3 13.0 - - - -
326F ARG* 3.2 37.9 - - + +
327F ILE* 4.2 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 316 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296F PHE* 3.6 46.9 - - + -
301F ASN* 4.2 22.2 - - + +
302F LEU 3.2 4.3 - - - +
303F ALA* 4.2 0.2 - - - +
304F PHE* 4.0 1.6 - - - -
315F TYR* 1.3 75.4 - - - +
317F VAL* 1.3 64.9 + - - +
323F ALA 4.7 0.5 - - - +
324F PRO* 3.4 1.2 - - - +
325F GLN* 2.9 37.1 + - + +
327F ILE* 3.8 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 317 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270F LEU* 4.4 6.1 - - + -
283F VAL* 4.0 26.9 - - + +
284F THR* 4.5 3.6 - - + -
301F ASN* 3.4 5.2 - - - -
302F LEU* 2.9 35.0 + - + +
304F PHE* 3.5 26.2 - - + -
316F LYS* 1.3 76.7 - - - +
318F ASN* 1.3 72.3 + - - +
319F ILE 3.7 0.5 + - - -
322F GLY 3.6 24.2 - - - +
323F ALA 4.5 0.9 - - - +
324F PRO* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 318 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283F VAL* 4.6 1.4 - - - +
300F GLN* 3.4 11.1 + - - +
301F ASN* 3.1 26.9 + - - +
317F VAL* 1.3 86.4 - - - +
319F ILE* 1.3 63.4 + - - +
320F ASN* 2.9 55.7 + - - +
321F GLY 3.5 22.8 + - - +
----------------------------------------------------------
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