Contacts of the strand formed by residues 313 - 319 (chain F) in PDB entry 5IJ7
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 ALA 313 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F HIS* 4.5 2.3 + - - -
307F SER 4.0 0.2 - - - +
308F LYS* 3.6 15.2 - - - +
309F SER 4.3 3.8 + - - -
311F GLU* 3.3 11.3 + - + +
312F ASN* 1.3 79.8 - - - +
314F ILE* 1.4 58.9 + - - +
315F VAL* 3.9 9.3 + - + +
341F ARG* 3.8 19.7 - - + -
342F PHE 3.3 8.5 - - - +
343F ASP* 3.5 19.1 - - - +
344F TYR* 3.2 15.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 314 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F LEU* 3.9 29.8 - - + -
307F SER 3.5 15.7 - - - +
308F LYS* 4.0 7.2 - - + -
313F ALA* 1.4 71.1 - - - +
315F VAL* 1.3 59.5 + - - +
341F ARG* 3.2 4.3 - - - +
342F PHE* 2.8 44.9 + - + -
344F TYR* 3.8 10.5 - - + +
354F PHE* 3.9 30.7 - - + -
363F LEU* 3.7 25.4 - - + -
365F LEU* 3.8 21.5 - - + -
375F TRP* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 315 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290F ILE* 3.7 25.6 - - + +
291F HIS* 3.6 29.8 - - + +
305F ILE 3.4 4.3 - - - +
306F LEU* 3.4 2.1 - - - -
307F SER 2.8 30.0 + - - -
311F GLU* 5.5 1.3 - - - +
313F ALA* 4.4 9.4 - - + +
314F ILE* 1.3 75.9 - - - +
316F CYS* 1.3 64.4 + - - +
317F TRP* 3.6 5.4 - - + -
338F ILE* 3.9 31.2 - - + -
340F GLY 3.8 3.4 - - - +
341F ARG* 4.4 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 316 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE* 3.8 32.8 - - + -
301F LEU* 4.4 4.7 - - - -
304F LEU* 4.1 20.2 - - - -
305F ILE 3.3 8.7 - - - -
306F LEU* 3.8 18.8 - - + -
314F ILE 4.0 1.0 + - - -
315F VAL* 1.3 70.8 - - - +
317F TRP* 1.3 64.9 + - - +
338F ILE* 3.7 1.9 - - - -
339F LEU* 2.9 26.1 + - - -
340F GLY 2.8 25.2 + - - +
342F PHE* 4.5 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 317 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238F MET* 4.6 7.0 - - + -
246F LEU* 3.8 27.6 - - + -
285F PHE* 3.8 20.2 - + - -
287F THR* 3.8 14.6 - - + -
290F ILE* 3.6 39.7 - - + +
304F LEU* 3.7 3.5 - - - +
305F ILE* 2.8 71.2 + - + +
307F SER* 3.1 18.4 + - - -
315F VAL* 3.6 12.8 - - + -
316F CYS* 1.3 76.9 - - - +
318F LYS* 1.3 83.6 + - - +
319F PRO* 3.7 17.7 - - + -
336F VAL* 4.0 7.2 - - + -
337F THR 3.2 14.1 - - - +
338F ILE* 4.0 9.6 - - + -
339F LEU* 4.1 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 318 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B MET* 4.2 15.0 - - + -
303F ASP 4.7 4.3 - - - +
304F LEU* 4.0 23.8 - - + -
305F ILE* 4.5 0.4 - - - -
317F TRP* 1.3 84.9 - - - +
319F PRO* 1.4 87.3 + - + +
321F LYS 2.8 20.9 + - - +
322F MET* 3.2 24.5 - - - +
324F ASP 2.7 27.5 + - - -
326F ILE 5.9 0.4 - - - +
329F ILE* 5.0 0.4 - - - +
336F VAL* 3.6 3.1 - - - -
337F THR* 2.9 42.6 + - - +
339F LEU* 4.3 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 319 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238F MET* 4.6 4.7 - - + -
248F LEU* 5.4 0.4 - - + -
285F PHE* 3.6 48.5 - - + -
303F ASP 4.8 1.3 - - - +
305F ILE* 3.6 20.2 - - + -
317F TRP* 3.7 4.9 - - + -
318F LYS* 1.4 109.6 + - + +
320F GLY* 1.3 58.0 + - - +
326F ILE* 3.5 26.5 - - + -
329F ILE* 3.4 21.8 - - + +
335F ASN 4.1 0.4 - - - +
336F VAL* 4.6 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