Contacts of the strand formed by residues 301 - 305 (chain F) in PDB entry 2HU4
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 PRO 301 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274F HIS 3.5 20.2 - - - +
275F TYR* 3.7 22.9 - - + -
290F VAL* 3.7 2.3 - - - +
291F CYS* 2.9 45.3 + - + +
292F ARG 4.0 0.9 - - - +
293F ASP* 3.7 16.4 - - + +
299F ASN 3.9 3.8 - - - +
300F ARG* 1.3 86.0 - - - +
302F TRP* 1.3 62.9 + - - +
315F GLY 3.4 7.9 - - - +
316F TYR* 3.6 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 302 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275F TYR* 2.8 23.2 + - - -
288F THR* 5.6 1.6 - - + -
289F CYS 3.0 14.4 - - - +
290F VAL* 4.5 3.4 - - + -
291F CYS 4.8 0.2 - - - +
300F ARG 4.4 0.2 - - - -
301F PRO* 1.3 75.5 - - - +
303F VAL* 1.3 69.8 + - - +
304F SER* 3.5 27.6 - - - -
313F GLN* 3.7 27.8 - - + -
314F ILE* 3.6 21.4 - - - -
315F GLY* 2.9 51.5 + - - -
316F TYR* 3.0 22.3 + - - +
317F ILE* 3.8 5.6 - - + -
383F TRP* 3.6 50.9 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 303 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240F VAL* 5.7 4.0 - - + -
254F ILE* 4.1 4.5 - - + -
268F LEU* 3.8 23.1 - - + -
275F TYR* 2.9 41.3 - - + +
278F CYS* 5.5 1.6 - - - -
287F ILE 3.8 1.2 - - - +
288F THR* 3.6 0.7 - - - -
289F CYS* 2.7 46.4 + - + +
291F CYS* 5.0 3.6 - - - -
302F TRP* 1.3 75.7 - - - +
304F SER* 1.3 67.2 + - - +
305F PHE* 3.9 15.9 - - + -
312F TYR* 4.1 9.9 - - + -
313F GLN 3.6 12.8 - - - +
314F ILE* 4.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 304 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286F GLU* 5.5 5.6 - - - -
287F ILE 3.0 12.3 - - - -
288F THR* 4.4 13.5 - - - -
302F TRP* 3.5 21.9 - - - -
303F VAL* 1.3 74.9 - - - +
305F PHE* 1.3 69.3 + - - +
312F TYR* 3.0 21.8 - - - +
313F GLN* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 305 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238F PHE* 3.6 28.3 - + + -
239F THR 5.2 0.9 - - - -
240F VAL* 4.6 4.5 - - + -
254F ILE* 3.4 49.8 - - + -
280F CYS* 5.5 0.4 - - - -
286F GLU* 3.8 10.9 + - - +
287F ILE* 3.1 52.5 + - + +
289F CYS* 4.0 23.6 - - - -
303F VAL* 3.9 8.7 - - + -
304F SER* 1.3 82.4 - - - +
306F ASN* 1.3 70.3 + - - +
310F LEU* 4.2 6.5 - - + -
311F GLU 3.0 18.6 - - - +
312F TYR* 3.6 9.0 - - + +
----------------------------------------------------------
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