Contacts of the helix formed by residues 261 - 265 (chain F) in PDB entry 5JA0
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 ASP 261 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F ASP* 4.0 12.1 - - - +
247F ASP* 3.1 41.2 + - + +
260F THR* 1.3 77.5 + - - +
262F ILE* 1.3 67.3 + - + +
264F ASP* 3.2 4.6 + - - -
266F LYS* 3.1 59.0 + - + +
268F SER* 3.7 23.9 + - - +
290F TYR* 3.9 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 262 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F LEU* 4.2 20.6 - - + -
260F THR* 3.1 1.2 - - - +
261F ASP* 1.3 80.9 - - + +
263F GLN* 1.4 59.1 + - - +
264F ASP 2.8 6.8 + - - -
265F ASN* 3.2 9.2 + - - -
289F ASN 4.5 2.2 - - - +
290F TYR* 3.7 34.3 - - + +
291F GLY 3.4 16.4 + - - +
292F GLN 5.5 1.1 - - - +
298F VAL* 4.2 19.3 - - + +
301F VAL* 3.5 41.5 - - + -
302F LYS 4.2 7.4 - - - +
305F TYR* 3.9 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 263 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258F ILE* 5.3 4.8 - - - +
259F GLY 3.6 10.0 + - - -
260F THR* 3.0 41.3 + - + +
262F ILE* 1.4 76.9 - - - +
264F ASP* 1.4 66.3 + - - +
265F ASN 3.8 0.7 - - - -
291F GLY 4.7 5.3 - - - +
292F GLN 3.2 29.3 - - - +
293F LYS* 4.3 15.1 + - - +
295F ALA* 5.7 0.7 - - - -
298F VAL* 3.4 27.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 264 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178F ALA 5.0 4.3 - - - +
180F GLN* 5.1 20.0 - - - +
260F THR* 2.8 38.6 + - - +
261F ASP 3.2 2.0 + - - +
262F ILE 2.8 3.4 + - - -
263F GLN* 1.4 93.6 - - - +
265F ASN* 1.3 73.5 + - - +
266F LYS* 3.1 36.2 + - + +
291F GLY* 4.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 265 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177F THR 5.2 0.6 + - - -
178F ALA* 3.4 22.3 - - - +
179F PRO* 3.5 13.1 + - - +
180F GLN* 5.2 1.6 - - - -
181F GLY 5.2 7.4 - - - +
182F ASN 2.6 32.0 + - - +
183F VAL* 3.6 18.0 - - - +
184F ASP 4.3 1.9 + - - +
185F LEU* 5.0 0.2 - - - +
188F PHE* 3.3 24.3 - - - -
262F ILE 3.2 7.7 + - - -
263F GLN 3.8 1.0 - - - -
264F ASP* 1.3 79.7 - - - +
266F LYS* 1.4 63.3 + - - +
290F TYR* 3.4 24.6 - - - -
291F GLY* 3.8 13.7 - - - +
----------------------------------------------------------
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