Contacts of the helix formed by residues 233 - 239 (chain A) in PDB entry 5Y9F
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 233 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ILE* 2.9 20.2 + - + +
167A GLU* 4.0 17.4 - - + +
192A ASN* 2.8 29.2 + - - +
231A TYR 3.3 3.0 + - - -
232A PRO* 1.3 67.4 - - - +
234A TYR* 1.3 65.3 + - - +
235A LEU* 3.6 9.2 + - - +
236A GLN* 3.1 22.1 + - + +
237A MET* 2.9 27.7 + - - +
41B ARG* 2.3 34.7 + - - -
110B GLY* 5.9 0.2 - - - -
370B GLU* 3.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 4.2 12.6 - - - +
158A ILE* 4.0 8.3 - - + -
231A TYR* 3.5 31.6 + + - -
232A PRO* 3.0 50.7 + - + +
233A ASP* 1.3 72.3 - - - +
235A LEU* 1.3 63.6 + - + +
237A MET* 4.1 12.8 - - + -
238A SER* 2.9 35.0 + - - -
246A MET* 4.3 6.1 - - + +
249A CYS* 3.6 31.2 - - - -
251A ARG* 3.8 33.6 - - + +
253A GLU* 4.8 0.5 + - - -
109B ARG 6.0 0.9 - - - -
110B GLY 5.5 1.1 - - - -
308B ASN* 5.3 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ASP* 3.1 9.3 + - - +
234A TYR* 1.3 85.0 - - + +
236A GLN* 1.3 59.9 + - - +
238A SER* 3.5 6.1 + - - -
239A ALA* 3.3 23.7 + - - +
41B ARG* 4.9 6.3 - - + -
108B GLY* 4.4 3.1 - - - -
109B ARG 3.3 28.9 - - - +
110B GLY* 3.8 15.7 - - - +
308B ASN* 4.3 10.1 - - - +
370B GLU* 3.3 29.2 - - + +
371B PHE 4.2 4.3 - - - +
372B ASP* 3.6 40.5 - - + +
374B GLN* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ILE* 3.5 34.3 - - - +
192A ASN* 4.5 10.7 + - - +
233A ASP* 3.1 29.0 + - - +
235A LEU* 1.3 77.7 - - - +
237A MET* 1.3 74.8 + - - +
239A ALA* 3.4 5.5 + - - +
240A ASP* 3.2 23.4 + - - +
245A SER* 5.1 1.4 + - - -
41B ARG* 4.6 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ILE* 3.8 26.0 - - + -
164A ALA* 4.0 10.8 - - - -
165A ILE* 3.3 38.4 - - + +
232A PRO* 4.3 0.4 - - + -
233A ASP 2.9 27.8 + - - +
234A TYR* 4.1 6.1 - - + +
236A GLN* 1.3 88.0 + - - +
238A SER* 1.3 59.9 + - - +
240A ASP* 3.3 19.7 - - - +
243A GLY* 4.9 1.2 - - - -
245A SER* 3.8 18.1 - - - -
246A MET* 3.7 38.4 + - + +
317A GLN* 3.6 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TYR* 2.9 21.1 + - - -
235A LEU* 3.5 7.1 + - - -
237A MET* 1.3 76.8 - - - +
239A ALA* 1.3 62.8 + - - +
240A ASP 3.2 4.5 + - - +
246A MET* 3.6 8.9 - - - +
317A GLN* 3.7 19.5 + - - +
106B GLU* 5.8 0.5 + - - -
372B ASP* 5.6 0.7 + - - -
374B GLN* 5.2 5.4 + - - -
464B PRO* 3.7 20.0 - - - +
467B ARG* 3.7 21.8 + - - -
468B LYS* 6.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU 3.3 17.8 + - - +
236A GLN* 3.4 6.0 + - - +
238A SER* 1.3 78.7 + - - +
240A ASP* 1.3 66.2 + - - +
241A ALA* 3.6 1.4 + - - -
372B ASP* 5.0 7.2 - - - +
374B GLN* 6.3 0.2 - - - +
462B GLN 5.6 1.4 - - - +
464B PRO* 4.4 14.8 - - + +
----------------------------------------------------------
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