Contacts of the helix formed by residues 235 - 242 (chain B) in PDB entry 4IA4
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 SER 235 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ALA 4.5 1.0 + - - -
233B PHE* 3.6 33.4 - - - -
234B ASN* 1.3 76.3 - - - +
236B ASN* 1.3 60.5 + - - +
237B LYS* 3.4 16.3 + - - +
238B VAL* 3.0 13.8 + - - +
239B TRP* 2.8 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ASN 4.3 0.2 - - - -
235B SER* 1.3 70.1 + - - +
237B LYS* 1.3 57.9 + - - +
238B VAL 2.9 0.3 + - - -
239B TRP* 3.0 13.5 + - - +
240B ASP* 2.7 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 3.1 25.0 + - - -
155B VAL 3.0 27.6 + - - -
157B LEU* 5.9 5.6 - - - +
235B SER* 3.4 9.3 + - - +
236B ASN* 1.3 79.4 - - - +
238B VAL* 1.3 62.4 + - + +
240B ASP* 3.5 17.1 + - - +
241B ASP* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ALA* 4.0 17.7 - - + +
153B ASN 3.6 25.5 - - - +
154B SER* 4.3 11.0 - - - -
230B ALA* 4.0 25.1 - - + +
233B PHE* 3.8 28.7 - - + -
235B SER* 3.0 15.3 + - - +
236B ASN 3.0 0.4 - - - -
237B LYS* 1.3 78.2 - - + +
239B TRP* 1.3 67.5 + - + +
240B ASP 2.9 2.4 + - - -
241B ASP* 3.0 4.3 + - - +
242B GLN* 2.9 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B PHE* 3.7 28.9 - + - -
230B ALA* 3.8 18.8 - - + -
231B VAL* 3.8 24.0 - - + -
234B ASN* 3.1 29.5 + - - +
235B SER 2.8 29.6 + - - +
236B ASN* 3.6 12.6 - - - +
238B VAL* 1.3 73.0 - - + +
240B ASP* 1.3 64.6 + - - +
242B GLN* 3.2 41.4 - - + +
243B TRP 4.5 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LYS* 3.7 9.3 + - - +
236B ASN* 2.7 34.4 + - - +
237B LYS* 3.5 13.3 - - - +
238B VAL 2.9 1.0 - - - -
239B TRP* 1.3 81.4 - - - +
241B ASP* 1.3 61.4 + - - +
243B TRP* 3.3 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 3.9 9.5 - - - -
155B VAL* 3.5 43.4 + - + +
161B LYS* 2.6 39.6 + - - +
237B LYS* 3.2 29.0 + - - +
238B VAL 3.0 6.2 + - - +
240B ASP* 1.3 73.0 - - - +
242B GLN* 1.3 65.0 + - - +
243B TRP* 3.1 3.6 - - - -
244B ILE* 2.8 24.4 + - + +
245B PHE* 3.8 7.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ASN* 5.0 1.4 + - - +
226B SER* 3.7 8.2 + - - -
227B PHE* 3.6 20.2 + - + -
230B ALA* 3.6 22.8 - - - +
238B VAL* 2.9 15.2 + - - +
239B TRP* 3.2 40.6 - - + +
240B ASP 3.2 1.2 - - - -
241B ASP* 1.3 76.0 - - - +
243B TRP* 1.3 61.6 + - - +
244B ILE 3.2 1.0 + - - -
245B PHE* 3.2 30.1 + - - +
246B TRP* 3.0 36.1 + - + +
----------------------------------------------------------
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