Contacts of the strand formed by residues 233 - 237 (chain F) in PDB entry 3EXG
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 CYS 233 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F ARG* 2.9 29.0 + - - +
203F GLN 3.4 1.6 - - - +
204F GLY* 3.3 7.0 - - - -
207F ILE* 3.7 25.8 - - + -
209F VAL* 4.4 9.2 - - + -
223F ALA* 3.8 27.6 - - + -
226F LEU* 3.8 28.9 - - - -
231F VAL* 3.6 7.7 + - - -
232F GLU* 1.3 74.8 - - - +
234F GLU* 1.3 58.1 + - - +
235F VAL* 3.6 4.0 - - + -
323F ILE* 4.3 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 234 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200F ILE* 3.7 25.8 - - + +
202F ARG 3.2 13.5 - - - +
203F GLN* 3.3 8.8 - - - +
204F GLY* 2.8 26.0 + - - +
207F ILE 2.9 16.2 + - - +
208F THR* 3.9 1.6 - - - -
209F VAL 3.3 18.2 + - - +
233F CYS* 1.3 70.7 - - - +
235F VAL* 1.3 64.3 + - - +
236F ILE* 3.4 7.7 + - + +
252F SER* 2.8 37.8 + - - +
255F LYS* 2.7 36.6 + - - -
256F THR* 4.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 235 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200F ILE* 3.8 2.9 - - - +
201F GLU* 3.0 25.2 + - + -
202F ARG* 3.4 25.9 + - + +
209F VAL* 3.4 12.3 - - + +
211F SER* 5.9 0.7 - - - -
216F VAL* 4.6 8.5 - - + +
219F CYS* 3.8 29.6 - - + -
220F LEU* 3.7 33.2 - - + -
223F ALA* 4.0 13.5 - - + -
233F CYS* 3.6 5.3 - - + -
234F GLU* 1.3 71.4 - - - +
236F ILE* 1.3 73.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 236 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F ALA* 3.8 26.5 - - + -
199F LYS 3.8 5.2 - - - +
200F ILE* 4.7 12.1 - - + -
201F GLU 5.0 0.2 - - - -
208F THR* 3.7 23.8 - - + -
209F VAL 2.7 14.9 + - - +
210F VAL* 3.9 8.9 - - + -
211F SER* 3.2 24.8 + - - +
216F VAL* 4.4 1.0 - - - +
234F GLU* 3.9 8.5 - - + +
235F VAL* 1.3 85.3 - - - +
237F ASN* 1.3 64.0 + - - +
238F MET* 4.3 2.0 - - - +
248F THR* 4.3 9.6 - - + +
249F ILE* 4.0 26.9 - - + -
252F SER* 4.0 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 237 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146F SER 4.8 2.8 + - - -
148F TRP* 3.9 9.9 - - - +
152F ASP* 3.0 28.9 - - - +
198F ALA* 3.5 0.2 - - - -
199F LYS* 2.9 32.8 + - + +
201F GLU* 3.4 31.3 - - + +
211F SER 3.6 3.6 + - - -
212F HIS* 4.2 4.8 - - - +
216F VAL* 3.7 23.5 - - + +
236F ILE* 1.3 74.1 - - - +
238F MET* 1.3 66.5 + - - +
239F ARG* 3.6 21.0 + - - +
----------------------------------------------------------
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