Contacts of the strand formed by residues 238 - 242 (chain A) in PDB entry 2VZ3
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 GLN 238 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A MET* 4.3 1.6 - - - -
234A ASP* 2.7 50.1 + - - +
236A ASN* 3.7 15.4 - - + +
237A GLY* 1.3 79.7 - - - +
239A ILE* 1.3 64.1 + - - +
240A VAL 3.4 0.9 + - - -
252A LEU* 3.5 31.9 - - + +
253A TYR 3.4 9.9 - - - +
254A ASP* 3.0 31.6 + - - +
261A ILE* 3.7 24.0 - - - +
302A TYR* 4.8 1.2 + - - -
304A PRO* 6.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ALA* 3.6 28.3 - - + -
176A ILE 4.2 12.1 - - - +
178A PRO* 5.4 5.2 - - + -
184A LEU* 4.6 4.0 - - + -
186A TRP* 5.0 2.5 - - + -
231A ILE* 3.6 30.1 - - + -
232A SER 3.3 6.1 - - - +
233A MET* 4.2 13.0 - - + +
237A GLY 5.4 1.6 - - - +
238A GLN* 1.3 71.4 - - - +
240A VAL* 1.3 61.8 + - - +
241A VAL* 3.6 12.2 + - + +
251A SER 3.4 2.8 - - - +
252A LEU* 3.3 5.8 - - - -
253A TYR* 2.8 66.8 + - + +
255A SER* 6.4 0.4 - - - -
260A TRP* 5.8 0.4 - - + -
578A THR* 4.4 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLY 3.6 1.4 - - - +
231A ILE* 3.3 5.4 - - - -
232A SER* 2.6 35.2 + - - +
234A ASP* 3.5 31.4 - - + +
238A GLN 3.8 4.0 - - - +
239A ILE* 1.3 72.5 - - - +
241A VAL* 1.3 60.9 + - - +
242A THR* 4.1 13.0 + - + -
250A THR* 3.8 22.9 - - + -
251A SER 3.7 2.9 - - - -
252A LEU* 3.8 7.6 - - + -
275A SER* 4.7 0.7 + - - -
283A VAL* 4.2 11.2 - - + -
302A TYR* 3.7 20.6 - - + -
309A TRP* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TRP* 3.9 22.7 - - + -
224A HIS* 3.3 5.5 - - + -
226A MET* 3.8 31.2 - - + -
229A PRO* 3.5 27.6 - - + -
230A GLY 3.3 3.8 - - - +
231A ILE* 4.5 2.0 - - + -
239A ILE* 4.0 14.1 - - + +
240A VAL* 1.3 75.6 - - - +
242A THR* 1.3 61.4 + - - +
250A THR* 3.3 2.3 - - - -
251A SER 2.8 41.6 + - - +
260A TRP* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A HIS* 4.0 0.2 - - - -
229A PRO* 3.1 3.2 - - - +
230A GLY* 2.9 35.6 + - - -
240A VAL* 4.1 10.1 - - + +
241A VAL* 1.3 78.0 - - - +
243A GLY* 1.3 67.0 + - - +
249A LYS 3.4 1.8 - - - -
250A THR* 3.7 12.8 - - - +
266A MET* 3.7 12.6 - - - -
273A GLN* 2.8 38.2 + - - +
275A SER* 4.6 7.1 + - - -
285A THR* 5.0 0.9 + - - -
309A TRP* 3.3 35.9 - - + -
----------------------------------------------------------
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