Contacts of the strand formed by residues 233 - 238 (chain A) in PDB entry 3F7F
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 TYR 233 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 3.3 3.6 - - - +
229A PHE* 2.7 63.5 + + + +
230A HIS* 4.6 8.5 - + + -
232A ARG* 1.3 119.3 + - + +
234A LEU* 1.3 58.7 + - - +
235A ILE* 3.5 1.9 - - + +
245A ILE* 4.2 3.1 - - + -
246A TRP 3.1 8.7 - - - +
247A ASP* 3.2 26.2 - - + -
254A ILE* 5.6 2.0 - - + -
305A VAL* 4.5 14.7 - - + +
311A LEU* 3.1 52.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A PHE* 3.3 24.9 - - + -
169A VAL* 4.9 2.5 - - + -
175A VAL* 3.9 26.0 - - + -
177A PHE* 3.9 23.1 - - + -
183A LEU* 5.4 2.9 - - + -
199A PHE* 5.7 0.7 - - + -
226A CYS* 3.3 26.0 - - - -
227A LYS 3.9 0.4 - - - -
228A LEU* 4.1 14.4 - - + -
232A ARG 3.7 0.4 + - - -
233A TYR* 1.3 72.3 - - - +
235A ILE* 1.3 64.1 + - - +
236A VAL* 3.4 10.7 + - + +
245A ILE* 4.7 0.7 - - - -
246A TRP* 2.7 40.9 + - + +
248A LEU* 4.6 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A CYS* 3.3 3.8 - - - -
227A LYS* 2.9 53.0 + - + +
229A PHE* 3.1 33.9 - - + -
233A TYR* 3.5 9.6 - - + +
234A LEU* 1.3 70.6 - - - +
236A VAL* 1.3 63.2 + - - +
243A LEU* 3.4 35.2 - - + -
244A LYS 4.2 2.5 - - - -
245A ILE* 4.5 19.3 - - + +
280A LEU* 5.0 4.7 - - + +
282A LEU* 5.4 1.6 - - + -
287A LEU* 4.7 17.7 - - + -
303A LEU* 4.2 17.3 - - + -
311A LEU* 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PHE* 3.9 30.1 - - + -
223A VAL* 3.5 20.6 - - + -
225A SER 3.5 4.9 - - - +
226A CYS* 4.1 5.4 - - - -
234A LEU* 3.4 12.3 - - + +
235A ILE* 1.3 80.8 - - - +
237A LEU* 1.3 62.5 + - - +
238A THR* 5.2 1.1 - - + -
242A HIS 5.1 0.4 - - - +
243A LEU* 3.2 20.2 - - - +
244A LYS* 2.8 53.0 + - + +
246A TRP* 4.1 12.6 - - + +
280A LEU* 5.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A VAL* 3.2 2.6 - - - -
224A ILE* 2.6 51.5 + - + +
225A SER* 3.0 15.8 + - - -
236A VAL* 1.3 75.4 - - - +
238A THR* 1.3 55.6 + - - +
241A CYS* 3.5 40.2 - - + -
242A HIS 3.6 4.3 - - - +
243A LEU* 5.0 2.7 - - + +
259A MET* 4.6 4.5 - - + -
279A TYR* 3.5 33.0 - - + -
280A LEU* 3.8 15.7 - - + -
289A THR* 3.8 26.0 - - + -
290A LEU 4.9 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ASP* 3.1 43.1 + - - +
222A SER 3.4 8.3 - - - +
223A VAL* 4.6 9.2 - - + -
224A ILE* 3.6 12.0 - - - +
236A VAL* 5.2 1.1 - - + -
237A LEU* 1.3 78.1 - - - +
239A GLN* 1.3 57.3 + - - +
240A ASN 3.0 2.0 + - - -
241A CYS* 2.8 22.7 + - - -
242A HIS* 2.9 39.4 + - - +
244A LYS* 4.2 20.9 - - + +
----------------------------------------------------------
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