Contacts of the strand formed by residues 265 - 269 (chain A) in PDB entry 4Z3A
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 LEU 265 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ARG 3.1 13.6 + - - +
226A ILE* 4.5 6.7 - - + -
227A ALA* 2.7 32.4 + - - +
254A LEU* 3.8 30.3 - - + -
255A GLN 5.9 1.1 - - - +
257A HIS 4.8 3.4 - - - +
258A LYS* 3.8 28.0 - - + -
263A GLU 3.8 12.6 - - - +
264A THR* 1.3 74.8 - - - +
266A CYS* 1.4 57.8 + - - +
295A LEU* 4.2 11.7 - - + -
299A LEU* 3.8 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ALA* 3.4 4.9 - - - -
229A PHE* 4.0 13.2 - - + -
235A TYR* 3.9 22.4 - - + -
238A PHE* 4.7 0.4 - - - -
243A PHE* 4.1 12.8 - - - -
254A LEU* 3.6 6.8 - - - +
255A GLN* 2.9 33.0 + - + -
257A HIS 3.7 21.9 + - - +
259A ILE* 3.5 33.7 - - - -
265A LEU* 1.4 74.6 - - - +
267A TYR* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ILE* 3.8 21.1 - - + -
227A ALA 2.9 6.6 + - - +
228A VAL* 3.3 7.9 - - + +
229A PHE* 2.8 32.3 + - - +
253A GLY* 3.5 18.9 - - - -
254A LEU* 3.4 22.9 - - + -
266A CYS* 1.3 75.1 - - - +
268A VAL* 1.3 59.8 + - - +
269A MET* 3.5 26.0 - - + -
288A TYR* 2.8 39.3 + - + -
291A LYS* 3.2 22.4 - - + +
292A LEU* 3.9 22.9 - - + -
295A LEU* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PHE* 3.7 5.4 - - + +
231A GLY 4.0 7.4 - - - +
232A LYS* 3.9 32.8 - - + -
235A TYR* 3.5 36.8 - - + -
250A LEU* 5.3 0.4 - - + -
251A GLU 4.8 0.9 - - - +
252A PHE* 3.6 17.4 - - + +
253A GLY* 2.7 34.5 + - - +
255A GLN* 3.5 29.2 - - + +
267A TYR* 1.3 78.5 - - - +
269A MET* 1.4 68.7 + - - +
288A TYR* 4.5 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 5.0 5.6 - - + -
159A PHE* 5.6 1.1 - - + -
228A VAL* 3.7 23.6 - - + -
229A PHE 2.9 9.6 + - - +
230A ASN* 5.0 10.8 - - + +
231A GLY* 3.0 25.6 + - - -
232A LYS 3.8 0.5 + - - -
252A PHE* 3.5 5.2 - - - -
267A TYR* 3.5 25.4 - - + -
268A VAL* 1.4 73.7 - - - +
270A PRO* 1.4 80.6 - - + +
288A TYR* 3.8 25.8 - - + +
289A TYR* 3.5 50.7 - - + +
292A LEU* 4.3 8.1 - - + -
----------------------------------------------------------
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