Contacts of the strand formed by residues 269 - 274 (chain C) in PDB entry 1ZR3
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 PHE 269 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C ASP 2.9 4.8 + - - +
211C ALA* 3.0 6.4 - - + -
212C VAL 3.0 23.4 + - - -
259C VAL* 3.6 12.6 - - + -
260C SER 3.2 16.2 - - - +
261C ALA* 3.8 14.4 - - + -
262C GLY* 3.6 2.0 - - - +
267C ALA* 3.3 5.7 - - - +
268C LYS* 1.3 103.0 - - + +
270C VAL* 1.3 64.4 + - - +
301C LYS* 3.4 37.7 - - + -
303C LEU* 3.7 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C VAL* 3.2 8.7 - - + +
214C HIS* 3.6 20.9 - - + -
230C LEU* 4.3 7.6 - - + -
238C PHE* 4.1 11.7 - - + -
259C VAL* 3.3 2.8 - - - -
260C SER* 2.8 37.2 + - - +
261C ALA 4.8 0.4 - - - +
262C GLY* 4.2 7.2 - - - -
265C LEU* 3.4 31.9 - - + -
267C ALA* 5.2 3.4 - - + -
269C PHE* 1.3 77.2 - - - +
271C ILE* 1.3 62.7 + - - +
272C HIS* 3.3 33.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C ALA* 3.6 28.7 - - + -
212C VAL 2.7 10.7 + - - +
213C VAL* 3.1 10.5 - - + +
214C HIS 2.7 30.0 + - - -
257C ALA* 3.9 2.7 - - + -
258C ALA 3.4 2.5 - - - -
259C VAL* 3.8 18.6 - - + -
269C PHE* 5.0 0.2 - - + -
270C VAL* 1.3 74.9 - - - +
272C HIS* 1.3 58.0 + - - +
294C CYS* 3.5 52.7 - - + +
297C LEU* 3.8 16.4 - - + -
298C ALA* 3.9 15.3 - - + +
303C LEU* 4.9 0.7 - - + -
306C ILE* 3.8 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C HIS* 2.8 31.1 + - - +
216C THR* 3.9 14.1 - - + -
220C PHE* 3.9 16.4 - + + -
238C PHE* 4.2 0.9 - + - -
242C VAL* 3.5 31.1 - - + +
245C LEU* 3.2 26.3 - - + +
252C LEU* 3.8 3.1 - - - +
257C ALA* 3.0 4.6 - - - +
258C ALA 2.7 39.0 + - - +
260C SER* 2.8 23.4 + - - -
270C VAL* 3.3 28.1 - - + +
271C ILE* 1.3 72.9 - - - +
273C CYS* 1.3 59.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C VAL* 3.6 25.1 - - - -
214C HIS 2.9 7.5 + - - -
215C PRO* 3.6 15.4 - - - +
216C THR* 2.7 28.6 + - - +
252C LEU* 3.7 3.1 - - - -
256C GLY 3.1 7.0 - - - +
257C ALA* 4.4 0.2 - - + -
272C HIS* 1.3 74.6 - - - +
274C ASN* 1.3 59.8 + - - +
275C SER 3.8 1.7 + - - -
290C THR* 3.4 26.9 - - + -
294C CYS* 3.5 17.0 - - - -
311C ILE* 4.2 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C THR 3.6 3.4 + - - -
217C ASN* 3.5 25.9 - - - +
218C THR* 3.2 15.7 - - - +
252C LEU* 2.9 33.7 - - + +
253C GLU 3.4 20.1 - - - +
254C VAL* 3.5 10.4 + - - +
255C ALA* 2.6 32.4 + - - -
256C GLY 2.8 8.7 + - - -
273C CYS* 1.3 74.4 - - - +
275C SER* 1.3 71.2 + - - +
290C THR* 4.3 2.5 - - - -
316C ASN* 5.0 1.2 - - - +
----------------------------------------------------------
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