Contacts of the strand formed by residues 225 - 230 (chain D) in PDB entry 3ZXR
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 225 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D GLU* 4.5 3.2 - - - +
136D PHE 3.3 15.9 - - - +
137D TYR* 3.5 34.6 + - + -
218D HIS* 3.1 14.4 + - - -
219D GLU* 2.8 37.4 + - + +
220D VAL 3.5 1.6 + - - -
221D GLY* 2.8 42.0 + - - +
224D GLY* 1.3 77.2 - - - +
226D ALA* 1.3 62.6 + - - +
271D ASN* 3.7 7.7 + - - +
272D GLY 2.7 30.1 + - - -
273D SER* 3.0 19.6 + - - +
505D P3S 4.2 2.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D GLU* 3.4 7.1 - - - +
136D PHE* 2.7 62.0 + - + -
138D ILE* 4.3 4.3 - - + -
199D ARG* 3.6 27.8 - - - +
217D HIS 3.5 4.9 - - - -
219D GLU* 3.9 5.3 - - - +
224D GLY 4.2 5.2 - - - +
225D GLN* 1.3 75.8 - - - +
227D GLU* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D GLU* 2.9 15.1 - - + +
134D ALA 4.8 1.8 - - - +
135D GLU* 3.2 13.7 - - + +
136D PHE* 4.6 2.7 - - - -
199D ARG* 4.9 0.2 - - - -
216D GLY* 3.2 2.3 - - - -
217D HIS* 2.8 61.2 + - + +
219D GLU* 2.9 7.7 - - + +
226D ALA* 1.3 76.4 - - - +
228D ILE* 1.3 68.8 + - - +
229D ASN* 3.0 24.2 + - - +
502D MG 2.0 32.1 - - - -
504D MG 2.2 25.6 - - - -
505D P3S 2.9 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ALA 5.1 0.5 - - - +
133D GLU* 5.0 0.7 - - - -
134D ALA 4.8 5.2 + - - +
136D PHE* 4.4 6.0 - - + -
199D ARG* 4.1 17.5 - - + +
202D MET* 3.7 36.3 - - + -
203D LEU* 3.7 9.9 - - + +
206D LEU* 3.7 22.9 - - + -
213D LEU* 3.7 15.7 - - + -
215D LYS 3.3 9.2 - - - +
216D GLY* 3.9 11.2 - - - -
217D HIS 4.9 0.2 - - - +
227D GLU* 1.3 81.5 - - - +
229D ASN* 1.3 74.1 + - - +
230D TYR* 4.3 2.8 + - - -
245D TYR* 3.3 33.4 + - + +
249D ILE* 4.1 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ALA 4.4 2.0 + - - -
133D GLU* 3.9 14.3 - - - +
213D LEU* 3.4 10.3 - - - +
214D GLU* 2.9 30.6 + - + -
215D LYS* 2.6 51.2 + - - +
227D GLU* 3.0 31.4 + - - +
228D ILE* 1.3 82.7 + - - +
230D TYR* 1.3 60.0 + - - +
501D IQ1 3.9 28.5 - - + +
504D MG 4.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ALA* 4.6 19.3 + - + +
134D ALA 6.2 1.1 - - - -
206D LEU* 5.5 0.2 - - + -
211D PHE* 3.8 25.1 - + + -
212D ILE 3.2 16.8 - - - +
213D LEU* 4.4 7.9 - - + -
214D GLU* 4.2 5.2 - - - +
228D ILE* 4.7 4.0 - - + -
229D ASN* 1.3 76.9 - - - +
231D GLN* 1.3 79.5 + - - +
232D PHE* 3.5 1.2 + - - -
238D ALA* 4.3 4.4 + - + -
241D ASP* 3.7 25.6 - - + -
242D MET* 3.3 43.9 + - + +
245D TYR* 3.5 44.2 - + + -
501D IQ1 3.4 17.0 - - - +
----------------------------------------------------------
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