Contacts of the helix formed by residues 238 - 246 (chain D) in PDB entry 2UZ1
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 ASP 238 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D VAL* 4.7 1.8 - - - +
211D LEU 3.1 13.8 + - - +
212D GLY* 3.5 15.7 - - - -
213D SER* 4.2 3.3 + - - -
237D ALA* 1.3 78.3 - - - +
239D TYR* 1.3 67.7 + - - +
240D GLU* 3.3 8.2 + - - +
241D GLY 2.9 28.4 + - - -
242D LEU 3.0 6.9 + - - -
256D LEU* 3.8 4.1 - - - +
257D VAL* 4.0 12.5 - - + +
277D GLY 5.3 0.2 - - - +
278D ALA* 4.7 7.7 - - + +
279D ARG 5.4 0.7 + - - -
283D ASN* 3.7 34.9 + - + +
284D THR* 5.2 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D ASP* 1.3 73.9 - - - +
240D GLU* 1.3 64.1 + - - +
242D LEU* 3.1 17.3 + - - +
243D SER 4.7 0.2 + - - -
256D LEU* 3.9 14.4 - - + -
258D GLN* 3.9 26.2 + - - -
283D ASN* 3.6 25.5 - - + +
397D TYR* 3.4 32.7 + + - -
398D LEU* 4.2 9.4 - - - +
401D SER* 4.3 14.0 + - - -
412D PHE* 3.6 32.0 - + + +
414D CYS* 3.8 25.1 - - + +
415D HIS 3.6 23.6 - - - +
552D GLU* 5.5 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ARG* 2.8 47.8 + - - +
91D ASP* 5.1 4.0 - - - +
213D SER* 3.5 33.4 - - - -
216D SER* 3.5 18.2 + - - -
217D ARG* 2.9 29.8 + - - +
238D ASP* 3.2 8.2 + - - +
239D TYR* 1.3 79.2 - - - +
241D GLY* 1.3 58.9 + - - +
242D LEU 3.7 0.2 + - - -
243D SER* 4.7 5.0 + - - -
412D PHE 4.1 11.8 - - - +
413D LEU* 4.3 4.6 - - - +
414D CYS 4.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D LEU* 4.2 6.1 - - - +
212D GLY 4.1 14.8 - - - -
216D SER* 4.8 0.2 - - - -
237D ALA* 3.3 16.8 - - - +
238D ASP* 2.9 16.8 + - - -
240D GLU* 1.3 78.4 - - - +
242D LEU* 1.3 64.0 + - - +
243D SER 3.3 2.0 - - - -
244D MET* 3.0 27.9 + - - +
245D LEU* 4.1 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D ALA* 3.8 5.8 - - - -
238D ASP 3.0 9.0 + - - +
239D TYR 3.1 15.4 + - - +
240D GLU 3.4 0.2 - - - -
241D GLY* 1.3 77.0 - - - +
243D SER* 1.3 57.6 + - - +
244D MET 3.1 0.2 - - - -
245D LEU* 2.9 40.5 + - + +
246D SER* 4.1 2.3 + - - -
253D ARG* 4.8 8.4 + - - +
255D GLY* 4.2 4.3 - - - +
256D LEU* 3.9 37.5 - - + +
404D MET* 3.9 42.6 - - + +
405D SER* 4.8 0.9 - - - -
409D PRO* 4.5 8.5 - - + +
412D PHE* 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D SER* 4.5 11.8 + - - -
221D LYS* 4.0 17.5 + - - -
239D TYR 4.7 0.6 + - - -
240D GLU 4.7 3.7 + - - -
241D GLY 3.2 0.8 + - - -
242D LEU* 1.3 78.7 - - - +
244D MET* 1.3 60.8 + - - +
245D LEU 3.1 1.6 - - - -
246D SER* 3.3 24.9 + - - -
409D PRO* 3.8 10.5 - - - +
410D GLY 3.7 22.3 + - - +
411D GLY* 3.8 14.2 - - - -
412D PHE* 4.0 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D LEU* 3.7 13.2 - - + -
215D ALA* 3.4 30.1 - - + +
216D SER* 3.9 28.3 - - - +
219D ALA* 3.9 8.3 - - - -
220D ARG 3.8 18.8 - - - +
221D LYS* 3.7 48.5 - - + +
224D LEU* 3.5 28.4 - - + +
241D GLY 3.0 16.0 + - - +
243D SER* 1.3 79.1 + - - +
245D LEU* 1.3 60.3 + - - +
246D SER 3.3 1.0 + - - -
247D GLY 4.7 2.1 + - - -
248D LEU* 4.2 4.0 - - - +
326D ILE* 5.1 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D LEU* 3.6 16.8 - - + -
235D VAL* 3.4 53.4 - - + +
236D PHE* 4.2 7.0 - - - +
237D ALA* 4.3 4.9 - - + -
241D GLY 4.5 0.2 - - - +
242D LEU* 2.9 23.2 + - + +
244D MET* 1.3 76.8 - - - +
246D SER* 1.3 62.4 + - - +
247D GLY 3.3 2.7 - - - -
248D LEU* 3.3 24.0 + - + +
253D ARG* 2.9 35.8 + - + +
254D GLY 4.7 1.3 - - - +
255D GLY* 3.6 32.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D LYS* 6.0 1.6 - - - -
242D LEU 4.4 0.9 + - - -
243D SER* 3.3 18.1 + - - -
244D MET 3.3 0.6 - - - -
245D LEU* 1.3 79.5 - - - +
247D GLY* 1.3 56.9 + - - +
248D LEU 3.4 1.3 + - - +
253D ARG* 4.3 0.8 + - - +
385D ALA* 6.2 2.2 - - - -
408D LYS* 3.3 49.2 - - - +
409D PRO* 2.6 32.7 + - - +
410D GLY* 5.5 0.7 - - - -
----------------------------------------------------------
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