Contacts of the helix formed by residues 233 - 245 (chain D) in PDB entry 3MA2
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 ILE 233 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D THR* 3.4 22.0 - - + -
135D VAL* 3.4 34.8 - - + -
140D THR* 3.9 11.7 - - + +
143D ALA* 4.1 10.5 - - + -
144D ILE* 4.3 20.6 - - + -
181D PHE* 4.0 18.2 - - + -
215D PHE* 4.6 8.0 - - + -
221D TRP* 3.6 27.6 - - + -
222D THR 3.0 11.4 + - - +
223D VAL* 4.3 0.9 - - + +
231D ASN 3.3 0.8 + - - -
232D ASP* 1.3 71.6 + - - +
234D PHE* 1.3 59.3 + - - +
236D VAL* 3.4 1.4 + - - +
237D ALA* 2.8 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 234 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D ALA* 3.4 39.7 - - + +
146D LYS* 3.6 31.9 - - + +
147D ALA* 3.5 20.0 - - - -
150D VAL* 3.8 9.0 - - + -
223D VAL* 4.9 1.3 - - + +
232D ASP* 3.0 8.5 + - - +
233D ILE* 1.3 80.2 - - - +
235D LEU* 1.4 66.5 + - + +
237D ALA* 3.2 2.6 + - - +
238D VAL* 2.8 48.4 + - + +
266D THR* 3.7 25.6 - - + -
269D PHE* 3.7 42.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D ASP* 2.8 36.5 + - + +
234D PHE* 1.4 78.5 - - + +
236D VAL* 1.3 63.5 + - - +
238D VAL* 3.2 6.6 + - - +
239D HIS* 3.2 17.7 + - - +
256D ILE* 3.7 21.0 - - + +
261D TYR* 3.7 18.8 - - + +
262D GLN 4.1 6.3 - - - +
263D TRP* 4.5 1.8 - - + -
264D MET* 3.6 33.9 - - + +
266D THR* 3.6 27.8 - - + -
269D PHE* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C THR* 3.8 22.7 - - + +
199D LEU* 4.8 2.0 - - + -
200D ALA* 3.6 31.0 - - + -
215D PHE* 3.8 11.0 - - + -
221D TRP* 3.9 20.0 - - + -
231D ASN* 5.0 0.2 - - + -
232D ASP 3.2 17.5 + - - +
233D ILE 3.9 2.7 - - - +
235D LEU* 1.3 73.4 - - - +
237D ALA* 1.3 67.1 + - - +
239D HIS* 3.3 5.1 + - - +
240D GLU* 2.9 22.8 + - + +
261D TYR* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ILE* 4.3 17.9 - - + -
147D ALA* 3.7 16.2 - - + -
215D PHE* 3.9 24.2 - - + -
233D ILE 2.8 19.8 + - - +
234D PHE* 3.7 4.5 - - - +
236D VAL* 1.3 77.8 - - - +
238D VAL* 1.4 62.8 + - - +
240D GLU* 4.6 1.1 - - - +
241D LEU* 2.8 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D ALA* 3.4 24.2 - - + +
150D VAL* 4.4 8.7 - - + -
151D TRP* 3.0 38.0 + - + +
234D PHE* 2.8 49.0 + - + +
235D LEU* 3.2 7.8 + - - +
237D ALA* 1.4 71.3 - - - +
239D HIS* 1.3 64.9 + - - +
242D GLY 2.9 17.5 + - - -
256D ILE* 3.9 21.1 - - + -
269D PHE* 4.5 5.6 - - + -
271D LEU* 4.4 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C CYS 2.8 6.9 + - - -
302C THR* 3.7 8.8 + - + +
235D LEU 3.2 10.0 + - - +
236D VAL* 3.6 7.6 - - - +
237D ALA 3.3 0.2 - - - -
238D VAL* 1.3 79.0 - - - +
240D GLU* 1.3 81.3 + - - +
242D GLY 3.0 10.2 + - - -
243D HIS* 3.0 9.6 + + - -
249D HIS* 3.4 13.2 - + - -
256D ILE* 2.9 28.4 + - + +
257D MET* 3.3 27.5 - - + +
258D ALA 3.3 19.9 + - - -
259D PRO* 4.2 0.7 - - + -
294D ZN 2.0 37.5 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
301C CYS* 2.9 35.8 + - - -
302C THR* 2.6 27.2 + - - +
200D ALA* 3.5 17.3 - - + +
201D HIS* 3.0 27.3 - - - +
202D ALA* 3.3 16.9 + - + +
213D THR* 3.9 17.5 - - - +
214D HIS 5.6 0.2 - - - +
215D PHE* 4.8 2.5 - - + -
236D VAL* 2.9 21.5 + - + +
237D ALA* 4.4 2.5 - - - +
239D HIS* 1.3 75.9 - - - +
241D LEU* 1.3 59.5 + - - +
243D HIS* 3.1 6.7 + - - +
244D ALA* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ILE* 4.2 10.1 - - + +
147D ALA* 4.0 18.2 - - + -
148D PHE* 3.6 54.7 - - + +
151D TRP* 4.0 14.8 - - + +
177D ILE* 3.9 8.7 - - + -
179D ILE* 4.1 6.3 - - + -
213D THR* 3.6 28.0 - - + +
215D PHE* 5.9 0.9 - - + -
237D ALA* 2.8 23.4 + - + +
240D GLU* 1.3 76.1 - - - +
242D GLY* 1.3 61.7 + - - +
244D ALA* 3.1 6.3 + - + +
245D LEU* 3.0 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D TRP* 3.5 24.7 - - - +
238D VAL 2.9 11.7 + - - -
239D HIS 3.0 6.9 + - - -
241D LEU* 1.3 76.4 - - - +
243D HIS* 1.4 52.9 + - - +
245D LEU* 3.3 6.2 + - - +
246D GLY 3.1 5.5 + - - -
247D LEU* 2.8 44.4 + - - +
257D MET* 4.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C CYS 3.1 12.0 + - - -
368C SER* 3.6 26.2 - - - -
202D ALA* 4.0 8.3 - - + +
203D TYR 4.3 0.9 - - - -
204D PHE* 3.5 24.1 - + + -
239D HIS* 3.0 11.9 + + - -
240D GLU* 3.1 17.9 + - - +
242D GLY* 1.4 75.5 - - - +
244D ALA* 1.3 58.7 + - - +
246D GLY* 2.8 17.2 + - - -
247D LEU 2.7 26.7 + - - -
248D GLU* 4.2 0.9 - - - -
249D HIS* 3.0 29.3 + + - -
257D MET* 3.5 10.6 - - + +
294D ZN 2.1 36.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D TRP* 2.9 26.2 + - - -
177D ILE* 4.2 12.1 - - + -
202D ALA* 4.4 0.2 - - - +
203D TYR 3.6 11.9 - - - +
205D PRO* 3.3 9.5 - - - +
211D GLY* 3.1 26.2 - - - +
213D THR* 3.4 20.0 - - + -
240D GLU 3.0 5.4 + - - +
241D LEU* 3.1 12.3 + - + +
243D HIS* 1.3 77.7 - - - +
245D LEU* 1.4 57.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
117D LEU 4.6 1.0 - - - +
119D TRP* 3.9 22.2 - - + +
124D ILE* 4.1 4.7 - - + -
148D PHE* 5.5 0.7 - - + -
151D TRP* 3.7 41.7 - - + -
157D LEU* 4.3 10.1 - - + -
159D PHE* 3.8 31.6 - - + -
177D ILE* 4.2 9.6 - - + -
205D PRO* 3.5 6.5 - - - +
241D LEU* 3.0 14.6 + - + +
242D GLY* 3.7 7.0 - - - +
243D HIS 3.1 0.4 - - - -
244D ALA* 1.4 76.5 - - - +
246D GLY* 1.3 56.6 + - - +
247D LEU 3.7 0.2 - - - -
279D ILE* 4.5 11.7 - - + -
282D LEU* 3.8 1.8 - - - +
283D TYR* 2.6 39.3 + - + -
----------------------------------------------------------
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