Contacts of the strand formed by residues 211 - 223 (chain B) in PDB entry 2MPR
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 211 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B TYR* 2.8 31.4 + - + +
194B GLY 3.2 14.6 - - - +
195B ARG* 3.7 5.4 - - + -
209B SER 2.8 14.9 + - - +
210B LYS* 1.3 90.4 + - - +
212B GLY* 1.3 61.3 + - - +
213B TRP* 5.5 1.3 + - - -
237B ASP* 3.3 13.5 - - - +
238B ALA* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B TYR* 3.3 8.7 - - - -
194B GLY 3.0 26.9 + - - -
211B ASP* 1.3 82.5 - - - +
213B TRP* 1.3 67.3 + - - -
236B THR* 3.4 22.4 - - - -
237B ASP* 5.3 0.2 - - - -
238B ALA* 3.9 1.2 - - - +
239B MET* 3.5 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 3.7 32.1 - - + -
192B ASP 3.3 11.9 - - - -
193B TYR* 3.4 39.0 - + + -
211B ASP* 5.5 1.3 + - - -
212B GLY* 1.3 80.8 - - - -
214B MET* 1.3 61.6 + - - +
215B PHE* 3.8 29.2 - + + -
234B TYR 4.0 0.8 - - - +
235B ALA* 3.3 1.9 - - - -
236B THR* 2.7 44.2 + - + +
239B MET* 3.5 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B TRP* 5.2 1.3 - - - -
190B GLY 4.1 0.3 - - - +
191B VAL* 3.5 4.0 - - - +
192B ASP* 2.9 40.5 + - + +
213B TRP* 1.3 75.5 - - - +
215B PHE* 1.3 73.6 + - - +
216B THR* 4.5 4.3 - - - +
233B GLN* 4.3 17.3 - - + +
234B TYR 3.3 12.8 - - - +
235B ALA* 3.7 9.4 - - + -
239B MET* 4.1 17.7 - - + +
243B GLY* 3.3 35.0 - - - +
244B LYS* 3.9 3.6 - - - +
245B GLY* 3.6 22.2 - - - +
279B MET* 3.5 22.0 - - + -
281B ARG* 4.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B GLY 3.6 3.8 - - - +
191B VAL* 3.9 34.5 - - + -
213B TRP* 3.8 36.6 - + + -
214B MET* 1.3 74.5 - - - +
216B THR* 1.3 63.3 + - - +
232B VAL 3.8 0.6 - - - +
233B GLN* 3.1 8.0 - - - +
234B TYR* 2.9 65.0 + + + +
236B THR* 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B TYR* 5.7 0.7 - - + -
120B TRP* 3.6 45.7 + - + -
188B GLU 5.3 0.2 - - - +
189B LEU* 3.4 5.9 - - - +
190B GLY 2.9 36.3 + - - +
192B ASP* 5.2 1.2 + - - -
214B MET* 4.5 6.1 - - - +
215B PHE* 1.3 73.5 + - - +
217B ALA* 1.3 70.8 + - - +
218B GLU* 4.2 3.6 - - + +
231B VAL* 4.4 6.7 - - + -
232B VAL 3.6 3.6 - - - -
233B GLN* 2.8 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU* 4.7 7.0 - - + -
188B GLU 3.4 5.8 - - - -
189B LEU* 4.0 16.2 - - + -
216B THR* 1.3 75.6 - - - +
218B GLU* 1.3 60.6 + - - +
219B HIS 4.3 0.2 - - - -
230B PHE* 3.7 1.3 - - - +
231B VAL* 3.4 4.7 - - - +
232B VAL* 3.0 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B HIS* 2.9 32.6 + - + +
119B TYR* 2.6 36.3 + - - -
120B TRP* 5.4 0.4 - - + -
186B VAL 3.8 0.7 - - - +
187B LEU* 3.4 4.6 - - - +
188B GLU* 2.9 51.4 + - + +
216B THR* 4.2 6.9 - - + -
217B ALA* 1.3 74.8 - - - +
219B HIS* 1.3 67.0 + - - +
220B THR* 4.1 7.3 + - - +
229B LYS* 3.3 27.9 + - + +
230B PHE 3.4 3.4 - - - +
231B VAL* 3.7 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B THR* 3.4 15.4 + - + -
182B ASN* 3.0 22.4 + - - -
185B GLY* 3.6 5.1 - - - -
186B VAL 3.2 20.0 - - - -
187B LEU* 4.2 13.7 - - + +
218B GLU* 1.3 74.5 - - - +
220B THR* 1.3 68.7 + - - +
221B GLN* 3.3 31.8 + - + +
228B ASN* 3.5 3.5 + - - +
229B LYS* 3.2 5.4 - - - +
230B PHE* 2.9 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASP 3.6 1.2 - - - +
185B GLY* 3.3 2.9 - - - -
186B VAL* 2.8 43.4 + - - +
218B GLU* 4.1 6.4 + - - +
219B HIS* 1.3 75.9 - - - +
221B GLN* 1.3 64.0 + - - +
222B SER* 5.1 4.7 - - - +
227B TYR* 4.2 18.2 - - + -
228B ASN 3.5 1.8 - - - -
229B LYS* 2.9 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ASN* 2.7 25.6 + - - +
183B PRO 3.0 17.8 + - - -
184B ASP* 3.0 26.6 + - - +
185B GLY* 3.3 7.8 - - - -
219B HIS* 3.3 14.8 - - + +
220B THR* 1.3 74.7 - - - +
222B SER* 1.3 68.7 + - - +
223B MET* 3.7 14.6 + - + +
227B TYR* 3.2 6.3 - - - -
228B ASN* 2.9 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASP* 2.9 33.1 + - - +
220B THR* 5.2 5.4 + - - +
221B GLN* 1.3 81.8 + - - +
223B MET* 1.3 65.9 + - - +
226B GLY 3.5 9.6 - - - -
227B TYR* 4.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLN* 3.9 20.0 - - + +
222B SER* 1.3 77.4 - - - +
224B LEU* 1.3 84.2 + - + +
225B LYS 3.1 3.4 - - - -
226B GLY* 2.7 34.3 + - - +
227B TYR* 3.8 3.1 + - - -
228B ASN* 4.4 14.6 - - + -
288B ILE* 3.9 22.0 - - + +
298B TYR* 4.5 11.0 - - - +
----------------------------------------------------------
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