Contacts of the helix formed by residues 208 - 227 (chain B) in PDB entry 2B9R
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 THR 208 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLN* 3.4 7.0 - - - +
207B TYR* 1.3 74.3 - - - +
209B GLU* 1.3 81.3 + - - +
210B GLU* 3.6 21.1 - - + -
211B SER* 2.7 38.6 + - - -
212B LEU* 3.3 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B TRP* 3.6 40.5 - - + +
199B PRO* 5.1 2.8 - - - +
202B GLN* 2.4 45.9 + - - +
207B TYR 3.7 0.6 + - - -
208B THR* 1.3 82.9 - - - +
210B GLU* 1.3 62.4 + - + +
211B SER 3.0 0.3 + - - -
212B LEU* 3.2 15.7 + - - +
213B LEU* 3.7 7.6 + - - +
216B MET* 5.9 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B THR* 3.6 20.6 - - + +
209B GLU* 1.3 81.2 - - + +
211B SER* 1.3 59.0 + - - +
213B LEU* 3.5 30.8 - - - +
214B PRO* 4.0 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B GLN* 3.1 22.5 + - - -
207B TYR* 3.6 18.2 - - - +
208B THR* 2.7 44.6 + - - -
210B GLU* 1.3 72.8 - - - +
212B LEU* 1.3 60.8 + - - +
213B LEU 3.3 2.0 - - - -
214B PRO* 3.7 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B GLN* 3.8 20.2 - - + +
182B ALA* 3.3 27.4 - - + +
183B GLY* 3.6 17.3 - - - +
186B SER* 4.1 13.7 - - - +
197B TRP* 3.8 39.3 - - + +
207B TYR* 4.1 11.0 - - + -
208B THR 3.7 14.4 - - - +
209B GLU* 3.2 7.2 + - - +
211B SER* 1.3 78.5 - - - +
213B LEU* 1.3 55.8 + - - +
214B PRO* 3.2 2.2 - - - -
215B VAL* 2.8 10.3 + - + +
216B MET* 2.7 43.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B GLU 3.7 5.8 + - - +
210B GLU* 3.5 24.9 + - - +
212B LEU* 1.3 76.6 - - - +
214B PRO* 1.3 61.4 - - + +
216B MET* 4.4 10.5 - - + -
217B GLN* 2.8 67.3 + - + +
260B GLN* 5.8 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B PHE* 3.9 20.9 - - + -
179B GLN* 5.4 0.7 - - - +
210B GLU 4.0 3.4 - - - +
211B SER* 3.7 15.3 - - - +
212B LEU 3.3 2.7 - - - -
213B LEU* 1.3 101.8 - - + +
215B VAL* 1.3 63.0 + - + +
217B GLN* 3.3 11.2 + - - +
218B HIS* 3.0 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B MET* 3.9 11.6 - - + +
175B PHE* 3.9 25.1 - - + -
179B GLN* 3.7 44.6 - - + +
180B ILE* 4.4 7.0 - - + +
183B GLY* 3.7 24.7 - - - -
211B SER 4.3 0.2 - - - +
212B LEU* 2.8 21.2 + - - +
214B PRO* 1.3 70.7 - - + +
216B MET* 1.3 66.0 + - - +
218B HIS* 3.6 1.7 + - - +
219B LEU* 3.1 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLY* 3.9 11.9 - - - +
186B SER* 3.2 27.4 - - - +
187B LEU* 3.5 49.3 - - + +
190B LYS* 3.7 29.2 - - + +
209B GLU 5.9 1.1 - - - +
212B LEU* 2.7 26.5 + - - +
213B LEU* 3.7 11.9 - - + +
215B VAL* 1.3 73.0 - - - +
217B GLN* 1.3 67.5 + - - +
219B LEU* 3.0 15.9 + - - +
220B ALA* 3.0 14.0 + - - +
260B GLN* 5.0 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LEU* 2.8 51.4 + - + +
214B PRO* 3.5 12.2 - - - +
216B MET* 1.3 73.5 - - - +
218B HIS* 1.3 66.5 + - + +
220B ALA* 3.2 4.2 + - - +
221B LYS* 3.0 19.8 + - - +
260B GLN* 3.9 43.6 + - + +
261B ASP 4.3 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ASP* 4.0 4.0 - - - +
171B ASP* 3.6 31.0 + - + +
172B MET* 3.6 22.9 - - + -
174B HIS* 5.5 1.3 - - - -
175B PHE* 3.9 17.7 - + - -
214B PRO* 3.0 28.6 + - + -
215B VAL 3.9 2.9 - - - +
217B GLN* 1.3 77.7 - - + +
219B LEU* 1.3 68.2 + - - +
221B LYS* 2.9 46.7 - - + +
222B ASN* 2.9 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU* 3.3 39.7 - - + +
165B LEU* 4.7 3.8 - - + +
166B THR* 3.4 21.1 - - + -
172B MET* 4.4 3.1 - - + -
180B ILE* 5.2 0.7 - - + +
183B GLY 3.9 6.5 - - - +
184B ALA* 3.6 33.4 - - + +
187B LEU* 4.0 16.6 - - + -
215B VAL* 3.1 26.2 + - + +
216B MET* 3.0 15.1 + - - +
218B HIS* 1.3 73.5 - - - +
220B ALA* 1.3 67.6 + - - +
222B ASN* 2.5 22.3 + - + +
223B VAL* 2.9 15.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU* 4.3 13.3 - - + +
216B MET 3.0 6.2 + - - +
217B GLN 3.4 7.9 - - - +
219B LEU* 1.3 76.8 - - - +
221B LYS* 1.3 53.9 + - - +
223B VAL* 2.9 14.3 + - - +
224B VAL* 2.5 40.7 + - + +
257B ALA* 3.6 22.4 - - + +
259B VAL* 5.2 0.7 - - - -
260B GLN* 3.6 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ASP* 3.2 35.7 + - - -
171B ASP* 4.4 14.3 - - - +
217B GLN 3.0 10.6 + - - +
218B HIS* 2.9 28.8 + - + +
220B ALA* 1.3 75.7 - - - +
222B ASN* 1.3 56.8 + - - +
224B VAL* 3.3 9.7 - - - +
225B MET* 2.7 54.8 + - + +
260B GLN* 5.1 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 3.7 31.6 + - + +
166B THR* 5.6 1.3 - - + -
168B LEU* 5.4 5.7 - - - +
169B ASP* 3.4 41.2 + - - +
172B MET* 4.5 3.5 - - - +
218B HIS 2.9 14.1 + - - +
219B LEU* 2.5 16.0 + - + +
221B LYS* 1.3 72.5 + - - +
223B VAL* 1.3 65.7 + - - +
225B MET* 3.0 15.0 + - - +
226B VAL* 2.8 29.2 + - + +
231B THR* 5.7 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B TYR* 4.7 6.7 - - + +
162B LEU* 3.6 28.3 - - + -
165B LEU* 3.4 15.0 - - + +
187B LEU* 4.8 3.1 - - + -
191B ILE* 6.0 1.8 - - + -
219B LEU* 2.9 19.6 + - + +
220B ALA* 3.3 10.8 - - - +
222B ASN* 1.3 70.8 - - - +
224B VAL* 1.3 62.6 + - - +
226B VAL* 4.0 3.0 - - - +
227B ASN* 3.0 33.8 + - - +
253B GLN* 3.5 35.4 - - + +
254B LEU* 4.8 0.4 - - + -
257B ALA* 4.8 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ALA* 2.5 20.5 + - + +
221B LYS* 3.3 13.2 - - - +
223B VAL* 1.3 71.0 - - - +
225B MET* 1.3 63.7 + - + +
227B ASN* 2.7 31.4 + - - +
228B GLN* 3.7 20.7 + - + +
229B GLY* 6.2 0.7 - - - -
254B LEU* 4.0 21.8 - - + -
257B ALA* 4.2 12.1 - - + +
259B VAL* 4.3 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LYS* 2.7 46.8 + - + +
222B ASN* 3.0 16.1 + - - +
224B VAL* 1.3 78.1 - - + +
226B VAL* 1.3 61.2 + - - +
229B GLY* 3.2 32.2 + - - -
230B LEU* 3.5 27.8 - - + +
231B THR* 3.4 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B TYR* 3.7 11.0 - - - +
165B LEU* 4.1 20.2 - - + -
168B LEU* 6.1 1.1 - - + -
222B ASN* 2.8 14.6 + - + +
223B VAL* 4.0 2.7 - - - +
225B MET* 1.3 75.3 - - + +
227B ASN* 1.3 64.0 + - - +
228B GLN* 2.6 19.4 + - - -
230B LEU 5.2 0.2 - - - +
231B THR* 4.6 10.1 - - + -
233B HIS 4.5 12.6 - - - +
234B MET* 3.5 38.6 - - - +
237B LYS* 3.4 37.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B TYR* 4.4 5.9 + - - -
223B VAL* 3.0 22.1 + - - +
224B VAL 2.7 10.7 + - - +
226B VAL* 1.3 82.3 - - - +
228B GLN* 1.3 71.3 + - - +
237B LYS* 4.8 9.5 - - - +
249B SER 4.4 9.5 + - - +
251B LEU 5.3 2.0 + - - -
252B PRO 5.5 0.4 - - - -
253B GLN* 4.0 10.2 - - - +
254B LEU* 3.2 50.2 - - + +
----------------------------------------------------------
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