Contacts of the helix formed by residues 227 - 248 (chain B) in PDB entry 2XVU
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 GLU 227 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LYS 3.8 7.8 + - - +
226B ALA* 1.3 78.7 - - - +
228B PHE* 1.3 57.5 + - - +
229B ALA* 4.2 7.6 - - + +
230B GLU* 2.7 34.0 + - + +
231B VAL* 3.1 10.9 + - - +
270B SER 4.9 1.0 + - - -
332B TYR* 3.8 5.9 + - - -
336B ARG* 4.8 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B VAL* 5.1 9.2 - - + -
227B GLU* 1.3 72.5 - - - +
229B ALA* 1.3 61.3 + - + +
231B VAL* 4.0 4.8 - - + +
232B SER* 3.0 41.2 + - - -
325B VAL* 4.4 12.6 - - + -
328B GLY* 3.7 26.7 - - - -
329B MET* 3.7 38.8 - - + -
332B TYR* 3.6 49.8 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLU* 3.1 6.1 - - + +
228B PHE* 1.3 82.3 - - + +
230B GLU* 1.3 65.4 + - - +
232B SER* 3.8 7.3 - - - -
233B LYS* 3.2 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ALA* 4.4 4.5 - - + -
227B GLU* 2.7 24.4 + - + +
229B ALA* 1.3 77.8 - - - +
231B VAL* 1.3 65.8 + - - +
233B LYS* 2.9 20.1 + - - +
234B LEU* 2.9 20.8 + - + +
263B TYR* 3.0 32.4 + - - -
267B ASN* 4.2 9.4 + - - +
270B SER* 4.1 14.2 - - - +
271B ILE* 3.8 33.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B VAL* 4.4 10.8 - - + +
219B LEU* 4.2 21.8 - - + -
220B SER* 4.0 22.0 - - - +
223B PHE* 4.5 8.5 - - + +
226B ALA* 4.2 17.9 - - + -
227B GLU 3.1 10.7 + - - +
228B PHE* 4.1 10.3 - - + +
230B GLU* 1.3 74.5 - - - +
232B SER* 1.3 58.9 + - - +
234B LEU* 3.1 12.7 + - + +
235B VAL* 2.8 37.8 + - + +
332B TYR* 4.3 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B VAL* 5.9 3.4 - - - -
228B PHE* 3.0 38.3 + - - -
229B ALA* 3.8 9.0 - - - -
230B GLU 3.1 0.2 - - - -
231B VAL* 1.3 80.1 - - - +
233B LYS* 1.3 57.6 + - - +
235B VAL* 4.0 7.3 - - - +
236B THR* 2.9 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ALA 3.2 14.6 + - - +
230B GLU* 2.9 14.0 + - - +
232B SER* 1.3 74.5 - - - +
234B LEU* 1.3 69.4 + - - +
236B THR* 3.3 13.7 + - - -
237B ASP* 3.1 44.3 + - - +
263B TYR* 3.6 49.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 3.9 15.5 - - + -
223B PHE* 3.9 33.2 - - + -
230B GLU* 2.9 19.6 + - + +
231B VAL* 3.4 13.5 - - + +
233B LYS* 1.3 78.2 - - + +
235B VAL* 1.3 57.9 + - - +
237B ASP* 3.0 10.0 + - - +
238B LEU* 2.9 30.8 + - - +
260B LEU* 4.3 9.3 - - + +
263B TYR* 4.0 27.6 - - + -
264B ILE* 4.2 22.0 - - + -
271B ILE* 4.4 16.8 - - + -
2001B 9DN 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B LYS* 3.9 33.2 - - + +
215B ALA* 3.6 32.8 - - + +
216B VAL* 3.6 26.9 - - + +
219B LEU* 4.2 8.5 - - + +
231B VAL* 2.8 24.6 + - + +
232B SER* 4.0 7.2 - - - +
234B LEU* 1.3 72.7 - - - +
236B THR* 1.3 60.2 + - - +
238B LEU* 3.8 6.6 - - - +
239B THR* 2.9 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B LYS* 5.4 10.3 + - - +
232B SER* 2.9 15.6 + - - -
233B LYS* 3.3 12.2 + - - -
234B LEU 3.2 1.0 - - - -
235B VAL* 1.3 81.3 - - - +
237B ASP* 1.3 66.4 + - - +
239B THR* 3.7 7.1 - - - +
240B LYS* 3.4 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LYS* 3.1 46.8 + - - +
234B LEU* 3.0 6.5 + - - +
236B THR* 1.3 78.7 - - - +
238B LEU* 1.3 61.3 + - - +
239B THR 3.0 1.6 - - - -
240B LYS* 2.7 28.4 + - - +
241B VAL* 2.9 14.7 + - + +
260B LEU* 3.4 25.5 - - + +
263B TYR* 5.8 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B PHE* 4.6 6.7 - - + -
214B TRP* 5.4 2.5 - - + -
215B ALA* 4.9 11.0 - - + -
219B LEU* 4.2 22.4 - - + -
234B LEU 2.9 16.2 + - - +
235B VAL* 3.8 5.4 - - - +
237B ASP* 1.3 75.6 - - - +
239B THR* 1.3 61.7 + - - +
241B VAL* 3.3 6.7 + - + +
242B HIS* 3.1 56.4 + - + +
260B LEU* 3.4 11.5 - - + +
2001B 9DN 3.5 58.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU* 4.8 2.5 - - + +
208B GLU* 4.2 30.7 - - + +
211B PHE* 3.3 29.8 - - + -
212B LYS* 3.7 17.5 - - - +
235B VAL* 2.9 24.6 + - - +
236B THR* 3.7 7.9 - - - +
238B LEU* 1.3 78.0 - - - +
240B LYS* 1.3 53.7 + - - +
242B HIS* 3.9 0.9 - - - +
243B THR* 2.4 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B THR 3.4 9.6 + - - +
237B ASP* 2.7 16.6 + - - +
239B THR* 1.3 73.7 - - - +
241B VAL* 1.3 67.3 + - + +
243B THR* 3.2 5.1 + - - -
244B GLU* 2.8 39.4 + - - +
256B ASP* 5.7 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TYR* 3.3 29.2 - - + +
237B ASP* 2.9 18.3 + - + +
238B LEU* 3.3 9.8 + - + +
240B LYS* 1.3 77.6 - - - +
242B HIS* 1.3 63.5 + - + +
244B GLU* 3.0 9.2 + - - +
245B CYS 2.8 25.3 + - - -
253B CYS* 3.5 19.4 - - - +
256B ASP* 4.1 10.8 - - + +
257B ARG* 3.9 31.9 - - + +
260B LEU* 4.4 10.3 - - + -
2001B 9DN 5.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TYR* 4.0 19.0 - + - -
196B GLN* 3.2 23.4 + - - +
199B LYS* 3.4 31.7 - - + +
203B LEU* 4.0 9.6 - - + -
211B PHE* 3.5 26.9 - + + -
238B LEU* 3.1 44.6 + - + +
239B THR 4.2 1.6 - - - +
241B VAL* 1.3 79.5 - - + +
243B THR* 1.3 63.7 + - - +
245B CYS* 4.4 4.0 - - - +
246B CYS* 2.8 31.2 + - - +
2001B 9DN 3.5 18.8 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU* 3.8 20.8 - - + +
208B GLU* 5.9 0.2 - - - +
239B THR* 2.4 41.0 + - - +
240B LYS* 3.5 7.9 - - - -
242B HIS* 1.3 75.9 - - - +
244B GLU* 1.3 60.7 + - + +
246B CYS* 3.9 2.4 - - - +
247B HIS* 3.0 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LYS* 2.8 30.0 + - + +
241B VAL 3.5 2.0 - - - +
243B THR* 1.3 77.3 - - + +
245B CYS* 1.3 66.6 + - - +
247B HIS 3.2 1.6 + - - -
248B GLY 3.2 4.9 + - - -
249B ASP* 3.1 52.3 + - + +
252B GLU* 3.3 23.7 - - + +
253B CYS* 3.8 5.3 + - + -
256B ASP* 2.7 36.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLN* 5.6 0.5 - - - +
106B LYS* 5.1 4.2 + - - -
148B TYR* 5.6 4.3 - - - +
149B PHE 5.7 0.7 - - - +
150B TYR* 3.7 19.1 - - + -
151B ALA* 4.0 13.9 - - - +
152B PRO* 3.6 22.7 - - - -
196B GLN* 4.7 3.1 - - - +
200B CYS* 5.2 0.4 - - - -
241B VAL 2.8 13.5 + - - +
242B HIS* 4.1 3.8 - - - +
244B GLU* 1.3 74.2 - - - +
246B CYS* 1.3 61.2 + - - +
247B HIS 3.4 0.3 + - - -
248B GLY* 3.5 7.1 + - - -
250B LEU* 3.6 16.2 - - + +
253B CYS* 2.0 46.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 4.9 2.4 - - - +
106B LYS* 4.3 11.4 + - - -
148B TYR* 4.4 12.2 - - - +
196B GLN* 3.9 11.0 - - - -
199B LYS 4.2 2.7 - - - -
200B CYS* 2.0 65.3 - - + +
203B LEU* 4.4 9.6 - - + -
242B HIS* 2.8 27.4 + - - +
243B THR 3.9 2.9 - - - +
245B CYS* 1.3 77.8 - - - +
247B HIS* 1.3 60.0 + - + +
248B GLY 3.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 3.7 2.6 + - - -
67B HIS* 4.2 7.4 - - - -
99B ASN* 3.3 26.9 - - - -
100B GLU* 3.2 25.8 + - + -
103B LEU* 3.2 34.0 - - + +
243B THR* 3.0 21.4 + - + +
244B GLU 3.2 2.9 + - - +
246B CYS* 1.3 78.5 - - - +
248B GLY* 1.3 56.9 + - - +
249B ASP* 3.4 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA* 4.8 6.1 - - - +
29B GLN* 6.0 0.4 - - - -
30B TYR* 4.0 19.9 + - - -
67B HIS* 5.3 1.6 - - - -
103B LEU* 4.3 3.6 - - - +
106B LYS* 4.9 5.3 - - - +
244B GLU 3.2 3.4 + - - -
245B CYS 3.5 2.8 + - - -
246B CYS 3.4 4.4 + - - -
247B HIS* 1.3 78.1 - - - +
249B ASP* 1.3 51.5 + - - +
250B LEU* 2.5 39.9 + - - +
----------------------------------------------------------
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