Contacts of the helix formed by residues 249 - 265 (chain L) in PDB entry 5GJQ
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 ALA 249 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279K THR* 5.5 0.2 - - - +
247L THR* 3.0 16.1 - - + +
248L SER* 1.3 74.4 - - - +
250L ASP* 1.3 60.2 + - - +
251L ARG 3.0 2.0 - - - -
252L GLU* 2.7 39.9 + - - +
253L ILE* 3.6 6.3 + - - +
259M MET 5.7 3.6 - - - +
261M ILE* 4.5 19.9 - - + +
308M ARG* 5.8 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 250 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243L PHE* 2.9 42.0 - - + -
245L GLU* 5.8 0.4 - - + -
246L GLY* 4.0 14.4 - - - +
247L THR* 3.2 20.5 + - - +
249L ALA* 1.3 82.8 - - - +
251L ARG* 1.3 57.7 + - - +
253L ILE* 3.1 10.6 + - - +
254L GLN* 2.5 40.1 + - - +
301M ALA* 5.1 0.2 - - - +
302M GLY 4.4 6.1 + - - +
304M ARG* 3.4 26.7 - - - +
308M ARG* 4.4 1.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 251 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272K THR* 4.0 27.0 + - + +
274K ARG* 1.8 58.8 + - - +
275K PHE* 4.2 5.5 + - - +
276K ASP* 5.1 1.6 - - - +
282K ASP* 4.9 5.1 + - - +
245L GLU* 3.1 42.4 + - - +
246L GLY 3.8 13.4 + - - -
247L THR 3.8 11.4 + - - -
248L SER* 3.6 21.9 + - - +
249L ALA 2.9 0.2 + - - -
250L ASP* 1.3 80.9 - - - +
252L GLU* 1.3 52.2 + - - +
254L GLN* 3.6 10.0 - - + +
255L ARG* 2.6 59.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 252 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281K ALA* 3.7 24.4 - - + +
206L LYS* 4.1 9.7 - - - +
207L TYR 4.8 0.3 + - - -
208L ILE* 3.7 29.8 + - - +
248L SER 4.8 4.9 - - - +
249L ALA* 2.7 20.0 + - - +
251L ARG* 1.3 73.8 - - - +
253L ILE* 1.3 57.8 + - - +
255L ARG* 3.2 27.5 + - - +
256L THR* 2.7 32.0 + - - -
261M ILE* 3.3 37.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 253 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204L VAL* 3.9 15.7 - - + -
211L SER* 5.1 2.5 - - - +
237L ALA 4.1 4.0 - - - +
238L ILE* 3.4 32.8 - - + +
240L GLY* 5.8 2.0 - - - -
249L ALA 4.2 3.8 - - - +
250L ASP* 3.1 8.4 + - - +
252L GLU* 1.3 73.4 - - - +
254L GLN* 1.3 60.4 - - - +
256L THR* 2.9 11.2 + - + +
257L LEU* 2.2 38.7 + - + +
261M ILE* 3.0 35.2 - - + -
304M ARG* 5.9 1.3 - - + +
308M ARG* 3.0 42.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 254 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268K ASP* 4.8 4.7 - - - +
240L GLY* 5.1 2.4 - - - -
241L ARG 4.6 4.2 - - - +
242L ARG* 3.3 50.6 - - - +
243L PHE* 3.7 17.5 + - - +
245L GLU* 4.6 9.4 - - - +
250L ASP* 2.5 41.2 + - - +
251L ARG* 3.6 11.0 + - + +
253L ILE* 1.3 75.8 - - - +
255L ARG* 1.3 58.4 + - + +
257L LEU* 2.2 40.4 + - - +
258L MET* 2.5 23.5 + - + -
304M ARG* 4.7 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 255 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233K SER* 3.6 21.9 + - - +
236K VAL* 4.4 19.7 - - + +
268K ASP* 4.9 0.9 + - - -
269K ALA* 3.1 39.9 + - + +
272K THR* 5.7 2.5 + - - -
281K ALA* 5.2 3.8 + - - +
282K ASP* 5.1 4.2 + - - -
285K VAL* 3.9 26.3 - - - +
208L ILE 4.5 4.0 + - - -
248L SER 5.1 1.2 + - - -
251L ARG* 2.6 52.4 + - - +
252L GLU* 3.2 31.1 + - - +
254L GLN* 1.3 75.1 - - - +
256L THR* 1.3 50.0 + - - +
258L MET* 2.4 21.8 + - - +
259L GLU* 2.4 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 256 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203L ILE* 5.1 4.0 - - + -
204L VAL* 5.5 2.9 - - + -
209L GLY* 6.0 1.0 - - - -
211L SER* 3.2 40.7 - - - +
212L ALA* 4.3 2.1 + - - +
215L ILE* 3.2 34.4 - - + +
238L ILE* 4.1 12.1 - - + -
252L GLU 2.7 14.1 + - - -
253L ILE* 2.9 19.2 + - + +
254L GLN 2.7 1.8 + - - -
255L ARG* 1.3 74.2 - - - +
257L LEU* 1.3 59.8 + - - +
259L GLU* 3.2 19.4 + - - +
260L LEU* 3.2 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235L ILE* 6.1 0.2 - - + -
238L ILE* 2.1 54.8 - - + +
239L GLY 3.7 14.4 - - - +
240L GLY* 5.1 3.4 - - - -
241L ARG 5.4 0.7 - - - +
242L ARG* 4.6 8.5 - - + +
253L ILE* 2.2 15.5 + - + +
254L GLN* 2.2 33.4 + - - +
256L THR 1.3 64.0 - - - -
258L MET* 1.3 58.0 - - + +
260L LEU* 3.3 13.0 - - + +
261L LEU* 2.2 47.9 - - + +
286L ASP* 4.1 21.1 - - + +
289L LEU* 4.5 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 258 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233K SER* 4.3 4.9 - - - +
266K GLU* 3.5 41.4 - - + +
268K ASP* 2.7 40.8 - - + +
269K ALA* 4.1 9.0 - - + +
312K ASN* 6.0 0.2 - - - -
242L ARG* 3.8 26.7 - - - +
254L GLN* 2.5 6.7 + - + -
255L ARG* 2.4 45.6 + - + +
257L LEU* 1.3 67.2 - - + +
259L GLU* 1.3 64.3 + - - +
260L LEU 3.1 2.7 - - - -
261L LEU* 2.7 29.5 + - + +
262L ASN* 2.8 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231K VAL* 4.6 1.1 - - - +
233K SER* 2.6 32.0 + - - +
212L ALA* 3.3 21.4 - - + +
215L ILE* 3.9 13.8 - - + +
216L ARG* 2.1 55.5 + - - +
255L ARG* 2.4 24.3 + - + +
256L THR* 3.3 18.4 - - - +
258L MET* 1.3 73.6 - - - +
260L LEU* 1.3 60.3 + - - +
262L ASN* 3.5 8.9 + - - +
263L GLN* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203L ILE* 5.7 1.6 - - + -
215L ILE* 2.6 50.7 - - + -
218L MET* 5.5 0.9 - - + -
219L PHE* 4.7 4.7 - - + -
232L MET* 4.6 22.4 - - + -
235L ILE* 5.6 3.8 - - + -
238L ILE* 3.4 28.5 - - + -
256L THR 3.2 6.3 - - - +
257L LEU* 3.3 23.6 - - + +
259L GLU* 1.3 72.6 - - - +
261L LEU* 1.3 57.3 + - + +
263L GLN* 3.0 4.8 + - - +
264L MET* 2.7 57.9 + - + +
277L MET* 5.8 1.3 - - + -
289L LEU* 5.7 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266K GLU* 3.9 6.7 - - - +
242L ARG* 5.0 1.8 - - - +
257L LEU* 2.2 48.2 - - + +
258L MET* 2.7 32.6 + - + +
260L LEU* 1.3 73.0 - - + +
262L ASN* 1.3 61.1 + - - +
264L MET* 3.6 5.1 + - - +
265L ASP* 3.4 13.9 + - - +
286L ASP* 5.3 0.9 - - - +
288L ALA* 3.6 34.3 - - + +
289L LEU* 3.6 30.1 - - + -
294L ARG* 3.3 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 262 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231K VAL* 3.3 43.7 - - + +
233K SER* 6.2 0.2 - - - -
265K ASP* 4.9 9.0 - - - +
266K GLU* 4.2 19.2 + - - +
216L ARG* 5.6 1.2 - - - +
258L MET 2.8 10.4 + - - +
259L GLU* 3.7 13.9 + - - +
261L LEU* 1.3 78.5 - - - +
263L GLN* 1.3 64.7 + - - +
265L ASP 3.5 0.9 - - - +
266L GLY* 3.1 34.6 + - - +
267L PHE* 4.2 4.3 + - - +
268L ASP 5.2 0.2 - - - +
294L ARG* 5.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 263 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215L ILE* 3.6 11.1 - - - +
216L ARG* 3.8 28.6 + - - +
219L PHE* 3.0 50.1 - - + +
220L ASN* 5.4 3.2 + - - -
223L ARG* 3.9 22.5 + - - +
259L GLU* 2.9 20.1 + - - +
260L LEU* 3.0 6.4 + - - +
262L ASN* 1.3 83.1 - - - +
264L MET* 1.3 62.9 + - - +
265L ASP 2.9 6.0 + - - -
268L ASP 3.7 16.0 - - - +
270L LEU* 4.6 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 264 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168L LYS* 3.1 15.4 + - - +
219L PHE* 4.3 7.2 - - + -
232L MET* 5.1 2.2 - - + -
260L LEU* 2.7 43.3 + - + +
261L LEU* 4.0 5.2 - - - +
262L ASN 3.6 0.2 - - - -
263L GLN* 1.3 72.5 - - - +
265L ASP* 1.3 57.4 + - - +
270L LEU* 5.0 13.2 + - + +
275L MET* 2.6 40.8 - - + -
277L MET* 3.0 33.2 - - + -
289L LEU* 4.1 9.0 - - + -
293L GLY 3.1 12.9 - - - +
294L ARG* 3.6 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 265 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213K THR* 5.8 3.6 - - - +
217K LYS* 4.6 4.7 + - - -
501K ADP 4.5 8.2 + - - +
168L LYS* 3.2 17.1 + - - +
261L LEU 3.4 10.4 + - - +
262L ASN 3.5 2.4 - - - +
263L GLN 2.9 1.0 + - - -
264L MET* 1.3 78.9 - - - +
266L GLY* 1.3 79.1 + - - +
267L PHE 3.3 1.4 + - - +
268L ASP 3.3 17.7 - - - +
269L THR* 4.7 2.8 - - - -
291L ARG* 1.6 46.0 + - - +
293L GLY* 3.3 12.2 - - - +
294L ARG* 4.4 5.8 - - + +
----------------------------------------------------------
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