Contacts of the helix formed by residues 239 - 260 (chain G) in PDB entry 2I2X
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 239 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179G ASN* 6.1 0.2 - - - +
238G LEU* 1.3 76.8 - - - +
240G HIS* 1.3 59.2 + - - +
241G THR* 3.8 16.2 - - - +
242G ILE* 2.8 31.2 + - + +
243G ALA 3.1 9.2 + - - -
417G PHE* 4.5 8.5 - - + -
418G GLU* 5.0 3.8 - - + -
421G ALA* 3.9 21.1 - - + -
94H PHE* 3.4 22.6 - - + +
96H PRO* 5.5 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 240 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230G GLY* 2.7 28.1 + - - -
231G GLY 3.3 10.9 + - - -
232G GLY 3.0 26.0 + - - -
233G LEU* 3.9 12.6 - - + +
235G ASN* 4.9 2.5 + - - +
238G LEU 3.4 13.7 - - - -
239G ALA* 1.3 71.8 - - - +
241G THR* 1.3 56.3 + - - +
242G ILE 3.2 0.2 - - - -
243G ALA* 3.4 8.5 + - - +
244G VAL* 3.1 27.0 + - - +
298G VAL* 5.9 2.2 - - + -
364G ASP* 2.8 36.0 + - - +
365G PRO* 3.9 7.3 - - + +
366G GLN* 3.4 20.4 + - - +
418G GLU* 4.2 14.9 + - - +
15H ARG* 4.7 1.2 + - - -
94H PHE* 5.0 2.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 241 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239G ALA* 3.8 7.3 - - - +
240G HIS* 1.3 76.6 - - - +
242G ILE* 1.3 58.3 + - - -
244G VAL* 3.3 16.7 - - - +
245G ILE* 3.3 21.3 - - - +
365G PRO* 3.9 20.2 - - + -
404G ILE* 4.4 9.0 - - + -
414G LEU* 4.2 15.7 - - + -
418G GLU* 2.8 49.7 + - + +
421G ALA* 4.1 2.9 - - - +
422G LEU* 4.2 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 242 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176G VAL* 5.7 0.9 - - + +
179G ASN* 3.5 38.1 - - + +
181G ILE* 4.0 18.6 - - + -
184G LEU* 4.0 23.0 - - + +
238G LEU* 3.8 21.3 - - + -
239G ALA* 2.8 17.1 + - + +
241G THR* 1.3 78.9 + - - +
243G ALA* 1.3 66.8 + - - +
244G VAL 3.2 1.1 - - - -
245G ILE* 3.1 17.9 + - + +
246G ALA* 3.2 11.5 + - + +
421G ALA* 4.1 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 243 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223G ALA 5.3 1.7 - - - +
226G ALA* 4.2 18.7 - - - +
227G MET* 4.6 0.9 - - - +
230G GLY* 5.5 2.2 - - - -
238G LEU* 4.2 18.5 - - + +
239G ALA 3.1 10.8 + - - +
240G HIS* 3.5 11.7 - - - +
242G ILE* 1.3 77.5 - - - +
244G VAL* 1.3 62.4 + - - +
246G ALA* 3.1 8.0 + - - +
247G ARG* 3.1 18.7 + - - +
366G GLN* 3.7 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 244 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240G HIS 3.1 11.5 + - - +
241G THR* 3.3 24.0 - - - +
243G ALA* 1.3 78.7 - - - +
245G ILE* 1.3 66.0 + - + +
247G ARG* 3.0 7.9 + - + +
248G ALA* 2.9 20.3 + - - +
365G PRO* 3.3 29.8 - - + +
366G GLN* 4.0 17.0 - - - +
369G MET* 3.4 30.9 - - + +
400G CYS* 3.9 12.3 - - - -
404G ILE* 4.3 8.5 - - + -
422G LEU* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G ILE* 4.6 11.4 - - + -
184G LEU* 5.4 2.5 - - + -
241G THR 3.3 19.1 - - - +
242G ILE* 3.1 13.7 + - + +
244G VAL* 1.3 76.8 - - + +
246G ALA* 1.3 62.1 + - - +
248G ALA* 3.2 4.1 + - - +
249G ILE* 3.1 39.3 + - + +
397G ALA* 4.3 14.8 - - + +
400G CYS* 4.1 15.5 - - - -
401G CYS* 4.0 21.1 - - - -
422G LEU* 4.2 8.3 - - + -
425G ALA* 3.5 31.4 - - + -
429G LEU* 4.4 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 246 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172G PHE* 4.8 1.3 - - + -
184G LEU* 4.6 13.3 - - + +
188G ILE* 4.0 24.6 - - + +
223G ALA* 4.5 6.5 - - - -
226G ALA* 4.2 21.1 - - + -
242G ILE* 3.2 9.6 + - + +
243G ALA 3.1 11.0 + - - +
245G ILE* 1.3 76.7 - - - +
247G ARG* 1.3 56.5 + - - +
249G ILE* 3.1 10.3 + - - +
250G SER* 2.9 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 247 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G ASP* 5.5 0.6 - - - +
223G ALA* 3.6 29.8 + - + +
224G ASN* 2.9 30.3 + - - -
227G MET* 3.4 29.5 - - - +
243G ALA 3.1 9.7 + - - +
244G VAL* 3.0 13.2 + - + +
246G ALA* 1.3 73.9 - - - +
248G ALA* 1.3 65.4 + - - +
250G SER* 2.4 29.0 + - - -
251G ALA* 3.4 3.5 + - - +
269G CYS 4.1 0.4 + - - -
271G TYR* 3.5 22.0 - - - +
272G GLU* 3.3 44.0 + - + +
275G ILE* 5.0 0.4 - - + +
299G MET* 4.8 3.0 - - - +
366G GLN* 5.1 2.5 + - - +
369G MET* 3.8 3.6 - - + -
370G LEU* 3.8 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G VAL 2.9 7.4 + - - +
245G ILE 3.6 8.3 - - - +
247G ARG* 1.3 76.0 - - - +
249G ILE* 1.3 60.8 + - - +
251G ALA* 3.3 12.1 + - - +
252G PRO* 3.3 10.2 - - - +
275G ILE* 4.8 5.4 - - - -
369G MET* 3.3 16.7 - - + +
378G VAL* 4.6 4.3 - - + +
396G ALA* 3.4 23.5 - - + +
397G ALA 4.6 0.7 - - - +
400G CYS* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 249 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G ILE* 5.0 1.6 - - + +
184G LEU* 4.3 13.2 - - + +
185G LEU* 4.2 32.5 - - + +
188G ILE* 3.7 13.1 - - + +
189G GLY* 3.6 29.6 - - - +
245G ILE* 3.1 33.2 + - + +
246G ALA* 3.5 7.6 - - - +
248G ALA* 1.3 75.9 - - - +
250G SER* 1.3 62.0 + - - +
252G PRO* 3.1 20.2 - - - +
253G ARG* 3.8 4.0 + - - +
393G ALA* 4.1 8.3 - - + +
396G ALA* 4.6 2.5 - - - -
397G ALA* 3.9 22.2 - - + -
429G LEU* 5.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 250 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G ILE* 3.7 11.0 - - - -
219G ASP* 3.1 34.1 - - - -
223G ALA* 3.9 4.3 - - - -
246G ALA 2.9 10.6 + - - -
247G ARG* 2.4 26.5 + - - -
249G ILE* 1.3 78.9 - - - +
251G ALA* 1.3 55.9 + - - +
253G ARG* 3.4 2.9 + - - +
254G SER* 2.9 32.1 + - - -
272G GLU* 3.2 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 251 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247G ARG 3.4 0.2 + - - -
248G ALA 3.3 9.1 + - - +
249G ILE 3.1 0.2 - - - -
250G SER* 1.3 80.1 + - - +
252G PRO* 1.4 58.7 - - + +
254G SER 3.3 1.7 + - - -
255G LEU* 2.7 34.1 + - - +
272G GLU* 3.9 14.6 - - + +
275G ILE* 3.6 45.5 - - + -
276G VAL* 3.7 7.8 - - + +
279G ILE* 6.0 0.8 - - - +
382G ILE* 4.2 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 252 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G GLY* 5.4 0.7 - - - +
193G SER* 4.5 2.9 - - - +
248G ALA 3.3 11.4 - - - +
249G ILE 3.1 17.3 - - - +
251G ALA* 1.4 88.7 - - + +
253G ARG* 1.3 64.6 + - - +
255G LEU* 3.3 17.2 - - + +
256G VAL* 3.3 3.0 - - - +
382G ILE* 4.0 16.8 - - + -
389G ILE 5.3 0.4 - - - +
392G ARG* 3.0 51.4 + - + +
393G ALA* 3.8 27.6 - - + -
396G ALA* 4.4 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 253 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G SER* 2.8 40.6 + - - -
167G GLY 5.4 3.6 + - - +
188G ILE* 3.6 40.4 - - + +
189G GLY* 4.7 1.0 - - - -
192G GLY* 4.0 16.9 - - - -
193G SER* 3.9 11.2 + - - +
196G MET* 3.5 22.2 - - + +
217G ASP* 3.0 19.7 + - - +
218G THR 2.9 35.9 + - - +
219G ASP* 3.6 16.9 + - - +
222G GLN* 4.5 2.9 + - - +
249G ILE 4.1 0.9 - - - +
250G SER 3.4 8.1 - - - +
251G ALA 3.3 0.4 - - - -
252G PRO* 1.3 80.3 - - - +
254G SER* 1.3 74.4 + - - +
256G VAL* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 254 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G MET* 4.0 3.1 - - - +
217G ASP* 5.3 3.5 - - - +
218G THR* 5.2 4.0 - - - -
219G ASP* 3.8 0.9 + - - +
250G SER 2.9 15.0 + - - -
251G ALA 4.0 2.7 - - - -
253G ARG* 1.3 95.9 + - - +
255G LEU* 1.3 66.2 + - - +
256G VAL 2.9 3.4 + - - -
257G ALA* 3.2 13.5 + - - +
258G TYR* 3.4 19.1 - - - -
272G GLU* 2.9 31.2 + - - -
273G ASN* 5.3 3.8 - - - -
276G VAL* 4.4 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 255 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G TYR* 3.5 27.8 - - + +
251G ALA 2.7 18.1 + - - +
252G PRO* 3.3 9.6 - - + +
253G ARG 3.2 0.2 - - - -
254G SER* 1.3 77.3 - - - +
256G VAL* 1.3 60.1 + - - +
258G TYR* 3.1 17.5 + - - -
259G GLU* 3.2 30.5 + - - +
276G VAL* 4.0 10.2 - - + +
279G ILE* 3.8 24.9 - - + -
280G THR* 3.7 20.4 - - + -
382G ILE* 4.1 24.9 - - + -
383G VAL* 5.5 0.2 - - + -
392G ARG* 4.0 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ARG* 3.9 19.5 - - - +
193G SER* 3.9 20.0 - - - +
196G MET* 3.8 6.1 - - + -
197G GLU* 3.6 37.7 - - + +
252G PRO 3.3 12.3 - - - +
253G ARG 3.2 17.0 - - - +
254G SER 2.9 1.0 + - - -
255G LEU* 1.3 75.3 - - - +
257G ALA* 1.3 55.9 + - - +
259G GLU* 3.2 9.8 + - + +
260G ALA* 2.7 33.5 + - + +
392G ARG* 3.6 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G MET* 3.7 16.4 - - + +
200G TRP* 3.8 31.0 - - + +
217G ASP 4.3 7.9 - - - +
254G SER 3.2 14.0 + - - +
256G VAL* 1.3 77.8 - - - +
258G TYR* 1.3 67.1 + - + +
260G ALA* 3.2 4.2 + - - +
261G GLY 3.2 9.7 + - - -
262G ALA* 2.9 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 258 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G TYR* 4.4 7.1 + - + +
215G ALA 3.3 20.6 - - - -
216G GLY* 3.7 10.3 - - - -
217G ASP 4.1 5.1 + - - -
254G SER* 3.4 25.6 - - - -
255G LEU 3.1 7.2 + - - +
256G VAL 3.1 0.2 - - - -
257G ALA* 1.3 78.3 - - + +
259G GLU* 1.3 63.9 + - - +
260G ALA 3.1 1.6 - - - -
261G GLY* 3.0 13.9 + - - -
262G ALA* 3.3 34.1 - - + +
264G GLY* 3.9 6.1 - - - -
266G GLY* 3.2 26.5 - - - -
273G ASN* 4.5 4.3 + - - -
276G VAL* 3.6 27.4 - - + -
280G THR* 4.1 10.8 - - + -
282G MET* 3.7 24.4 - - + +
284G MET* 3.6 19.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G ALA* 4.2 8.7 - - - +
4G LYS* 3.2 47.8 + - - +
5G ARG* 3.3 21.8 + - - +
6G TYR* 3.2 29.6 + - + -
255G LEU* 3.2 19.6 + - - +
256G VAL* 3.2 17.0 + - + +
258G TYR* 1.3 75.7 - - - +
260G ALA* 1.3 59.2 + - - +
261G GLY 3.6 0.5 + - - -
392G ARG* 2.6 47.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G ALA* 4.3 15.5 - - - +
197G GLU* 4.2 8.3 - - - +
200G TRP* 3.3 12.3 - - + +
201G THR* 3.7 36.0 - - - +
204G SER* 3.2 14.4 + - - -
256G VAL 2.7 16.4 + - - +
257G ALA 3.2 6.9 + - - +
258G TYR 3.1 0.2 - - - -
259G GLU* 1.3 77.6 - - - +
261G GLY* 1.3 52.9 + - - +
----------------------------------------------------------
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