Contacts of the helix formed by residues 239 - 260 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ASN* 5.5 0.4 + - - -
238C LEU* 1.3 76.6 - - - +
240C HIS* 1.3 60.7 + - - +
241C THR* 3.8 7.9 - - - +
242C ILE* 2.8 30.2 + - + +
243C ALA 3.0 9.7 + - - -
417C PHE* 4.5 16.2 - - + -
418C GLU* 5.1 5.2 - - + -
421C ALA* 3.7 29.4 - - + -
94D PHE* 3.7 14.6 - - - -
96D PRO* 5.6 0.6 - - - +
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Residues in contact with HIS 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C GLY* 2.7 27.7 + - - -
231C GLY 3.2 12.9 + - - -
232C GLY 3.1 26.2 + - - -
233C LEU* 3.9 9.8 - - + +
235C ASN* 5.2 2.3 + - - +
238C LEU 3.4 14.4 - - - -
239C ALA* 1.3 74.0 - - - +
241C THR* 1.3 56.9 + - - +
243C ALA* 3.2 7.5 + - - +
244C VAL* 3.0 30.7 + - - +
298C VAL* 5.8 2.0 - - + -
364C ASP* 2.6 40.7 + - - +
365C PRO* 4.0 5.4 - - + -
366C GLN* 3.5 13.9 + - - +
418C GLU* 4.0 18.7 + - - +
15D ARG* 4.5 1.2 + - - -
94D PHE* 5.4 2.7 - + - -
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Residues in contact with THR 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C ALA* 3.8 9.2 - - - +
240C HIS* 1.3 74.8 - - - +
242C ILE* 1.3 59.3 + - - +
244C VAL* 3.4 16.5 - - - +
245C ILE* 3.3 21.1 - - - +
365C PRO* 4.0 17.5 - - + -
404C ILE* 4.4 6.3 - - + -
414C LEU* 4.1 13.2 - - + -
418C GLU* 2.8 48.1 + - + +
421C ALA* 3.8 5.0 - - - +
422C LEU* 3.9 21.2 - - + +
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Residues in contact with ILE 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C VAL* 6.1 1.1 - - + -
179C ASN* 3.4 34.1 - - + +
181C ILE* 3.7 31.6 - - + -
184C LEU* 4.0 12.7 - - + +
238C LEU* 4.2 15.9 - - + -
239C ALA* 2.8 21.4 + - + +
241C THR* 1.3 79.3 - - - +
243C ALA* 1.3 66.2 + - - +
244C VAL 3.1 1.3 - - - -
245C ILE* 3.1 14.1 + - + +
246C ALA* 3.1 12.5 + - - +
421C ALA* 4.0 31.2 - - + +
425C ALA* 5.1 3.1 - - + -
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Residues in contact with ALA 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C ALA 5.3 1.7 - - - +
226C ALA* 4.2 19.8 - - - +
227C MET* 4.4 0.9 - - - +
230C GLY* 5.5 2.2 - - - -
238C LEU* 4.1 19.6 - - + +
239C ALA 3.0 10.7 + - - +
240C HIS* 3.6 9.0 - - - +
242C ILE* 1.3 76.9 - - - +
244C VAL* 1.3 62.4 + - - +
246C ALA* 3.1 13.9 + - - +
247C ARG* 3.1 11.8 + - - +
366C GLN* 3.6 28.0 - - - +
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Residues in contact with VAL 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C HIS 3.0 17.3 + - - +
241C THR* 3.4 24.7 - - - +
243C ALA* 1.3 77.3 - - - +
245C ILE* 1.3 56.7 + - - +
247C ARG* 3.2 8.1 + - + +
248C ALA 3.0 22.2 + - - -
365C PRO* 3.5 21.3 - - + +
366C GLN* 3.9 19.9 - - - +
369C MET* 3.4 41.2 - - + +
400C CYS* 3.8 14.7 - - - -
404C ILE* 4.3 7.0 - - + -
422C LEU* 5.7 0.4 - - + -
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Residues in contact with ILE 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ILE* 4.6 9.0 - - + -
184C LEU* 5.5 2.7 - - + -
241C THR 3.3 20.6 - - - +
242C ILE* 3.1 13.1 + - + +
244C VAL* 1.3 75.2 - - + +
246C ALA* 1.3 65.4 + - - +
248C ALA* 3.2 2.9 + - - +
249C ILE* 3.1 39.6 + - + +
397C ALA* 4.2 16.6 - - + +
400C CYS* 4.1 19.3 - - - -
401C CYS* 3.8 20.6 - - - -
422C LEU* 4.5 7.0 - - + -
425C ALA* 3.7 28.7 - - + -
429C LEU* 4.4 8.1 - - + -
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Residues in contact with ALA 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C PHE* 4.9 1.1 - - + -
184C LEU* 4.8 12.5 - - + +
188C ILE* 4.0 23.8 - - + +
223C ALA* 4.5 9.6 - - - -
226C ALA* 4.0 22.2 - - + -
242C ILE 3.1 10.3 + - - +
243C ALA 3.1 10.2 + - - +
245C ILE* 1.3 77.1 - - - +
247C ARG* 1.3 56.0 + - - +
249C ILE* 3.2 8.0 + - - +
250C SER* 2.9 28.8 + - - -
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Residues in contact with ARG 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C ASP 5.4 0.8 + - - -
223C ALA* 3.5 24.6 + - - +
224C ASN* 2.9 29.1 + - - -
227C MET* 3.6 35.2 - - - +
243C ALA 3.1 11.0 + - - +
244C VAL* 3.3 13.2 - - + +
246C ALA* 1.3 75.9 - - - +
248C ALA* 1.3 63.8 + - - +
250C SER* 2.7 25.1 + - - -
251C ALA* 3.4 3.5 + - - +
269C CYS 4.3 0.4 + - - -
271C TYR* 3.5 22.4 - - - +
272C GLU* 3.1 43.7 + - + +
275C ILE* 4.9 0.4 - - + +
299C MET* 5.0 2.2 - - - +
366C GLN* 5.2 2.9 + - + +
369C MET* 3.7 16.2 - - + -
370C LEU* 3.8 19.0 - - + +
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Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C VAL 3.0 9.2 + - - +
245C ILE 3.2 7.8 + - - +
247C ARG* 1.3 76.8 - - - +
249C ILE* 1.3 60.7 + - - +
251C ALA* 3.3 12.6 + - - +
252C PRO* 3.3 10.0 - - - +
275C ILE* 4.8 4.5 - - - -
369C MET* 3.5 13.5 - - + +
378C VAL* 4.6 4.2 - - + +
396C ALA* 3.6 22.9 - - + +
397C ALA* 4.3 1.6 - - - -
400C CYS* 3.5 33.2 - - + -
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Residues in contact with ILE 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ILE* 5.1 1.8 - - + +
184C LEU* 4.4 10.1 - - + -
185C LEU* 4.1 31.4 - - + +
188C ILE* 3.7 11.2 - - + +
189C GLY* 3.4 32.4 - - - +
245C ILE* 3.1 32.3 + - + +
246C ALA* 3.7 7.0 - - - +
248C ALA* 1.3 70.9 - - - +
250C SER* 1.3 58.2 + - - +
251C ALA 3.1 4.9 - - - -
252C PRO* 3.0 24.0 - - - +
253C ARG* 3.7 4.9 + - - +
393C ALA* 4.2 14.8 - - + +
397C ALA* 3.8 22.4 - - + -
429C LEU* 5.3 1.6 - - + -
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Residues in contact with SER 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ILE* 3.6 11.4 - - - +
219C ASP* 3.3 32.8 - - - -
223C ALA* 3.7 4.7 - - - -
246C ALA 2.9 10.9 + - - -
247C ARG* 2.7 21.5 + - - -
249C ILE* 1.3 76.8 - - - +
251C ALA* 1.3 56.7 + - - +
253C ARG* 3.4 1.8 + - - +
254C SER* 2.9 32.7 + - - -
272C GLU* 3.0 23.7 + - - +
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Residues in contact with ALA 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ARG 3.4 0.6 + - - +
248C ALA 3.3 8.2 + - - +
249C ILE 3.1 1.8 - - - -
250C SER* 1.3 81.8 + - - +
252C PRO* 1.4 63.6 - - + +
254C SER 3.3 0.5 + - - -
255C LEU* 2.8 30.1 + - - +
272C GLU* 4.0 14.1 - - + +
275C ILE* 3.6 45.1 - - + -
276C VAL* 3.8 7.1 - - + +
279C ILE* 5.9 0.8 - - - +
382C ILE* 4.2 3.1 - - + -
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Residues in contact with PRO 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C GLY* 5.5 0.2 - - - -
193C SER* 4.0 3.5 + - - +
248C ALA 3.3 11.4 - - - +
249C ILE 3.0 24.5 - - - +
251C ALA* 1.4 80.7 - - + +
253C ARG* 1.3 64.6 + - - +
255C LEU* 3.5 13.6 - - + +
256C VAL* 3.5 3.8 - - - +
382C ILE* 3.8 19.4 - - + -
389C ILE 5.3 0.7 - - - +
392C ARG* 3.1 49.9 + - + +
393C ALA* 3.7 28.7 - - + -
396C ALA* 4.5 0.4 - - + -
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Residues in contact with ARG 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C SER* 3.1 29.7 + - - -
167C GLY 5.5 3.2 + - - +
188C ILE* 3.5 35.4 - - + +
189C GLY* 4.8 0.4 - - - -
192C GLY* 3.9 20.1 - - - -
193C SER* 3.6 11.2 + - - +
196C MET* 3.5 25.7 - - + +
217C ASP* 3.1 21.8 + - - -
218C THR 3.0 27.9 + - - +
219C ASP* 3.1 25.9 + - - +
221C ALA* 6.1 0.2 - - - +
222C GLN* 4.2 2.4 + - - -
249C ILE 4.1 0.9 - - - +
250C SER 3.4 5.6 + - - +
251C ALA 3.2 0.8 - - - -
252C PRO* 1.3 82.5 - - - +
254C SER* 1.3 83.2 + - - +
256C VAL* 3.0 22.0 + - - +
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Residues in contact with SER 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C MET* 3.9 2.6 - - - +
217C ASP* 5.2 3.7 + - - +
218C THR* 3.9 4.5 - - - -
219C ASP 3.4 1.2 + - - -
250C SER 2.9 18.3 + - - -
251C ALA 4.1 1.3 - - - -
253C ARG* 1.3 98.9 + - - +
255C LEU* 1.3 62.8 + - - +
256C VAL 3.1 1.0 + - - -
257C ALA* 3.3 14.2 + - - +
258C TYR* 3.5 17.7 - - - -
272C GLU* 2.6 35.4 + - - -
273C ASN* 5.1 4.0 - - - -
276C VAL* 4.3 6.3 - - - -
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Residues in contact with LEU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C TYR* 3.8 17.9 - - + +
251C ALA 2.8 19.4 + - - +
252C PRO* 3.5 8.3 - - + +
254C SER* 1.3 77.8 - - - +
256C VAL* 1.3 62.2 + - - +
258C TYR* 3.1 16.7 + - - -
259C GLU* 3.2 31.1 + - - +
276C VAL* 4.1 11.4 - - + +
279C ILE* 4.0 30.5 - - + -
280C THR* 3.6 29.4 - - + -
382C ILE* 4.2 10.3 - - + -
383C VAL* 5.6 0.2 - - + -
392C ARG* 3.9 13.9 - - - +
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Residues in contact with VAL 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 4.0 13.9 - - - +
193C SER* 3.7 25.6 - - - +
196C MET* 3.8 6.1 - - + -
197C GLU* 3.5 42.6 - - + +
252C PRO 3.5 3.1 - - - +
253C ARG 3.0 18.8 + - - +
255C LEU* 1.3 73.2 - - - +
257C ALA* 1.3 65.7 + - - +
259C GLU* 3.1 10.6 + - + +
260C ALA* 2.9 21.3 + - + +
389C ILE* 5.0 0.2 - - + -
392C ARG* 3.4 22.9 - - - +
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Residues in contact with ALA 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C MET* 3.6 17.7 - - + +
200C TRP* 3.7 34.7 - - + +
217C ASP 4.4 7.6 - - - +
254C SER 3.3 13.2 + - - +
255C LEU 3.2 0.6 - - - -
256C VAL* 1.3 76.5 - - - +
258C TYR* 1.3 67.0 + - + +
260C ALA* 3.2 13.3 + - - +
261C GLY 3.2 1.4 + - - -
262C ALA* 3.0 28.0 + - + +
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Residues in contact with TYR 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C TYR* 4.4 7.8 + - + +
215C ALA 3.2 20.0 - - - -
216C GLY* 3.6 11.5 - - - -
217C ASP 4.2 5.3 + - - -
254C SER* 3.5 25.1 - - - -
255C LEU 3.1 7.9 + - - +
257C ALA* 1.3 74.1 - - + +
259C GLU* 1.3 67.3 + - - +
260C ALA 3.0 1.6 + - - -
261C GLY* 3.3 8.8 + - - -
262C ALA* 3.4 22.5 - - + +
264C GLY* 3.7 10.3 - - - -
266C GLY* 3.1 28.2 - - - -
273C ASN* 4.8 2.5 + - - -
276C VAL* 3.6 25.6 - - + -
280C THR* 3.9 11.9 - - + -
282C MET* 3.5 35.1 - - + +
284C MET* 3.7 12.5 - - + -
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Residues in contact with GLU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ALA* 4.0 13.7 - - - +
4C LYS* 3.1 44.9 + - - +
5C ARG* 3.3 19.7 + - - +
6C TYR* 3.0 32.9 + - + -
255C LEU* 3.2 18.0 + - - +
256C VAL* 3.1 13.0 + - - +
258C TYR* 1.3 76.8 - - - +
260C ALA* 1.3 57.9 + - - +
261C GLY 3.8 0.5 + - - -
392C ARG* 2.5 46.9 + - - -
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Residues in contact with ALA 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ALA* 4.3 15.5 - - - +
197C GLU* 4.5 9.4 - - + +
200C TRP* 3.4 22.9 - - + +
201C THR* 3.9 22.5 + - - +
204C SER* 3.3 13.7 + - - -
256C VAL 2.9 16.4 + - - +
257C ALA 3.2 6.5 + - - +
258C TYR 3.0 0.6 - - - -
259C GLU* 1.3 77.2 - - - +
261C GLY* 1.3 54.2 + - - +
262C ALA 3.8 0.2 - - - -
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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