Contacts of the helix formed by residues 239 - 260 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179M ASN* 5.8 0.2 + - - -
238M LEU* 1.3 76.1 - - - +
240M HIS* 1.3 60.3 + - - +
241M THR* 3.9 5.8 - - - +
242M ILE* 2.9 29.5 + - + +
243M ALA* 3.1 9.9 + - - +
417M PHE* 4.5 15.5 - - + -
418M GLU* 5.2 4.9 - - - -
421M ALA* 3.7 30.3 - - + -
94N PHE* 3.4 16.4 - - - -
96N PRO* 5.7 0.4 - - - +
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Residues in contact with HIS 240 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230M GLY* 2.8 27.6 + - - -
231M GLY 3.2 12.1 + - - -
232M GLY 3.2 25.5 + - - -
233M LEU* 4.2 9.4 + - + -
235M ASN* 5.2 2.4 + - - +
238M LEU 3.2 15.5 - - - -
239M ALA* 1.3 68.0 - - - +
241M THR* 1.3 64.7 + - - +
242M ILE 3.0 1.8 - - - -
243M ALA* 3.3 4.3 + - + +
244M VAL* 3.1 25.8 + - - +
298M VAL* 5.9 2.0 - - + -
364M ASP* 2.6 37.4 + - - +
365M PRO* 3.8 9.4 - - + -
366M GLN* 3.4 18.8 + - - +
418M GLU* 3.9 14.8 + - - +
15N ARG* 4.4 3.2 + - - -
94N PHE* 5.7 2.0 - + - -
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Residues in contact with THR 241 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239M ALA* 3.9 1.7 - - - +
240M HIS* 1.3 79.4 - - - +
242M ILE* 1.3 58.1 + - - +
244M VAL* 3.2 21.3 - - - +
245M ILE* 3.4 18.5 - - - +
365M PRO* 3.9 10.5 - - + +
404M ILE* 4.2 9.6 - - + -
414M LEU* 3.9 22.0 - - + -
418M GLU* 2.9 43.0 + - + +
421M ALA* 3.6 14.0 - - - +
422M LEU* 3.8 21.0 - - + +
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Residues in contact with ILE 242 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176M VAL* 5.9 1.3 - - + -
179M ASN* 3.3 39.3 - - + +
181M ILE* 4.0 25.6 - - + -
184M LEU* 4.1 12.5 - - + +
226M ALA* 6.4 0.2 - - + -
238M LEU* 4.1 17.0 - - + -
239M ALA* 2.9 20.1 + - + +
241M THR* 1.3 77.4 + - - +
243M ALA* 1.3 66.3 + - - +
244M VAL 3.1 2.0 - - - -
245M ILE* 3.1 17.0 + - + +
246M ALA* 3.3 11.1 + - + +
421M ALA* 4.1 30.1 - - + +
425M ALA* 4.8 4.5 - - + -
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Residues in contact with ALA 243 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223M ALA 5.1 2.4 - - - +
226M ALA* 4.2 20.3 - - - +
227M MET* 4.4 1.3 - - - +
230M GLY* 5.4 0.7 - - - -
238M LEU* 4.0 22.4 - - + +
239M ALA 3.1 8.7 + - - +
240M HIS* 3.6 10.5 - - + +
242M ILE* 1.3 76.4 - - - +
244M VAL* 1.3 60.8 + - - +
246M ALA* 3.5 5.5 + - - +
247M ARG* 3.2 19.2 + - - +
366M GLN* 3.6 27.3 - - - +
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Residues in contact with VAL 244 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240M HIS 3.1 15.2 + - - +
241M THR* 3.2 24.7 - - - +
242M ILE 3.1 0.2 - - - -
243M ALA* 1.3 76.3 - - - +
245M ILE* 1.3 62.5 + - + +
247M ARG* 3.2 6.6 + - + -
248M ALA 3.1 18.0 + - - -
365M PRO* 3.4 30.7 - - + +
366M GLN* 3.7 21.7 - - - +
369M MET* 3.4 31.4 - - + +
400M CYS* 3.7 12.8 - - - -
404M ILE* 4.3 7.0 - - + -
422M LEU* 5.7 0.7 - - + -
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Residues in contact with ILE 245 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181M ILE* 4.5 9.9 - - + -
184M LEU* 5.3 4.3 - - + -
241M THR 3.4 19.1 - - - +
242M ILE* 3.1 10.6 + - + +
244M VAL* 1.3 74.3 - - + +
246M ALA* 1.3 67.3 + - - +
248M ALA* 3.1 3.9 + - - +
249M ILE* 3.0 40.5 + - + +
397M ALA* 4.1 14.6 - - + +
400M CYS* 4.1 15.9 - - - -
401M CYS* 3.7 25.4 - - - -
422M LEU* 4.4 6.3 - - + -
425M ALA* 3.6 30.5 - - + -
429M LEU* 4.4 7.6 - - + -
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Residues in contact with ALA 246 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172M PHE* 5.0 1.3 - - + -
184M LEU* 4.6 13.2 - - + +
188M ILE* 4.0 25.5 - - + +
223M ALA* 4.1 7.3 - - - +
226M ALA* 4.3 17.9 - - + -
242M ILE* 3.3 8.6 + - + +
243M ALA 3.5 10.5 - - - +
245M ILE* 1.3 78.6 - - - +
247M ARG* 1.3 57.0 + - - +
249M ILE* 3.4 8.1 + - - +
250M SER* 3.0 28.8 + - - -
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Residues in contact with ARG 247 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219M ASP 5.3 1.2 + - - -
223M ALA* 3.4 32.6 + - + +
224M ASN* 2.6 32.3 + - - -
227M MET* 3.8 21.0 - - - +
243M ALA 3.2 10.5 + - - +
244M VAL* 3.4 14.1 - - + +
245M ILE 3.2 0.6 - - - -
246M ALA* 1.3 76.2 - - - +
248M ALA* 1.3 63.9 + - - +
250M SER* 2.7 21.9 + - - -
251M ALA* 3.3 5.5 + - - +
269M CYS 4.2 0.4 + - - -
271M TYR* 3.6 27.0 - - - +
272M GLU* 3.0 44.3 + - + +
275M ILE* 4.8 0.6 - - + +
299M MET* 5.5 1.6 - - - +
366M GLN* 5.6 1.3 + - + +
369M MET* 3.9 13.0 - - + -
370M LEU* 4.0 19.4 - - + +
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Residues in contact with ALA 248 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244M VAL 3.1 6.6 + - - +
245M ILE 3.1 8.2 + - - +
247M ARG* 1.3 75.4 - - - +
249M ILE* 1.3 62.7 + - - +
251M ALA* 3.2 7.3 + - - +
252M PRO* 3.1 17.8 - - - +
275M ILE* 4.7 6.3 - - - -
369M MET* 3.5 16.5 - - + +
378M VAL* 4.7 3.9 - - + +
396M ALA* 3.5 34.4 - - + +
397M ALA* 4.5 1.1 - - - -
400M CYS* 3.6 19.5 - - + -
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Residues in contact with ILE 249 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181M ILE* 5.0 1.8 - - + +
184M LEU* 4.2 11.7 - - + +
185M LEU* 3.9 28.7 - - + +
188M ILE* 3.8 11.6 - - + +
189M GLY* 3.5 32.0 - - - +
245M ILE* 3.0 33.4 + - + +
246M ALA* 3.8 5.8 - - - +
247M ARG 3.3 0.2 - - - -
248M ALA* 1.3 76.3 - - - +
250M SER* 1.3 58.4 + - - +
252M PRO* 3.0 22.8 - - - +
253M ARG* 3.7 5.5 + - - +
393M ALA* 4.0 15.9 - - + +
397M ALA* 3.7 21.8 - - + -
429M LEU* 5.3 1.3 - - + -
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Residues in contact with SER 250 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188M ILE* 3.6 10.3 - - - +
219M ASP* 3.1 33.4 - - - -
223M ALA* 3.8 4.3 - - - +
246M ALA 3.0 13.9 + - - -
247M ARG* 2.7 20.8 + - - -
249M ILE* 1.3 74.8 - - - +
251M ALA* 1.3 64.4 + - - +
253M ARG* 3.3 2.8 + - - +
254M SER* 2.9 29.6 + - - -
272M GLU* 3.4 19.9 + - - +
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Residues in contact with ALA 251 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247M ARG 3.3 1.2 + - - +
248M ALA 3.2 9.3 + - - +
250M SER* 1.3 83.0 + - - +
252M PRO* 1.4 64.8 - - + +
254M SER 3.3 0.9 + - - -
255M LEU* 2.8 28.4 + - - +
272M GLU* 3.9 12.6 - - + +
275M ILE* 3.6 45.5 - - + -
276M VAL* 3.8 7.3 - - + +
279M ILE* 6.1 0.4 - - - -
382M ILE* 4.0 4.7 - - + -
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Residues in contact with PRO 252 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189M GLY 6.2 0.2 - - - +
193M SER* 4.1 3.6 + - - +
248M ALA 3.1 13.7 - - - +
249M ILE 3.0 23.6 - - - +
251M ALA* 1.4 80.9 - - + +
253M ARG* 1.3 64.0 + - - +
255M LEU* 3.5 12.8 - - + +
256M VAL* 3.4 2.9 - - - +
382M ILE* 3.8 20.8 - - + -
389M ILE 5.5 0.4 - - - +
392M ARG* 2.9 52.2 + - + +
393M ALA* 3.7 28.5 - - + +
396M ALA* 4.4 0.2 - - + -
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Residues in contact with ARG 253 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165M SER* 2.9 28.5 + - - -
167M GLY 5.6 2.8 + - - +
188M ILE* 3.5 29.4 - - + +
189M GLY* 4.9 0.6 - - - -
192M GLY* 4.0 17.4 - - - -
193M SER* 3.6 11.8 + - - +
196M MET* 3.4 21.7 - - + +
217M ASP* 2.9 28.1 + - - +
218M THR 3.0 36.2 + - - +
219M ASP* 3.2 26.3 + - - +
222M GLN* 4.4 2.0 + - - +
249M ILE 3.7 5.6 + - - +
250M SER 3.3 9.8 + - - +
251M ALA 3.2 0.8 - - - -
252M PRO* 1.3 78.1 - - - +
254M SER* 1.3 74.7 + - - +
256M VAL* 3.1 23.6 + - - +
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Residues in contact with SER 254 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196M MET* 4.0 2.6 - - - +
217M ASP* 5.4 4.8 - - - +
218M THR* 5.2 2.7 - - - -
219M ASP 3.6 0.6 + - - -
250M SER 2.9 13.8 + - - -
251M ALA 4.0 2.7 - - - -
253M ARG* 1.3 97.5 + - - +
255M LEU* 1.3 65.4 + - - +
256M VAL 3.0 2.8 + - - -
257M ALA* 3.4 9.6 + - - +
258M TYR* 3.3 24.2 - - - -
272M GLU* 2.8 33.2 + - - -
273M ASN* 5.2 3.4 - - - -
276M VAL* 4.5 5.6 - - - -
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Residues in contact with LEU 255 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M TYR* 3.8 11.0 - - + +
251M ALA 2.8 17.4 + - - +
252M PRO* 3.5 8.1 - - + +
253M ARG 3.2 0.4 - - - -
254M SER* 1.3 77.8 - - - +
256M VAL* 1.3 62.3 + - - +
257M ALA 3.3 0.2 - - - -
258M TYR* 3.1 12.1 + - - +
259M GLU* 3.1 39.2 + - - +
276M VAL* 4.1 9.6 - - + +
279M ILE* 3.8 26.7 - - + -
280M THR* 3.3 33.9 - - + -
382M ILE* 4.1 20.6 - - + -
392M ARG* 3.9 14.1 - - - +
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Residues in contact with VAL 256 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M ARG* 3.7 17.7 - - - +
193M SER* 3.6 21.8 - - - +
196M MET* 3.5 9.2 - - + -
197M GLU* 3.3 36.6 - - + +
252M PRO 3.4 2.9 - - - +
253M ARG 3.2 16.6 - - - +
254M SER 3.0 1.0 - - - -
255M LEU* 1.3 78.0 - - - +
257M ALA* 1.3 61.9 + - - +
259M GLU* 3.1 11.0 + - - +
260M ALA* 3.0 22.4 + - + +
392M ARG* 3.3 23.3 - - - +
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Residues in contact with ALA 257 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196M MET* 3.5 22.7 - - + +
200M TRP* 3.5 37.2 - - + +
217M ASP* 4.5 7.9 - - + +
254M SER 3.4 8.3 + - - +
255M LEU 3.3 0.6 - - - -
256M VAL* 1.3 76.5 - - - +
258M TYR* 1.3 62.6 + - + +
260M ALA* 3.2 4.5 + - - +
261M GLY 3.2 9.9 + - - -
262M ALA* 3.0 30.1 + - + +
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Residues in contact with TYR 258 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M TYR* 4.3 9.8 + - + -
215M ALA 3.3 20.9 - - - -
216M GLY* 3.7 10.9 - - - -
217M ASP 4.0 5.3 + - - -
254M SER* 3.3 26.2 - - - -
255M LEU 3.1 6.9 + - - +
256M VAL 3.1 0.4 - - - -
257M ALA* 1.3 75.3 - - + +
259M GLU* 1.3 64.3 + - - +
260M ALA 3.1 2.1 + - - -
261M GLY* 3.4 8.3 + - - -
262M ALA* 3.4 31.5 - - + +
264M GLY* 3.8 6.5 - - - -
266M GLY* 3.0 28.6 - - - -
273M ASN* 4.4 4.9 + - - -
276M VAL* 3.5 27.6 - - + -
280M THR* 4.1 11.7 - - + -
282M MET* 3.9 22.4 - - - +
284M MET* 3.7 15.8 - - + -
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Residues in contact with GLU 259 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M ALA* 4.0 8.8 - - - +
4M LYS* 3.1 48.9 + - - +
5M ARG* 3.2 16.8 + - - -
6M TYR* 3.0 35.4 + - + -
255M LEU* 3.1 18.4 + - - +
256M VAL* 3.1 15.3 + - - +
258M TYR* 1.3 77.1 - - - +
260M ALA* 1.3 58.3 + - - +
261M GLY 3.5 0.6 + - - -
392M ARG* 2.5 48.0 + - - -
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Residues in contact with ALA 260 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M ALA* 4.2 19.7 - - + +
197M GLU* 4.5 9.2 - - - +
200M TRP* 3.3 13.0 - - + +
201M THR* 4.0 28.9 - - - +
204M SER* 3.1 14.3 + - - -
256M VAL 3.0 15.8 + - - +
257M ALA 3.4 6.7 - - - +
258M TYR 3.1 0.2 - - - -
259M GLU* 1.3 78.6 - - - +
261M GLY* 1.3 54.7 + - - +
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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