Contacts of the helix formed by residues 239 - 260 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E ASN* 5.5 1.1 + - - +
238E LEU* 1.3 75.3 - - - +
240E HIS* 1.3 58.3 + - - +
241E THR* 3.9 6.7 - - - +
242E ILE* 2.8 46.4 + - + +
243E ALA* 3.1 9.0 + - - +
417E PHE* 4.7 17.0 - - + +
418E GLU* 5.2 4.0 - - + -
421E ALA* 3.8 18.8 - - + -
94F PHE* 3.6 14.2 - - - -
96F PRO* 5.7 0.4 - - - +
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Residues in contact with HIS 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E GLY* 2.9 27.3 + - - -
231E GLY 3.3 11.9 + - - -
232E GLY 3.1 26.3 + - - -
233E LEU* 4.1 10.7 + - + +
235E ASN* 5.0 2.5 + - - +
238E LEU 3.4 14.4 - - - -
239E ALA* 1.3 70.9 - - - +
241E THR* 1.3 60.9 + - - +
242E ILE 3.1 1.0 + - - -
243E ALA* 3.2 8.8 + - - +
244E VAL* 3.1 26.0 + - - +
298E VAL* 5.7 2.7 - - + -
364E ASP* 2.8 39.1 + - - +
365E PRO* 3.9 5.8 - - + +
366E GLN* 3.6 12.5 + - - +
418E GLU* 3.8 21.4 + - - +
94F PHE* 5.5 3.8 - + - -
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Residues in contact with THR 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239E ALA* 3.9 2.3 - - - +
240E HIS* 1.3 77.9 - - - +
242E ILE* 1.3 57.5 + - - +
244E VAL* 3.3 18.7 - - - +
245E ILE* 3.5 17.3 - - - +
365E PRO* 3.9 19.1 - - + -
404E ILE* 4.5 5.8 - - + -
414E LEU* 4.2 16.4 - - + -
418E GLU* 2.7 52.7 + - + +
421E ALA* 3.9 9.0 - - - +
422E LEU* 4.1 18.9 - - + +
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Residues in contact with ILE 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E VAL* 6.2 0.4 - - + -
179E ASN* 3.3 39.9 - - + +
181E ILE* 3.9 27.1 - - + -
184E LEU* 4.0 15.0 - - + -
238E LEU* 4.4 16.2 - - + -
239E ALA* 2.8 28.0 + - + +
241E THR* 1.3 77.9 - - - +
243E ALA* 1.3 65.2 + - - +
244E VAL 3.1 2.2 - - - -
245E ILE* 3.0 16.9 + - + +
246E ALA* 3.1 11.5 + - + +
421E ALA* 4.2 23.1 - - + +
425E ALA* 5.2 2.2 - - + -
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Residues in contact with ALA 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223E ALA 5.2 1.6 - - - +
226E ALA* 4.2 20.1 - - - +
227E MET* 4.4 1.9 + - - +
230E GLY* 5.2 2.5 - - - -
238E LEU* 4.1 19.7 - - + +
239E ALA 3.1 10.5 + - - +
240E HIS* 3.2 10.3 + - - +
242E ILE* 1.3 75.7 - - - +
244E VAL* 1.3 61.6 + - - +
246E ALA* 3.3 6.7 - - - +
247E ARG* 3.2 20.0 + - - +
366E GLN* 3.8 26.1 - - - +
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Residues in contact with VAL 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E HIS 3.1 13.5 + - - +
241E THR* 3.3 23.1 - - - +
243E ALA* 1.3 75.7 - - - +
245E ILE* 1.3 62.3 + - + +
247E ARG* 3.0 9.4 + - + +
248E ALA* 2.9 23.9 + - - +
365E PRO* 3.4 30.1 - - + +
366E GLN* 3.7 21.7 - - - +
369E MET* 3.4 30.6 - - + +
400E CYS* 4.0 11.9 - - - -
404E ILE* 4.4 7.2 - - + -
422E LEU* 5.7 0.2 - - + -
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Residues in contact with ILE 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181E ILE* 4.8 8.5 - - + -
184E LEU* 5.5 2.2 - - + -
241E THR 3.5 20.9 - - - +
242E ILE* 3.0 11.7 + - + +
244E VAL* 1.3 73.5 - - + +
246E ALA* 1.3 68.2 + - - +
248E ALA* 3.0 3.9 + - - +
249E ILE* 2.9 39.3 + - + +
397E ALA* 3.9 18.4 - - + +
400E CYS* 4.1 19.3 - - - -
401E CYS* 3.9 22.0 - - - -
422E LEU* 4.3 5.6 - - + -
425E ALA* 3.5 31.4 - - + -
429E LEU* 4.5 7.2 - - + -
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Residues in contact with ALA 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E PHE* 5.0 1.8 - - + -
184E LEU* 4.4 14.6 - - + +
188E ILE* 3.9 23.9 - - + +
223E ALA* 4.7 7.0 - - - +
226E ALA* 4.0 21.1 - - + -
242E ILE* 3.1 10.4 + - + +
243E ALA 3.3 11.7 - - - +
245E ILE* 1.3 77.7 - - - +
247E ARG* 1.3 55.7 + - - +
249E ILE* 3.3 8.6 + - - +
250E SER* 3.0 26.2 + - - -
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Residues in contact with ARG 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E THR* 6.0 0.2 - - - +
219E ASP 5.9 0.2 - - - -
223E ALA* 3.4 22.7 + - - +
224E ASN* 2.9 29.9 + - - -
227E MET* 3.5 37.4 - - - +
243E ALA 3.2 10.1 + - - +
244E VAL* 3.0 14.6 + - + +
246E ALA* 1.3 76.9 - - - +
248E ALA* 1.3 66.0 + - - +
250E SER* 2.3 27.5 + - - -
251E ALA* 3.4 2.8 + - - +
271E TYR* 3.5 20.6 - - - +
272E GLU* 3.0 42.7 + - + +
275E ILE* 4.7 0.7 - - + +
299E MET* 5.1 2.0 - - - +
366E GLN* 4.9 5.1 + - + +
369E MET* 4.0 2.2 - - + -
370E LEU* 4.0 28.3 - - + +
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Residues in contact with ALA 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244E VAL 2.9 6.8 + - - +
245E ILE 3.0 8.7 + - - +
247E ARG* 1.3 76.0 - - - +
249E ILE* 1.3 61.6 + - - +
251E ALA* 2.9 22.0 + - - +
252E PRO* 3.3 5.4 - - - +
275E ILE* 4.8 5.2 - - - -
369E MET* 3.6 16.3 - - + +
378E VAL* 4.8 3.6 - - + -
396E ALA* 3.8 21.5 - - + +
397E ALA* 4.3 2.0 - - - -
400E CYS* 3.7 29.4 - - + -
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Residues in contact with ILE 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181E ILE* 4.8 2.2 - - + +
184E LEU* 4.3 12.3 - - + -
185E LEU* 4.0 33.0 - - + +
188E ILE* 3.6 13.2 - - + +
189E GLY* 3.5 31.5 - - - +
245E ILE* 2.9 36.8 + - + +
246E ALA* 3.7 6.7 - - - +
248E ALA* 1.3 74.8 - - - +
250E SER* 1.3 61.7 + - - +
251E ALA 3.3 0.7 + - - -
252E PRO* 3.4 17.7 - - - +
253E ARG* 3.8 4.5 + - - +
393E ALA* 4.2 16.8 - - + +
397E ALA* 3.8 20.6 - - + -
429E LEU* 5.5 1.6 - - + -
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Residues in contact with SER 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188E ILE* 3.6 11.2 - - - -
219E ASP* 3.1 28.7 - - - -
223E ALA* 3.7 9.0 - - - -
246E ALA 3.0 12.2 + - - -
247E ARG* 2.3 25.5 + - - -
248E ALA 3.0 0.2 + - - -
249E ILE* 1.3 78.4 - - - +
251E ALA* 1.3 55.6 + - - +
253E ARG* 3.4 3.1 - - - +
254E SER* 2.9 32.2 + - - -
272E GLU* 3.2 20.0 + - - +
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Residues in contact with ALA 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248E ALA 2.9 11.2 + - - +
250E SER* 1.3 78.2 + - - +
252E PRO* 1.4 64.8 - - + +
254E SER* 3.2 2.3 + - - -
255E LEU* 2.8 28.8 + - - +
272E GLU* 4.1 13.0 - - + +
275E ILE* 3.6 45.1 - - + -
276E VAL* 3.7 7.6 - - + +
279E ILE* 6.2 0.4 - - - -
378E VAL* 5.1 0.2 - - + -
382E ILE* 4.2 3.6 - - + -
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Residues in contact with PRO 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E GLY* 5.7 0.9 - - - +
193E SER* 4.6 2.2 - - - +
248E ALA 3.3 10.3 - - - +
249E ILE 3.4 11.7 - - - +
251E ALA* 1.4 90.9 - - + +
253E ARG* 1.3 63.1 + - - +
255E LEU* 3.2 19.4 + - + +
256E VAL* 3.3 1.7 - - - +
382E ILE* 3.7 20.4 - - + -
389E ILE 5.1 0.9 - - - +
392E ARG* 3.1 49.2 + - + +
393E ALA* 3.7 29.4 - - + +
396E ALA* 4.3 0.9 - - + -
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Residues in contact with ARG 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E SER* 3.3 27.1 + - - -
167E GLY 5.2 3.8 + - - +
188E ILE* 3.3 30.1 - - + +
189E GLY* 4.8 1.6 + - - -
192E GLY* 3.9 17.8 + - - -
193E SER* 3.6 12.3 + - - -
196E MET* 3.2 34.9 - - - +
217E ASP* 3.2 17.6 + - - +
218E THR 3.1 37.5 + - - -
219E ASP* 3.2 26.6 + - - +
221E ALA* 5.6 0.4 - - - +
222E GLN* 4.6 2.0 + - - -
249E ILE 3.8 7.2 + - - +
250E SER 3.4 9.6 + - - +
251E ALA 3.3 0.4 - - - -
252E PRO* 1.3 81.7 - - - +
254E SER* 1.3 73.9 + - - +
256E VAL* 3.3 18.0 + - - +
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Residues in contact with SER 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196E MET* 3.8 5.8 - - - +
217E ASP* 5.5 4.1 - - - +
218E THR* 4.3 1.8 - - - -
219E ASP 3.6 1.0 + - - -
250E SER 2.9 16.1 + - - -
251E ALA 3.7 3.6 - - - -
253E ARG* 1.3 92.3 + - - +
255E LEU* 1.3 64.4 + - - +
256E VAL 3.1 2.5 + - - -
257E ALA* 3.4 13.2 + - - +
258E TYR* 3.6 17.7 - - - -
272E GLU* 3.1 32.6 + - - -
273E ASN* 5.3 2.7 - - - -
276E VAL* 4.2 8.1 - - - -
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Residues in contact with LEU 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E TYR* 3.7 19.3 - - + +
251E ALA 2.8 13.6 + - - +
252E PRO* 3.2 10.1 + - + +
254E SER* 1.3 77.3 - - - +
256E VAL* 1.3 61.2 + - - +
258E TYR* 3.1 17.7 + - - +
259E GLU* 3.1 27.6 + - - +
276E VAL* 4.2 9.1 - - + +
279E ILE* 3.8 36.3 - - + -
280E THR* 3.5 30.5 - - + -
382E ILE* 4.1 18.2 - - + -
383E VAL* 5.6 0.2 - - + -
392E ARG* 4.3 7.4 - - - +
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Residues in contact with VAL 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ARG* 3.8 17.3 - - - +
193E SER* 3.9 21.3 - - - +
196E MET* 4.1 3.6 - - + -
197E GLU* 3.6 38.8 - - + +
252E PRO 3.3 7.2 - - - +
253E ARG 3.3 11.7 - - - +
254E SER 3.1 1.0 - - - -
255E LEU* 1.3 73.9 - - - +
257E ALA* 1.3 67.1 + - - +
259E GLU* 3.2 10.5 + - - +
260E ALA* 2.9 21.2 + - + +
392E ARG* 3.2 26.9 - - - +
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Residues in contact with ALA 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196E MET* 3.8 8.3 - - + +
200E TRP* 3.7 44.5 - - + +
217E ASP 4.4 7.9 - - - +
254E SER 3.4 12.8 + - - +
255E LEU 3.3 0.2 - - - -
256E VAL* 1.3 76.4 - - - +
258E TYR* 1.3 65.8 + - + +
260E ALA* 3.1 15.2 + - - +
262E ALA* 3.1 28.0 + - + +
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Residues in contact with TYR 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E TYR* 4.6 7.7 + - + -
215E ALA 3.2 22.3 + - - -
216E GLY* 3.8 9.0 - - - -
217E ASP 4.3 5.3 + - - -
254E SER* 3.6 22.4 - - - -
255E LEU* 3.1 8.1 + - - +
257E ALA* 1.3 74.2 - - + +
259E GLU* 1.3 62.0 + - - +
260E ALA 2.9 5.6 + - - -
261E GLY* 3.3 9.9 + - - -
262E ALA* 3.3 36.6 - - + +
263E VAL 3.6 1.6 - - - -
264E GLY* 3.4 11.4 - - - -
266E GLY* 3.0 29.5 - - - -
267E LYS 4.5 0.3 + - - -
273E ASN* 4.9 2.3 + - - -
276E VAL* 3.7 27.6 - - + -
280E THR* 4.2 8.7 - - + -
282E MET* 3.7 23.0 - - - +
284E MET* 3.4 12.1 - - + +
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Residues in contact with GLU 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ALA* 4.1 2.7 - - - +
4E LYS* 3.2 45.9 + - - +
5E ARG* 2.9 29.0 + - - +
6E TYR* 3.1 37.0 + - + -
255E LEU* 3.1 19.9 + - - +
256E VAL* 3.3 15.7 - - - +
258E TYR* 1.3 74.8 - - - +
260E ALA* 1.3 56.8 + - - +
261E GLY 3.6 0.8 + - - -
392E ARG* 2.7 46.6 + - - -
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Residues in contact with ALA 260 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ALA* 4.4 14.4 - - + +
197E GLU* 4.3 7.6 - - - +
200E TRP* 3.2 23.7 - - + +
201E THR* 3.6 34.6 - - - +
204E SER* 3.4 3.0 + - - -
256E VAL 2.9 15.2 + - - +
257E ALA 3.1 7.4 + - - +
258E TYR 2.9 1.8 - - - -
259E GLU* 1.3 79.3 - - - +
261E GLY* 1.3 56.4 + - - +
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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