Contacts of the helix formed by residues 220 - 246 (chain C) in PDB entry 2M6I
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 LEU 220 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C LEU 3.5 3.0 + - - +
217C GLU 3.5 13.5 - - - +
218C ARG 3.2 1.2 - - - -
219C GLN* 1.3 76.0 - - - +
221C GLY* 1.3 67.8 + - - +
222C TYR 3.0 2.5 - - - -
223C TYR* 2.9 32.6 + - + +
224C LEU* 3.1 19.2 + - + +
268C SER* 4.2 11.9 - - - +
273C SER* 3.2 32.1 - - - +
274C LEU 4.9 0.2 - - - -
275C PRO* 3.6 39.0 - - + -
278C SER* 3.8 18.2 - - - +
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Residues in contact with GLY 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C GLU 5.0 0.2 + - - -
218C ARG 4.2 7.3 + - - -
219C GLN 3.5 0.6 - - - -
220C LEU* 1.3 78.1 - - - +
222C TYR* 1.3 56.8 + - - +
224C LEU* 3.6 14.8 - - - +
225C ILE* 2.9 41.0 + - - +
278C SER* 5.8 0.4 - - - -
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Residues in contact with TYR 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C ARG 4.2 5.4 - - - -
219C GLN* 3.3 48.0 + - + +
220C LEU 2.9 0.8 + - - -
221C GLY* 1.3 78.8 - - - +
223C TYR* 1.3 61.1 + - - +
225C ILE* 3.4 22.1 + - + +
226C GLN* 3.5 21.0 + - - +
421C VAL* 5.3 17.0 - - + +
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Residues in contact with TYR 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C GLN 4.7 0.9 + - - +
220C LEU* 2.9 26.8 + - + +
222C TYR* 1.3 78.7 - - - +
224C LEU* 1.3 61.6 + - + +
225C ILE 3.3 0.2 - - - -
226C GLN* 4.3 4.6 - - + +
227C LEU* 2.9 61.9 + - + +
267C SER* 3.8 23.8 - - - -
279D TYR* 5.9 3.5 - - - -
283D ILE* 5.6 17.8 - - + +
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Residues in contact with LEU 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C LEU* 3.1 32.9 + - + +
221C GLY* 3.2 13.0 + - - +
223C TYR* 1.3 80.1 - - + +
225C ILE* 1.3 59.4 + - + +
227C LEU* 4.3 4.7 - - + -
228C TYR* 2.8 73.3 + - + +
264C THR* 4.9 9.4 - - + -
267C SER* 5.1 10.5 - - - +
268C SER* 5.6 5.2 - - - +
278C SER* 3.6 24.0 - - - +
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Residues in contact with ILE 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C GLY* 2.9 33.0 + - - +
222C TYR* 3.7 16.6 - - + +
223C TYR 3.3 0.4 - - - -
224C LEU* 1.3 74.8 - - + +
226C GLN* 1.3 70.2 + - + +
227C LEU 3.1 1.3 - - - -
228C TYR* 3.1 12.4 + - - +
229C ILE* 3.3 17.7 + - + +
414C TYR* 6.3 1.8 - - + -
417C ILE* 3.5 60.3 - - + +
418C TYR* 5.6 4.3 - - + -
420C ILE* 6.2 1.6 - - + -
421C VAL* 5.5 7.0 - - + -
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Residues in contact with GLN 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C TYR 3.5 16.9 + - - +
223C TYR* 4.7 6.1 - - + +
225C ILE* 1.3 81.7 - - + +
227C LEU* 1.3 57.1 + - - +
229C ILE* 3.8 7.5 - - - +
230C PRO* 3.0 21.4 - - - +
287D LEU* 4.5 14.3 - - + +
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Residues in contact with LEU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C TYR* 2.9 61.1 + - + +
224C LEU* 4.0 5.2 - - + +
225C ILE 3.1 0.6 - - - -
226C GLN* 1.3 76.2 - - - +
228C TYR* 1.3 75.7 + - + +
229C ILE 3.3 0.4 - - - -
230C PRO* 3.2 20.1 - - + +
231C SER* 3.3 15.6 - - - -
263C LEU* 4.9 7.6 - - + +
264C THR* 5.7 3.1 - - + -
267C SER* 3.5 25.6 - - - +
287D LEU* 5.9 1.1 - - - -
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Residues in contact with TYR 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C LEU* 2.8 54.2 + - + +
225C ILE* 3.1 7.4 + - - +
227C LEU* 1.3 85.8 - - + +
229C ILE* 1.3 56.2 + - - +
231C SER* 2.9 12.3 + - - -
232C LEU* 2.7 47.1 + - + +
264C THR* 4.3 20.3 - - + +
282C ALA* 6.2 0.5 - - - +
413C PHE* 3.6 48.7 - + - -
417C ILE* 5.2 7.9 - - + -
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Residues in contact with ILE 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C ILE* 3.3 13.9 + - + +
226C GLN* 3.8 9.2 - - - +
228C TYR* 1.3 79.5 - - - +
230C PRO* 1.3 68.3 - - + +
232C LEU* 3.7 6.5 - - + +
233C LEU* 3.0 48.1 + - + +
410C PHE* 3.6 33.5 - - + -
414C TYR* 5.5 10.1 - - + -
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Residues in contact with PRO 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C GLN 3.0 16.8 - - - +
227C LEU* 3.2 20.9 - - + +
229C ILE* 1.3 104.1 - - + +
231C SER* 1.3 61.6 + - - +
233C LEU* 4.0 9.6 - - + -
234C ILE* 3.1 39.9 + - + +
287D LEU* 4.8 17.9 - - + -
290D CYS* 5.7 6.3 - - - -
291D LEU* 5.3 12.3 - - + -
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Residues in contact with SER 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C LEU* 3.3 21.5 - - - -
228C TYR* 2.9 28.6 + - - +
230C PRO* 1.3 81.0 - - - +
232C LEU* 1.3 61.7 + - - +
234C ILE* 4.2 6.2 + - - +
235C VAL* 2.9 28.8 + - - +
260C VAL* 4.9 7.0 - - - +
263C LEU* 5.5 15.9 - - - -
264C THR* 6.0 2.2 - - - -
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Residues in contact with LEU 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C TYR* 2.7 33.5 + - + +
229C ILE* 3.7 6.5 - - + +
231C SER* 1.3 81.2 + - - +
233C LEU* 1.3 65.5 + - + +
234C ILE 3.3 0.2 - - - -
235C VAL* 3.0 13.7 + - + +
236C ILE* 3.0 33.5 + - + +
409C ILE* 3.2 34.5 - - + +
410C PHE* 5.1 17.3 - - + +
413C PHE* 4.0 35.4 - - + -
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Residues in contact with LEU 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C ILE* 3.0 46.5 + - + +
230C PRO* 3.5 8.9 + - + +
232C LEU* 1.3 76.5 - - + +
234C ILE* 1.3 61.9 + - - +
235C VAL 3.3 0.5 + - - -
236C ILE* 3.3 22.0 + - + +
237C LEU* 3.2 23.0 + - + +
410C PHE* 5.6 16.2 - - + -
291D LEU* 4.1 28.9 - - + -
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Residues in contact with ILE 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C PRO* 3.1 23.5 + - + +
231C SER* 4.5 5.4 - - - +
233C LEU* 1.3 77.1 - - - +
235C VAL* 1.3 61.0 + - + +
237C LEU* 3.7 12.8 + - + +
238C SER* 3.3 19.2 + - - -
252C ARG* 4.8 9.1 + - - +
259C THR* 5.7 8.7 - - + -
260C VAL* 6.1 1.3 - - + -
263C LEU* 5.2 13.0 - - + -
290D CYS* 4.6 24.5 - - + +
291D LEU* 4.1 23.6 - - + -
294D VAL* 4.6 23.6 - - + -
298D LEU* 4.8 0.8 - - + +
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Residues in contact with VAL 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C SER 2.9 22.9 - - - +
232C LEU* 3.0 19.1 + - + +
234C ILE* 1.3 77.7 - - + +
236C ILE* 1.3 70.0 + - + +
238C SER* 3.1 24.3 + - - +
239C TRP* 3.6 7.4 + - + +
260C VAL* 3.2 40.4 - - + -
293C PHE* 5.3 15.0 - - + -
409C ILE* 6.2 4.7 - - + -
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Residues in contact with ILE 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C LEU* 3.0 22.7 + - + +
233C LEU* 3.3 17.7 + - + +
235C VAL* 1.3 79.4 - - + +
237C LEU* 1.3 67.3 + - + +
238C SER 3.4 0.3 + - - -
239C TRP* 3.5 8.2 + - - +
240C ILE* 3.2 27.0 + - + +
405C LEU* 6.4 1.3 - - - -
406C ALA* 3.2 48.5 - - + +
409C ILE* 6.3 2.0 - - + -
410C PHE* 4.7 13.5 - - + -
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Residues in contact with LEU 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C LEU* 3.2 20.2 + - + +
234C ILE* 3.9 13.0 - - + +
235C VAL 3.2 0.4 - - - -
236C ILE* 1.3 77.2 - - + +
238C SER* 1.3 67.6 + - - +
240C ILE* 3.1 23.0 + - + +
241C SER 3.2 7.8 + - - -
291D LEU* 4.8 12.1 - - + -
294D VAL 5.1 0.4 - - - +
295D PHE* 4.8 27.8 - - + -
298D LEU* 3.4 40.0 - - + +
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Residues in contact with SER 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ILE 3.3 11.5 + - - -
235C VAL* 3.1 17.3 + - - +
237C LEU* 1.3 77.8 - - - +
239C TRP* 1.3 67.4 + - - +
241C SER* 2.8 24.1 + - - -
242C PHE* 3.0 15.3 + - - +
252C ARG* 3.9 25.2 + - - +
253C VAL* 5.1 4.1 - - - +
256C GLY* 5.2 9.7 - - - -
257C ILE* 5.5 4.3 - - - +
260C VAL* 6.5 0.7 - - - -
293C PHE* 5.4 6.4 - - - -
298D LEU* 4.3 1.1 - - - +
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Residues in contact with TRP 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C VAL* 3.6 6.6 + - + +
236C ILE* 3.5 9.9 + - - +
237C LEU 3.3 0.4 - - - -
238C SER* 1.3 81.2 + - - +
240C ILE* 1.3 60.4 + - + +
241C SER 2.9 4.9 - - - -
242C PHE* 2.8 48.4 + + + +
243C TRP* 3.4 8.4 + - + +
293C PHE* 4.5 24.4 + + - -
296C SER* 4.4 31.4 - - - -
297C ALA* 4.7 9.6 - - - +
300C GLU* 5.1 2.5 - - + -
398C ILE* 3.4 35.2 - - + -
399C SER* 6.1 0.4 - - - -
401C ILE* 3.2 35.0 - - + -
402C GLY* 4.1 16.6 - - - -
405C LEU* 5.1 20.7 - - + +
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Residues in contact with ILE 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C ILE* 3.2 25.6 - - + +
237C LEU* 3.1 20.1 + - + +
239C TRP* 1.3 77.2 - - + +
241C SER* 1.3 55.1 + - - +
243C TRP* 2.8 28.5 + - + +
399C SER* 5.9 1.3 - - - -
402C GLY 6.0 1.6 - - - -
403C PHE* 3.4 39.0 - - + +
302D ALA* 3.5 13.5 - - + +
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Residues in contact with SER 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C LEU 3.2 1.0 + - - -
238C SER 2.8 15.2 + - - -
239C TRP 2.9 0.6 - - - -
240C ILE* 1.3 76.1 - - - +
242C PHE* 1.3 58.1 + - - +
243C TRP* 3.3 4.5 - - - -
244C ILE* 2.9 20.1 - - - +
245C ASN* 2.7 25.4 + - - -
252C ARG* 3.3 14.0 - - - -
298D LEU* 3.2 31.5 - - - +
301D TYR* 4.4 9.4 - - - -
302D ALA* 3.8 16.2 - - - -
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Residues in contact with PHE 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C SER* 3.0 11.5 + - - +
239C TRP* 2.8 48.0 + + + +
241C SER* 1.3 75.3 - - - +
243C TRP* 1.3 70.3 + - - +
244C ILE 2.9 6.4 + - - -
246C LEU* 2.9 34.7 + - + +
253C VAL* 3.6 37.2 - - + -
297C ALA* 3.9 29.2 - - + -
300C GLU* 4.0 25.6 - - + -
301C TYR* 3.9 23.3 - + - -
398C ILE* 4.8 3.4 - - + -
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Residues in contact with TRP 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C TRP 3.4 5.7 + - - +
240C ILE* 2.8 32.9 + - + -
242C PHE* 1.3 86.7 - - - +
244C ILE* 1.3 90.4 + - + +
246C LEU* 4.2 7.4 - - - +
394C LYS* 3.2 29.5 - - + -
396C ASP* 3.2 46.2 - - + -
398C ILE* 3.4 29.4 - - + -
399C SER* 5.5 6.3 - - - -
302D ALA* 3.3 19.3 + - + +
305D ASN* 3.2 45.5 - - + -
306D PHE* 3.4 21.5 - + - -
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Residues in contact with ILE 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C SER* 2.9 21.8 - - - +
243C TRP* 1.3 91.5 - - + +
245C ASN* 1.3 60.3 + - - +
246C LEU* 3.0 10.4 + - - +
247C ASP 3.6 0.9 + - - -
248C ALA* 3.0 36.4 + - + +
394C LYS* 4.8 1.9 - - - +
246D LEU* 6.0 0.2 - - + -
247D ASP* 4.6 5.4 - - - +
301D TYR* 3.2 26.7 - - + +
302D ALA* 4.3 0.4 - - - -
304D VAL* 3.5 33.0 - - + -
305D ASN* 3.2 38.6 - - - +
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Residues in contact with ASN 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C SER* 2.7 28.7 + - - +
242C PHE 3.2 0.6 + - - +
244C ILE* 1.3 75.3 - - - +
246C LEU* 1.3 62.1 + - - +
247C ASP 2.7 8.4 + - - -
249C ALA* 2.6 31.5 - - - +
250C PRO* 2.8 27.3 - - - +
252C ARG* 3.3 34.8 - - - +
253C VAL* 3.3 23.8 - - + +
301D TYR* 3.2 25.1 - - - -
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Residues in contact with LEU 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ILE* 6.1 1.6 - - + -
249B ALA* 4.0 3.1 - - - +
242C PHE* 2.9 25.4 + - + +
243C TRP* 4.2 10.5 - - - +
244C ILE 3.0 1.3 - - - +
245C ASN* 1.3 77.0 - - - +
247C ASP* 1.3 66.5 + - + +
250C PRO* 4.6 0.2 - - - -
300C GLU* 3.8 13.0 - - + +
301C TYR* 3.4 60.6 + - + +
304C VAL* 3.2 29.4 - - + -
394C LYS* 4.8 16.4 - - - +
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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