Contacts of the helix formed by residues 220 - 246 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216E LEU 3.5 2.6 + - - +
217E GLU 3.5 13.7 - - - +
218E ARG 3.2 1.0 - - - -
219E GLN* 1.3 77.2 - - - +
221E GLY* 1.3 66.6 + - - +
222E TYR 3.0 2.9 - - - -
223E TYR* 2.8 33.4 + - + +
224E LEU* 3.1 19.2 + - + +
267E SER 6.2 0.4 - - - +
268E SER* 4.2 11.7 - - - +
273E SER* 3.2 32.3 - - - +
274E LEU 4.9 0.2 - - - -
275E PRO* 3.6 39.0 - - + -
278E SER* 3.8 16.8 - - - +
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Residues in contact with GLY 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E ARG 4.2 6.3 + - - -
219E GLN 3.5 1.0 - - - -
220E LEU* 1.3 78.7 - - - +
222E TYR* 1.3 56.4 + - - +
224E LEU* 3.2 15.1 + - - +
225E ILE* 2.9 41.4 + - - +
278E SER* 5.2 1.2 + - - -
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Residues in contact with TYR 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E ARG 4.2 6.1 - - - -
219E GLN* 3.3 46.6 + - + +
220E LEU 2.9 0.8 + - - -
221E GLY* 1.3 79.6 - - - +
223E TYR* 1.3 61.2 + - - +
225E ILE* 3.4 21.9 + - + +
226E GLN* 3.5 21.1 + - - +
421E VAL* 5.3 16.5 - - + +
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Residues in contact with TYR 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR* 5.9 2.9 - - - -
283A ILE* 5.6 16.3 - - + +
219E GLN 4.7 1.5 + - - +
220E LEU* 2.8 25.5 + - + +
222E TYR* 1.3 78.4 - - - +
224E LEU* 1.3 61.7 + - + +
226E GLN* 4.3 5.1 - - + +
227E LEU* 2.9 62.7 + - + +
267E SER* 3.8 24.0 - - - -
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Residues in contact with LEU 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220E LEU* 3.1 30.5 + - + +
221E GLY* 3.2 11.6 + - - +
223E TYR* 1.3 80.4 - - + +
225E ILE* 1.3 59.6 + - + +
227E LEU* 3.8 5.6 - - + -
228E TYR* 2.9 71.6 + - + +
264E THR* 4.9 10.1 - - + -
267E SER* 5.1 10.5 - - - +
268E SER* 5.6 5.8 - - - +
278E SER* 3.5 24.9 - - - +
286E TRP* 5.9 2.2 - - + -
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Residues in contact with ILE 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221E GLY* 2.9 33.7 + - - +
222E TYR* 3.7 16.8 - - + +
223E TYR 3.3 0.4 - - - -
224E LEU* 1.3 75.4 - - + +
226E GLN* 1.3 70.0 + - + +
227E LEU 3.1 1.1 - - - -
228E TYR* 3.1 12.7 + - - +
229E ILE* 3.3 17.9 + - + +
414E TYR* 6.3 1.6 - - + -
417E ILE* 3.5 60.1 - - + +
418E TYR* 5.7 4.3 - - + -
420E ILE* 6.2 1.8 - - + -
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Residues in contact with GLN 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 4.6 13.1 - - + +
222E TYR 3.5 17.3 + - - +
223E TYR* 4.7 6.1 - - + +
225E ILE* 1.3 80.7 - - + +
227E LEU* 1.3 57.8 + - - +
229E ILE* 3.8 8.2 - - - +
230E PRO* 3.0 21.4 - - - +
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Residues in contact with LEU 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 6.0 1.1 - - - -
223E TYR* 2.9 62.6 + - + +
224E LEU* 4.0 4.9 - - + +
225E ILE 3.1 0.6 - - - -
226E GLN* 1.3 76.0 - - - +
228E TYR* 1.3 74.7 + - + +
229E ILE 3.3 0.7 - - - -
230E PRO* 3.2 20.8 - - + +
231E SER* 3.3 14.9 - - - -
263E LEU* 4.9 7.9 - - + +
264E THR* 5.7 3.1 - - + -
267E SER* 3.5 25.8 - - - +
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Residues in contact with TYR 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E LEU* 2.9 55.3 + - + +
225E ILE* 3.1 7.4 + - - +
227E LEU* 1.3 87.0 - - + +
229E ILE* 1.3 56.1 + - - +
231E SER* 2.9 13.3 + - - -
232E LEU* 2.7 47.7 + - + +
264E THR* 4.3 16.0 - - + +
286E TRP* 3.9 20.6 + - - -
413E PHE* 3.6 49.5 - + - -
417E ILE* 5.2 7.2 - - + -
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Residues in contact with ILE 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E ILE* 3.3 14.4 + - + +
226E GLN* 3.8 9.0 - - - +
228E TYR* 1.3 79.4 - - - +
230E PRO* 1.3 67.7 - - + +
232E LEU* 3.7 5.5 - - + +
233E LEU* 3.0 49.4 + - + +
410E PHE* 3.7 34.1 - - + -
414E TYR* 5.5 9.0 - - + -
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Residues in contact with PRO 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 4.9 17.5 - - + -
290A CYS* 5.7 6.1 - - - -
291A LEU* 5.3 12.6 - - + -
226E GLN 3.0 16.8 - - - +
227E LEU* 3.2 20.2 - - + +
229E ILE* 1.3 104.4 - - + +
231E SER* 1.3 60.2 - - - +
233E LEU* 3.9 8.7 - - + +
234E ILE* 3.1 40.6 + - + +
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Residues in contact with SER 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E LEU* 3.3 21.3 - - - -
228E TYR* 2.9 28.9 + - - +
230E PRO* 1.3 81.6 - - - +
232E LEU* 1.3 60.6 + - - +
234E ILE* 4.5 6.0 - - - +
235E VAL* 2.9 28.6 + - - +
260E VAL* 4.9 6.5 - - - +
263E LEU* 5.5 15.0 - - - -
264E THR* 6.0 2.7 - - - -
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Residues in contact with LEU 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228E TYR* 2.7 34.0 + - + +
229E ILE* 3.7 5.8 - - + +
231E SER* 1.3 82.1 - - - +
233E LEU* 1.3 64.6 + - + +
234E ILE 3.3 0.2 - - - -
235E VAL* 3.0 13.3 + - + +
236E ILE* 3.0 34.4 + - + +
409E ILE* 3.2 33.4 - - + +
410E PHE* 5.1 18.2 - - + +
413E PHE* 4.0 35.0 - - + -
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Residues in contact with LEU 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU* 4.1 29.6 - - + -
229E ILE* 3.0 47.5 + - + +
230E PRO* 3.9 8.1 - - + +
232E LEU* 1.3 76.8 - - + +
234E ILE* 1.3 61.9 + - - +
235E VAL 3.3 0.5 + - - -
236E ILE* 3.3 21.7 + - + +
237E LEU* 3.2 23.2 + - + +
410E PHE* 5.6 15.9 - - + -
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Residues in contact with ILE 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A CYS* 4.6 24.0 - - + +
291A LEU* 4.1 23.8 - - + -
294A VAL* 4.7 22.7 - - + -
298A LEU* 4.9 0.6 - - + +
230E PRO* 3.1 22.3 + - + +
231E SER* 4.5 6.3 - - - +
233E LEU* 1.3 76.1 - - - +
235E VAL* 1.3 60.8 + - + +
237E LEU* 3.7 13.3 + - + +
238E SER* 3.3 20.3 + - - -
252E ARG* 4.7 9.1 + - - +
259E THR* 5.7 8.5 - - + -
260E VAL* 6.5 0.9 - - + -
263E LEU* 5.2 13.5 - - + -
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Residues in contact with VAL 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E SER 2.9 22.2 + - - +
232E LEU* 3.0 19.1 + - + +
234E ILE* 1.3 77.7 - - + +
236E ILE* 1.3 69.5 + - + +
238E SER* 3.1 24.2 + - - +
239E TRP* 3.6 7.2 + - + +
260E VAL* 3.2 41.3 - - + -
293E PHE* 5.3 14.1 - - + -
409E ILE* 6.2 4.5 - - + -
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Residues in contact with ILE 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E LEU* 3.0 22.5 + - + +
233E LEU* 3.3 17.5 + - + +
235E VAL* 1.3 80.5 - - + +
237E LEU* 1.3 67.6 + - + +
238E SER 3.4 0.3 + - - -
239E TRP* 3.5 6.7 + - - +
240E ILE* 3.2 28.2 + - + +
405E LEU* 6.4 0.9 - - - -
406E ALA* 3.2 49.4 - - + +
409E ILE* 6.3 1.8 - - + -
410E PHE* 4.7 13.2 - - + -
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Residues in contact with LEU 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU* 4.8 12.8 - - + +
294A VAL* 5.5 0.7 - - + -
295A PHE* 4.8 26.0 - - + -
298A LEU* 3.4 40.8 - - + +
233E LEU* 3.2 20.2 + - + +
234E ILE* 3.9 12.6 - - + +
235E VAL 3.2 0.6 - - - -
236E ILE* 1.3 76.7 - - + +
238E SER* 1.3 67.5 + - - +
240E ILE* 3.1 23.8 + - + +
241E SER* 3.2 8.0 + - - -
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Residues in contact with SER 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 4.4 0.9 - - - +
234E ILE 3.3 11.4 + - - -
235E VAL* 3.1 17.6 + - - +
237E LEU* 1.3 77.6 - - - +
239E TRP* 1.3 67.9 + - - +
241E SER* 2.8 24.4 + - - -
242E PHE* 2.9 14.9 + - - +
252E ARG* 3.9 23.9 + - - +
253E VAL* 5.1 3.8 - - - +
256E GLY* 5.2 10.6 - - - -
257E ILE* 5.5 4.0 - - - +
260E VAL* 6.5 0.7 - - - -
293E PHE* 5.4 6.6 - - - -
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Residues in contact with TRP 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235E VAL* 3.6 6.4 + - + +
236E ILE* 3.5 10.4 + - - +
237E LEU 3.3 0.4 - - - -
238E SER* 1.3 81.1 + - - +
240E ILE* 1.3 59.9 + - + +
241E SER 2.9 4.9 - - - -
242E PHE* 2.8 48.6 + + + +
243E TRP* 3.4 8.4 + - + +
293E PHE* 4.5 24.6 + + - -
296E SER* 4.4 31.8 - - - -
297E ALA* 4.7 9.7 - - - +
300E GLU* 5.6 1.3 - - + -
398E ILE* 3.4 37.0 - - + -
399E SER* 6.1 0.4 - - - -
401E ILE* 3.2 34.5 - - + -
402E GLY* 4.1 16.6 - - - -
405E LEU* 5.1 19.1 - - + +
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Residues in contact with ILE 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ALA* 3.5 13.6 - - + +
306A PHE* 6.2 4.7 - - + -
236E ILE* 3.2 25.6 - - + +
237E LEU* 3.1 20.3 + - + +
239E TRP* 1.3 76.6 - - + +
241E SER* 1.3 55.8 + - - +
243E TRP* 2.8 28.7 + - + -
399E SER* 5.9 1.3 - - - -
402E GLY 6.0 1.3 - - - -
403E PHE* 3.4 38.4 - - + +
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Residues in contact with SER 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 3.3 30.2 - - - +
301A TYR* 4.4 8.7 - - - -
302A ALA* 3.9 16.6 - - - -
237E LEU 3.2 1.8 + - - -
238E SER 2.8 15.1 + - - -
239E TRP 2.9 0.6 - - - -
240E ILE* 1.3 76.8 - - - +
242E PHE* 1.3 58.0 + - - +
243E TRP* 3.3 4.9 - - - -
244E ILE* 2.9 19.3 - - - +
245E ASN* 2.7 25.7 + - - -
252E ARG* 3.3 15.7 - - - -
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Residues in contact with PHE 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238E SER* 2.9 11.8 + - - +
239E TRP* 2.8 48.1 + + + +
241E SER* 1.3 74.6 - - - +
243E TRP* 1.3 66.4 + - - +
244E ILE 2.9 6.6 + - - -
245E ASN 3.6 0.2 - - - -
246E LEU* 2.9 57.6 + - + +
253E VAL* 3.6 35.7 - - + -
297E ALA* 4.0 31.9 - - + -
300E GLU* 4.0 15.9 - - + -
301E TYR* 4.5 15.7 - + - -
398E ILE* 4.8 3.1 - - + -
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Residues in contact with TRP 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ALA* 3.3 20.3 + - + +
305A ASN* 3.2 47.1 + - + -
306A PHE* 3.4 23.8 - + - -
239E TRP 3.4 5.9 + - - +
240E ILE* 2.8 30.9 + - + -
242E PHE* 1.3 86.3 - - - +
244E ILE* 1.3 89.3 + - + +
246E LEU* 4.2 10.8 - - - +
394E LYS* 3.1 29.5 - - + -
396E ASP* 3.3 46.0 - - + -
398E ILE* 3.4 30.1 - - + -
399E SER* 5.5 6.1 - - - -
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Residues in contact with ILE 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 5.7 0.9 - - + -
301A TYR* 3.2 29.2 - - + +
302A ALA* 4.3 0.4 - - - -
304A VAL* 3.6 32.3 - - + -
305A ASN* 3.2 38.6 - - - +
241E SER* 2.9 21.5 - - - +
243E TRP* 1.3 92.5 - - + +
245E ASN* 1.3 59.5 + - - +
246E LEU* 3.0 10.2 + - - +
247E ASP 3.6 1.0 + - - -
248E ALA* 3.0 36.2 + - + +
394E LYS* 4.9 1.6 - - - +
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Residues in contact with ASN 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A TYR* 3.2 24.5 - - - -
241E SER* 2.7 27.0 + - - +
242E PHE 3.2 0.8 + - - +
244E ILE* 1.3 74.5 - - - +
246E LEU* 1.3 62.5 + - - +
247E ASP 2.7 8.2 + - - -
249E ALA* 2.6 31.3 - - - +
250E PRO* 2.8 27.6 - - - +
252E ARG* 3.3 34.6 - - - +
253E VAL* 3.3 24.9 - - + +
301E TYR* 5.0 0.2 - - - -
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Residues in contact with LEU 246 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D ILE* 5.8 0.4 - - + -
242E PHE* 2.9 49.4 + - + +
243E TRP* 4.2 15.0 - - - +
244E ILE 3.0 2.1 - - - +
245E ASN* 1.3 76.2 - - - +
247E ASP* 1.3 77.8 + - - +
300E GLU* 3.8 24.9 - - + +
301E TYR* 3.3 39.5 + - + +
304E VAL* 3.4 31.9 - - + -
391E ARG* 5.9 4.0 - - - +
394E LYS* 5.6 7.4 - - - +
398E ILE* 6.0 1.8 - - + -
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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