Contacts of the helix formed by residues 220 - 246 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LEU 3.5 2.8 + - - +
217A GLU 3.5 13.7 - - - +
218A ARG 3.2 1.4 - - - -
219A GLN* 1.3 76.4 - - - +
221A GLY* 1.3 66.8 + - - +
222A TYR 3.0 3.1 - - - -
223A TYR* 2.9 34.2 + - + +
224A LEU* 3.1 19.6 + - + +
267A SER 6.2 0.2 - - - +
268A SER* 4.2 12.1 - - - +
273A SER* 3.2 32.3 - - - +
275A PRO* 3.7 39.5 - - + -
278A SER* 3.8 16.8 - - - +
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Residues in contact with GLY 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLU 5.0 0.2 + - - -
218A ARG 4.2 6.3 + - - -
219A GLN 3.5 0.8 - - - -
220A LEU* 1.3 78.0 - - - +
222A TYR* 1.3 56.7 + - - +
224A LEU* 3.6 14.0 - - - +
225A ILE* 2.9 43.0 + - - +
278A SER* 5.2 1.4 + - - -
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Residues in contact with TYR 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ARG 4.2 5.6 - - - -
219A GLN* 3.3 46.9 + - + +
220A LEU 2.9 0.4 + - - -
221A GLY* 1.3 78.2 - - - +
223A TYR* 1.3 61.4 + - - +
225A ILE* 3.4 20.1 + - + +
226A GLN* 3.5 21.8 + - - +
421A VAL* 5.2 17.8 - - + +
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Residues in contact with TYR 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A GLN 4.7 1.3 + - - +
220A LEU* 2.9 26.8 + - + +
222A TYR* 1.3 78.4 - - - +
224A LEU* 1.3 62.1 + - + +
226A GLN* 4.3 5.3 - - + +
227A LEU* 2.9 61.9 + - + +
267A SER* 3.8 23.6 - - - -
279B TYR* 5.9 3.1 - - - -
283B ILE* 5.5 18.4 - - + +
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Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LEU* 3.1 31.6 + - + +
221A GLY* 3.2 12.1 + - - +
223A TYR* 1.3 80.5 - - + +
225A ILE* 1.3 58.6 + - + +
227A LEU* 4.3 4.9 - - + -
228A TYR* 2.8 73.0 + - + +
264A THR* 4.9 9.9 - - + -
267A SER* 5.1 10.5 - - - +
268A SER* 5.6 5.2 - - - +
278A SER* 3.5 25.4 - - - +
286A TRP* 5.9 1.8 - - + -
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Residues in contact with ILE 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLY* 2.9 33.4 + - - +
222A TYR* 3.7 16.8 - - + +
224A LEU* 1.3 74.4 - - + +
226A GLN* 1.3 69.6 + - + +
227A LEU 3.1 1.1 - - - -
228A TYR* 3.1 12.5 + - - +
229A ILE* 3.3 17.9 + - + +
414A TYR* 6.3 2.0 - - + -
417A ILE* 3.4 59.1 - - + +
418A TYR* 5.6 4.7 - - + -
420A ILE* 6.2 1.3 - - + -
421A VAL* 5.5 7.2 - - + -
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Residues in contact with GLN 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A TYR 3.5 16.0 + - - +
223A TYR* 4.7 5.6 - - + +
225A ILE* 1.3 80.1 - - + +
227A LEU* 1.3 57.6 + - - +
228A TYR 3.4 0.2 - - - -
229A ILE* 3.8 7.8 - - - +
230A PRO* 3.0 21.0 - - - +
287B LEU* 4.5 13.2 - - + +
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A TYR* 2.9 61.9 + - + +
224A LEU* 4.0 4.7 - - + +
225A ILE 3.1 0.6 - - - -
226A GLN* 1.3 76.2 - - - +
228A TYR* 1.3 76.3 + - + +
229A ILE 3.3 0.7 - - - -
230A PRO* 3.2 20.3 - - + +
231A SER* 3.3 15.5 - - - -
263A LEU* 4.9 7.9 - - + +
264A THR* 5.7 2.5 - - + -
267A SER* 3.5 25.4 - - - +
287B LEU* 5.9 1.6 - - - -
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Residues in contact with TYR 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LEU* 2.8 56.5 + - + +
225A ILE* 3.1 8.0 + - - +
227A LEU* 1.3 86.6 - - + +
229A ILE* 1.3 55.9 + - - +
231A SER* 2.9 12.5 + - - -
232A LEU* 2.7 48.8 + - + +
264A THR* 4.3 16.7 - - + +
286A TRP* 3.9 21.1 + - - -
413A PHE* 3.5 50.3 - + - -
417A ILE* 5.2 6.7 - - + -
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Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ILE* 3.3 14.1 + - + +
226A GLN* 3.8 8.1 - - - +
228A TYR* 1.3 78.1 - - - +
230A PRO* 1.3 69.6 - - + +
232A LEU* 3.7 5.8 - - + +
233A LEU* 3.0 48.9 + - + +
410A PHE* 3.6 33.5 - - + -
414A TYR* 5.5 9.4 - - + -
291B LEU* 6.3 0.2 - - + -
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Residues in contact with PRO 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLN 3.0 16.6 - - - +
227A LEU* 3.2 20.2 - - + +
229A ILE* 1.3 103.7 - - + +
231A SER* 1.3 60.7 - - - +
233A LEU* 3.9 9.1 - - + +
234A ILE* 3.1 39.4 + - + +
287B LEU* 4.8 18.6 - - + -
290B CYS* 5.7 6.3 - - - -
291B LEU* 5.3 12.6 - - + -
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Residues in contact with SER 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 3.3 21.8 - - - -
228A TYR* 2.9 28.6 + - - +
230A PRO* 1.3 81.2 - - - +
232A LEU* 1.3 61.8 + - - +
234A ILE* 4.5 5.6 - - - +
235A VAL* 2.9 28.9 + - - +
260A VAL* 4.9 6.2 - - - +
263A LEU* 5.5 15.3 - - - -
264A THR* 6.0 2.0 - - - -
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A TYR* 2.7 33.7 + - + +
229A ILE* 3.7 5.6 - - + +
231A SER* 1.3 81.9 - - - +
233A LEU* 1.3 65.6 + - + +
234A ILE 3.3 0.2 - - - -
235A VAL* 3.0 13.9 + - + +
236A ILE* 3.0 33.2 + - + +
409A ILE* 3.2 34.1 - - + +
410A PHE* 5.1 18.4 - - + +
413A PHE* 4.0 34.1 - - + -
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ILE* 3.0 46.5 + - + +
230A PRO* 3.9 8.5 - - + +
232A LEU* 1.3 76.3 - - + +
234A ILE* 1.3 62.1 + - - +
235A VAL 3.2 0.5 + - - -
236A ILE* 3.3 22.4 + - + +
237A LEU* 3.2 23.0 + - + +
410A PHE* 5.6 16.4 - - + -
291B LEU* 4.1 29.6 - - + -
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Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PRO* 3.1 23.0 + - + +
231A SER* 4.5 6.1 - - - +
233A LEU* 1.3 75.3 - - - +
235A VAL* 1.3 62.5 + - + +
237A LEU* 3.7 11.5 + - + +
238A SER* 3.3 19.8 + - - -
252A ARG* 4.7 7.5 + - - +
259A THR* 5.8 8.3 - - + -
260A VAL* 6.5 1.1 - - + -
263A LEU* 5.2 12.3 - - + -
290B CYS* 4.6 25.1 - - + +
291B LEU* 4.0 22.7 - - + -
294B VAL* 4.6 23.3 - - + -
298B LEU* 4.8 3.3 - - + +
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A SER 2.9 22.7 - - - +
232A LEU* 3.0 18.9 + - + +
234A ILE* 1.3 77.5 - - + +
236A ILE* 1.3 68.8 + - + +
238A SER* 3.1 25.5 + - - +
239A TRP* 3.5 7.1 + - + +
260A VAL* 3.2 38.8 - - + -
293A PHE* 5.3 15.0 - - + -
409A ILE* 6.2 4.7 - - + -
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Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 3.0 22.9 + - + +
233A LEU* 3.3 17.2 + - + +
235A VAL* 1.3 79.3 - - + +
237A LEU* 1.3 67.0 + - + +
238A SER 3.4 0.3 + - - -
239A TRP* 3.5 7.9 + - - +
240A ILE* 3.2 27.3 + - + +
405A LEU* 6.4 0.9 - - - -
406A ALA* 3.2 49.6 - - + +
409A ILE* 6.3 1.1 - - + -
410A PHE* 4.7 13.2 - - + -
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Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 3.2 19.3 - - + +
234A ILE* 3.9 13.2 - - + +
235A VAL 3.2 0.4 - - - -
236A ILE* 1.3 77.9 - - + +
238A SER* 1.3 67.2 + - - +
240A ILE* 3.2 24.3 + - + +
241A SER* 3.3 7.8 + - - -
291B LEU* 4.8 11.4 - - + +
294B VAL* 5.5 0.7 - - + -
295B PHE* 4.8 27.4 - - + +
298B LEU* 3.4 39.3 - - + +
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Residues in contact with SER 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE 3.3 8.6 + - - -
235A VAL* 3.1 18.2 + - - +
237A LEU* 1.3 77.6 - - - +
239A TRP* 1.3 67.0 + - - +
241A SER* 2.8 23.0 + - - -
242A PHE* 2.9 13.5 + - - +
252A ARG* 3.6 31.8 + - - +
253A VAL* 5.0 3.9 - - - +
256A GLY* 5.2 8.9 - - - -
257A ILE* 5.5 4.0 - - - +
260A VAL* 6.5 0.7 - - - -
293A PHE* 5.4 6.8 - - - -
298B LEU* 4.4 0.2 - - - +
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Residues in contact with TRP 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A VAL* 3.5 6.4 + - + +
236A ILE* 3.5 9.9 + - - +
237A LEU 3.3 0.2 - - - -
238A SER* 1.3 80.9 + - - +
240A ILE* 1.3 61.0 + - + +
241A SER 2.9 2.2 - - - -
242A PHE* 2.7 46.2 + + + +
243A TRP* 3.0 36.4 + + + -
293A PHE* 4.5 24.4 + + - -
296A SER* 4.4 31.4 - - - -
297A ALA* 4.6 9.2 - - - +
300A GLU* 5.6 1.3 - - + -
398A ILE* 3.3 30.7 - - + -
401A ILE* 3.2 35.2 - - + -
402A GLY* 4.1 15.9 - - - -
405A LEU* 5.1 19.8 - - + +
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Residues in contact with ILE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ILE* 3.2 25.1 - - + +
237A LEU* 3.2 19.7 + - + +
239A TRP* 1.3 77.8 - - + +
241A SER* 1.3 56.2 + - - +
243A TRP* 3.2 44.4 - - + +
244A ILE* 5.6 0.2 - - - +
402A GLY 6.1 1.1 - - - -
403A PHE* 3.4 36.3 - - + +
302B ALA* 3.7 19.9 - - + +
306B PHE* 5.5 6.1 - - + -
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Residues in contact with SER 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU 3.3 1.0 + - - -
238A SER 2.8 16.5 + - - -
239A TRP 2.9 0.4 - - - -
240A ILE* 1.3 75.5 - - - +
242A PHE* 1.3 64.4 + - - +
243A TRP 3.0 3.6 + - - -
244A ILE* 3.1 9.6 - - - +
245A ASN* 2.7 41.6 + - - -
252A ARG* 3.2 14.5 - - - -
298B LEU* 3.4 20.1 - - - +
301B TYR* 4.3 9.2 - - - -
302B ALA* 3.8 18.2 - - - -
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Residues in contact with PHE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A SER* 2.9 12.9 + - - +
239A TRP* 2.7 41.6 + + + +
241A SER* 1.3 77.6 + - - +
243A TRP* 1.3 75.9 + + - +
244A ILE 3.3 0.2 - - - -
245A ASN* 3.7 0.4 - - - +
246A LEU* 2.9 34.0 + - + +
253A VAL* 3.5 41.7 - - + -
257A ILE* 6.0 0.4 - - + -
297A ALA* 3.8 33.7 - - + -
300A GLU* 4.0 24.7 - - + -
301A TYR* 4.5 18.6 - + - -
398A ILE* 4.9 2.5 - - + -
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Residues in contact with TRP 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TRP* 3.0 31.6 + + - -
240A ILE* 3.2 51.1 - - + +
241A SER 3.0 0.2 - - - -
242A PHE* 1.3 87.8 - + - +
244A ILE* 1.3 58.4 + - + +
246A LEU* 3.3 18.1 - - - +
394A LYS* 3.3 22.8 + - + +
396A ASP* 3.3 28.7 - - - +
398A ILE* 3.4 39.9 + - + +
399A SER* 3.2 29.8 - - - -
402A GLY* 5.8 1.3 - - - -
403A PHE* 3.8 10.5 - + - -
302B ALA* 5.8 1.6 - - + -
305B ASN* 4.4 13.2 - - + +
306B PHE* 4.1 22.4 - + - -
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Residues in contact with ILE 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ILE 5.6 0.2 - - - +
241A SER* 3.1 15.5 - - - +
243A TRP* 1.3 75.4 - - - +
245A ASN* 1.3 62.6 + - - +
246A LEU* 2.9 10.2 + - - +
247A ASP* 3.4 1.6 + - - +
248A ALA* 3.0 47.7 + - + +
249A ALA* 6.1 0.7 - - + -
394A LYS* 4.6 0.4 - - - +
246B LEU* 5.5 3.8 - - + -
247B ASP* 6.5 0.2 - - + -
301B TYR* 3.2 26.2 - - + +
302B ALA* 4.5 5.8 - - - -
304B VAL* 3.4 41.5 - - + -
305B ASN* 3.3 33.9 - - + +
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Residues in contact with ASN 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A SER* 2.7 47.0 + - - +
242A PHE 3.6 1.9 - - - +
244A ILE* 1.3 74.9 - - - +
246A LEU* 1.3 61.7 + - - +
247A ASP 2.8 8.5 + - - -
249A ALA* 2.7 31.3 - - - +
250A PRO* 2.8 28.2 - - - +
252A ARG* 3.3 17.4 - - - +
253A VAL* 3.2 24.3 - - + +
301A TYR* 5.0 0.2 - - - -
301B TYR* 3.3 24.8 - - - -
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Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 2.9 25.2 + - + +
243A TRP* 3.3 14.6 - - - +
244A ILE 2.9 0.8 - - - +
245A ASN* 1.3 77.0 - - - +
247A ASP* 1.3 64.2 + - + +
300A GLU* 4.0 11.4 - - + +
301A TYR* 3.3 51.0 + - + -
304A VAL* 3.3 35.9 - - + -
394A LYS* 4.1 20.2 - - - +
244E ILE* 5.7 1.6 - - + -
249E ALA* 4.1 1.6 - - - +
----------------------------------------------------------
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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