Contacts of the helix formed by residues 275 - 302 (chain B) 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 PRO 275 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 3.6 28.3 - - + -
268B SER* 4.0 20.0 - - - +
271B ARG* 3.2 49.4 - - + +
273B SER* 3.6 2.9 - - - +
274B LEU* 1.3 88.3 - - - +
276B LYS* 1.3 56.4 + - + +
277B VAL 3.3 0.4 - - - -
278B SER* 2.9 5.9 + - - -
279B TYR* 2.7 44.9 + - + +
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Residues in contact with LYS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A SER* 4.8 11.7 + - - -
271B ARG* 4.9 18.8 - - - +
274B LEU* 3.0 14.9 - - + +
275B PRO* 1.3 77.5 - - + +
277B VAL* 1.3 63.4 + - + +
279B TYR* 2.8 51.9 + - - +
280B VAL* 3.4 7.3 + - - +
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLU* 3.1 48.2 - - + +
218B ARG* 3.2 28.7 - - - +
274B LEU 3.9 0.8 + - - -
275B PRO 3.3 0.4 - - - -
276B LYS* 1.3 78.6 - - + +
278B SER* 1.3 62.1 + - - +
279B TYR 3.1 1.2 + - - -
280B VAL* 3.5 13.3 + - - +
281B LYS* 3.5 14.3 + - + +
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Residues in contact with SER 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLU 4.2 10.3 + - - -
220B LEU* 3.8 22.9 - - - +
221B GLY* 5.2 1.0 + - - -
224B LEU* 3.5 25.3 - - - +
275B PRO* 2.9 11.2 + - - -
277B VAL* 1.3 77.9 - - - +
279B TYR* 1.3 56.7 + - - +
281B LYS* 4.4 5.1 - - - +
282B ALA* 2.9 32.1 + - - +
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Residues in contact with TYR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A TYR* 5.9 2.9 - - - -
266A GLN* 5.0 9.9 + - - -
265B THR* 5.6 6.1 - - - +
268B SER* 5.9 6.1 - - - -
271B ARG* 4.9 16.4 + - - -
275B PRO* 2.7 20.9 + - + +
276B LYS* 2.8 38.4 + - + +
278B SER* 1.3 76.8 - - - +
280B VAL* 1.3 53.7 + - + +
282B ALA* 2.9 6.1 + - - +
283B ILE* 2.7 66.2 + - + +
286B TRP* 4.9 21.5 - + - -
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LYS 3.4 6.7 + - - +
277B VAL* 3.5 7.8 + - - +
279B TYR* 1.3 78.3 - - + +
281B LYS* 1.3 74.2 + - + +
283B ILE* 3.0 30.8 + - + +
284B ASP* 3.3 7.8 + - - +
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Residues in contact with LYS 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B VAL* 3.5 14.6 + - + +
278B SER* 4.4 5.2 - - - +
279B TYR 3.2 0.4 - - - -
280B VAL* 1.3 88.4 + - + +
282B ALA* 1.3 61.1 + - - +
283B ILE 3.4 0.3 + - - -
284B ASP* 3.4 41.9 + - - +
285B ILE* 3.4 24.0 - - + +
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B SER* 2.9 24.0 + - - +
279B TYR* 2.9 7.0 + - - +
281B LYS* 1.3 76.0 - - - +
283B ILE* 1.3 54.7 + - - +
285B ILE* 3.9 4.0 - - - +
286B TRP* 2.7 71.1 + - + +
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Residues in contact with ILE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A TYR* 5.5 17.5 - - + +
279B TYR* 2.7 48.3 + - + +
280B VAL* 3.0 25.1 + - + +
282B ALA* 1.3 74.7 - - - +
284B ASP* 1.3 64.0 + - - +
285B ILE 3.1 2.0 - - - -
286B TRP* 4.2 9.6 - - + +
287B LEU* 3.1 35.4 + - + +
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Residues in contact with ASP 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B VAL 3.3 5.3 + - - +
281B LYS* 3.4 28.5 + - - +
282B ALA 3.3 0.6 - - - -
283B ILE* 1.3 79.5 - - - +
285B ILE* 1.3 82.6 + - - +
287B LEU* 4.3 10.6 + - - +
288B ALA* 5.4 2.3 - - - +
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Residues in contact with ILE 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LYS* 3.4 19.1 - - + +
282B ALA* 3.5 6.4 + - - +
284B ASP* 1.3 105.7 - - - +
286B TRP* 1.3 70.9 + - + +
287B LEU 3.1 6.5 + - - -
288B ALA* 3.7 5.0 + - - +
289B VAL* 3.5 25.3 + - + +
413B PHE* 5.0 17.5 - - + -
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Residues in contact with TRP 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B LEU* 5.9 2.2 - - + -
228B TYR* 3.9 16.3 + - - -
264B THR* 3.5 38.5 - - + +
265B THR* 5.3 7.9 - - - -
279B TYR* 4.9 23.8 - + - -
282B ALA* 2.7 45.5 + - + +
283B ILE* 3.5 11.6 + - + -
285B ILE* 1.3 83.6 - - + +
287B LEU* 1.3 56.0 + - - +
288B ALA 3.1 4.6 + - - -
289B VAL* 3.6 19.6 - - + +
290B CYS* 3.1 28.3 - - + -
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLN* 4.5 20.9 - - + +
227A LEU* 5.9 1.1 - - - -
230A PRO* 4.8 16.2 - - + -
283B ILE* 3.1 26.9 + - + +
284B ASP* 4.5 7.9 - - - +
285B ILE 3.1 2.2 - - - -
286B TRP* 1.3 75.7 - - - +
288B ALA* 1.3 63.3 + - - +
290B CYS* 4.9 3.1 - - - -
291B LEU* 5.4 5.1 - - - +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ASP 5.4 2.7 - - - +
285B ILE* 3.7 6.0 + - - +
286B TRP 3.1 3.2 + - - -
287B LEU* 1.3 77.5 - - - +
289B VAL* 1.3 63.1 + - - +
290B CYS* 3.2 4.0 - - - +
291B LEU* 3.8 12.8 - - - +
292B LEU* 2.9 50.4 + - + +
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ILE* 3.5 24.0 + - + +
286B TRP* 3.6 26.5 - - + +
288B ALA* 1.3 78.5 - - - +
290B CYS* 1.3 62.1 - - + +
292B LEU* 4.4 4.2 - - - +
293B PHE* 2.9 34.7 + - + +
409B ILE* 6.4 2.5 - - + -
413B PHE* 5.9 7.9 - - + -
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Residues in contact with CYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PRO* 5.7 6.3 - - - -
234A ILE* 4.6 15.2 - - + +
261B LEU* 5.5 16.4 - - + -
286B TRP 3.1 24.9 - - - +
287B LEU* 4.9 2.0 - - - -
288B ALA 4.5 2.9 - - - -
289B VAL* 1.3 83.4 - - + +
291B LEU* 1.3 70.0 + - - +
292B LEU 3.3 0.4 - - - -
293B PHE* 4.4 5.4 - - - -
294B VAL* 3.2 33.2 + - + +
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PRO* 4.9 10.3 - - + +
233A LEU* 4.1 35.4 - - + -
234A ILE* 4.0 28.3 - - + +
237A LEU* 4.8 10.2 - - + +
287B LEU 5.4 2.9 - - - +
288B ALA* 3.5 16.3 + - - +
289B VAL 3.4 0.2 - - - -
290B CYS* 1.3 85.6 - - - +
292B LEU* 1.3 62.0 + - + +
294B VAL* 5.2 0.4 - - - +
295B PHE* 2.9 25.0 + - + +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ALA* 2.9 37.1 + - + +
289B VAL* 4.4 3.1 - - - +
291B LEU* 1.3 84.5 - - + +
293B PHE* 1.3 63.8 + - - +
294B VAL 3.3 0.4 - - - -
295B PHE* 3.3 31.2 + - + +
296B SER* 3.4 16.1 + - - -
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Residues in contact with PHE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B VAL* 5.3 14.4 - - + -
238B SER* 5.4 4.9 - - - -
239B TRP* 4.5 25.0 + + - -
257B ILE* 3.8 51.6 - - + -
260B VAL* 5.3 13.2 - - + -
261B LEU* 5.3 11.0 - - + -
289B VAL* 2.9 25.7 + - + +
290B CYS* 3.9 4.9 + - - +
292B LEU* 1.3 79.3 - - - +
294B VAL* 1.3 68.7 - - + +
295B PHE 3.2 0.6 + - - -
296B SER* 3.9 2.8 + - - -
297B ALA* 3.7 17.5 + - + +
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Residues in contact with VAL 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE* 4.6 19.3 - - + -
237A LEU* 5.5 0.7 - - + -
252A ARG* 4.2 13.5 - - - +
257B ILE* 5.1 13.5 - - + -
261B LEU* 6.0 5.8 - - + -
290B CYS* 3.2 20.9 + - + +
291B LEU* 5.2 0.9 - - - +
292B LEU 3.3 0.2 - - - -
293B PHE* 1.3 92.1 - - + +
295B PHE* 1.3 61.0 + - - +
296B SER 3.4 0.2 - - - -
297B ALA* 4.0 9.9 - - + -
298B LEU* 2.9 50.7 + - + +
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Residues in contact with PHE 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU* 4.8 23.1 - - + -
291B LEU* 2.9 25.1 + - + +
292B LEU* 3.5 27.4 - - + +
293B PHE 3.2 0.2 - - - -
294B VAL* 1.3 79.9 - - - +
296B SER* 1.3 71.6 + - - +
297B ALA 3.4 0.2 - - - -
298B LEU* 3.8 5.9 + - - +
299B LEU* 3.4 33.2 + - + +
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Residues in contact with SER 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TRP* 4.4 21.1 - - - -
292B LEU 3.4 11.6 + - - -
293B PHE* 4.5 3.6 - - - -
295B PHE* 1.3 87.6 - - - +
297B ALA* 1.3 65.0 + - - +
299B LEU* 3.5 22.4 + - - +
300B GLU* 3.6 10.2 + - - +
401B ILE* 5.3 6.1 - - - +
405B LEU* 5.4 9.8 - - - +
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TRP* 4.7 12.9 - - - +
242B PHE* 3.9 24.6 - - + -
257B ILE* 5.0 15.9 - - + -
293B PHE* 3.7 17.2 + - + +
294B VAL* 4.2 10.8 - - + +
295B PHE 3.4 0.4 - - - -
296B SER* 1.3 80.3 - - - +
298B LEU* 1.3 57.5 + - + +
300B GLU 3.5 1.2 + - - -
301B TYR* 3.0 30.5 + - + +
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE* 4.8 4.5 - - + +
237A LEU* 3.4 50.7 - - + +
238A SER 4.7 1.1 - - - +
241A SER* 3.4 26.2 - - - +
252A ARG* 3.1 33.4 - - - +
294B VAL* 2.9 33.3 + - + +
295B PHE* 4.2 3.6 - - - +
296B SER 3.3 0.2 - - - -
297B ALA* 1.3 74.6 - - + +
299B LEU* 1.3 61.0 + - - +
300B GLU 3.1 2.2 - - - -
301B TYR* 3.5 5.1 - - + -
302B ALA* 2.8 36.8 + - + +
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B PHE* 3.4 28.2 + - + +
296B SER* 3.5 16.8 - - - +
297B ALA 3.3 0.2 - - - -
298B LEU* 1.3 78.2 - - - +
300B GLU* 1.3 67.0 + - - +
302B ALA* 3.9 2.4 - - - +
303B ALA* 2.9 32.6 + - + +
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Residues in contact with GLU 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TRP* 5.6 0.9 - - + -
242B PHE* 4.0 16.6 - - + -
246B LEU* 4.2 16.7 - - + +
296B SER 3.6 7.4 + - - +
297B ALA 3.5 6.5 + - - +
299B LEU* 1.3 93.3 - - - +
301B TYR* 1.3 60.8 + - - +
302B ALA 2.9 6.8 + - - -
303B ALA* 3.1 17.8 + - + +
304B VAL* 3.5 19.2 + - - +
397B LYS* 6.1 0.3 - - - +
398B ILE* 3.3 36.2 - - + +
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Residues in contact with TYR 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A SER* 4.3 7.4 - - - -
244A ILE* 3.2 25.7 - - + +
245A ASN* 3.3 13.9 - - - -
249A ALA* 2.9 26.3 + - + +
252A ARG* 3.5 33.3 + - + +
242B PHE* 4.5 17.2 - + + -
245B ASN 5.5 0.4 - - - -
246B LEU* 3.3 35.2 - - + -
250B PRO* 2.9 34.3 - - + +
253B VAL* 4.9 11.2 - - + -
297B ALA* 3.0 21.7 + - + +
298B LEU* 3.1 9.2 + - + +
300B GLU* 1.3 75.7 - - - +
302B ALA* 1.3 57.8 + - - +
304B VAL 4.8 0.7 - - - -
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU 5.9 0.2 - - - +
240A ILE* 3.7 35.2 - - + +
241A SER* 3.8 10.5 - - - -
243A TRP* 5.8 1.4 - - - -
244A ILE* 4.5 6.1 - - - -
298B LEU* 2.8 16.5 + - + +
299B LEU* 4.5 2.0 - - - +
301B TYR* 1.3 78.9 - - - +
303B ALA* 1.3 62.4 + - - +
304B VAL 3.3 2.0 - - - -
305B ASN* 3.5 7.6 + - - +
306B PHE* 3.2 23.9 + - + +
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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