Contacts of the helix formed by residues 259 - 287 (chain B) in PDB entry 4O6M
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 259 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TRP* 4.9 8.5 - - + +
255B SER 3.6 11.9 - - - +
256B ALA 5.8 0.4 - - - +
257B SER 4.7 1.1 - - - +
258B ASN* 1.3 90.4 - - - +
260B VAL* 1.3 59.4 + - + +
261B TYR 3.0 2.5 + - - -
262B TRP* 3.1 36.0 + - + +
263B ILE* 4.3 2.4 + - - +
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ASN* 3.0 25.0 + - - +
259B PRO* 1.3 78.1 - - + +
261B TYR* 1.3 61.8 + - + +
263B ILE* 3.1 31.9 + - + +
264B ILE* 3.4 25.7 + - + +
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Residues in contact with TYR 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B THR* 3.4 11.3 + - + +
254B LEU* 3.9 47.3 - - + -
255B SER 4.5 1.8 - - - +
257B SER* 4.9 4.3 - - - -
258B ASN* 3.1 40.4 + - + +
259B PRO 3.0 1.0 - - - -
260B VAL* 1.3 77.0 - - + +
262B TRP* 1.3 55.5 + - - +
263B ILE 3.2 0.2 - - - -
264B ILE* 3.7 30.8 - - + +
265B GLY* 2.7 28.9 + - - -
318B SER* 3.6 35.0 + - - -
321B LEU* 4.8 4.2 - - + +
322B VAL* 5.1 3.8 - - + +
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Residues in contact with TRP 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PRO* 5.2 4.3 + - - +
262A TRP* 3.3 62.3 - + + -
263A ILE* 4.1 13.7 - - + -
266A PHE* 3.3 42.8 - + - -
248B PHE* 3.9 21.1 - + - -
251B THR* 3.5 16.8 - - + -
252B TYR* 4.0 24.5 - + - -
255B SER* 3.1 35.7 + - - -
259B PRO* 3.1 23.7 + - + +
261B TYR* 1.3 78.6 - - - +
263B ILE* 1.3 56.8 + - - +
265B GLY* 3.8 0.3 - - - -
266B PHE* 2.9 37.0 + - - -
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Residues in contact with ILE 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PHE* 3.9 23.6 - - + -
252A TYR* 4.2 21.5 - - + +
262A TRP* 4.1 19.3 - - + -
259B PRO 5.0 1.1 - - - +
260B VAL* 3.1 27.5 + - + +
262B TRP* 1.3 75.1 - - - +
264B ILE* 1.3 66.9 + - + +
266B PHE* 3.4 2.9 + - - +
267B LEU* 3.1 36.5 + - + +
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Residues in contact with ILE 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B VAL* 3.4 24.1 + - + +
261B TYR* 3.4 34.1 + - + +
263B ILE* 1.3 78.8 - - + +
265B GLY* 1.3 58.3 + - - +
267B LEU* 3.3 8.7 + - + +
268B ALA* 2.9 27.4 + - - +
321B LEU* 3.9 33.4 - - + +
322B VAL* 4.0 13.7 - - + +
325B ALA* 4.1 5.5 - - + +
405B MPG 4.3 33.0 - - + -
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Residues in contact with GLY 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PHE* 3.8 7.2 - - - -
247B VAL* 3.4 11.2 - - - +
251B THR* 3.2 25.6 - - - -
261B TYR 2.7 18.5 + - - -
262B TRP 3.8 0.9 - - - -
264B ILE* 1.3 71.0 - - - +
266B PHE* 1.3 64.3 + - - +
268B ALA* 3.2 1.2 + - - -
269B ALA* 2.9 22.7 + - - +
321B LEU* 4.3 7.1 - - - +
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Residues in contact with PHE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PHE* 3.5 32.8 - + + -
247A VAL* 4.8 0.4 - - + -
248A PHE* 3.9 37.9 - + + -
251A THR* 4.2 8.3 - - + -
262A TRP* 3.5 28.7 - + - -
265A GLY 3.7 4.9 - - - -
266A PHE* 3.0 67.3 - + - -
269A ALA* 4.4 14.6 - - + -
262B TRP 2.9 20.9 + - - +
263B ILE 3.5 5.8 - - - +
265B GLY* 1.3 74.8 - - - +
267B LEU* 1.3 57.6 + - - +
269B ALA* 3.8 2.0 - - - +
270B PHE* 2.9 30.3 + - - +
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PHE* 4.2 13.2 - - + -
248A PHE* 4.2 17.9 - - + -
263B ILE* 3.1 32.3 + - + +
264B ILE* 3.7 5.4 - - - +
265B GLY 3.2 0.2 - - - -
266B PHE* 1.3 77.4 - - - +
268B ALA* 1.3 60.7 + - - +
270B PHE* 3.7 3.4 - - + +
271B ALA* 2.9 23.7 + - - +
325B ALA* 4.0 7.2 - - + -
329B ASN* 3.2 33.0 + - - +
405B MPG 4.0 31.2 - - + -
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Residues in contact with ALA 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B VAL* 4.2 13.5 - - + -
264B ILE 2.9 16.8 + - - +
265B GLY 3.7 4.3 - - - +
267B LEU* 1.3 75.4 - - - +
269B ALA* 1.3 60.0 + - - +
271B ALA 3.5 0.2 + - - -
272B SER* 2.8 34.4 + - - -
321B LEU* 3.6 32.1 - - + +
324B ILE* 3.7 8.8 - - + +
325B ALA* 3.8 13.4 - - - +
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Residues in contact with ALA 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PHE* 4.1 16.8 - - + -
243B ASP 5.5 0.9 - - - -
244B PHE* 4.3 19.1 - - + +
247B VAL* 3.9 19.2 - - + +
265B GLY 2.9 16.6 + - - +
266B PHE 3.8 3.8 - - - +
268B ALA* 1.3 74.9 - - - +
270B PHE* 1.3 64.6 + - - +
272B SER* 3.3 5.7 + - - -
273B LEU* 3.0 32.1 + - + +
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Residues in contact with PHE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ARG 4.0 7.2 - - - -
241A TYR* 3.6 47.3 - + - -
244A PHE* 3.4 57.6 - + + -
273A LEU* 4.2 11.4 - - + -
266B PHE 2.9 18.0 + - - +
267B LEU* 3.7 4.5 - - + +
269B ALA* 1.3 78.4 - - - +
271B ALA* 1.3 56.3 + - - +
273B LEU* 3.3 7.3 + - - +
274B MET* 2.8 65.7 + - + +
329B ASN* 3.4 24.7 - - - -
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Residues in contact with ALA 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU 2.9 19.1 + - - +
268B ALA 3.7 3.6 - - - +
270B PHE* 1.3 76.8 - - - +
272B SER* 1.3 63.7 + - - +
274B MET* 3.2 4.5 + - - +
275B ILE* 2.9 30.7 + - - +
324B ILE* 3.7 16.6 - - + +
328B GLY* 3.7 6.5 - - - +
329B ASN* 3.6 36.1 - - - +
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Residues in contact with SER 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ASP* 4.2 22.9 - - - +
247B VAL* 4.6 7.1 - - - +
268B ALA 2.8 21.6 + - - -
269B ALA* 3.7 6.6 - - - -
270B PHE 3.3 0.2 - - - -
271B ALA* 1.3 76.6 - - - +
273B LEU* 1.3 65.4 + - - +
275B ILE 3.5 0.3 + - - -
276B ALA* 3.5 14.7 + - - +
304B ARG* 3.6 38.4 + - - +
324B ILE* 3.5 16.8 - - - +
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A PHE* 4.1 23.3 - - + -
273A LEU* 3.9 33.9 - - + -
274A MET* 5.0 2.2 - - - -
277A TYR* 5.4 0.7 - - - -
240B ARG* 3.5 50.0 - - + +
243B ASP* 4.6 4.7 - - + -
244B PHE* 4.5 16.2 - - + +
269B ALA* 3.0 21.9 + - + +
270B PHE 3.8 2.9 - - - +
272B SER* 1.3 77.0 - - - +
274B MET* 1.3 60.7 + - + +
276B ALA* 3.2 8.3 + - - +
277B TYR* 2.8 28.4 + - - +
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Residues in contact with MET 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A VAL* 4.0 12.3 - - + -
240A ARG* 3.6 38.4 - - + -
241A TYR* 3.9 21.8 - - + -
273A LEU* 5.1 3.1 - - - -
270B PHE* 2.8 50.7 + - + +
271B ALA* 3.2 4.2 + - - +
273B LEU* 1.3 76.8 - - + +
275B ILE* 1.3 61.0 + - - +
277B TYR* 3.9 22.2 - - + -
278B THR* 2.9 41.3 + - + +
332B ALA* 4.5 14.8 - - + -
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Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ALA 2.9 21.9 + - - +
272B SER 3.9 0.2 - - - +
273B LEU 3.4 0.2 - - - -
274B MET* 1.3 75.0 - - - +
276B ALA* 1.3 63.5 + - - +
278B THR* 3.1 5.8 + - - -
279B GLY* 3.4 2.8 + - - -
299B ILE* 4.0 16.4 - - + +
300B THR* 4.3 4.9 - - - -
304B ARG* 3.6 21.1 - - - +
328B GLY* 3.5 25.4 - - - +
331B GLU* 3.5 27.8 - - + -
332B ALA* 4.0 10.3 - - + +
335B ARG* 2.9 41.0 + - - +
419B SO4 3.5 21.6 + - - +
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TYR* 4.5 1.8 - - + -
146B TYR* 4.4 3.2 + - - +
240B ARG* 3.2 51.8 - - - +
272B SER 3.5 4.7 + - - +
273B LEU 3.2 8.1 + - - +
275B ILE* 1.3 80.8 - - - +
277B TYR* 1.3 63.8 + - - +
279B GLY* 3.2 2.9 + - - -
280B ASP* 3.0 27.6 + - - +
419B SO4 3.4 15.6 + - - +
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Residues in contact with TYR 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLY* 3.5 23.8 + - - -
237A VAL* 3.9 8.7 - - + -
240A ARG* 3.1 43.0 + - + -
273A LEU 5.4 0.4 - - - -
276A ALA 4.3 7.2 - - - -
277A TYR* 4.1 30.7 - + + -
280A ASP* 2.7 39.0 + - + -
273B LEU 2.8 20.0 + - - +
274B MET* 3.9 27.4 - - + +
275B ILE 3.4 0.4 - - - -
276B ALA* 1.3 73.6 - - - +
278B THR* 1.3 59.4 + - - +
280B ASP* 5.9 0.4 - - + -
281B LYS* 2.8 56.0 + - + +
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Residues in contact with THR 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TRP* 3.0 49.4 + - + +
237A VAL* 4.2 15.3 - - + -
241A TYR* 6.0 0.2 - - + -
274B MET* 2.9 38.7 + - + +
275B ILE* 3.8 1.0 - - - +
277B TYR* 1.3 74.1 - - - +
279B GLY* 1.3 59.1 + - - +
281B LYS* 4.6 0.2 - - - -
282B PHE* 3.2 9.4 + - - +
290B TYR* 5.0 2.2 - - - -
332B ALA* 4.9 13.9 - - + +
335B ARG* 2.9 41.9 + - - -
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Residues in contact with GLY 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B TYR* 4.4 13.9 - - - -
275B ILE 3.4 5.6 + - - -
276B ALA 3.2 5.9 + - - -
277B TYR 3.1 0.6 - - - -
278B THR* 1.3 81.8 + - - +
280B ASP* 1.3 63.7 + - - +
282B PHE* 3.3 6.4 + - - +
283B VAL* 3.2 23.4 + - - +
290B TYR* 3.8 26.7 - - - +
335B ARG* 4.0 1.7 - - - +
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Residues in contact with ASP 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TYR* 2.7 37.9 + - + -
280A ASP* 4.5 2.6 - - + +
281A LYS* 2.9 42.1 + - + +
284A ALA* 3.8 7.4 - - + +
145B ALA* 3.8 6.8 - - - +
146B TYR* 3.7 21.6 + - - -
240B ARG* 4.5 0.2 + - - -
276B ALA 3.0 15.5 + - - +
277B TYR* 4.1 2.0 - - + +
279B GLY* 1.3 73.7 - - - +
281B LYS* 1.3 61.3 - - - +
283B VAL* 3.2 6.7 + - - +
284B ALA* 2.9 27.4 + - - +
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Residues in contact with LYS 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ALA* 3.5 27.5 + - - +
233A TRP* 3.5 27.4 - - + +
236A GLY* 4.1 7.8 - - - -
237A VAL* 4.7 0.4 - - + -
280A ASP* 3.0 32.2 + - - +
277B TYR* 2.8 57.7 + - + +
278B THR* 4.6 0.2 - - - -
280B ASP* 1.3 70.2 - - - +
282B PHE* 1.3 61.4 + - - +
284B ALA* 3.5 8.7 - - + +
285B ALA* 2.9 32.9 + - - +
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Residues in contact with PHE 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TRP* 3.4 9.8 - - - +
278B THR 3.2 15.2 + - - +
279B GLY 3.3 9.6 - - - +
280B ASP 3.2 0.2 - - - -
281B LYS* 1.3 76.5 - - - +
283B VAL* 1.3 56.2 + - - +
285B ALA 3.2 0.2 + - - -
286B TYR* 2.7 78.1 + + + +
288B ARG* 3.6 44.0 - - + -
289B THR 3.4 21.3 - - - -
290B TYR* 3.5 27.6 - + + -
291B SER 5.6 1.3 - - - -
339B LEU* 3.7 34.1 - - + -
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Residues in contact with VAL 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ALA* 3.9 28.7 - - + +
287A MET* 5.6 1.8 - - - -
143B LYS* 5.7 4.7 - - - +
145B ALA* 3.3 45.3 - - + +
279B GLY 3.2 12.7 + - - +
280B ASP* 3.2 6.9 + - - +
282B PHE* 1.3 76.7 - - - +
284B ALA* 1.3 58.5 + - - +
287B MET* 2.8 32.7 + - + +
288B ARG 3.6 26.9 - - - +
290B TYR 4.0 2.2 - - - +
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Residues in contact with ALA 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ASP* 3.7 22.4 - - - +
283A VAL* 3.8 26.5 - - + +
284A ALA* 4.2 5.4 - - - +
280B ASP 2.9 16.6 + - - +
281B LYS* 3.5 20.4 - - + +
282B PHE 3.2 0.2 - - - -
283B VAL* 1.3 80.6 - - - +
285B ALA* 1.3 59.3 + - - +
287B MET* 3.6 15.9 - - - +
----------------------------------------------------------
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LYS* 3.5 40.1 - - - +
232A ALA* 4.4 9.9 - - + -
233A TRP* 4.2 14.1 - - + +
281B LYS* 2.9 20.9 + - - +
284B ALA* 1.3 77.7 - - + +
286B TYR* 1.3 69.1 + - + +
287B MET* 4.8 3.6 - - - +
----------------------------------------------------------
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Residues in contact with TYR 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LYS* 3.7 53.7 + - + -
230A TYR* 3.3 27.5 + - - +
233A TRP* 4.2 7.2 - - + -
282B PHE* 2.7 71.1 + + + +
285B ALA* 1.3 78.2 - - + +
287B MET* 1.3 72.1 + - - +
288B ARG* 3.2 26.2 + - + +
339B LEU* 3.9 21.0 + - + +
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Residues in contact with MET 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LYS* 6.3 1.1 - - - -
283A VAL* 4.2 14.4 - - + +
284A ALA* 5.2 0.7 - - - -
287A MET* 3.2 57.7 - - + +
143B LYS* 4.4 10.9 + - - -
283B VAL* 2.8 40.5 + - - +
284B ALA* 3.6 17.0 - - - +
285B ALA 4.8 3.1 - - - +
286B TYR* 1.3 80.9 - - - +
288B ARG* 1.3 59.2 + - - +
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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