Contacts of the helix formed by residues 259 - 287 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A SER 3.7 12.5 - - - +
256A ALA 5.8 0.4 - - - +
257A SER 4.7 1.3 - - - +
258A ASN* 1.3 90.5 - - - +
260A VAL* 1.3 61.8 + - + +
261A TYR 3.0 0.7 - - - -
262A TRP* 3.0 35.8 + - + +
263A ILE* 4.2 2.8 + - - +
262B TRP* 5.2 4.7 + - - +
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ASN* 3.0 26.1 + - - +
259A PRO* 1.3 77.6 - - + +
261A TYR* 1.3 57.5 + - + +
263A ILE* 3.0 35.5 + - + +
264A ILE* 3.3 26.2 + - + +
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Residues in contact with TYR 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A THR* 3.3 12.2 + - + +
254A LEU* 3.9 42.8 - - + -
255A SER 4.5 1.6 - - - +
257A SER* 4.5 6.5 - - - -
258A ASN* 3.1 40.9 + - + +
259A PRO 3.0 1.0 - - - -
260A VAL* 1.3 76.8 - - + +
262A TRP* 1.3 59.5 + - - +
264A ILE* 3.8 28.9 - - + +
265A GLY* 2.7 25.8 + - - -
318A SER* 3.6 35.8 + - - -
321A LEU* 4.9 3.9 - - + +
322A VAL* 5.0 3.6 - - + -
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Residues in contact with TRP 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PHE* 3.9 18.6 - + - -
251A THR* 3.5 17.5 - - + +
252A TYR* 4.0 27.1 - + - -
255A SER* 3.2 36.5 + - - -
259A PRO* 3.0 26.3 + - + +
261A TYR* 1.3 78.8 - - - +
263A ILE* 1.3 55.4 + - - +
265A GLY* 3.9 0.2 - - - -
266A PHE* 2.9 34.5 + - - +
259B PRO* 4.9 8.5 + - + +
262B TRP* 3.3 67.3 - + + -
263B ILE* 4.1 9.9 - - + -
266B PHE* 3.5 37.6 - + - -
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Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PRO 5.0 1.1 - - - +
260A VAL* 3.0 27.2 + - + +
262A TRP* 1.3 74.7 - - - +
264A ILE* 1.3 68.6 + - + +
266A PHE* 3.4 3.9 + - - +
267A LEU* 3.1 37.0 + - + +
248B PHE* 3.9 23.1 - - + -
252B TYR* 4.1 22.9 - - + +
262B TRP* 4.1 19.1 - - + -
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Residues in contact with ILE 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A VAL* 3.3 24.3 + - + +
261A TYR* 4.0 33.2 - - + +
263A ILE* 1.3 79.9 - - + +
265A GLY* 1.3 57.6 + - - +
267A LEU* 3.2 9.2 + - - +
268A ALA* 2.8 27.7 + - - +
321A LEU* 3.9 31.9 - - + +
322A VAL* 3.9 21.3 - - + +
325A ALA* 4.0 5.9 - - + +
407A MPG 4.4 16.4 - - + -
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Residues in contact with GLY 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A VAL* 3.4 10.4 - - - +
251A THR* 3.2 25.4 - - - -
261A TYR 2.7 19.1 + - - -
262A TRP 3.9 0.7 - - - -
264A ILE* 1.3 70.9 - - - +
266A PHE* 1.3 58.0 + - - +
268A ALA* 3.2 1.5 + - - -
269A ALA* 2.8 28.6 + - - +
321A LEU* 4.2 8.9 - - - +
266B PHE* 3.7 6.5 - - - -
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Residues in contact with PHE 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TRP 2.9 13.1 + - - +
263A ILE 3.4 5.8 - - - +
265A GLY* 1.3 74.6 - - - +
267A LEU* 1.3 57.6 + - - +
269A ALA* 3.4 2.5 + - - +
270A PHE* 3.0 29.6 + - - +
244B PHE* 3.3 37.1 - + - -
247B VAL* 4.9 0.2 - - + -
248B PHE* 4.0 27.6 - + + -
251B THR* 4.2 11.9 - - + -
262B TRP* 3.3 35.2 - + - -
265B GLY 3.8 5.8 - - - -
266B PHE* 3.0 65.0 - + - -
269B ALA* 4.1 15.3 - - + -
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ILE* 3.1 32.8 + - + +
264A ILE* 3.2 7.4 + - - +
266A PHE* 1.3 74.4 - - - +
268A ALA* 1.3 59.9 + - - +
270A PHE* 3.9 4.1 - - + +
271A ALA* 3.0 29.8 + - - +
325A ALA* 4.0 12.6 - - + -
329A ASN* 3.3 21.3 + - - +
407A MPG 3.8 34.3 - - + -
244B PHE* 4.4 12.6 - - + -
248B PHE* 4.1 20.0 - - + -
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A VAL* 4.2 4.5 - - + -
264A ILE 2.8 16.1 + - - +
265A GLY 3.6 4.5 - - - +
267A LEU* 1.3 75.0 - - - +
269A ALA* 1.3 64.0 + - - +
271A ALA 3.5 0.2 + - - -
272A SER* 2.8 30.0 + - - -
321A LEU* 3.6 41.5 - - + +
324A ILE* 3.7 8.7 - - + +
325A ALA* 3.8 12.7 - - - +
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Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ASP 5.5 1.1 - - - -
244A PHE* 4.3 26.7 - - + +
247A VAL* 3.8 18.8 - - + +
265A GLY 2.8 16.5 + - - +
266A PHE* 3.7 4.5 - - - +
268A ALA* 1.3 76.5 - - - +
270A PHE* 1.3 62.9 + - - +
272A SER* 3.2 6.4 + - - -
273A LEU* 3.0 31.4 + - + +
266B PHE* 4.4 9.0 - - + -
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Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PHE 3.0 17.2 + - - +
267A LEU* 3.9 4.5 - - + +
269A ALA* 1.3 76.4 - - - +
271A ALA* 1.3 57.2 + - - +
273A LEU* 3.2 7.4 + - - +
274A MET* 2.7 72.1 + - + +
329A ASN* 3.5 22.7 - - - -
240B ARG 4.1 6.1 - - - -
241B TYR* 3.6 46.9 - + - -
244B PHE* 3.3 58.5 - + + -
273B LEU* 4.1 11.4 - - + -
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU 3.0 19.3 + - - +
268A ALA 3.7 4.0 - - - +
270A PHE* 1.3 82.4 - - - +
272A SER* 1.3 62.9 + - - +
274A MET* 3.2 4.1 + - - +
275A ILE* 2.9 30.8 + - - +
304A ARG* 5.6 0.2 - - - -
324A ILE* 3.7 22.0 - - + +
328A GLY* 3.8 5.6 - - - +
329A ASN* 3.7 26.5 - - - +
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Residues in contact with SER 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ARG* 5.2 0.2 + - - -
243A ASP* 4.1 22.5 - - - +
247A VAL* 4.5 7.8 - - - +
268A ALA 2.8 23.1 + - - -
269A ALA* 3.2 6.2 + - - -
271A ALA* 1.3 76.5 - - - +
273A LEU* 1.3 63.4 + - - +
275A ILE 3.7 0.2 + - - -
276A ALA* 3.5 16.1 + - - +
304A ARG* 3.7 38.9 + - - +
324A ILE* 3.5 16.1 - - - +
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ARG* 3.6 47.7 - - + +
243A ASP* 4.7 4.0 - - + -
244A PHE* 4.6 17.7 - - + +
269A ALA* 3.0 21.2 + - + +
270A PHE* 3.7 4.0 - - - +
272A SER* 1.3 79.0 - - - +
274A MET* 1.3 58.0 + - + +
276A ALA* 3.4 6.4 + - - +
277A TYR* 2.8 29.0 + - - +
270B PHE* 4.2 23.8 - - + -
273B LEU* 3.9 34.1 - - + -
274B MET* 5.1 2.0 - - - -
277B TYR* 5.4 0.7 - - - -
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Residues in contact with MET 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A PHE* 2.7 56.7 + - + +
271A ALA* 3.8 4.9 - - - +
273A LEU* 1.3 73.6 - - - +
275A ILE* 1.3 61.6 + - - +
277A TYR* 4.0 21.1 - - + -
278A THR* 2.8 37.5 + - + +
332A ALA* 4.6 13.7 - - + -
237B VAL* 4.0 12.1 - - + +
240B ARG* 3.7 36.8 - - + -
241B TYR* 3.8 22.7 - - + -
273B LEU* 5.0 3.6 - - - -
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Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ALA 2.9 20.0 + - - +
272A SER* 4.0 0.4 - - - +
274A MET* 1.3 74.1 - - - +
276A ALA* 1.3 63.5 + - - +
278A THR* 3.0 14.8 + - - -
279A GLY* 3.2 4.3 + - - -
299A ILE* 3.9 20.9 - - + +
300A THR* 4.2 5.4 - - - -
304A ARG* 3.5 25.8 - - - +
328A GLY* 3.6 21.8 - - - +
331A GLU* 3.5 33.0 - - + -
332A ALA* 4.0 9.2 - - + +
335A ARG* 3.0 32.0 + - - +
411A SO4 3.6 12.3 + - - +
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Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ARG* 3.3 47.6 - - - +
272A SER 3.5 6.3 + - - +
273A LEU 3.4 8.4 + - - +
275A ILE* 1.3 79.6 - - - +
277A TYR* 1.3 57.6 + - - +
279A GLY* 3.2 1.7 + - - -
280A ASP* 2.9 35.7 + - - +
411A SO4 3.5 20.1 + - - +
277B TYR* 4.4 1.6 - - + -
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Residues in contact with TYR 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU 2.8 20.7 + - - +
274A MET* 4.0 25.8 - - + +
275A ILE 3.4 0.2 - - - -
276A ALA* 1.3 74.1 - - - +
278A THR* 1.3 55.5 + - - +
280A ASP* 6.0 0.2 - - + -
281A LYS* 2.7 58.4 + - + +
236B GLY* 3.5 25.0 + - - -
237B VAL* 3.8 8.7 - - + -
240B ARG* 3.3 43.0 + - + -
273B LEU 5.4 0.4 - - - -
276B ALA 4.4 1.3 - - - -
277B TYR* 4.1 35.9 - + + -
280B ASP* 2.7 37.8 + - + -
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Residues in contact with THR 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A MET* 2.8 41.3 + - + +
275A ILE* 3.0 2.1 + - - +
277A TYR* 1.3 74.3 - - - +
279A GLY* 1.3 58.7 + - - +
282A PHE* 3.1 10.4 + - - +
290A TYR* 5.3 1.1 - - - -
332A ALA* 4.9 14.1 - - + +
335A ARG* 2.9 38.8 + - - -
233B TRP* 3.0 49.4 + - + +
237B VAL* 4.0 16.2 - - + -
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Residues in contact with GLY 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ILE 3.2 9.0 + - - -
276A ALA* 3.7 3.6 - - - -
277A TYR 3.1 0.4 - - - -
278A THR* 1.3 82.7 + - - +
280A ASP* 1.3 61.9 + - - +
282A PHE* 3.3 17.0 + - - +
283A VAL* 3.3 13.5 + - - +
290A TYR* 4.0 18.8 - - - +
335A ARG* 4.2 8.3 - - - -
411A SO4 5.5 2.9 - - - -
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Residues in contact with ASP 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ARG* 4.2 5.0 + - - -
276A ALA* 2.9 17.8 + - - +
277A TYR* 4.2 1.3 - - + +
279A GLY* 1.3 74.4 - - - +
281A LYS* 1.3 59.4 + - - +
283A VAL* 3.3 12.3 + - - +
284A ALA* 3.0 27.4 + - - +
411A SO4 5.7 0.3 + - - -
277B TYR* 2.7 36.9 + - + -
280B ASP* 4.5 2.9 - - + +
281B LYS* 3.0 41.1 + - + +
284B ALA* 3.7 8.8 - - + +
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Residues in contact with LYS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TYR* 2.7 53.1 + - + +
280A ASP* 1.3 69.4 - - - +
282A PHE* 1.3 60.7 + - - +
284A ALA* 3.3 8.8 + - + +
285A ALA* 2.9 32.3 + - - +
145B ALA* 4.1 14.3 - - - +
146B TYR* 5.4 2.6 + - - -
232B ALA* 3.6 26.5 + - - +
233B TRP* 3.6 28.0 - - + +
236B GLY* 4.2 7.5 - - - -
237B VAL* 4.7 0.2 - - + -
280B ASP* 2.9 38.6 + - + +
422B C5P 5.6 2.4 + - - -
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Residues in contact with PHE 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A THR 3.1 16.3 + - - +
279A GLY 3.3 10.1 - - - +
280A ASP 3.2 0.2 - - - -
281A LYS* 1.3 76.5 - - - +
283A VAL* 1.3 53.6 + - - +
286A TYR* 2.7 80.3 + + + +
288A ARG* 3.3 46.2 - - + -
289A THR 3.6 13.5 - - - -
290A TYR* 3.7 30.7 - + + -
291A SER 5.6 0.7 - - - -
339A LEU* 3.5 34.8 - - + -
342A TYR 5.1 0.7 - - - -
233B TRP* 3.4 9.3 - - - +
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLY 3.3 13.2 + - - +
280A ASP* 3.3 14.5 + - - +
282A PHE* 1.3 75.1 - - - +
284A ALA* 1.3 58.6 + - - +
287A MET* 2.8 30.4 + - - -
288A ARG 3.4 27.8 - - - +
289A THR* 4.2 11.0 - - + -
290A TYR* 4.2 4.5 - - + +
284B ALA* 3.8 29.4 - - + +
287B MET* 4.2 8.3 - - + +
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ASP 3.0 13.7 + - - +
281A LYS* 3.6 22.4 - - + +
283A VAL* 1.3 80.2 - - - +
285A ALA* 1.3 60.2 + - - +
287A MET* 4.1 10.9 - - - +
145B ALA* 5.8 1.1 - - + -
280B ASP* 3.8 22.7 - - - +
283B VAL* 3.9 29.1 - - + +
284B ALA* 4.2 5.8 - - - +
287B MET* 5.2 0.7 - - - -
----------------------------------------------------------
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LYS* 2.9 21.4 + - - +
284A ALA* 1.3 78.0 - - + +
286A TYR* 1.3 69.9 + - + +
287A MET* 3.6 3.0 - - - +
229B LYS* 3.6 42.8 + - - +
232B ALA* 4.5 9.2 - - + -
233B TRP* 4.2 14.1 - - + +
----------------------------------------------------------
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Residues in contact with TYR 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE* 2.7 66.6 + + + +
285A ALA* 1.3 77.6 - - + +
287A MET* 1.3 71.7 + - - +
288A ARG* 3.2 27.2 + - + +
339A LEU* 4.1 10.7 + - + +
342A TYR 3.8 21.0 + - - -
229B LYS* 3.6 55.2 + - + -
230B TYR* 3.2 33.3 + - - +
233B TRP* 4.2 13.5 - + + -
----------------------------------------------------------
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Residues in contact with MET 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A VAL* 2.8 20.3 + - - +
284A ALA 4.1 14.4 - - - +
285A ALA 4.7 3.1 - - - +
286A TYR* 1.3 82.2 - - - +
288A ARG* 1.3 60.7 + - - +
143B LYS* 5.9 6.1 - - - +
229B LYS* 5.3 4.3 - - - +
283B VAL* 5.6 2.5 - - - -
287B MET* 3.2 61.8 - - + +
----------------------------------------------------------
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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