Contacts of the helix formed by residues 253 - 282 (chain C) in PDB entry 5J0Z
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 THR 253 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C PHE* 3.6 24.5 + - + +
117C ARG* 3.9 4.7 - - - +
119C TYR* 4.0 15.3 - - + -
246C LEU* 4.1 16.4 - - + +
249C THR* 3.9 14.6 + - - +
251C TYR* 3.4 5.4 + - - -
252C MET* 1.3 81.9 - - - +
254C TYR* 1.3 62.1 + - - +
255C THR* 3.5 20.6 - - - +
256C GLY* 3.6 15.4 - - - +
257C ALA* 3.0 23.0 + - - +
314C PHE* 3.7 1.6 - - - -
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Residues in contact with TYR 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ARG 2.8 23.1 + - - +
118C ARG* 4.4 2.7 - - - -
119C TYR 3.7 13.9 - - - +
120C PRO* 5.3 0.7 - - + -
121C PHE* 3.9 28.0 - + - -
253C THR* 1.3 70.5 - - - +
255C THR* 1.3 69.8 + - - +
256C GLY 3.2 0.2 - - - -
257C ALA* 3.3 4.0 + - - +
258C ILE* 3.1 52.4 + - + +
307C ASN* 5.1 4.3 + - - -
310C LEU* 4.6 4.5 - - + -
311C ALA* 4.3 26.1 - - - +
314C PHE* 3.6 37.5 - + + -
315C PHE* 4.1 22.4 - + - -
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Residues in contact with THR 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C TYR* 2.5 42.8 + - + -
120C PRO* 3.3 11.0 - - + +
201C ILE* 5.4 6.1 - - + -
202C ILE* 6.6 0.2 - - + -
242C VAL* 4.1 30.5 - - + -
246C LEU* 5.7 0.4 - - - -
253C THR* 3.9 8.1 - - - -
254C TYR* 1.3 80.3 - - - +
256C GLY* 1.3 57.0 + - - +
258C ILE* 3.5 10.4 + - + +
259C ILE* 2.9 36.4 + - + +
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Residues in contact with GLY 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PRO 5.5 0.2 - - - +
200B ASN* 5.7 6.8 + - - -
242C VAL* 5.8 2.9 - - - -
246C LEU* 6.2 0.2 - - - +
252C MET* 3.6 10.6 - - - +
253C THR* 3.5 18.8 + - - -
254C TYR 3.2 0.6 - - - -
255C THR* 1.3 76.3 - - - +
257C ALA* 1.3 56.8 + - - +
259C ILE* 3.8 7.9 - - - +
260C PHE* 2.8 34.8 + - - +
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Residues in contact with ALA 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C MET* 3.3 12.5 - - + +
253C THR 3.0 14.0 + - - +
254C TYR 3.5 8.7 - - - +
256C GLY* 1.3 73.4 - - - +
258C ILE* 1.3 56.8 + - - +
260C PHE* 3.0 7.7 + - - +
261C MET* 2.6 36.3 + - - +
310C LEU* 3.8 23.3 - - + -
314C PHE* 4.1 14.6 - - + -
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Residues in contact with ILE 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ILE* 6.4 1.8 - - + -
205C MET* 5.4 2.9 - - - -
254C TYR* 3.1 56.5 + - + +
255C THR* 3.6 12.3 - - + +
257C ALA* 1.3 77.8 - - - +
259C ILE* 1.3 62.1 - - + +
261C MET* 3.3 7.7 + - + +
262C ILE* 3.0 45.4 + - + +
303C PHE* 5.8 1.1 - - + -
307C ASN* 4.0 27.1 - - - +
310C LEU* 4.0 13.6 - - + +
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Residues in contact with ILE 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C ILE* 5.7 0.2 - - + -
205C MET* 3.8 37.5 - - + -
235C HIS* 3.9 3.3 + - + +
238C PHE 4.3 4.0 - - - +
239C ASN* 3.7 31.4 - - + +
242C VAL* 3.6 37.5 - - + -
255C THR* 2.9 25.2 + - + +
256C GLY* 3.8 6.7 - - - +
258C ILE* 1.3 79.3 - - + +
260C PHE* 1.3 63.8 + - - +
262C ILE* 3.2 17.6 + - - +
263C TYR* 3.2 21.5 + - + -
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Residues in contact with PHE 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PRO* 3.7 38.8 - - + +
203B LEU* 3.5 44.9 - - + -
204B PRO* 4.8 4.5 - - + -
207B PHE* 3.9 20.2 - + - -
252C MET* 5.6 1.6 - - + -
256C GLY 2.8 22.7 + - - +
257C ALA* 3.6 6.3 - - - +
259C ILE* 1.3 75.3 - - - +
261C MET* 1.3 67.6 + - + +
263C TYR* 3.3 21.8 + - + +
264C LEU* 3.9 18.4 + - + +
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Residues in contact with MET 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C ALA 2.6 20.8 + - - +
258C ILE* 3.7 7.9 - - + +
260C PHE* 1.3 77.9 - - + +
262C ILE* 1.3 66.2 + - + +
264C LEU* 3.0 30.9 + - + +
265C PHE* 3.5 22.4 - - + -
303C PHE* 3.3 30.1 - - + -
306C ALA* 4.0 29.6 - - + +
307C ASN* 3.2 26.2 - - - +
310C LEU* 4.4 13.7 - - + -
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Residues in contact with ILE 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C MET* 4.1 18.6 - - + +
206C LEU* 5.3 4.5 - - + -
209C LEU* 4.5 14.1 - - + -
235C HIS* 3.2 38.1 - - + +
258C ILE* 3.0 37.8 + - + +
259C ILE* 3.2 8.3 + - - +
261C MET* 1.3 76.3 - - - +
263C TYR* 1.3 56.4 + - - +
264C LEU 2.8 6.8 + - - -
265C PHE* 2.9 18.3 + - - +
266C TYR* 3.2 30.3 + - + -
303C PHE* 4.2 26.0 - - + -
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Residues in contact with TYR 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PRO* 3.6 34.5 - - + -
207B PHE* 3.8 23.8 - + + +
208B ILE* 5.0 5.4 - - + -
211B ILE* 5.8 0.3 - - - +
238B PHE* 3.5 12.8 - + - -
232C LEU* 4.6 12.5 - - + +
235C HIS* 3.4 26.0 - + - -
236C ILE* 3.5 24.5 - - + +
239C ASN* 2.7 45.5 + - - +
259C ILE* 3.2 23.8 - - + -
260C PHE* 3.3 15.1 + - + +
261C MET 3.3 0.8 - - - -
262C ILE* 1.3 74.7 - - - +
264C LEU* 1.3 58.3 + - - +
266C TYR* 4.4 8.3 - - - +
267C PHE* 3.4 21.1 + - - +
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Residues in contact with LEU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B PHE* 3.3 43.7 - - + -
260C PHE* 4.0 21.1 - - + +
261C MET* 3.0 22.8 + - + +
262C ILE 2.8 1.4 + - - -
263C TYR* 1.3 72.5 - - - +
265C PHE* 1.3 64.6 + - + +
266C TYR 3.0 4.5 - - - -
267C PHE* 2.6 11.1 + - + -
268C VAL* 2.5 44.6 + - + +
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Residues in contact with PHE 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C LEU* 4.3 14.4 - - + +
212C SER* 4.2 8.1 + - - -
213C TRP* 3.9 22.4 + + - +
261C MET* 3.5 33.9 - - + +
262C ILE* 2.9 11.5 + - - +
264C LEU* 1.3 81.7 - - + +
266C TYR* 1.3 58.9 + - - +
268C VAL* 4.7 6.7 - - + -
269C ALA* 3.3 21.7 + - - +
299C PHE* 4.0 16.9 - + - -
302C VAL* 3.9 26.7 - - + -
303C PHE* 3.3 50.5 - + + -
306C ALA* 5.0 2.0 - - + -
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Residues in contact with TYR 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ILE* 4.9 1.3 - - + -
208C ILE* 3.2 37.8 + - - +
209C LEU* 3.3 16.7 - - + +
212C SER* 3.7 16.2 - - - -
228C VAL* 3.9 19.0 - - + +
231C THR* 3.4 26.0 + - - -
232C LEU* 3.6 38.1 - - + -
235C HIS* 3.8 11.4 - + + -
262C ILE* 3.2 46.8 + - + +
263C TYR* 4.4 4.7 - - - +
264C LEU 3.0 0.4 - - - -
265C PHE* 1.3 78.4 - - - +
267C PHE* 1.3 65.4 + - - +
268C VAL 3.3 0.2 - - - -
269C ALA* 3.3 4.0 + - - +
270C VAL* 2.9 28.3 + - - +
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Residues in contact with PHE 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B PHE* 4.0 26.5 - + + -
210B PHE* 3.4 40.4 - + + -
211B ILE* 3.6 30.5 - - + +
214B THR* 5.7 1.6 - - + -
263C TYR 3.4 16.3 + - - +
264C LEU* 2.6 17.9 + - + +
266C TYR* 1.3 75.7 - - - +
268C VAL* 1.3 64.2 + - + +
270C VAL* 3.3 5.5 + - - +
271C ILE* 3.1 50.1 + - + +
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Residues in contact with VAL 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C LEU* 2.5 28.0 + - + +
265C PHE* 4.7 4.5 - - + -
267C PHE* 1.3 80.3 - - + +
269C ALA* 1.3 64.1 + - - +
271C ILE* 3.0 12.3 + - + +
272C GLU* 2.9 21.9 + - + +
299C PHE* 3.4 28.0 - - + -
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Residues in contact with ALA 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C SER* 4.5 7.2 - - - +
213C TRP* 5.2 0.2 - - + -
216C PHE* 4.5 9.6 - - + -
228C VAL* 4.3 18.4 - - + -
265C PHE 3.3 21.2 + - - +
266C TYR* 3.3 8.1 + - - +
268C VAL* 1.3 79.0 - - - +
270C VAL* 1.3 62.8 + - - +
272C GLU* 3.2 5.3 + - - +
273C VAL* 2.9 27.7 + - - +
299C PHE* 3.7 20.0 - - + -
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Residues in contact with VAL 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ILE* 4.0 34.3 - - + -
214B THR* 3.4 35.2 - - + +
227B LEU* 4.9 2.0 - - + -
228C VAL* 3.3 27.3 - - + +
229C VAL* 4.8 6.3 - - + -
232C LEU* 6.1 0.7 - - + -
266C TYR 2.9 13.4 + - - +
267C PHE 3.4 8.7 - - - +
269C ALA* 1.3 74.4 - - - +
271C ILE* 1.3 54.3 + - + +
273C VAL* 3.2 6.9 + - + +
274C THR* 2.6 44.3 + - - +
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Residues in contact with ILE 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B THR* 4.8 13.5 - - + -
267C PHE* 3.1 45.3 + - + +
268C VAL* 3.0 17.7 + - + +
270C VAL* 1.3 77.3 - - - +
272C GLU* 1.3 53.9 + - - +
274C THR* 3.6 5.2 - - + -
275C VAL* 2.8 46.2 + - + +
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Residues in contact with GLU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C ALA 4.4 0.5 - - - +
216C PHE* 3.2 26.5 - - + -
268C VAL 2.9 11.9 + - - +
269C ALA 3.5 6.1 - - - +
271C ILE* 1.3 76.8 - - - +
273C VAL* 1.3 89.1 + - - +
275C VAL* 3.3 7.9 + - - +
276C GLN* 2.8 32.7 + - - +
291C ILE* 4.0 13.1 - - + +
292C THR* 2.6 35.3 + - - -
295C SER* 3.5 21.5 - - - +
299C PHE* 4.5 7.2 - - + -
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Residues in contact with VAL 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C ALA* 4.1 13.2 - - + -
216C PHE* 5.1 1.3 - - + -
221C TYR* 3.6 24.5 - - + -
224C ASN* 3.7 38.6 - - + +
225C VAL* 4.6 7.2 - - + +
228C VAL* 4.6 9.0 - - + -
269C ALA 2.9 16.3 + - - +
270C VAL* 3.7 6.3 - - + +
272C GLU* 1.3 97.5 + - - +
274C THR* 1.3 65.8 + - - +
276C GLN* 3.4 6.1 + - - +
277C HIS* 3.0 23.9 + - - +
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Residues in contact with THR 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B THR* 3.2 48.5 + - + +
217B TRP* 4.0 22.7 - - + +
227B LEU* 5.1 0.2 - - - +
221C TYR* 3.3 19.8 + - - +
225C VAL* 5.8 0.2 - - - +
270C VAL* 2.6 26.2 + - - +
271C ILE* 3.6 5.8 - - + +
273C VAL* 1.3 73.2 - - - +
275C VAL* 1.3 57.2 + - + +
277C HIS* 3.8 5.4 - - - +
278C TYR* 2.9 25.0 + - - +
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Residues in contact with VAL 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TRP* 6.6 0.2 - - + -
271C ILE* 2.8 27.7 + - + +
272C GLU* 3.4 11.0 - - - +
274C THR* 1.3 74.3 - - + +
276C GLN* 1.3 63.8 + - - +
277C HIS 3.2 1.3 - - - -
278C TYR* 2.7 26.8 + - + +
279C LEU* 2.8 25.7 + - + +
291C ILE* 3.8 31.6 - - + -
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Residues in contact with GLN 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C ALA 4.2 0.7 - - - +
218C SER 3.0 19.7 + - - -
219C THR* 3.7 18.9 - - - +
224C ASN* 3.5 21.0 + - - -
272C GLU* 2.8 28.2 + - - +
273C VAL* 3.7 9.5 - - - +
275C VAL* 1.3 75.5 - - - +
277C HIS* 1.3 63.0 + - - +
279C LEU 3.6 0.3 + - - -
280C LYS* 3.2 30.9 + - - +
288C ALA* 3.7 26.3 - - + +
289C ALA* 5.4 0.8 - - - +
291C ILE* 5.7 1.1 - - + -
292C THR* 2.7 38.6 + - - +
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Residues in contact with HIS 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TRP 4.0 15.9 + - - -
218B SER* 4.1 16.3 + - - -
219B THR* 4.5 6.4 + - - -
220B SER* 4.8 9.4 - - - -
221C TYR* 3.4 59.9 - + + +
222C GLU* 5.7 0.4 + - - -
273C VAL 3.0 10.1 + - - +
274C THR 3.8 3.6 - - - +
276C GLN* 1.3 77.0 + - - +
278C TYR* 1.3 71.9 + + - +
280C LYS* 3.3 8.8 + - - +
281C VAL* 3.3 37.8 + - + +
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Residues in contact with TYR 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TRP* 3.8 35.2 - + + +
293B ARG* 5.6 1.9 - - - -
296B ARG* 3.8 33.5 + - - -
274C THR* 2.9 18.1 + - + +
275C VAL* 2.7 19.4 + - + +
277C HIS* 1.3 75.0 - + - +
279C LEU* 1.3 67.5 + - + +
281C VAL* 2.9 27.4 + - + +
282C GLU* 3.0 51.9 + - + +
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Residues in contact with LEU 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C VAL* 2.8 28.3 + - + +
278C TYR* 1.3 86.1 - - + +
280C LYS* 1.3 52.2 + - - +
282C GLU* 3.0 11.1 + - + +
283C SER 2.7 31.4 + - - -
284C GLN* 3.2 26.0 + - + +
287C ARG* 3.9 25.6 - - + +
288C ALA* 3.5 40.2 - - + +
291C ILE* 3.9 14.8 - - + -
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Residues in contact with LYS 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C THR* 4.1 35.1 - - - +
276C GLN* 3.2 22.8 + - - +
277C HIS* 3.7 11.4 - - - +
278C TYR 3.2 0.4 + - - -
279C LEU* 1.3 77.2 - - - +
281C VAL* 1.3 61.4 + - + +
283C SER* 3.7 9.9 + - - +
285C PRO* 3.8 43.9 + - + +
288C ALA* 4.2 8.2 - - + +
289C ALA* 4.4 12.0 - - - +
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Residues in contact with VAL 281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B THR* 4.8 15.0 - - + +
277C HIS* 3.3 36.2 + - + +
278C TYR* 2.9 14.1 + - + +
280C LYS* 1.3 77.2 - - + +
282C GLU* 1.3 72.9 + - - +
283C SER* 3.2 8.2 + - - -
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Residues in contact with GLU 282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C TYR* 3.0 56.9 + - + +
279C LEU* 3.0 11.9 + - + +
281C VAL* 1.3 93.7 - - - +
283C SER* 1.3 69.7 + - - +
284C GLN* 3.3 15.4 - - - +
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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).
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