Contacts of the helix formed by residues 241 - 266 (chain C) in PDB entry 3RHW
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 ALA 241 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B ILE* 4.0 24.9 - - + -
243B PRO* 5.5 3.1 - - + -
298B ASN* 5.5 0.2 - - - +
237C PHE* 4.8 2.5 - - + +
238C ASP* 3.0 32.4 + - - +
239C ARG 4.8 0.2 - - - -
240C THR* 1.3 77.3 + - - +
242C ILE* 1.3 63.1 - - - +
243C PRO* 3.2 8.1 - - + -
244C ALA* 3.5 13.8 + - + +
245C ARG* 3.8 7.3 + - - +
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Residues in contact with ILE 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C ARG* 4.7 5.4 - - - +
240C THR 3.1 7.3 + - - +
241C ALA* 1.3 71.8 - - - +
243C PRO* 1.3 81.6 - - + +
244C ALA 3.1 2.5 - - - -
245C ARG* 2.9 40.5 + - + +
246C VAL* 3.0 27.6 + - + +
294C PHE* 3.9 28.0 - - + +
297C VAL* 6.3 0.9 - - + -
298C ASN* 4.0 30.5 - - + +
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Residues in contact with PRO 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B PRO* 4.3 25.4 - - + -
240C THR 4.4 2.2 - - - +
241C ALA* 3.2 10.1 - - + -
242C ILE* 1.3 100.8 - - + +
244C ALA* 1.3 61.7 + - - +
246C VAL* 3.7 5.3 + - + +
247C THR* 3.1 29.4 + - - -
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Residues in contact with ALA 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ILE* 3.7 29.8 - - + -
243B PRO* 4.9 5.5 - - - +
246B VAL* 3.8 22.7 - - + +
237C PHE* 4.5 13.9 - - + -
241C ALA* 3.5 9.7 + - - +
242C ILE 3.1 0.8 - - - -
243C PRO* 1.3 80.3 - - - +
245C ARG* 1.3 61.9 + - - +
247C THR* 3.5 4.8 + - - -
248C LEU* 3.2 29.0 + - - +
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Residues in contact with ARG 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C SER* 2.7 37.6 + - - +
235C PHE* 3.7 8.7 + - - +
237C PHE* 3.1 29.9 + - + -
238C ASP 4.5 3.1 + - - -
239C ARG* 4.2 8.8 - - - +
241C ALA 4.1 10.3 - - - +
242C ILE* 2.9 24.6 + - + +
244C ALA* 1.3 74.7 - - - +
246C VAL* 1.3 61.5 + - - +
248C LEU* 3.3 2.1 + - - +
249C GLY 2.9 25.8 + - - -
293C GLU* 3.4 17.0 + - - -
294C PHE* 3.1 34.9 + - + +
297C VAL* 4.0 14.8 - - - +
316C ASP* 2.6 43.0 + - - -
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Residues in contact with VAL 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C ILE* 3.0 34.8 + - + +
243C PRO* 4.1 4.7 - - + +
245C ARG* 1.3 72.3 - - - +
247C THR* 1.3 67.9 + - - +
250C VAL* 2.8 48.1 + - + +
291C LEU* 4.4 13.7 - - + -
294C PHE* 5.0 4.7 - - + -
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Residues in contact with THR 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B PRO 5.6 0.8 + - - -
246B VAL* 3.5 24.2 - - + +
247B THR* 4.5 22.6 + - - +
250B VAL* 4.6 5.6 - - + -
243C PRO 3.1 20.5 + - - -
244C ALA* 3.7 5.2 - - - -
245C ARG 3.3 0.2 - - - -
246C VAL* 1.3 77.3 - - - +
248C LEU* 1.3 60.6 + - - +
250C VAL* 4.4 1.7 - - - +
251C THR* 2.7 38.8 + - - +
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Residues in contact with LEU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B VAL* 3.8 8.7 - - + -
250B VAL* 3.2 29.6 - - + -
291B LEU* 4.2 8.7 - - + -
230C VAL* 3.6 29.8 - - + +
231C SER* 5.2 1.3 - - - -
233C VAL* 3.6 13.5 - - + -
234C SER* 3.6 28.5 - - - +
237C PHE* 3.6 25.6 - - + -
244C ALA 3.2 12.0 + - - +
245C ARG 3.6 5.8 - - - +
247C THR* 1.3 78.0 - - - +
249C GLY* 1.3 65.6 + - - +
250C VAL 3.0 0.7 + - - -
251C THR* 3.1 2.1 + - - -
252C THR* 3.0 30.4 + - + +
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Residues in contact with GLY 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C SER* 4.9 6.9 - - - +
245C ARG 2.9 19.2 + - - -
246C VAL 3.9 0.4 - - - -
248C LEU* 1.3 73.1 - - - +
250C VAL* 1.3 57.7 + - - +
252C THR* 3.2 16.2 + - - -
253C LEU* 3.3 14.9 + - - +
287C ILE* 3.4 10.5 - - - +
290C ALA* 5.5 0.2 - - - -
291C LEU* 3.9 21.3 - - - +
294C PHE* 4.1 8.9 - - - -
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Residues in contact with VAL 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C VAL* 2.8 41.4 + - + +
247C THR* 4.4 2.0 - - - +
249C GLY* 1.3 72.0 - - - +
251C THR* 1.3 62.6 + - - +
252C THR 3.3 0.4 - - - -
253C LEU* 3.3 7.2 + - + +
254C LEU* 2.9 36.7 + - + +
291C LEU* 4.0 20.9 - - + -
230D VAL* 5.3 7.6 - - + -
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Residues in contact with THR 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B VAL* 3.1 33.2 - - + +
251B THR* 5.7 0.2 - - - -
254B LEU* 3.3 30.7 - - + +
247C THR* 2.7 27.1 + - - +
248C LEU 3.1 2.5 + - - -
250C VAL* 1.3 79.1 - - - +
252C THR* 1.3 60.3 + - + +
254C LEU* 3.9 5.8 - - - +
255C THR* 2.9 35.4 + - - +
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Residues in contact with THR 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B VAL* 5.9 1.3 - - + -
253B LEU* 6.2 0.9 - - + -
227C LEU* 3.7 37.4 - - + +
230C VAL* 3.6 31.6 - - + -
231C SER* 3.8 7.4 - - - +
248C LEU* 3.0 21.4 + - + +
249C GLY* 3.2 10.7 + - - -
251C THR* 1.3 80.3 - - + +
253C LEU* 1.3 58.9 + - - +
255C THR* 4.5 1.1 - - - -
256C MET* 3.0 27.2 + - - +
287C ILE* 3.3 18.8 - - - +
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Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C GLY 3.3 15.9 + - - +
250C VAL* 3.3 6.7 + - + +
251C THR 3.2 0.4 - - - -
252C THR* 1.3 79.8 + - - +
254C LEU* 1.3 66.1 + - - +
256C MET* 3.2 6.7 - - - +
257C THR* 3.1 22.0 + - - +
284C MET* 3.8 24.7 - - + +
287C ILE* 3.7 16.2 - - + -
288C PHE* 4.1 7.9 - - + +
291C LEU* 4.7 9.9 - - + -
226D MET* 3.3 38.4 - - + -
227D LEU* 5.2 7.0 - - + -
230D VAL* 4.2 22.7 - - + -
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Residues in contact with LEU 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B LEU* 5.2 10.5 - - + -
250C VAL* 2.9 25.1 + - + +
251C THR* 3.9 6.3 - - - +
253C LEU* 1.3 76.9 - - - +
255C THR* 1.3 69.0 + - - +
257C THR* 3.0 19.4 + - + -
258C ALA* 3.1 18.0 + - + +
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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
----------------------------------------------------------
254B LEU* 3.0 35.2 - - + +
257B THR* 4.5 22.9 - - + +
227C LEU* 3.5 31.1 - - + +
251C THR* 2.9 21.8 + - - +
252C THR* 3.9 1.8 - - - -
254C LEU* 1.3 79.1 - - - +
256C MET* 1.3 62.7 + - - +
258C ALA* 3.2 7.1 + - + +
259C GLN* 2.9 24.9 + - + +
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Residues in contact with MET 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C SER* 3.3 30.5 - - - +
227C LEU* 3.7 17.5 - - - +
252C THR 3.0 15.4 + - - +
253C LEU* 3.2 14.1 - - + +
254C LEU 3.2 0.2 - - - -
255C THR* 1.3 77.2 - - - +
257C THR* 1.3 62.0 + - - +
259C GLN* 3.3 6.9 + - - +
260C SER* 3.1 22.2 + - - -
279C TRP* 4.6 0.2 - - + -
280C ILE* 4.0 28.9 - - + +
283C CYS* 3.3 32.8 - - + -
284C MET* 3.4 27.8 - - - -
287C ILE* 4.4 10.5 - - + -
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Residues in contact with THR 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C LEU* 3.1 4.9 + - - +
254C LEU* 3.0 15.4 + - + -
256C MET* 1.3 78.2 - - - +
258C ALA* 1.3 66.0 + - - +
260C SER* 3.1 9.0 + - - -
261C ALA* 2.9 24.5 + - + +
284C MET* 2.9 28.6 - - - +
223D PRO* 6.1 4.7 - - + +
226D MET* 5.3 0.3 - - - +
227D LEU* 5.3 8.3 - - + +
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Residues in contact with ALA 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C LEU* 3.1 15.1 + - + +
255C THR* 3.5 12.1 - - + +
257C THR* 1.3 79.4 - - - +
259C GLN* 1.3 65.7 + - - +
261C ALA* 3.0 12.2 + - - +
262C GLY* 3.0 17.8 + - - -
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Residues in contact with GLN 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B THR* 6.0 5.4 - - + -
219C GLN 3.8 9.3 + - - +
220C LEU* 2.9 52.7 + - + +
223C PRO* 4.0 8.9 - - - +
224C SER* 3.0 21.6 + - - -
227C LEU* 4.2 17.2 - - - +
255C THR* 2.9 16.3 + - + +
256C MET* 3.6 11.6 - - - +
258C ALA* 1.3 74.2 - - - +
260C SER* 1.3 63.3 + - - +
262C GLY* 3.1 11.7 + - - -
263C ILE* 3.3 15.3 + - + +
280C ILE* 4.8 1.7 - - - +
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Residues in contact with SER 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C MET 3.1 6.5 + - - -
257C THR* 3.1 9.5 + - - -
259C GLN* 1.3 76.5 - - - +
261C ALA* 1.3 61.3 + - - +
262C GLY 3.2 0.2 + - - -
263C ILE* 3.2 6.3 + - - +
264C ASN* 2.8 51.5 + - - +
280C ILE* 3.6 42.6 - - - +
219D GLN* 4.6 2.6 + - - -
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Residues in contact with ALA 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C THR* 2.9 15.7 + - + +
258C ALA* 3.0 14.1 + - - +
260C SER* 1.3 76.7 + - - +
262C GLY* 1.3 63.2 + - - +
264C ASN* 3.9 4.6 - - - +
265C SER* 3.1 26.0 + - - -
219D GLN* 5.7 2.5 - - - -
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Residues in contact with GLY 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C ALA 3.0 12.3 + - - -
259C GLN* 3.1 5.6 + - - -
260C SER 3.1 0.6 - - - -
261C ALA* 1.3 75.4 - - - +
263C ILE* 1.3 62.7 + - - +
265C SER* 2.6 24.7 + - - -
266C GLN* 3.9 11.3 + - - +
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Residues in contact with ILE 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C TYR* 4.1 29.6 + - + +
215C PHE* 5.0 18.6 - - + -
216C TYR* 5.4 5.4 - - + -
219C GLN* 4.8 13.2 - - + +
220C LEU* 3.8 28.7 - - + -
259C GLN* 3.3 14.7 + - + +
260C SER* 3.2 7.7 + - - +
262C GLY* 1.3 74.4 - - - +
264C ASN* 1.3 65.0 + - - +
265C SER 3.1 1.0 + - - -
266C GLN* 3.3 22.5 + - - +
267C LEU* 3.8 12.2 - - + +
276C ILE* 4.3 18.6 - - + -
280C ILE* 6.0 0.4 - - + -
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Residues in contact with ASN 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C SER* 2.8 40.3 + - - +
261C ALA* 3.9 4.5 - - - +
263C ILE* 1.3 74.3 - - - +
265C SER* 1.3 60.8 + - - +
266C GLN 3.3 0.4 - - - -
267C LEU* 3.4 35.8 + - - +
274C LYS* 4.3 6.9 + - - -
276C ILE* 5.1 5.5 - - - +
277C ASP* 4.1 13.1 + - - +
280C ILE* 5.6 3.0 - - - +
215D PHE* 4.9 10.5 - - + -
219D GLN* 3.0 43.8 + - + +
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Residues in contact with SER 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C VAL* 5.3 2.1 - - - +
261C ALA 3.1 14.9 + - - -
262C GLY* 2.6 21.2 + - - -
264C ASN* 1.3 76.0 - - - +
266C GLN* 1.3 64.8 + - - +
267C LEU 3.2 7.1 + - - +
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Residues in contact with GLN 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B SER* 5.7 10.3 + - - +
44C VAL* 4.8 5.7 - - - +
45C VAL* 3.5 18.1 - - - +
137C TYR* 5.1 7.4 + - - +
215C PHE* 5.4 13.0 - - - -
216C TYR* 5.7 0.5 + - - -
262C GLY 4.1 10.4 + - - +
263C ILE* 3.3 14.7 + - - +
265C SER* 1.3 85.8 + - - +
267C LEU* 1.3 66.1 + - + +
268C PRO* 4.4 0.5 - - - +
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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