Contacts of the helix formed by residues 251 - 279 (chain C) in PDB entry 1RFU
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 ASN 251 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C GLN* 3.5 4.8 + - - +
248C HIS* 3.2 35.0 + - + +
249C PRO 3.6 0.6 - - - -
250C ASN* 1.3 80.1 + - - +
252C LEU* 1.3 67.2 + - - +
253C LYS* 2.9 9.0 - - - +
254C VAL* 2.7 41.9 + - + +
255C ALA* 2.8 10.6 + - - +
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Residues in contact with LEU 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C THR* 3.8 24.0 - - + -
184C VAL* 4.5 5.2 - - + -
203C GLY* 3.3 37.0 - - - +
204C SER 3.5 18.6 - - - +
205C GLN* 3.5 23.3 + - + +
217C GLN* 3.1 16.9 - - + +
219C ILE* 3.7 6.1 - - + -
241C LEU* 5.4 0.9 - - + -
245C THR* 5.0 11.4 - - + -
248C HIS 4.5 0.6 + - - -
249C PRO 5.5 0.2 - - - -
251C ASN* 1.3 75.0 - - - +
253C LYS* 1.3 57.7 + - - +
255C ALA* 4.5 4.0 - - + -
256C CYS* 2.8 59.0 + - - -
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Residues in contact with LYS 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C GLN* 4.2 4.6 - - - +
219C ILE* 3.6 22.6 - - + +
251C ASN* 2.8 7.7 + - - +
252C LEU* 1.3 79.2 - - - +
254C VAL* 1.3 58.7 + - + +
256C CYS* 3.5 1.9 - - - +
257C GLU* 2.6 65.1 + - - +
308C GLN* 3.1 21.3 - - - +
309C ALA* 3.2 35.9 - - + +
311C VAL* 3.9 23.1 - - + -
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Residues in contact with VAL 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C HIS* 3.6 26.7 - - + +
251C ASN* 2.7 37.1 + - + +
253C LYS* 1.3 82.4 - - + +
255C ALA* 1.3 63.8 + - - +
257C GLU* 2.8 24.4 + - + +
258C LYS* 2.9 31.2 + - + +
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Residues in contact with ALA 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C LEU* 4.8 1.6 - - + -
244C TRP* 3.7 16.3 - - + +
245C THR* 3.7 44.9 - - + +
248C HIS* 4.3 7.5 - - + +
251C ASN 2.8 17.5 + - - +
252C LEU* 4.0 4.0 - - - +
254C VAL* 1.3 77.1 - - - +
256C CYS* 1.3 61.2 + - - +
258C LYS* 3.7 0.4 + - - -
259C THR* 2.8 29.1 + - - -
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Residues in contact with CYS 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C VAL* 4.4 16.4 - - - -
203C GLY* 5.1 0.4 - - - -
219C ILE* 3.3 23.8 - - + -
221C MET* 3.8 17.7 - - + -
237C PHE* 5.8 3.4 - - + -
241C LEU* 4.6 9.4 - - - -
252C LEU* 2.8 46.5 + - - +
253C LYS 3.5 2.7 - - - +
255C ALA* 1.3 74.8 - - - +
257C GLU* 1.3 63.6 + - - +
259C THR* 3.7 4.4 - - - -
260C VAL* 2.8 34.3 + - + +
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Residues in contact with GLU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C MET* 5.0 0.9 - - - -
253C LYS* 2.6 56.2 + - - +
254C VAL* 2.8 17.1 + - + +
256C CYS* 1.3 71.7 - - - +
258C LYS* 1.3 66.8 + - + +
260C VAL 3.9 0.5 - - - -
261C SER* 2.8 28.4 + - - -
305C ILE* 4.4 16.2 - - + +
307C VAL* 3.8 18.8 - - + +
308C GLN* 3.0 13.7 + - - -
309C ALA* 2.5 41.6 + - + +
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Residues in contact with LYS 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C TRP* 3.5 52.4 - - + +
247C LYS* 4.2 8.3 - - - +
248C HIS* 2.7 33.4 + - + +
254C VAL* 2.9 33.1 + - + +
257C GLU* 1.3 70.2 - - + +
259C THR* 1.3 66.3 + - - +
261C SER* 2.8 16.3 + - - -
262C ALA* 2.8 12.1 + - - +
303C PRO* 3.5 19.3 - - + +
305C ILE* 5.1 17.0 - - + -
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Residues in contact with THR 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C PHE* 3.2 53.4 - - + +
240C MET* 4.1 9.6 - - + +
241C LEU* 3.7 17.2 - - + +
244C TRP* 3.2 20.5 - - - +
255C ALA 2.8 21.8 + - - -
256C CYS* 3.7 5.4 - - - -
258C LYS* 1.3 79.0 - - - +
260C VAL* 1.3 58.3 + - - +
262C ALA* 2.9 6.8 + - - +
263C MET* 2.8 25.8 + - - +
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Residues in contact with VAL 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C ALA* 5.8 1.1 - - + -
221C MET* 4.1 20.2 - - + -
223C MET* 3.5 39.9 - - + -
237C PHE* 3.9 20.6 - - + -
256C CYS* 2.8 22.3 + - - +
259C THR* 1.3 75.0 - - - +
261C SER* 1.3 57.3 + - - +
263C MET* 3.0 10.0 - - + +
264C HIS* 2.8 26.7 + - + +
307C VAL* 4.0 21.3 - - + +
2402C ADP 3.9 5.6 - - - +
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Residues in contact with SER 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C GLU 2.8 19.0 + - - -
258C LYS* 2.8 11.3 + - - -
260C VAL* 1.3 72.0 - - - +
262C ALA* 1.3 68.5 + - - +
264C HIS* 2.7 15.2 + - - +
265C HIS* 3.0 18.1 + - - -
303C PRO* 4.1 3.4 - - - -
304C GLU 3.1 23.1 - - - -
305C ILE* 3.2 9.7 - - - +
306C VAL* 3.2 28.4 + - - -
307C VAL* 3.9 7.1 - - - +
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Residues in contact with ALA 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C MET* 3.5 26.7 - - + -
244C TRP* 5.6 0.2 - - - +
258C LYS 2.8 7.6 + - - +
259C THR* 3.2 9.6 - - - +
261C SER* 1.3 73.9 - - - +
263C MET* 1.3 65.1 + - - +
265C HIS* 3.1 8.2 + - - +
266C VAL* 2.8 28.8 + - - +
299C ASP 4.2 8.5 - - - +
300C ILE* 4.7 6.5 - - + +
303C PRO* 3.5 24.8 - - + +
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Residues in contact with MET 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C THR* 3.0 45.3 - - + +
236C LEU* 3.4 24.5 - - + -
237C PHE* 3.9 20.6 - - + -
240C MET* 3.4 23.8 - - - -
259C THR 2.8 8.4 + - - +
260C VAL* 3.0 17.9 - - - +
262C ALA* 1.3 77.3 - - - +
264C HIS* 1.3 54.0 - - - +
266C VAL* 3.6 4.0 - - + +
267C LEU* 2.9 39.5 + - + +
2402C ADP 3.5 36.1 - - - +
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Residues in contact with HIS 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C HIS* 4.7 27.8 - - + +
226C VAL* 6.3 0.7 - - + -
260C VAL 2.8 11.7 + - - +
261C SER 2.7 15.0 + - - +
263C MET* 1.3 71.2 - - - +
265C HIS* 1.3 63.7 + + - +
267C LEU* 3.6 6.1 - - + +
268C GLN* 2.6 76.8 + - + +
306C VAL* 3.5 30.6 - - + +
307C VAL* 5.2 5.4 - - + -
2402C ADP 6.2 0.9 - - - -
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Residues in contact with HIS 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C SER 3.0 13.5 + - - -
262C ALA* 3.5 5.6 - - - +
264C HIS* 1.3 87.1 - + - +
266C VAL* 1.3 68.9 + - - +
268C GLN* 2.9 7.0 + - + +
269C ARG* 2.8 27.1 + - - +
299C ASP* 3.5 36.2 - - + +
303C PRO* 4.1 4.0 - - - +
304C GLU* 3.1 47.2 + - + +
306C VAL* 3.5 21.0 - - + +
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Residues in contact with VAL 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C LEU* 4.0 30.1 - - + -
240C MET* 5.4 0.2 - - + -
262C ALA* 2.8 23.3 + - + +
263C MET* 3.6 4.9 - - + +
265C HIS* 1.3 74.8 - - + +
267C LEU* 1.3 69.0 + - + +
269C ARG* 3.2 4.6 + - - +
270C THR* 3.0 30.7 + - - +
291C LEU* 4.5 18.2 - - + -
292C ARG 4.9 3.1 - - - +
293C MET* 5.6 2.0 - - - +
296C SER* 3.5 35.7 + - - +
299C ASP* 5.5 1.3 - - + -
300C ILE* 4.3 15.0 - - + -
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Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C VAL* 4.6 11.0 - - + -
230C PHE* 3.4 47.0 - - + -
233C THR* 3.8 14.1 - - + -
263C MET* 2.9 24.3 + - + +
264C HIS* 3.6 5.2 - - - +
266C VAL* 1.3 79.0 - - + +
268C GLN* 1.3 66.4 + - + +
270C THR* 3.0 5.0 + - - -
271C ILE* 2.9 25.7 + - - +
291C LEU* 4.1 7.4 - - + -
2402C ADP 3.4 51.6 - - + +
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Residues in contact with GLN 268 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C HIS* 5.1 9.1 - - - +
226C VAL* 4.0 18.8 - - - +
264C HIS* 2.6 64.8 + - + +
265C HIS* 2.9 6.7 + - - +
267C LEU* 1.3 71.0 - - - +
269C ARG* 1.3 63.5 + - - +
271C ILE* 3.1 14.4 - - - +
272C LYS* 3.1 24.0 + - - +
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Residues in contact with ARG 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C HIS 2.8 7.9 + - - +
266C VAL* 3.3 13.5 - - - +
268C GLN* 1.3 77.8 - - - +
270C THR* 1.3 62.9 + - - +
272C LYS* 3.5 11.9 - - - +
273C CYS* 3.2 20.8 + - + +
292C ARG* 4.1 15.5 - - + +
295C GLN* 3.4 44.8 + - - +
296C SER* 2.6 37.4 + - - -
299C ASP* 2.5 32.3 + - - -
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Residues in contact with THR 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C PHE* 3.9 14.4 - - + -
266C VAL* 3.0 16.7 + - - +
267C LEU* 3.0 12.0 + - - -
269C ARG* 1.3 75.9 - - - +
271C ILE* 1.3 55.7 + - - +
272C LYS 3.0 0.5 + - - -
273C CYS* 3.2 1.6 + - - +
274C ALA* 2.7 35.9 + - + +
288C GLN 4.9 0.6 - - - +
289C LEU* 3.5 20.0 - - - +
290C GLU 3.2 25.8 - - - +
291C LEU* 3.6 5.6 - - - +
292C ARG* 3.2 27.6 + - + +
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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
----------------------------------------------------------
226C VAL* 3.8 30.7 - - + -
227C ASP 4.8 1.8 - - - +
228C ALA* 4.1 16.8 - - + -
230C PHE* 4.4 3.5 - - + -
267C LEU 2.9 15.8 + - - +
268C GLN* 3.1 26.5 - - - +
270C THR* 1.3 73.6 - - - +
272C LYS* 1.3 64.4 + - + +
274C ALA* 3.7 4.7 - - + -
275C LYS* 2.8 64.7 + - + +
284C PRO* 4.5 5.2 - - + -
289C LEU* 4.1 12.6 - - + -
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Residues in contact with LYS 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C GLN 3.1 9.1 + - - +
269C ARG* 3.5 15.7 - - - +
270C THR 3.0 0.8 + - - -
271C ILE* 1.3 87.1 - - + +
273C CYS* 1.3 65.3 + - - +
275C LYS* 3.2 5.5 + - - +
276C ALA* 3.1 17.4 + - + +
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Residues in contact with CYS 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C ARG 3.2 3.1 + - - +
270C THR 3.2 2.3 + - - +
272C LYS* 1.3 79.5 - - - +
274C ALA* 1.3 64.8 + - - +
276C ALA* 2.7 23.2 + - - +
277C LYS* 2.9 43.0 + - - +
292C ARG* 3.6 46.7 - - - +
4H GLU* 5.2 1.6 - - - -
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Residues in contact with ALA 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C THR 2.7 21.9 + - - +
271C ILE* 3.4 7.0 - - - +
273C CYS* 1.3 75.0 - - - +
275C LYS* 1.3 63.7 + - - +
276C ALA 3.0 0.2 + - - -
277C LYS* 3.0 13.2 + - - +
278C SER* 3.1 12.6 + - - -
284C PRO* 3.8 9.5 - - + +
288C GLN* 3.2 30.1 + - - +
289C LEU* 3.5 25.6 - - + -
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Residues in contact with LYS 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C ASP* 4.2 20.8 + - - +
271C ILE* 2.8 46.3 + - + +
272C LYS* 3.7 4.9 - - - +
274C ALA* 1.3 71.9 - - - +
276C ALA* 1.3 56.4 + - - +
278C SER* 3.2 10.4 + - - +
279C GLY* 2.9 31.7 + - - +
282C VAL 5.5 2.2 - - - +
283C LYS* 4.5 16.8 - - - +
284C PRO* 3.7 14.6 - - + +
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Residues in contact with ALA 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C LYS* 3.1 11.6 + - + +
273C CYS* 2.7 23.9 + - - +
275C LYS* 1.3 80.6 - - - +
277C LYS* 1.3 59.5 + - + +
278C SER 3.3 0.7 + - - -
279C GLY* 3.6 6.8 + - - -
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Residues in contact with LYS 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ARG* 5.7 4.6 - - - +
273C CYS* 2.9 41.6 + - - +
274C ALA 3.0 4.7 + - - +
276C ALA* 1.3 75.8 - - + +
278C SER* 1.3 59.5 + - - +
287C ALA 5.8 0.6 + - - -
288C GLN* 3.0 46.1 + - + +
292C ARG* 5.5 3.8 - - - +
4H GLU* 5.0 9.0 + - - -
6H ARG* 5.3 9.5 - - - +
----------------------------------------------------------
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Residues in contact with SER 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C ALA 3.1 3.1 + - - -
275C LYS* 3.2 21.0 + - - -
277C LYS* 1.3 80.5 - - - +
279C GLY* 1.3 59.7 + - - +
282C VAL* 3.2 44.0 + - - +
283C LYS 4.0 3.1 - - - -
284C PRO* 3.4 17.8 - - - +
288C GLN* 3.5 20.6 - - - +
----------------------------------------------------------
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Residues in contact with GLY 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C LYS* 2.9 19.0 + - - +
276C ALA 3.6 5.5 + - - -
277C LYS 3.6 1.6 - - - -
278C SER* 1.3 84.5 + - - +
280C GLU* 1.3 68.8 + - - -
281C GLY 3.7 0.2 + - - -
282C VAL* 3.3 18.2 + - - +
----------------------------------------------------------
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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