Contacts of the helix formed by residues 251 - 279 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217F GLN* 3.6 4.3 + - - +
248F HIS* 3.1 35.3 + - + +
249F PRO 3.5 0.6 - - - -
250F ASN* 1.3 81.7 + - - +
252F LEU* 1.3 69.4 + - - +
253F LYS* 2.9 9.7 - - - +
254F VAL* 2.8 34.6 + - + +
255F ALA* 2.8 18.8 + - - +
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Residues in contact with LEU 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F THR* 3.7 26.5 - - + -
184F VAL* 4.5 5.6 - - + -
203F GLY* 3.1 40.2 - - - +
204F SER 3.5 17.0 - - - +
205F GLN* 3.4 22.2 + - + +
217F GLN* 3.2 15.9 - - + +
219F ILE* 3.7 12.3 - - + -
241F LEU* 5.3 1.3 - - + -
245F THR* 5.0 10.8 - - + -
248F HIS 4.5 0.8 + - - -
251F ASN* 1.3 73.7 - - - +
253F LYS* 1.3 54.0 + - - +
255F ALA* 4.3 4.3 - - - -
256F CYS* 2.7 54.2 + - - +
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Residues in contact with LYS 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217F GLN* 4.3 5.5 - - - +
219F ILE* 3.5 23.0 - - + +
251F ASN* 2.8 8.2 + - - +
252F LEU* 1.3 78.0 - - - +
254F VAL* 1.3 58.1 + - + +
256F CYS* 3.4 1.9 - - - +
257F GLU* 2.7 61.0 + - - +
308F GLN* 2.9 27.9 - - - +
309F ALA* 3.3 31.2 - - + -
311F VAL* 4.0 20.9 - - + -
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Residues in contact with VAL 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F HIS* 3.6 29.8 - - + +
251F ASN* 2.8 39.6 + - + +
253F LYS* 1.3 78.9 - - + +
255F ALA* 1.3 66.9 + - - +
257F GLU* 2.9 23.8 + - - +
258F LYS* 3.0 28.2 + - + +
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Residues in contact with ALA 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F LEU* 4.8 2.0 - - + -
244F TRP* 3.7 16.4 - - + +
245F THR* 3.7 44.0 - - + +
248F HIS* 4.4 6.4 - - + +
251F ASN 2.8 17.5 + - - +
252F LEU* 3.8 6.5 - - - +
254F VAL* 1.3 76.5 - - - +
256F CYS* 1.3 64.5 + - - +
258F LYS 3.5 0.2 + - - -
259F THR* 3.0 26.1 + - - -
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Residues in contact with CYS 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F VAL* 4.6 16.6 - - - -
203F GLY* 5.1 0.9 - - - -
219F ILE* 3.4 24.0 - - + -
221F MET* 3.9 18.8 - - + -
237F PHE* 5.7 3.1 - - - -
241F LEU* 4.7 8.1 - - - -
252F LEU* 2.7 48.0 + - - +
253F LYS 3.4 2.9 - - - +
255F ALA* 1.3 75.0 - - - +
257F GLU* 1.3 62.5 + - - +
259F THR* 3.4 5.4 + - - -
260F VAL* 2.9 32.7 + - + +
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Residues in contact with GLU 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221F MET* 4.9 0.4 - - - -
253F LYS* 2.7 65.3 + - - +
254F VAL* 2.9 13.2 + - - +
256F CYS* 1.3 72.3 - - - +
258F LYS* 1.3 59.7 + - + +
260F VAL* 3.9 0.2 - - - -
261F SER* 2.5 34.6 + - - -
305F ILE* 4.6 15.9 - - + +
307F VAL* 3.9 21.6 - - + +
308F GLN* 3.2 9.7 + - - -
309F ALA* 2.5 39.8 + - + +
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Residues in contact with LYS 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F TRP* 3.6 51.7 - - + +
247F LYS* 4.3 6.3 - - - +
248F HIS* 3.1 30.7 + - + +
254F VAL* 3.0 29.0 + - + +
255F ALA 3.9 0.2 - - - +
257F GLU* 1.3 73.2 - - + +
259F THR* 1.3 67.3 + - - +
261F SER* 2.8 17.0 + - - -
262F ALA 2.8 12.1 + - - -
303F PRO* 3.6 20.0 - - + +
305F ILE* 5.2 17.0 - - + -
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Residues in contact with THR 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F PHE* 3.3 53.2 - - + +
240F MET* 3.9 9.3 - - + +
241F LEU* 3.6 17.7 - - + +
244F TRP* 3.0 21.2 - - - +
255F ALA 3.0 17.1 + - - -
256F CYS* 3.6 5.8 - - - -
258F LYS* 1.3 79.0 - - - +
260F VAL* 1.3 63.9 + - - +
262F ALA* 3.0 6.9 + - - +
263F MET* 2.8 21.5 + - - +
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Residues in contact with VAL 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F ALA* 5.8 1.6 - - + -
221F MET* 4.0 19.3 - - + -
223F MET* 3.6 39.9 - - + -
237F PHE* 3.9 21.5 - - + -
256F CYS* 2.9 24.6 + - - +
259F THR* 1.3 72.3 - - - +
261F SER* 1.3 57.2 + - - +
263F MET* 3.0 9.6 - - - +
264F HIS* 2.8 27.3 + - + +
307F VAL* 4.0 22.6 - - + +
5402F ADP 4.0 4.9 - - - +
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Residues in contact with SER 261 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257F GLU 2.5 21.9 + - - -
258F LYS* 2.8 16.4 + - - -
260F VAL* 1.3 69.1 - - - +
262F ALA* 1.3 67.0 + - - -
264F HIS* 2.8 14.6 + - - +
265F HIS* 3.0 15.1 + - - -
303F PRO* 4.1 5.4 - - - -
304F GLU 3.1 24.5 - - - -
305F ILE* 3.4 8.0 - - - +
306F VAL* 3.3 26.7 + - - -
307F VAL* 3.9 7.4 - - - +
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Residues in contact with ALA 262 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240F MET* 3.3 28.0 - - + -
244F TRP* 5.5 0.2 - - - +
258F LYS 2.8 10.2 + - - +
259F THR* 3.3 9.4 - - - +
261F SER* 1.3 72.5 - - - +
263F MET* 1.3 65.6 + - - +
265F HIS* 3.1 5.5 + - - +
266F VAL* 2.9 29.6 + - - +
299F ASP 4.2 8.1 - - - +
300F ILE* 4.6 5.4 - - + -
303F PRO* 3.4 27.2 - - + +
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Residues in contact with MET 263 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F THR* 3.1 43.1 - - + +
236F LEU* 3.6 18.2 - - + -
237F PHE* 3.9 16.4 - - + +
240F MET* 3.5 23.8 - - - -
259F THR 2.8 9.5 + - - +
260F VAL* 3.0 19.3 - - - +
262F ALA* 1.3 78.0 - - - +
264F HIS* 1.3 60.7 + - - +
266F VAL* 3.6 2.9 - - + +
267F LEU* 2.9 33.7 + - + +
291F LEU* 5.4 0.2 - - + -
5402F ADP 3.5 43.5 - - - +
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Residues in contact with HIS 264 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224F HIS* 4.6 27.8 - - + +
226F VAL* 6.3 0.7 - - + -
260F VAL* 2.8 12.0 + - + +
261F SER 2.8 14.0 + - - +
263F MET* 1.3 70.9 - - - +
265F HIS* 1.3 63.1 + + - +
267F LEU* 3.2 6.4 + - - +
268F GLN* 2.6 75.7 + - + +
306F VAL* 3.5 32.0 - - + +
307F VAL* 5.2 6.1 - - + -
5402F ADP 6.3 0.2 - - - -
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Residues in contact with HIS 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F SER 3.0 9.5 + - - -
262F ALA 3.4 5.6 - - - +
264F HIS* 1.3 90.2 - + - +
266F VAL* 1.3 66.5 + - - +
268F GLN* 2.8 8.6 + - + +
269F ARG* 2.8 26.0 + - - +
299F ASP* 3.5 34.5 - - + +
303F PRO* 4.1 8.5 - - - +
304F GLU* 3.2 46.9 + - + +
306F VAL* 3.4 20.4 - - + +
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Residues in contact with VAL 266 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236F LEU* 4.2 29.2 - - + -
262F ALA* 2.9 20.9 + - + +
263F MET* 3.6 4.9 - - + +
265F HIS* 1.3 75.8 - - + +
267F LEU* 1.3 58.2 + - + +
269F ARG* 3.2 5.7 + - - +
270F THR* 2.7 43.1 + - - +
291F LEU* 4.4 18.4 - - + -
292F ARG 4.6 4.2 + - - +
293F MET* 5.6 2.7 - - - -
296F SER* 3.6 34.4 + - - +
299F ASP* 5.5 1.6 - - + -
300F ILE* 4.3 15.7 - - + -
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Residues in contact with LEU 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F VAL* 4.7 10.3 - - + -
230F PHE* 3.5 44.3 - - + -
233F THR* 3.8 11.9 - - + -
263F MET* 2.9 27.1 + - + +
264F HIS* 3.5 5.8 - - - +
266F VAL* 1.3 77.2 - - + +
268F GLN* 1.3 67.1 + - - +
270F THR* 3.0 4.8 + - - +
271F ILE* 2.9 25.8 + - - +
291F LEU* 4.1 9.0 - - + -
5402F ADP 3.5 51.1 - - + +
----------------------------------------------------------
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Residues in contact with GLN 268 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224F HIS* 4.9 10.4 - - - +
226F VAL* 3.9 20.3 - - - +
264F HIS* 2.6 60.8 + - + +
265F HIS* 2.8 5.1 + - - +
267F LEU* 1.3 71.2 - - + +
269F ARG* 1.3 62.3 + - - +
271F ILE* 3.1 26.6 - - - +
272F LYS* 3.1 11.1 + - - +
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Residues in contact with ARG 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265F HIS 2.8 7.5 + - - +
266F VAL* 3.3 15.1 - - - +
268F GLN* 1.3 77.5 - - - +
270F THR* 1.3 65.1 + - - +
272F LYS* 3.4 12.0 + - - +
273F CYS* 3.2 19.6 + - - +
292F ARG* 4.1 15.7 - - + +
295F GLN* 3.4 42.6 + - - +
296F SER* 2.7 36.8 + - - -
299F ASP* 2.6 32.5 + - - -
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Residues in contact with THR 270 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230F PHE* 4.0 13.9 - - + -
266F VAL* 2.7 23.3 + - - +
267F LEU* 3.3 10.9 - - - -
269F ARG* 1.3 73.5 - - - +
271F ILE* 1.3 63.1 + - - +
272F LYS 3.0 0.7 + - - -
273F CYS* 3.2 4.0 + - - +
274F ALA* 2.8 28.9 + - + +
288F GLN 4.9 0.6 - - - +
289F LEU* 3.3 20.9 - - - +
290F GLU 3.3 26.7 - - - +
291F LEU* 3.8 5.1 - - - +
292F ARG* 3.3 26.5 + - + +
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Residues in contact with ILE 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F VAL* 3.7 34.3 - - + -
227F ASP 4.8 1.3 - - - +
228F ALA* 4.1 9.0 - - + -
230F PHE* 4.4 3.5 - - + -
267F LEU 2.9 15.6 + - - +
268F GLN* 3.1 27.8 - - - +
270F THR* 1.3 73.8 - - - +
272F LYS* 1.3 61.8 + - + +
274F ALA* 3.9 4.0 - - + -
275F LYS* 2.9 61.1 + - + +
284F PRO* 4.5 4.5 - - + -
289F LEU* 4.1 21.3 - - + -
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Residues in contact with LYS 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F GLN 3.1 13.6 + - - +
269F ARG* 3.5 12.6 - - - +
270F THR 3.0 0.4 - - - -
271F ILE* 1.3 84.5 - - + +
273F CYS* 1.3 68.3 + - - +
275F LYS* 3.2 5.2 + - - +
276F ALA* 3.1 16.4 + - + +
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Residues in contact with CYS 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLU* 4.2 5.4 - - - -
269F ARG 3.2 3.1 + - - +
270F THR 3.2 2.9 + - - +
272F LYS* 1.3 78.7 - - - +
274F ALA* 1.3 56.7 + - - +
276F ALA* 2.6 37.1 + - - +
277F LYS* 2.9 39.1 + - - +
292F ARG* 3.7 46.4 - - - +
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Residues in contact with ALA 274 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270F THR 2.8 18.6 + - - +
271F ILE* 3.5 5.6 - - - +
273F CYS* 1.3 79.3 - - - +
275F LYS* 1.3 64.5 + - - +
276F ALA 3.0 0.3 + - - -
277F LYS* 3.1 6.0 + - - +
278F SER* 3.1 20.4 + - - -
284F PRO* 3.8 10.0 - - + +
288F GLN* 3.1 30.2 + - - +
289F LEU* 3.6 25.1 - - + -
----------------------------------------------------------
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Residues in contact with LYS 275 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227F ASP* 4.2 22.2 + - - +
271F ILE* 2.9 45.6 + - + +
272F LYS* 3.9 4.3 - - - +
274F ALA* 1.3 72.6 - - - +
276F ALA* 1.3 57.2 + - - +
278F SER* 3.2 8.6 + - - +
279F GLY* 2.9 31.7 + - - +
282F VAL 5.4 2.2 - - - +
283F LYS* 4.5 17.4 - - - +
284F PRO* 3.9 15.0 - - + -
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Residues in contact with ALA 276 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F LYS* 3.1 11.4 + - + +
273F CYS* 2.6 27.7 + - - +
275F LYS* 1.3 75.2 - - - +
277F LYS* 1.3 60.6 + - + +
278F SER 3.4 0.3 + - - -
279F GLY* 3.7 6.8 + - - -
----------------------------------------------------------
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Residues in contact with LYS 277 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLU* 4.1 15.5 + - - +
6B ARG* 5.0 11.1 - - - +
16F ARG* 5.8 2.2 - - - +
273F CYS* 2.9 39.7 + - - +
274F ALA 3.8 4.7 - - - +
276F ALA* 1.3 77.2 - - + +
278F SER* 1.3 60.0 + - - +
287F ALA 6.0 0.2 + - - -
288F GLN* 3.0 45.3 + - + +
292F ARG* 5.4 2.2 - - - +
----------------------------------------------------------
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Residues in contact with SER 278 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274F ALA 3.1 10.6 + - - -
275F LYS* 3.2 16.5 + - - -
277F LYS* 1.3 80.3 - - - +
279F GLY* 1.3 61.3 + - - +
282F VAL* 3.1 44.1 + - - +
283F LYS 4.0 2.9 - - - -
284F PRO* 3.3 17.0 - - - +
288F GLN* 3.4 20.9 - - - +
----------------------------------------------------------
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Residues in contact with GLY 279 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275F LYS* 2.9 18.4 + - - +
276F ALA 3.7 5.7 + - - -
277F LYS 3.6 1.6 - - - -
278F SER* 1.3 84.5 + - - +
280F GLU* 1.3 68.7 + - - +
282F VAL* 3.2 18.0 + - - +
----------------------------------------------------------
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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