Contacts of the helix formed by residues 260 - 285 (chain F) in PDB entry 5MGX
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 260 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259F MET* 1.3 76.5 - - - +
261F PHE* 1.3 64.1 + - - +
262F GLU* 3.8 16.4 + - - +
263F GLU* 2.8 41.2 + - - +
264F GLU* 3.1 22.2 + - - +
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Residues in contact with PHE 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260F THR* 1.3 72.4 - - - +
262F GLU* 1.3 77.7 + - + +
264F GLU* 3.2 13.1 + - + +
265F ALA* 2.9 42.1 + - + +
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Residues in contact with GLU 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260F THR* 3.8 14.9 - - - +
261F PHE* 1.3 99.7 + - + +
263F GLU* 1.3 57.1 + - + +
265F ALA* 3.7 5.3 + - - +
266F GLN* 3.1 29.8 + - - +
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Residues in contact with GLU 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213F THR* 5.3 1.4 + - - -
214F GLY* 3.8 21.1 + - - -
215F GLN* 3.8 28.0 + - + +
218F VAL* 5.0 1.3 - - + +
259F MET* 3.3 17.5 - - + +
260F THR* 2.8 46.4 + - - +
261F PHE 3.2 0.6 - - - -
262F GLU* 1.3 76.1 - - + +
264F GLU* 1.4 59.0 + - - +
266F GLN* 3.4 13.5 + - - +
267F LEU* 3.0 38.2 + - + +
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Residues in contact with GLU 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254F SER* 5.0 2.6 + - - -
257F VAL 5.4 0.9 - - - +
259F MET* 3.2 40.5 + - + +
260F THR 3.1 20.4 + - - +
261F PHE* 3.2 13.9 + - + +
263F GLU* 1.4 72.6 - - - +
265F ALA* 1.4 56.9 + - - +
267F LEU* 3.3 9.3 + - - +
268F LEU* 3.0 37.4 + - + +
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Residues in contact with ALA 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F PHE* 2.9 33.6 + - + +
262F GLU* 3.9 7.0 - - - +
264F GLU* 1.4 72.8 - - - +
266F GLN* 1.4 58.8 + - - +
268F LEU* 3.1 13.8 + - - +
269F GLN* 3.0 33.9 + - + +
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Residues in contact with GLN 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218F VAL* 3.8 36.1 - - + +
222F ASN* 5.9 0.2 - - - +
262F GLU 3.1 19.6 + - - +
263F GLU* 3.4 13.4 + - - +
265F ALA* 1.4 74.2 - - - +
267F LEU* 1.4 59.1 + - - +
269F GLN* 3.4 10.1 + - - +
270F LEU* 3.2 25.6 + - - +
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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
----------------------------------------------------------
214F GLY* 4.3 7.9 - - - +
217F ARG* 3.9 39.0 - - + +
218F VAL* 3.9 14.1 - - + -
251F ILE* 3.6 43.4 - - + +
259F MET* 3.8 30.7 - - + -
263F GLU* 3.0 21.7 + - + +
264F GLU* 3.7 6.1 - - - +
266F GLN* 1.4 73.0 - - - +
268F LEU* 1.4 59.4 + - - +
269F GLN 3.4 0.2 - - - -
270F LEU* 3.4 9.8 + - + +
271F LYS* 3.0 28.1 + - - +
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Residues in contact with LEU 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F GLU* 3.0 21.4 + - + +
265F ALA* 3.1 15.7 + - - +
267F LEU* 1.4 71.9 - - - +
269F GLN* 1.3 68.3 + - - +
271F LYS* 3.3 21.6 + - - +
272F VAL* 3.2 30.6 + - + +
301F HIS* 3.6 34.8 - - + +
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Residues in contact with GLN 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265F ALA* 3.0 19.2 + - + +
266F GLN* 3.5 11.0 - - - +
268F LEU* 1.3 80.1 - - - +
270F LEU* 1.3 58.7 + - - +
272F VAL* 3.8 6.5 + - - +
273F LYS* 3.4 33.6 + - + +
302F GLN* 3.7 26.2 + - - +
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Residues in contact with LEU 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F VAL* 3.9 15.7 - - + +
221F ALA* 3.7 27.1 - - + -
222F ASN* 3.5 40.8 - - - +
225F ARG* 4.1 14.6 - - - +
251F ILE* 4.0 8.7 - - + -
266F GLN* 3.2 13.2 + - + +
267F LEU* 3.5 16.2 - - + +
268F LEU 3.2 0.4 - - - -
269F GLN* 1.3 76.7 - - - +
271F LYS* 1.3 58.9 + - - +
273F LYS* 3.3 12.7 + - + +
274F CYS* 3.0 36.4 + - - -
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Residues in contact with LYS 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248F ILE* 4.9 9.4 - - + -
251F ILE* 3.7 23.1 - - + +
252F THR* 3.9 30.0 - - + +
267F LEU 3.0 17.7 + - - +
268F LEU* 3.3 28.3 + - + +
270F LEU* 1.3 74.9 - - - +
272F VAL* 1.4 52.7 + - - +
274F CYS* 3.3 4.2 + - - +
275F LEU* 2.8 54.2 + - + +
297F LEU* 6.4 0.2 - - - +
301F HIS* 4.5 14.9 + - - -
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Residues in contact with VAL 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F LEU 3.2 18.9 + - - +
269F GLN* 4.0 6.3 - - - +
270F LEU 3.4 0.2 - - - -
271F LYS* 1.4 72.3 - - + +
273F LYS* 1.3 61.4 + - + +
275F LEU* 3.4 7.3 + - + -
276F ASN* 3.0 29.9 + - - +
298F VAL* 3.5 33.4 - - + +
301F HIS* 3.7 35.0 - - + +
302F GLN* 3.7 32.5 - - - +
305F ASN* 4.5 2.7 - - - +
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Residues in contact with LYS 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709A ASP* 4.2 39.9 + - + +
225F ARG* 4.6 12.6 - - - +
269F GLN* 3.4 20.8 + - - +
270F LEU* 3.3 21.4 + - + +
272F VAL* 1.3 78.5 - - + +
274F CYS* 1.4 56.1 + - - +
276F ASN* 3.5 5.3 + - - +
277F ASN* 3.1 36.1 + - - +
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Residues in contact with CYS 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221F ALA 4.8 1.8 - - - -
225F ARG* 3.9 25.1 - - - -
244F TYR* 3.8 12.2 - - + +
247F ALA* 3.8 23.6 - - - -
248F ILE* 3.8 21.1 - - + -
251F ILE* 4.4 7.9 - - - -
270F LEU* 3.0 29.4 + - - +
271F LYS* 3.3 5.1 + - - +
273F LYS* 1.4 72.6 - - - +
275F LEU* 1.3 55.3 + - - +
277F ASN* 3.4 8.8 + - - +
278F LEU* 2.8 32.7 + - - +
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Residues in contact with LEU 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248F ILE* 3.9 24.0 - - + -
271F LYS* 2.8 43.5 + - + +
272F VAL* 3.8 2.9 - - + +
274F CYS* 1.3 68.4 - - - +
276F ASN* 1.3 60.5 - - - +
278F LEU* 3.4 9.4 + - + +
279F ALA* 3.0 22.2 + - - +
294F SER* 3.5 26.8 - - - +
297F LEU* 4.1 41.5 - - + +
298F VAL* 3.6 18.8 - - + -
301F HIS* 5.6 4.5 - - + -
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Residues in contact with ASN 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709A ASP* 4.7 10.4 + - - +
272F VAL 3.0 16.8 + - - +
273F LYS* 3.8 6.7 - - - +
275F LEU* 1.3 74.7 - - - +
277F ASN* 1.4 60.2 + - - +
279F ALA* 3.2 8.1 + - - +
280F ALA 2.9 23.9 + - - -
295F CYS* 5.9 0.2 - - - -
298F VAL* 3.5 13.6 - - + +
305F ASN* 2.9 40.4 + - - +
307F LYS* 3.8 6.3 - - - +
308F ALA* 3.6 19.4 + - - +
311F ARG* 3.1 36.0 + - - +
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Residues in contact with ASN 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708A VAL* 3.3 16.2 - - - +
709A ASP* 2.8 47.9 + - - +
225F ARG* 4.1 6.7 - - - +
229F ASN* 3.1 16.8 + - - -
244F TYR* 3.4 25.4 - - + -
273F LYS 3.1 23.2 + - - +
274F CYS 3.5 5.8 - - - +
276F ASN* 1.4 75.2 - - - +
278F LEU* 1.3 62.0 + - - +
280F ALA* 3.5 5.0 + - - +
281F SER* 3.0 27.9 + - - -
311F ARG* 5.0 1.9 + - - -
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Residues in contact with LEU 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241F ALA* 3.4 40.8 - - + +
244F TYR* 3.8 10.9 - - + -
245F ASP* 4.5 11.4 - - + +
248F ILE* 3.8 22.9 - - + -
274F CYS 2.8 17.1 + - - +
275F LEU* 3.5 12.3 - - + +
277F ASN* 1.3 75.1 - - - +
279F ALA* 1.4 51.6 + - - +
281F SER* 3.1 4.0 + - - -
282F GLN* 2.8 60.0 + - - +
294F SER* 4.0 12.3 - - - +
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Residues in contact with ALA 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275F LEU 3.0 14.1 + - - +
276F ASN* 3.4 13.7 - - - +
278F LEU* 1.4 72.3 - - - +
280F ALA* 1.4 59.8 + - - +
281F SER 3.2 0.2 + - - -
282F GLN* 3.3 11.9 + - - +
283F LEU* 2.9 33.6 + - - +
291F ALA* 3.8 11.9 - - - +
294F SER* 3.8 4.9 - - - -
295F CYS* 3.8 30.5 - - - +
311F ARG* 4.7 4.9 - - - -
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Residues in contact with ALA 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708A VAL* 4.7 2.5 - - + -
232F TYR* 3.8 25.5 + - + +
276F ASN 2.9 8.4 + - - +
277F ASN* 3.5 13.2 - - - +
279F ALA* 1.4 75.3 - - - +
281F SER* 1.3 59.5 + - - +
283F LEU* 3.9 6.7 + - - +
284F LYS* 3.3 28.1 + - - +
311F ARG* 3.6 37.3 - - - +
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Residues in contact with SER 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232F TYR* 3.5 16.9 - - - -
237F PHE* 3.8 23.1 - - - +
240F ALA* 3.7 4.1 - - - +
241F ALA* 4.1 12.6 - - - -
244F TYR* 3.4 17.0 - - - -
277F ASN 3.0 13.2 + - - -
278F LEU* 3.1 10.0 + - - -
280F ALA* 1.3 73.9 - - - +
282F GLN* 1.3 64.0 + - - +
284F LYS* 3.3 13.5 + - - +
285F LEU* 3.3 19.4 + - - +
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Residues in contact with GLN 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241F ALA* 5.2 4.7 - - + -
278F LEU* 2.8 48.3 + - + +
281F SER* 1.3 71.0 - - - +
283F LEU* 1.4 55.7 + - - +
285F LEU* 3.0 19.2 + - + +
287F HIS* 2.9 40.2 + - + +
290F ALA* 3.2 32.1 - - + +
291F ALA* 3.4 18.7 - - + -
294F SER* 2.7 26.8 + - - -
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Residues in contact with LEU 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A GLU* 5.6 1.3 - - - +
279F ALA 2.9 16.9 + - - +
280F ALA* 4.0 6.3 - - - +
282F GLN* 1.4 73.8 - - - +
284F LYS* 1.3 72.3 + - - +
286F ASP* 3.2 19.1 + - - +
287F HIS 4.9 1.3 - - - +
288F TYR* 4.2 4.8 - - + -
291F ALA* 3.9 5.7 - - + +
310F PHE* 6.0 0.4 - - + -
311F ARG* 4.0 34.5 - - + +
314F LYS* 4.0 23.1 - - + +
315F VAL* 3.5 28.9 - - + +
318F GLN* 3.6 29.0 - - - +
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Residues in contact with LYS 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A GLU* 3.0 40.2 + - - +
232F TYR* 4.4 8.3 + - - +
237F PHE* 3.6 47.7 - - + -
280F ALA 3.3 14.8 + - - +
281F SER 3.3 10.5 + - - +
282F GLN 3.3 0.6 - - - -
283F LEU* 1.3 87.1 - - - +
285F LEU* 1.3 59.5 + - - +
286F ASP* 3.4 6.6 + - - +
314F LYS* 4.7 5.5 - - - +
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Residues in contact with LEU 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F PHE* 3.7 39.7 - - + +
238F VAL* 3.7 27.8 - - + +
241F ALA* 4.9 6.3 - - + -
281F SER 3.3 13.2 + - - +
282F GLN* 3.0 12.7 + - + +
284F LYS* 1.3 76.6 - - - +
286F ASP* 1.4 68.8 + - - +
287F HIS* 3.1 9.7 + - + +
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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