Contacts of the helix formed by residues 242 - 270 (chain F) in PDB entry 5UHE
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 242 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240F LEU 4.0 0.8 + - - -
241F LEU* 1.3 74.2 - - - +
243F ALA* 1.3 91.8 + - - +
244F GLU* 3.3 28.7 + - - +
245F GLU* 3.2 34.5 + - + +
246F GLU* 3.0 27.0 + - - +
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Residues in contact with ALA 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F LEU 4.0 0.6 + - - -
242F ASN* 1.3 89.1 + - - +
244F GLU* 1.3 58.2 + - + +
246F GLU* 3.5 12.2 - - - +
247F VAL* 3.3 16.9 - - - +
342F LYS* 4.0 36.9 - - + +
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Residues in contact with GLU 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242F ASN* 3.8 24.5 + - + +
243F ALA* 1.3 75.9 - - + +
245F GLU* 1.3 68.1 - - + +
246F GLU 3.2 0.4 - - - -
247F VAL* 3.2 23.1 + - + +
248F GLU* 3.2 13.0 + - - +
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Residues in contact with GLU 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240F LEU 4.3 3.5 - - - +
241F LEU* 3.7 22.8 - - + +
242F ASN* 3.2 39.2 + - + +
244F GLU* 1.3 78.9 - - + +
246F GLU* 1.3 63.4 + - - +
248F GLU* 3.4 15.0 + - - +
249F LEU* 3.3 24.9 + - - +
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Residues in contact with GLU 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F LEU* 3.6 28.9 - - + +
242F ASN 3.0 18.3 + - - +
243F ALA 3.5 8.9 - - - +
245F GLU* 1.3 74.0 - - - +
247F VAL* 1.3 65.6 + - - +
249F LEU* 3.2 5.4 + - - +
250F ALA* 3.0 23.5 + - - +
295F LEU* 4.6 8.6 - - + +
299F ASN* 4.1 5.6 - - - +
335F PHE* 5.4 6.2 - - + -
342F LYS* 3.2 28.3 + - - -
343F PHE* 3.1 38.8 + - + +
6H T 3.4 22.2 - - - +
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Residues in contact with VAL 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243F ALA 3.3 18.4 - - - +
244F GLU* 3.3 15.7 - - + +
246F GLU* 1.3 77.7 - - + +
248F GLU* 1.3 51.5 + - - +
250F ALA* 3.2 7.7 + - - +
251F LYS* 2.7 46.2 + - + +
335F PHE* 5.9 0.7 - - - -
337F TYR* 4.0 31.1 - - + +
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Residues in contact with GLU 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F GLU 3.2 8.0 + - - +
245F GLU* 3.6 16.0 - - - +
246F GLU 3.3 0.2 - - - -
247F VAL* 1.3 80.4 - - - +
249F LEU* 1.3 62.8 + - - +
251F LYS* 3.1 12.4 + - + +
252F ARG* 2.8 58.6 + - + +
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Residues in contact with LEU 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F LEU* 3.6 22.9 - - + -
245F GLU 3.3 9.4 + - - +
246F GLU 3.2 8.8 + - - +
248F GLU* 1.3 84.6 - - - +
250F ALA* 1.3 56.0 + - - +
252F ARG* 3.0 36.0 + - - +
253F ILE* 2.8 36.1 + - + +
291F ALA* 4.1 12.6 - - + +
294F HIS* 3.3 32.3 - - + +
295F LEU* 3.7 32.3 - - + +
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Residues in contact with ALA 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246F GLU 3.0 13.0 + - - +
247F VAL* 3.5 7.2 - - - +
249F LEU* 1.3 75.5 - - - +
251F LYS* 1.3 63.2 + - - +
253F ILE* 3.4 12.1 + - - +
254F GLU* 3.0 29.3 + - + +
295F LEU* 4.7 4.2 - - + +
335F PHE* 3.9 33.0 - - + +
337F TYR* 4.0 16.4 - - + -
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Residues in contact with LYS 251 (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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247F VAL* 2.7 26.2 + - + +
248F GLU* 3.2 15.7 - - - +
250F ALA* 1.3 75.9 - - - +
252F ARG* 1.3 62.0 + - + +
254F GLU* 3.6 3.8 - - - +
255F ALA* 3.5 18.7 + - - +
337F TYR* 4.0 42.2 + - + +
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Residues in contact with ARG 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F GLU* 2.8 36.8 + - + +
249F LEU* 3.0 34.9 + - - +
251F LYS* 1.3 77.2 - - + +
253F ILE* 1.3 59.9 + - - +
255F ALA* 3.4 7.4 + - - +
256F GLY* 2.8 25.6 + - - -
284F ILE* 5.1 0.9 - - - +
287F ASP* 2.4 53.0 + - - +
288F GLY* 3.8 5.6 + - - -
290F ARG* 5.4 5.9 - - - +
291F ALA* 4.0 21.1 - - + +
294F HIS* 5.5 3.2 + - - +
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Residues in contact with ILE 253 (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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249F LEU 2.8 26.4 + - - +
250F ALA* 3.4 7.6 + - - +
252F ARG* 1.3 72.5 - - - +
254F GLU* 1.3 56.7 + - - +
256F GLY 3.0 0.6 + - - +
257F LEU* 2.4 55.1 + - + +
288F GLY 3.9 12.6 - - - +
291F ALA* 3.8 7.2 - - + -
292F LYS* 3.6 43.5 - - + +
295F LEU* 4.2 18.6 - - + -
332F VAL* 4.2 19.1 - - + +
333F GLU* 5.3 7.6 - - - +
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Residues in contact with GLU 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250F ALA 3.0 19.2 + - - +
251F LYS 3.6 7.0 - - - +
253F ILE* 1.3 75.5 - - - +
255F ALA* 1.3 52.8 + - - +
257F LEU* 3.6 7.5 - - + +
258F TYR* 2.8 38.1 + - - +
335F PHE 5.4 6.6 - - - +
336F ASP* 4.5 9.0 - - - +
337F TYR* 3.3 37.5 + - + +
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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
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251F LYS 3.5 8.8 + - - +
252F ARG* 3.4 9.8 + - - +
254F GLU* 1.3 78.5 - - - +
256F GLY* 1.3 58.3 + - - +
258F TYR* 3.1 5.1 + - - +
259F ALA* 2.9 32.2 + - - +
284F ILE* 3.6 16.6 - - + +
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Residues in contact with GLY 256 (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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252F ARG 2.8 15.3 + - - -
253F ILE 3.4 2.2 - - - -
255F ALA* 1.3 77.8 - - - +
257F LEU* 1.3 59.6 + - - +
258F TYR 3.2 0.7 + - - -
259F ALA* 3.4 2.8 + - - +
260F THR* 2.9 25.5 + - - -
284F ILE* 3.6 26.6 - - - +
285F CYS* 4.1 4.7 - - - -
288F GLY* 3.7 11.4 - - - -
289F ASP 5.5 0.4 - - - -
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Residues in contact with LEU 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253F ILE* 2.4 37.7 + - + +
254F GLU* 3.6 7.2 - - + +
256F GLY* 1.3 71.4 - - - -
258F TYR* 1.3 60.1 + - - +
260F THR* 3.9 8.7 + - - +
261F GLN* 3.6 17.5 + - - +
288F GLY 5.5 0.4 - - - -
333F GLU* 3.8 37.7 - - + +
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Residues in contact with TYR 258 (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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254F GLU 2.8 19.0 + - - +
255F ALA* 3.6 6.7 - - - +
256F GLY 3.1 0.2 - - - -
257F LEU* 1.3 76.9 - - - +
259F ALA* 1.3 66.2 + - - +
260F THR 3.0 1.8 - - - -
261F GLN* 2.9 32.4 + - + +
262F LEU* 3.2 11.4 + - - +
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Residues in contact with ALA 259 (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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255F ALA 2.9 15.7 + - - +
256F GLY 3.9 4.7 - - - +
258F TYR* 1.3 75.5 - - - +
260F THR* 1.3 61.1 + - - +
262F LEU* 3.4 16.8 - - - +
263F MET* 3.4 17.9 - - - +
281F MET* 3.9 40.7 - - + +
284F ILE* 4.3 11.2 - - + -
285F CYS* 4.4 5.2 - - + +
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Residues in contact with THR 260 (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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256F GLY 2.9 18.0 + - - -
257F LEU* 3.9 10.1 - - - -
258F TYR 3.0 0.6 - - - -
259F ALA* 1.3 76.2 - - - +
261F GLN* 1.3 58.9 + - - +
262F LEU 3.2 0.2 - - - -
263F MET* 3.6 11.0 + - + +
264F THR* 2.3 42.3 + - - +
285F CYS* 3.1 25.1 + - - -
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Residues in contact with GLN 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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257F LEU 3.6 10.5 + - - +
258F TYR* 2.9 26.9 + - + +
260F THR* 1.3 76.5 - - - +
262F LEU* 1.3 68.2 + - - +
264F THR* 4.0 8.8 - - - +
265F GLU* 3.8 33.8 + - - +
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Residues in contact with LEU 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258F TYR 3.2 9.7 + - - +
259F ALA* 3.4 9.6 - - - +
261F GLN* 1.3 81.2 - - - +
263F MET* 1.3 68.3 + - + +
264F THR 3.1 0.2 + - - -
265F GLU* 3.4 2.4 + - - +
266F LEU* 3.2 42.5 + - + +
273F LEU* 4.4 11.4 - - + -
281F MET* 3.5 41.1 - - + -
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Residues in contact with MET 263 (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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259F ALA 3.4 18.2 + - - +
260F THR* 4.3 13.2 - - + +
262F LEU* 1.3 78.3 - - + +
264F THR* 1.3 58.3 + - - +
266F LEU* 3.6 12.1 - - + +
267F SER* 2.9 31.2 + - - -
273F LEU* 5.7 3.1 - - + -
278F ARG* 4.9 13.0 - - + -
281F MET* 3.9 28.7 - - + -
282F MET* 3.8 33.2 - - + +
285F CYS* 4.3 15.3 - - + -
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Residues in contact with THR 264 (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* 2.3 36.6 + - - +
261F GLN* 3.9 15.3 - - - +
262F LEU 3.1 0.6 - - - -
263F MET* 1.3 78.6 - - - +
265F GLU* 1.3 64.0 + - + +
266F LEU 3.4 0.2 + - - -
267F SER* 3.5 10.5 + - - -
268F GLU* 3.8 9.7 + - - +
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Residues in contact with GLU 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 GLN* 3.8 27.4 + - - +
262F LEU 3.4 6.9 + - - +
264F THR* 1.3 78.6 - - + +
266F LEU* 1.3 65.1 + - + +
267F SER 3.4 0.2 - - - -
268F GLU* 3.7 16.6 + - - +
269F ARG* 3.4 22.2 + - - +
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Residues in contact with LEU 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262F LEU* 3.2 39.9 + - + +
263F MET* 3.3 12.1 + - + +
264F THR 3.2 0.2 - - - -
265F GLU* 1.3 82.5 - - + +
267F SER* 1.3 59.6 + - - +
268F GLU 3.2 0.7 - - - -
269F ARG* 3.2 25.4 - - - +
270F GLY 2.9 24.8 + - - -
271F GLU* 3.4 23.7 - - + +
272F LYS* 5.3 3.8 - - - -
273F LEU* 4.9 19.7 - - + -
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Residues in contact with SER 267 (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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263F MET 2.9 15.7 + - - -
264F THR* 3.5 6.9 + - - -
265F GLU 3.4 0.2 - - - -
266F LEU* 1.3 76.7 - - - +
268F GLU* 1.3 63.0 + - - +
270F GLY* 3.8 11.2 + - - +
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Residues in contact with GLU 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F THR 3.8 8.2 + - - +
265F GLU* 3.7 17.1 + - - +
266F LEU 3.2 0.4 - - - -
267F SER* 1.3 80.7 - - - +
269F ARG* 1.3 61.4 + - - +
270F GLY 3.6 0.3 + - - -
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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 GLU 3.4 12.7 + - - +
266F LEU* 3.2 32.6 - - - +
268F GLU* 1.3 80.9 - - + +
270F GLY* 1.3 56.2 + - - +
271F GLU* 2.6 50.9 + - - +
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Residues in contact with GLY 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F LEU 2.9 10.0 + - - +
267F SER* 3.8 10.2 + - - +
268F GLU 3.3 2.2 - - - -
269F ARG* 1.3 80.2 - - - +
271F GLU* 1.3 62.9 + - - +
272F LYS* 3.7 17.8 + - - +
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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