Contacts of the helix formed by residues 315 - 350 (chain F) in PDB entry 5UQ9
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 ASP 315 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312F PHE* 3.4 10.0 - - - -
314F GLY* 1.3 71.6 - - - -
316F LYS* 1.3 67.5 + - - +
317F LYS* 3.2 16.7 + - - +
318F SER* 3.0 32.7 + - - +
319F PHE* 3.1 18.2 + - - +
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Residues in contact with LYS 316 (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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209F LEU* 2.7 56.8 + - + +
210F GLY* 4.8 2.0 + - - -
211F MET* 4.5 10.7 - - + +
312F PHE* 3.5 30.7 - - + -
314F GLY 4.5 4.7 - - - +
315F ASP* 1.3 74.9 + - - +
317F LYS* 1.3 57.5 + - - +
320F LEU* 2.8 32.3 + - - +
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Residues in contact with LYS 317 (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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315F ASP* 3.2 15.2 + - - +
316F LYS* 1.3 79.2 - - - +
318F SER* 1.3 64.4 + - - +
320F LEU* 3.4 6.9 + - - +
321F GLU* 3.1 22.4 + - + +
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Residues in contact with SER 318 (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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315F ASP* 3.0 29.2 + - - +
317F LYS* 1.3 79.8 - - - +
319F PHE* 1.3 57.9 + - - +
321F GLU* 3.6 6.1 + - - +
322F ASP* 3.0 33.7 + - - +
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Residues in contact with PHE 319 (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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204F LEU* 4.9 7.2 - - + -
208F VAL* 3.7 20.6 - - + -
209F LEU* 3.5 25.8 - - + -
312F PHE* 3.8 17.3 - + + -
315F ASP 3.1 16.8 + - - +
318F SER* 1.3 75.5 - - - +
320F LEU* 1.3 60.8 + - - +
321F GLU 3.2 0.2 - - - -
322F ASP* 3.0 15.4 + - + +
323F ILE* 2.9 50.0 + - + +
408F ARG* 4.1 5.8 - - + -
409F ALA* 3.7 25.8 - - + -
412F THR* 3.5 42.2 - - + -
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Residues in contact with LEU 320 (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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205F MET* 3.5 30.3 - - + -
209F LEU* 3.9 6.2 - - + +
211F MET* 3.6 21.3 - - + -
219F ALA* 4.1 12.1 - - + -
223F TRP* 3.4 48.3 - - + +
316F LYS 2.8 20.5 + - - +
317F LYS* 3.6 7.2 - - - +
319F PHE* 1.3 76.7 - - - +
321F GLU* 1.3 64.6 + - - +
323F ILE* 3.2 4.0 + - + +
324F ARG* 3.1 16.8 + - - +
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Residues in contact with GLU 321 (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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223F TRP* 5.1 1.9 + - - -
317F LYS* 3.1 16.9 + - + +
318F SER* 3.7 7.9 - - - +
319F PHE 3.2 0.2 - - - -
320F LEU* 1.3 77.2 - - - +
322F ASP* 1.3 63.7 + - - +
324F ARG* 2.8 39.1 + - - +
325F LYS* 2.7 63.8 + - + +
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Residues in contact with ASP 322 (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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318F SER* 3.0 18.1 + - - +
319F PHE* 3.0 22.6 + - + +
321F GLU* 1.3 78.9 - - - +
323F ILE* 1.3 59.0 + - - +
325F LYS* 3.3 1.9 + - - +
326F ALA* 2.9 30.3 + - - +
405F SER* 2.9 37.2 + - - +
408F ARG* 2.7 43.1 + - - +
409F ALA* 4.4 5.2 - - + +
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Residues in contact with ILE 323 (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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201F ALA* 3.7 25.6 - - + +
204F LEU* 3.7 29.8 - - + -
205F MET* 4.0 11.2 - - + +
209F LEU* 3.8 17.9 - - + -
223F TRP* 3.6 19.3 - - + -
319F PHE* 2.9 48.1 + - + +
320F LEU* 3.2 7.4 + - - +
322F ASP* 1.3 75.9 - - - +
324F ARG* 1.3 57.1 + - - +
326F ALA* 3.5 5.6 + - - +
327F LEU* 2.9 27.7 + - - +
409F ALA* 4.7 2.9 - - + -
423F PHE* 4.8 2.3 - - + -
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Residues in contact with ARG 324 (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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223F TRP* 3.4 51.7 - - + +
226F THR* 2.9 27.5 + - - +
227F GLU* 2.7 34.9 + - - +
228F LEU* 4.3 13.5 - - + +
320F LEU 3.1 7.8 + - - +
321F GLU* 2.8 42.9 + - - +
323F ILE* 1.3 74.9 - - - +
325F LYS* 1.3 77.8 + - - +
327F LEU* 3.4 5.2 + - - +
328F TYR* 2.9 33.7 + - - +
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Residues in contact with LYS 325 (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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321F GLU* 2.7 54.9 + - + +
322F ASP 3.7 0.2 - - - +
324F ARG* 1.3 90.3 - - - +
326F ALA* 1.3 57.2 + - - +
328F TYR* 3.2 3.1 + - - +
329F ALA* 2.8 31.7 + - - +
401F ASN* 3.6 27.6 - - - +
402F CYS* 3.6 35.5 - - + +
405F SER* 3.6 32.3 - - - +
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Residues in contact with ALA 326 (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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322F ASP 2.9 17.8 + - - +
323F ILE* 3.9 4.9 - - - +
325F LYS* 1.3 75.8 - - - +
327F LEU* 1.3 58.4 + - - +
330F SER* 2.8 35.4 + - - -
406F TRP* 3.5 35.9 + - + +
409F ALA* 4.1 13.7 - - + -
410F VAL* 5.6 0.4 - - + -
423F PHE* 4.1 15.9 - - + -
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Residues in contact with LEU 327 (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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197F LEU* 3.5 47.6 - - + +
198F ILE* 4.0 8.1 - - + +
201F ALA* 4.3 7.0 - - + -
220F PHE* 4.8 0.7 - - + -
223F TRP* 4.1 21.8 - - + -
228F LEU* 3.8 28.0 - - + -
233F ILE* 4.4 12.8 - - + -
323F ILE 2.9 18.3 + - - +
324F ARG 3.7 4.3 - - - +
326F ALA* 1.3 74.8 - - - +
328F TYR* 1.3 59.4 + - - +
330F SER* 3.9 0.7 - - - -
331F LYS* 3.0 31.8 + - + +
423F PHE* 3.9 12.5 - - + -
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Residues in contact with TYR 328 (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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227F GLU* 3.5 44.4 - - + +
228F LEU* 3.7 27.1 - - + +
324F ARG* 2.9 22.9 + - - +
325F LYS* 3.7 4.7 - - - +
327F LEU* 1.3 75.4 - - - +
329F ALA* 1.3 64.5 + - - +
331F LYS* 3.3 7.0 + - + +
332F ILE* 3.2 36.9 + - + +
372F PHE* 4.3 20.8 - + + -
375F LYS* 5.1 1.6 + - - -
394F PHE* 3.9 22.3 - - - -
398F ALA* 3.8 30.7 - - + +
402F CYS* 3.6 22.4 - - - -
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Residues in contact with ALA 329 (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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325F LYS 2.8 20.5 + - - +
328F TYR* 1.3 70.7 - - - +
330F SER* 1.3 65.3 + - - +
332F ILE* 3.1 22.3 + - - +
333F ILE* 3.1 17.5 + - - +
399F VAL* 4.9 8.9 - - + +
402F CYS* 3.8 16.8 - - + -
406F TRP* 3.5 35.2 - - + -
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Residues in contact with SER 330 (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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197F LEU* 3.6 27.6 - - - -
280F LEU* 3.5 4.9 - - - +
326F ALA 2.8 23.1 + - - -
327F LEU 4.1 1.1 - - - -
329F ALA* 1.3 73.2 - - - +
331F LYS* 1.3 64.9 + - - +
333F ILE 3.9 0.4 - - - +
334F SER* 3.0 25.8 + - - -
406F TRP* 3.3 19.9 + - - -
422F CYS 4.6 0.2 - - - -
423F PHE* 3.4 10.9 - - - -
426F ALA* 3.9 18.9 - - - +
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Residues in contact with LYS 331 (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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194F ASP* 3.4 40.6 - - + +
197F LEU* 3.8 12.7 - - + +
228F LEU* 4.8 14.4 + - + +
230F SER* 3.4 24.9 + - - -
327F LEU* 3.0 21.9 + - + +
328F TYR* 3.3 11.9 - - + +
329F ALA 3.2 0.4 - - - -
330F SER* 1.3 78.3 - - - +
332F ILE* 1.3 60.4 + - + +
334F SER* 3.8 1.2 - - - -
335F TYR* 3.1 45.5 + - + +
370F SER* 4.2 5.4 + - - -
372F PHE* 3.9 32.4 - - + +
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Residues in contact with ILE 332 (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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328F TYR* 3.3 28.7 - - + +
329F ALA* 3.1 8.6 + - - +
331F LYS* 1.3 75.0 - - - +
333F ILE* 1.3 59.7 + - - +
335F TYR* 3.3 2.1 + - - +
336F ALA* 2.8 31.6 + - + +
372F PHE* 3.8 22.2 - - + -
389F LEU* 5.1 4.3 - - + +
390F LEU* 4.1 11.0 - - + -
395F PHE* 3.8 34.1 - - + -
398F ALA* 3.9 23.6 - - + -
399F VAL* 3.8 28.0 - - + +
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Residues in contact with ILE 333 (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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280F LEU* 5.1 0.4 - - + -
329F ALA 3.1 13.9 + - - +
330F SER 3.4 1.8 + - - +
332F ILE* 1.3 75.7 - - + +
334F SER* 1.3 57.5 + - - +
336F ALA* 3.6 3.4 - - - +
337F GLN* 2.9 39.0 + - - +
390F LEU* 3.6 38.6 - - + -
399F VAL* 5.2 3.4 - - + -
406F TRP* 3.6 20.0 - - + -
426F ALA* 3.8 26.2 - - + +
429F PHE* 3.6 24.9 - - + -
430F TYR* 4.1 19.7 - - + -
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Residues in contact with SER 334 (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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190F ILE* 5.1 7.0 + - - +
193F GLY* 4.5 2.6 - - - -
194F ASP* 4.5 7.7 + - - -
197F LEU* 4.7 3.6 - - - -
280F LEU* 3.4 32.7 - - - +
281F ILE* 4.0 16.5 - - - +
330F SER 3.0 18.0 + - - -
331F LYS* 3.8 6.7 - - - -
332F ILE 3.2 0.2 - - - -
333F ILE* 1.3 78.5 - - - +
335F TYR* 1.3 62.7 + - - +
337F GLN* 3.3 10.5 + - - +
338F GLY* 3.0 22.3 + - - -
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Residues in contact with TYR 335 (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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190F ILE* 3.4 35.8 - - + +
194F ASP* 2.5 40.2 + - - -
331F LYS* 3.1 39.3 + - - +
332F ILE 4.0 2.7 - - - +
334F SER* 1.3 80.3 - - - +
336F ALA* 1.3 65.6 + - - +
338F GLY* 3.1 3.0 + - - +
339F PHE* 3.1 36.2 + + + -
362F TRP* 4.6 0.9 - + - -
368F ILE* 3.7 20.5 + - + +
370F SER* 4.9 0.7 + - - -
372F PHE* 3.5 19.5 - + + -
373F LEU* 3.5 23.5 - - + +
376F ILE* 3.6 24.7 - - + -
389F LEU* 4.0 3.6 - - + -
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Residues in contact with ALA 336 (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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332F ILE 2.8 18.8 + - - +
333F ILE* 3.6 7.4 - - + +
335F TYR* 1.3 77.2 - - - +
337F GLN* 1.3 61.4 + - + +
339F PHE* 3.6 2.6 + - - +
340F MET* 3.1 28.6 + - - +
388F ASN* 4.1 7.2 + - - +
389F LEU* 4.0 27.5 + - + +
390F LEU* 4.0 25.6 - - + -
429F PHE* 5.7 1.6 - - + -
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Residues in contact with GLN 337 (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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277F PRO 3.2 21.1 + - - +
278F VAL* 3.4 29.4 - - + +
279F THR* 2.8 26.8 + - - -
280F LEU* 3.0 30.1 + - - +
333F ILE* 2.9 26.6 + - - +
334F SER* 3.6 4.7 - - - +
336F ALA* 1.3 76.4 - - - +
338F GLY* 1.3 62.9 + - - +
340F MET* 3.3 11.4 + - - +
341F LEU 3.3 16.3 + - - -
425F THR 5.0 0.2 + - - -
429F PHE* 3.4 36.6 - - + +
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Residues in contact with GLY 338 (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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186F VAL* 3.9 19.4 - - - +
190F ILE* 4.5 11.0 - - - -
278F VAL* 4.7 6.7 - - - +
281F ILE* 6.2 0.2 - - - -
334F SER 3.0 14.3 + - - -
335F TYR 3.1 4.8 + - - -
337F GLN* 1.3 77.8 - - - +
339F PHE* 1.3 61.8 + - - +
341F LEU* 3.3 9.4 + - - +
342F LEU* 3.3 23.7 + - - +
362F TRP* 6.4 0.2 - - - -
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Residues in contact with PHE 339 (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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190F ILE* 5.6 1.1 - - + -
335F TYR* 3.1 30.4 + + - +
336F ALA 4.2 3.1 - - - +
338F GLY* 1.3 74.9 - - - +
340F MET* 1.3 61.1 + - - +
341F LEU 3.2 0.2 - - - -
342F LEU* 3.7 21.7 - - + +
343F ARG* 2.8 31.2 + - - +
355F TYR* 3.8 27.7 - + + -
358F ILE* 4.5 2.7 - - + -
359F ALA* 4.1 13.9 - - + -
362F TRP* 4.5 21.5 - + - -
376F ILE* 3.6 37.7 - - + -
380F PHE* 3.7 31.4 - + + -
389F LEU* 3.9 14.1 - - + +
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Residues in contact with MET 340 (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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293E LEU* 3.6 31.0 - - + -
296E GLU* 4.8 1.1 - - - +
276F VAL* 3.7 8.8 - - + +
277F PRO* 3.8 22.9 - - + -
336F ALA* 3.1 19.0 + - - +
337F GLN* 3.3 17.5 + - - +
339F PHE* 1.3 76.5 - - - +
341F LEU* 1.3 56.4 + - - +
343F ARG* 3.4 28.4 + - - +
344F GLN* 3.0 29.8 + - - +
387F GLN 5.3 0.9 - - - +
388F ASN* 3.3 30.3 - - - +
429F PHE* 4.1 19.1 - - + -
433F TYR* 5.1 1.3 - - + -
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Residues in contact with LEU 341 (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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182F PHE* 3.8 12.1 - - + -
186F VAL* 3.7 23.6 - - + -
267F THR* 3.9 28.3 - - + +
270F SER* 3.9 33.7 - - - +
271F ALA* 4.0 10.1 - - - +
274F TYR* 4.0 10.1 - - + -
276F VAL* 3.6 14.9 - - + +
278F VAL* 4.0 18.6 - - + -
337F GLN 3.3 3.4 + - - -
338F GLY* 3.5 9.0 - - - +
339F PHE 3.2 0.4 - - - -
340F MET* 1.3 76.5 - - - +
342F LEU* 1.3 59.3 + - - +
344F GLN 3.3 0.3 + - - -
345F ALA* 3.0 27.9 + - - +
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Residues in contact with LEU 342 (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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182F PHE* 3.6 31.4 - - + -
183F VAL* 4.0 18.4 - - + -
186F VAL* 3.7 15.0 - - + -
338F GLY 3.3 13.5 + - - +
339F PHE* 3.3 35.6 + - + +
341F LEU* 1.3 77.2 - - - +
343F ARG* 1.3 58.7 + - - +
345F ALA* 3.9 0.9 - - - +
346F ALA* 3.0 30.0 + - - +
353F LEU* 3.4 16.7 - - + +
355F TYR* 4.1 5.6 - - + -
358F ILE* 4.3 21.1 - - + -
362F TRP* 4.5 11.7 - - + -
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Residues in contact with ARG 343 (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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293E LEU* 5.3 6.3 - - - +
296E GLU* 4.0 19.6 + - - -
276F VAL* 5.9 0.2 - - - +
339F PHE 2.8 16.4 + - - +
340F MET* 3.8 40.4 + - - +
342F LEU* 1.3 77.4 - - - +
344F GLN* 1.3 75.9 + - - +
346F ALA* 3.4 3.3 + - - +
347F THR* 2.8 36.6 + - - +
355F TYR* 3.6 23.7 + - + +
386F LEU 5.0 3.6 - - - -
387F GLN* 3.3 31.9 + - - +
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Residues in contact with GLN 344 (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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293E LEU* 6.0 1.6 - - - +
274F TYR* 4.0 24.0 + - + +
276F VAL* 3.6 25.8 - - + -
340F MET 3.0 17.0 + - - +
341F LEU 3.9 1.6 - - - +
343F ARG* 1.3 92.0 + - - +
345F ALA* 1.3 60.6 + - - +
347F THR* 3.0 16.1 + - - +
348F GLU* 2.9 31.6 + - - +
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Residues in contact with ALA 345 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F PHE* 3.4 43.5 - - + -
274F TYR* 4.6 17.8 - - + -
341F LEU 3.0 9.6 + - - +
342F LEU 4.1 2.0 - - - +
344F GLN* 1.3 77.3 - - - +
346F ALA* 1.3 60.5 + - - +
348F GLU 3.5 0.6 + - - +
349F PHE* 3.1 38.8 + - + +
351F TRP* 4.2 5.7 - - + -
353F LEU* 6.0 0.4 - - + -
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Residues in contact with ALA 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342F LEU 3.0 19.4 + - - +
343F ARG 3.6 5.6 - - - +
344F GLN 3.2 0.2 - - - -
345F ALA* 1.3 75.9 - - - +
347F THR* 1.3 57.8 + - - +
350F GLY* 3.0 6.4 + - - -
351F TRP* 2.8 49.3 + - + +
353F LEU* 3.7 19.3 - - + +
355F TYR* 3.7 16.2 - - - +
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Residues in contact with THR 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343F ARG* 2.8 24.9 + - - +
344F GLN* 3.0 22.7 + - - +
346F ALA* 1.3 76.9 - - - +
348F GLU* 1.3 64.8 + - - +
349F PHE 3.3 0.7 + - - -
350F GLY* 3.4 8.8 + - - -
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Residues in contact with GLU 348 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274F TYR* 3.6 28.4 - - + -
344F GLN* 2.9 19.4 + - - +
345F ALA 3.5 3.6 + - - +
347F THR* 1.3 76.9 - - - +
349F PHE* 1.3 94.4 + - - +
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Residues in contact with PHE 349 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F TYR* 4.3 15.0 - + - -
107F ARG* 5.2 5.6 - - + -
110F THR* 5.3 4.5 - - + -
114F ARG* 4.5 18.2 + - - -
177F GLU* 4.5 5.6 - - - +
274F TYR* 3.3 28.3 - + - -
345F ALA* 3.1 27.5 + - + +
347F THR 3.3 0.2 - - - -
348F GLU* 1.3 99.4 - - - +
350F GLY* 1.3 61.4 + - - +
351F TRP* 3.4 54.2 + + + +
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Residues in contact with GLY 350 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176F ASP* 4.6 4.3 - - - +
346F ALA 3.0 8.8 + - - -
347F THR* 3.4 9.7 + - - -
349F PHE* 1.3 79.2 - - - +
351F TRP* 1.3 66.2 + - - +
352F THR* 4.6 2.9 + - - -
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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