Contacts of the helix formed by residues 327 - 359 (chain A) in PDB entry 6FWF
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 PRO 327 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A TYR* 3.4 15.3 - - + +
322A MET 4.1 0.2 - - - -
323A SER* 3.8 16.6 - - - +
324A ASP 3.8 7.4 - - - +
325A TRP 3.1 15.0 - - - +
326A PHE* 1.4 90.0 - - - +
328A TYR* 1.3 64.2 + - - +
329A ALA* 4.2 9.6 - - + +
330A LEU* 3.5 23.0 + - + +
331A THR* 3.3 16.1 + - - +
393A LEU 5.1 5.2 - - - +
394A THR* 4.2 10.1 - - + -
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Residues in contact with TYR 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A VAL* 3.6 30.3 - - + -
77A ALA* 3.7 4.3 - - + +
79A GLN* 3.4 39.1 + - + +
164A PRO* 4.6 16.7 - - + +
301A THR* 3.8 18.4 - - + -
304A TYR* 3.6 41.0 - - + -
305A THR* 3.9 10.3 - - + -
327A PRO* 1.3 72.7 - - - +
329A ALA* 1.3 63.7 + - - +
331A THR* 2.9 6.4 + - - -
332A ARG* 2.8 74.8 + - + -
1002A HEM 3.8 6.2 + - - -
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLU 3.7 17.2 - - - +
69A VAL* 4.6 13.5 - - + +
164A PRO* 5.9 0.6 - - + +
327A PRO* 3.4 8.8 - - + +
328A TYR* 1.3 79.3 - - - +
330A LEU* 1.3 53.2 + - - +
332A ARG* 3.3 2.3 + - - +
333A THR* 2.8 38.1 + - - +
393A LEU* 3.8 34.5 - - + +
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A TRP 3.0 28.3 - - - +
326A PHE* 3.9 6.3 - - + -
327A PRO* 3.5 23.6 + - + +
328A TYR 3.2 0.4 - - - -
329A ALA* 1.3 78.2 - - - +
331A THR* 1.3 57.7 + - + +
333A THR* 3.2 2.7 + - - -
334A TRP* 2.8 56.2 + - + +
389A ASN 3.2 29.2 - - - +
390A PHE* 3.5 33.7 - - + +
393A LEU* 3.4 19.3 - - + -
394A THR* 4.6 0.9 - - + -
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Residues in contact with THR 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A LEU* 3.8 22.5 - - + +
300A LEU* 3.6 26.5 - - + -
301A THR* 2.4 31.1 + - - -
304A TYR* 3.5 19.4 - - + -
326A PHE* 4.5 3.1 - - + +
327A PRO 3.3 12.9 + - - +
328A TYR* 2.9 16.9 + - - -
330A LEU* 1.3 76.6 - - + +
332A ARG* 1.3 59.7 + - - +
334A TRP* 5.3 1.3 - - + -
335A HIS* 2.8 34.3 + - - +
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Residues in contact with ARG 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLU* 3.2 54.2 - - + +
77A ALA* 3.2 19.1 - - + +
301A THR* 3.6 16.7 + - - +
328A TYR* 2.8 46.6 + - + +
329A ALA 3.6 2.2 - - - +
331A THR* 1.3 74.6 + - - +
333A THR* 1.3 61.5 + - - +
335A HIS* 4.0 5.4 + - - +
336A ILE* 3.3 22.8 + - - +
1002A HEM 2.6 74.1 + - - +
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Residues in contact with THR 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLU* 3.2 22.7 - - + +
329A ALA 2.8 21.2 + - - +
330A LEU 3.2 3.6 + - - -
332A ARG* 1.3 71.2 - - - +
334A TRP* 1.3 76.8 + - - +
336A ILE 3.2 2.4 + - - -
337A GLN* 2.8 28.0 + - - +
389A ASN* 3.4 17.2 + - - -
393A LEU* 3.5 21.1 - - + +
407A HIS* 3.4 28.0 - - + +
414A ASP* 3.5 9.4 - - - +
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Residues in contact with TRP 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A LEU* 3.3 35.9 - - + -
326A PHE* 3.5 39.7 - + + -
330A LEU* 2.8 51.6 + - + +
331A THR* 5.4 0.7 - - + -
333A THR* 1.3 85.9 + - - +
335A HIS* 1.3 60.3 + - - +
337A GLN* 4.3 5.8 - - - +
338A SER* 2.8 36.4 + - - +
386A TYR* 2.8 61.4 + + + -
387A ALA* 5.4 0.2 - - - -
389A ASN* 4.0 1.0 - - - +
390A PHE* 3.8 12.8 - + + -
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Residues in contact with HIS 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A GLN* 3.4 20.0 - - - +
297A LEU* 3.8 16.7 - - + +
298A GLY* 3.1 30.3 - - - +
301A THR* 4.7 2.0 - - - +
331A THR 2.8 24.5 + - - +
332A ARG* 4.0 6.7 - - - +
334A TRP* 1.3 71.4 - - - +
336A ILE* 1.3 66.4 + - + +
339A ALA* 3.1 21.5 + - + +
1002A HEM 2.0 86.9 + + + -
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Residues in contact with ILE 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLU* 4.2 7.6 - - - +
332A ARG* 3.3 23.0 + - - +
333A THR 3.2 2.0 + - - -
335A HIS* 1.3 87.1 - - + +
337A GLN* 1.3 59.7 + - - +
339A ALA* 3.6 5.4 + - + +
340A ILE* 3.1 26.7 + - + +
412A TYR* 3.2 47.8 - - + +
414A ASP* 3.3 23.6 - - - +
1002A HEM 3.3 49.4 - - + +
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Residues in contact with GLN 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A THR 2.8 17.8 + - - +
334A TRP* 4.3 1.8 - - - +
336A ILE* 1.3 70.5 - - - +
338A SER* 1.3 60.5 + - - +
340A ILE* 3.1 26.8 + - - +
341A PHE* 2.8 51.4 + - + -
385A SER* 4.5 4.3 - - - +
386A TYR* 3.9 24.5 - - + -
389A ASN* 5.0 0.2 - - - +
412A TYR 3.4 7.7 + - - -
414A ASP* 2.9 48.7 + - + +
415A LEU* 3.0 38.8 - - + +
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Residues in contact with SER 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A LEU* 3.8 11.8 - - - +
293A VAL* 4.0 14.4 - - - +
294A GLN* 3.3 31.1 - - - -
297A LEU* 4.1 6.8 - - - +
334A TRP* 2.8 26.3 + - - -
337A GLN* 1.3 71.2 - - - +
339A ALA* 1.3 56.6 + - - +
341A PHE* 4.4 3.6 - - - +
342A TRP* 2.8 37.4 + - - +
386A TYR* 4.5 13.6 + - - -
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Residues in contact with ALA 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A GLN* 3.1 25.3 - - - +
335A HIS* 3.1 17.5 + - + +
336A ILE* 3.6 9.8 + - + +
337A GLN 3.4 0.2 - - - -
338A SER* 1.3 73.3 - - - +
340A ILE* 1.3 65.4 + - - +
342A TRP* 3.5 11.7 - - - +
343A ILE* 3.4 28.1 + - - +
638A LEU* 5.3 9.1 - - + +
1002A HEM 4.1 15.5 - - + -
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Residues in contact with ILE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A ILE* 3.1 15.7 + - + +
337A GLN* 3.1 27.6 - - - +
339A ALA* 1.3 79.3 - - + +
341A PHE* 1.3 75.8 + - + +
343A ILE* 4.1 0.9 - - - +
344A ALA* 2.8 36.5 + - + +
412A TYR* 3.1 48.5 - - + +
415A LEU* 5.1 1.1 - - + -
423A LEU* 5.1 7.4 - - + -
466A TYR* 5.6 4.5 - - + +
492A TRP* 6.1 7.4 - - + -
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Residues in contact with PHE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A LEU* 3.7 19.7 - - + -
337A GLN* 2.8 46.7 + - + +
338A SER* 4.2 0.9 - - - +
340A ILE* 1.3 79.0 - - + +
342A TRP* 1.3 56.4 + - - +
344A ALA* 3.8 5.8 - - + +
345A THR* 2.8 35.5 + - + +
378A LEU* 4.3 13.0 - - + -
381A VAL* 3.7 24.5 - - + -
382A VAL* 3.3 36.8 - - + -
385A SER* 3.5 22.0 - - - -
386A TYR* 4.6 1.3 - + - -
415A LEU* 4.7 6.5 - - + -
423A LEU* 3.4 31.6 - - + -
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Residues in contact with TRP 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A THR* 3.2 47.6 - - + +
290A LEU* 3.5 8.1 - - + +
291A PHE* 3.4 52.6 - + + +
294A GLN* 3.9 10.7 - - + -
338A SER 2.8 31.5 + - - +
339A ALA* 3.5 19.0 - - - +
341A PHE* 1.3 72.4 - - - +
343A ILE* 1.3 78.4 + - + +
345A THR* 3.7 4.9 - - - -
346A GLY* 2.8 22.5 + - - -
639A PHE* 3.8 20.2 - + - -
643A GLY* 3.6 21.8 - - - -
646A ALA* 3.8 19.5 - - + -
647A LEU* 4.5 13.2 - - + -
1002A HEM 4.1 4.7 - - + +
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Residues in contact with ILE 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A ALA 3.4 14.5 + - - +
340A ILE 4.1 0.7 - - - +
342A TRP* 1.3 113.4 - - + +
344A ALA* 1.3 60.0 + - - +
346A GLY* 3.0 3.6 + - - +
347A PHE* 2.8 40.4 + - + -
497A PHE* 3.6 31.2 - - + -
638A LEU* 4.2 15.5 - - + -
642A TYR* 4.1 3.6 - - + +
643A GLY* 3.8 21.5 - - - +
646A ALA* 4.4 2.2 - - + -
1002A HEM 4.0 16.6 - - + -
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Residues in contact with ALA 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A ILE* 2.8 31.3 + - + +
341A PHE* 3.8 9.9 - - + +
343A ILE* 1.3 73.3 - - - +
345A THR* 1.3 58.6 + - + +
347A PHE* 3.2 4.2 + - - -
348A LEU* 2.8 45.9 + - + +
378A LEU* 5.7 2.9 - - + -
423A LEU* 6.4 1.6 - - + -
492A TRP* 5.1 14.8 - - + -
496A PHE* 5.2 5.6 - - - -
497A PHE* 5.8 0.4 - - - -
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Residues in contact with THR 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A TYR* 4.4 12.6 - - + -
286A LEU* 3.5 30.1 - - + +
287A THR* 2.8 28.5 + - - -
290A LEU* 4.9 1.5 - - + +
341A PHE* 2.8 31.3 + - + +
342A TRP* 3.3 3.5 + - - -
344A ALA* 1.3 72.2 - - - +
346A GLY* 1.3 56.0 + - - +
348A LEU* 4.4 6.1 - - + +
349A THR* 2.8 37.0 + - - +
378A LEU* 3.9 29.6 - - + -
382A VAL* 5.6 1.3 - - + -
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Residues in contact with GLY 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A THR* 3.1 18.0 + - - -
342A TRP 2.8 21.6 + - - -
343A ILE* 3.0 7.8 + - - -
345A THR* 1.3 72.1 - - - +
347A PHE* 1.3 63.1 + - - +
349A THR* 3.6 14.5 - - - +
350A ALA* 4.2 0.7 - - - +
646A ALA* 4.1 18.4 - - - +
649A PHE* 4.1 10.4 - - - +
650A VAL* 4.6 2.7 - - - +
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Residues in contact with PHE 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A ILE* 2.8 22.3 + - + +
344A ALA 4.0 0.7 - - - +
346A GLY* 1.3 77.7 - - - +
348A LEU* 1.3 62.1 + - - +
349A THR 3.3 1.3 - - - -
350A ALA* 3.2 6.0 + - - +
351A GLY* 2.8 25.1 + - - -
496A PHE* 3.4 26.9 - + + -
497A PHE* 3.3 39.7 - + - -
500A PHE* 4.5 10.8 - + - -
501A ALA* 3.8 14.6 - - + -
642A TYR 3.8 6.5 - - - -
645A LEU* 3.6 28.7 - - + -
646A ALA* 3.6 26.9 - - + -
649A PHE* 3.6 29.6 - + - -
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Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A TYR* 5.1 8.9 - - + -
344A ALA* 2.8 31.8 + - + +
345A THR* 4.3 4.3 - - + +
347A PHE* 1.3 70.3 - - - +
349A THR* 1.3 57.7 + - - +
351A GLY* 4.7 0.2 - - - -
352A LEU* 2.8 37.8 + - + +
374A LEU* 5.5 3.4 - - + -
378A LEU* 5.3 19.5 - - + -
423A LEU* 6.4 1.1 - - + -
426A GLY 5.8 0.2 - - - +
427A LEU* 4.1 27.8 - - + +
430A TRP* 3.8 41.5 + - + +
462A VAL* 4.8 3.8 - - + -
492A TRP* 5.9 1.3 - - + -
496A PHE* 3.7 26.7 - - + -
500A PHE* 6.5 0.2 - - + -
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Residues in contact with THR 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A LEU* 3.3 24.3 + - - +
283A TYR* 2.9 35.5 - - - +
284A VAL* 3.7 22.6 - - + +
287A THR* 4.6 1.3 - - - +
345A THR 2.8 29.1 + - - +
346A GLY* 3.6 18.4 - - - +
348A LEU* 1.3 72.7 - - - +
350A ALA* 1.3 56.2 + - + +
353A PHE* 2.8 36.4 + - - +
649A PHE 5.5 2.7 - - - +
650A VAL* 4.9 2.0 - - + -
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Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A GLY 4.2 4.3 - - - +
347A PHE 3.2 8.4 + - - +
349A THR* 1.3 79.1 - - + +
351A GLY* 1.3 59.7 + - - +
353A PHE* 4.1 7.6 - - + -
354A LEU* 2.8 42.3 + - + +
500A PHE* 5.2 1.6 - - + -
649A PHE* 3.9 46.9 - - + +
652A LEU* 6.1 3.1 - - + -
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Residues in contact with GLY 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A PHE 2.8 16.5 + - - -
348A LEU* 3.4 3.3 + - - -
350A ALA* 1.3 72.9 - - - +
352A LEU* 1.3 56.2 + - - +
354A LEU* 3.6 2.2 - - - +
355A ALA 2.8 23.0 + - - -
430A TRP* 4.6 3.4 - - - -
434A MET* 3.2 18.9 - - - +
455A PHE* 5.7 0.2 - - - -
500A PHE* 3.6 31.0 - - - -
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A SER* 5.7 0.5 - - - -
280A LEU* 3.8 26.1 - - + +
283A TYR* 4.5 11.9 - - + +
348A LEU 2.8 16.9 + - - +
349A THR 3.7 0.4 - - - -
351A GLY* 1.3 70.3 - - - -
353A PHE* 1.3 56.6 + - - +
355A ALA* 3.8 11.7 - - + +
356A PRO* 3.5 16.6 - - - +
367A GLN* 5.1 2.0 - - - +
371A VAL* 4.4 11.2 - - + -
374A LEU* 3.8 21.8 - - + -
430A TRP* 3.5 28.5 - - + +
433A LEU* 4.1 29.2 - - + +
434A MET* 3.9 23.6 - - - +
437A CYS* 5.0 3.6 - - - -
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Residues in contact with PHE 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A GLN* 3.3 43.7 - - + -
280A LEU* 4.0 13.5 - - + -
349A THR* 2.8 25.6 + - - +
350A ALA* 3.9 6.3 - - + +
351A GLY 3.3 0.4 - - - -
352A LEU* 1.3 75.1 - - - +
354A LEU* 1.3 76.8 + - + +
355A ALA 3.3 0.4 - - - -
356A PRO* 3.2 14.5 - - - +
357A ILE* 4.9 7.0 - - + +
649A PHE 5.9 0.2 - - - -
652A LEU* 3.7 32.3 - - + -
654A ALA 6.0 0.2 - - - -
656A TYR* 4.1 33.9 - + + -
657A LEU* 4.3 7.9 - - + -
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ALA* 2.8 27.5 + - + +
351A GLY* 3.6 2.9 - - - +
353A PHE* 1.3 83.4 - - + +
355A ALA* 1.3 64.1 + - - +
356A PRO* 3.4 1.6 - - - -
357A ILE* 3.3 36.7 + - + +
358A VAL* 3.3 14.7 + - - +
434A MET* 5.1 0.7 - - - -
455A PHE* 5.3 7.2 - - + -
504A ALA* 4.2 22.0 - - + -
507A PHE* 4.2 9.2 - - + -
508A VAL* 3.4 33.9 - - + -
649A PHE* 6.1 3.6 - - + -
652A LEU* 4.0 22.9 - - + -
656A TYR* 5.4 3.4 - - + -
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Residues in contact with ALA 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A GLY 2.8 17.2 + - - +
352A LEU* 3.8 11.9 - - + +
354A LEU* 1.3 75.4 - - - +
356A PRO* 1.4 63.3 - - + +
357A ILE 3.1 0.2 - - - -
358A VAL* 2.8 33.7 + - - +
359A ASN* 3.7 1.2 - - - +
434A MET* 3.6 21.1 - - + -
437A CYS* 3.6 33.9 - - + +
438A THR* 5.8 0.2 - - - -
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Residues in contact with PRO 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER* 4.6 26.0 - - - +
277A GLN* 5.6 6.7 - - + -
352A LEU 3.5 11.7 - - - +
353A PHE* 3.2 19.7 - - - +
354A LEU 3.5 0.9 - - - -
355A ALA* 1.4 92.4 - - + +
357A ILE* 1.3 58.3 + - + +
358A VAL 3.4 0.2 - - - -
359A ASN* 3.4 10.3 - - - +
360A GLY 3.7 0.5 - - - -
361A GLY* 2.8 36.0 + - - +
437A CYS* 5.5 5.2 - - + -
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Residues in contact with ILE 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A VAL* 5.7 8.5 - - + -
353A PHE* 4.9 6.1 - - + +
354A LEU* 3.3 37.6 + - + +
355A ALA 3.1 1.4 - - - -
356A PRO* 1.3 79.0 - - + +
358A VAL* 1.3 64.7 + - - +
359A ASN 3.6 0.2 - - - -
360A GLY* 3.6 10.2 + - - +
507A PHE* 3.7 9.8 - - + -
508A VAL* 5.9 1.3 - - + -
511A ASN* 3.2 34.9 + - + +
656A TYR* 5.3 12.1 - - + -
----------------------------------------------------------
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LEU 3.3 17.9 - - - +
355A ALA* 2.8 16.2 + - - +
357A ILE* 1.3 79.8 - - - +
359A ASN* 1.3 60.0 + - - +
438A THR* 3.4 28.9 - - + -
441A ALA* 3.5 24.4 - - + +
444A GLU* 4.2 8.0 - - - +
452A LEU* 3.6 19.8 - - + +
455A PHE* 3.8 27.4 - - + -
456A VAL* 5.3 0.7 - - + -
507A PHE* 3.6 18.9 - - + -
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Residues in contact with ASN 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ALA 4.2 1.6 - - - -
356A PRO* 3.4 12.9 - - - +
358A VAL* 1.3 77.8 - - - +
360A GLY* 1.3 68.4 + - - +
361A GLY 3.1 11.5 + - - -
362A LYS* 2.6 42.3 + - + +
436A ARG 4.2 1.4 + - - -
437A CYS* 3.1 40.6 + - - +
440A SER* 3.5 39.1 + - - +
441A ALA 4.4 2.9 - - - +
444A GLU* 3.8 7.0 - - - +
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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