Contacts of the helix formed by residues 360 - 396 (chain A) in PDB entry 3VEY
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 SER 360 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A HIS* 5.6 9.5 - - - -
358A ARG 4.0 0.6 + - - -
359A PRO* 1.3 76.2 - - - +
361A THR* 1.3 63.6 + - - +
362A THR* 3.4 11.3 + - - -
363A ASP* 2.9 35.5 + - - -
364A CYS* 3.2 23.9 + - - -
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Residues in contact with THR 361 (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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345A ARG* 3.4 45.7 + - - +
360A SER* 1.3 73.3 - - - +
362A THR* 1.4 71.0 + - + +
364A CYS* 3.4 3.2 + - - +
365A ASP* 3.3 28.7 + - - +
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Residues in contact with THR 362 (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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360A SER* 3.3 9.8 + - - -
361A THR* 1.4 82.9 - - + +
363A ASP* 1.4 62.3 + - - +
365A ASP* 3.4 10.4 + - - +
366A ILE* 2.9 45.3 + - - +
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Residues in contact with ASP 363 (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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314A LEU 4.7 2.3 - - - +
315A LEU* 3.5 19.0 - - + +
316A PHE* 3.1 39.3 + - + -
317A HIS* 4.8 6.2 + - - -
358A ARG 4.4 1.7 - - - +
359A PRO* 3.5 16.3 - - + +
360A SER* 2.9 44.7 + - - +
362A THR* 1.4 76.3 + - - +
364A CYS* 1.4 56.4 + - - +
366A ILE* 3.4 4.2 + - - +
367A VAL* 3.0 35.5 + - - +
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Residues in contact with CYS 364 (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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345A ARG* 3.9 28.3 - - + -
348A ILE* 3.7 33.0 - - + +
349A TYR* 4.1 16.6 - - - -
352A LEU* 4.7 0.9 - - - -
359A PRO* 4.0 21.8 - - - -
360A SER 3.2 15.6 + - - -
361A THR* 3.5 9.0 - - - +
363A ASP* 1.4 78.5 - - - +
365A ASP* 1.3 56.4 + - - +
367A VAL* 3.3 5.1 + - - +
368A ARG* 3.0 26.7 + - - +
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Residues in contact with ASP 365 (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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345A ARG* 2.7 45.3 + - - +
348A ILE* 5.5 1.3 - - - +
361A THR* 3.3 13.6 + - - +
362A THR* 3.4 13.4 + - - +
364A CYS* 1.3 73.5 - - - +
366A ILE* 1.4 56.8 + - + +
368A ARG* 3.3 9.7 + - - +
369A ARG* 3.0 33.7 + - + +
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Residues in contact with ILE 366 (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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16A VAL* 4.0 29.4 - - + -
20A LEU* 4.7 0.4 - - + +
309A LEU* 3.8 21.8 - - + -
314A LEU 3.5 22.4 - - - +
315A LEU* 3.7 22.7 - - + -
362A THR* 2.9 34.3 + - - +
363A ASP* 3.7 9.2 - - - +
365A ASP* 1.4 72.3 - - + +
367A VAL* 1.4 54.2 + - - +
369A ARG* 3.2 9.2 + - - +
370A ALA* 2.8 32.6 + - - +
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Residues in contact with VAL 367 (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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306A LEU* 3.9 28.0 - - + -
315A LEU* 4.3 2.9 - - + -
316A PHE* 3.9 15.9 - - + -
330A PHE* 4.3 12.8 - - + -
338A VAL* 4.2 15.3 - - + -
348A ILE* 4.2 14.1 - - + -
352A LEU* 3.8 28.7 - - + -
363A ASP 3.0 21.2 + - - +
364A CYS 3.3 4.7 + - - +
366A ILE* 1.4 74.0 - - - +
368A ARG* 1.4 56.4 + - - +
370A ALA* 3.4 1.9 + - - +
371A CYS* 2.9 29.8 + - - -
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Residues in contact with ARG 368 (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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338A VAL* 3.5 26.7 + - + +
339A GLU* 3.1 37.2 + - - +
341A ASP* 3.0 28.3 + - - +
348A ILE* 3.7 11.7 - - + -
364A CYS 3.0 14.5 + - - +
365A ASP* 3.3 13.0 - - - +
366A ILE 3.3 0.2 - - - -
367A VAL* 1.4 74.3 - - - +
369A ARG* 1.3 58.3 + - + +
371A CYS* 3.1 4.7 + - - +
372A GLU* 2.7 74.0 + - - +
422A ARG* 5.4 2.2 - - - +
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Residues in contact with ARG 369 (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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16A VAL* 5.5 0.7 - - + -
17A GLU* 3.0 38.4 + - - +
20A LEU* 3.6 18.8 - - + +
365A ASP* 3.0 20.8 + - + +
366A ILE* 3.2 11.0 + - - +
368A ARG* 1.3 73.6 - - + +
370A ALA* 1.4 56.9 + - - +
372A GLU* 2.9 33.6 + - - +
373A SER* 2.9 47.5 + - - +
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Residues in contact with ALA 370 (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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20A LEU* 3.8 15.8 - - + +
302A VAL* 4.6 6.3 - - + -
305A VAL* 4.1 18.4 - - + -
306A LEU* 3.7 24.7 - - + -
309A LEU* 4.8 2.5 - - + -
366A ILE 2.8 19.4 + - - +
367A VAL 3.6 5.4 - - - +
369A ARG* 1.4 71.2 - - - +
371A CYS* 1.4 61.7 + - - +
373A SER* 3.6 2.1 + - - -
374A VAL* 3.3 29.8 + - - +
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Residues in contact with CYS 371 (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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302A VAL* 3.8 26.9 - - - -
330A PHE* 4.1 7.9 - - - -
335A VAL* 3.9 21.8 - - + +
338A VAL* 3.6 28.9 - - + -
339A GLU* 3.2 21.0 - - + +
367A VAL 2.9 17.9 + - - +
368A ARG 3.1 8.0 + - - +
370A ALA* 1.4 73.5 - - - +
372A GLU* 1.3 59.5 + - - +
374A VAL* 3.4 3.1 + - - +
375A SER* 3.0 25.3 + - - -
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Residues in contact with GLU 372 (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 GLU* 3.6 24.7 - - - +
368A ARG* 2.7 52.9 + - - +
369A ARG* 2.9 39.4 + - - +
371A CYS* 1.3 72.8 - - - +
373A SER* 1.3 59.4 + - - +
375A SER* 3.8 1.1 - - - -
376A THR* 2.7 38.1 + - - +
422A ARG* 4.1 13.1 + - - +
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Residues in contact with SER 373 (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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20A LEU* 3.6 31.1 + - - +
23A PHE* 3.8 28.2 - - - +
369A ARG* 2.9 30.9 + - - +
370A ALA 3.7 5.6 - - - -
372A GLU* 1.3 76.9 - - - +
374A VAL* 1.3 60.9 + - - +
376A THR* 4.2 2.8 - - - -
377A ARG* 3.3 24.1 + - - +
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Residues in contact with VAL 374 (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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23A PHE* 3.8 33.2 - - + -
292A LEU 4.8 2.3 - - - +
298A MET* 3.8 35.7 - - + +
301A LEU* 3.9 19.7 - - + -
302A VAL* 3.8 27.8 - - + +
305A VAL* 4.3 4.7 - - + -
370A ALA 3.3 15.9 + - - +
371A CYS 4.0 0.4 - - - +
373A SER* 1.3 74.4 - - - +
375A SER* 1.3 59.8 + - - +
377A ARG* 3.5 5.2 + - - +
378A ALA* 3.1 25.3 + - - +
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Residues in contact with SER 375 (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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298A MET* 4.2 17.9 - - - -
335A VAL* 4.4 0.7 - - - -
339A GLU* 2.7 27.7 + - - -
371A CYS 3.0 10.2 + - - -
372A GLU 3.6 0.7 + - - -
374A VAL* 1.3 75.1 - - - +
376A THR* 1.4 59.3 + - - +
378A ALA* 3.4 6.7 + - - +
379A ALA* 3.0 28.6 + - - +
416A HIS* 3.5 17.4 - - - -
419A PHE* 3.9 6.2 - - - -
422A ARG* 3.1 20.0 + - - -
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Residues in contact with THR 376 (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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372A GLU* 2.7 26.0 + - - +
373A SER* 4.2 4.0 - - - -
375A SER* 1.4 72.3 + - - +
377A ARG* 1.4 60.7 + - - +
379A ALA* 3.3 6.2 + - - +
380A HIS* 3.0 58.2 + - + +
422A ARG* 3.0 32.5 + - + +
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Residues in contact with ARG 377 (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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22A GLU 5.7 0.2 - - - -
23A PHE* 3.5 49.6 - - + +
25A LEU* 3.7 18.6 - - + -
269A PHE 4.2 10.1 + - - -
271A LEU* 3.8 14.9 - - - +
274A ASP* 2.7 43.8 + - - -
292A LEU* 3.5 27.3 + - - +
301A LEU* 3.6 20.0 - - - +
373A SER 3.3 17.4 + - - +
374A VAL* 3.8 6.1 + - - +
375A SER 3.4 0.2 - - - -
376A THR* 1.4 76.7 - - - +
378A ALA* 1.3 52.8 + - - +
380A HIS* 3.4 5.0 + - - +
381A MET* 2.8 46.7 + - + +
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Residues in contact with ALA 378 (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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292A LEU 3.4 24.4 + - - +
293A ILE* 3.6 13.3 - - - +
298A MET* 3.7 24.9 - - + -
374A VAL 3.1 13.0 + - - +
375A SER 3.5 8.5 - - - +
377A ARG* 1.3 76.9 - - - +
379A ALA* 1.4 56.9 + - - +
381A MET* 3.5 0.4 + - - -
382A CYS* 2.9 32.4 + - - +
419A PHE* 3.8 7.6 - - + -
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Residues in contact with ALA 379 (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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375A SER 3.0 16.7 + - - +
376A THR* 3.6 5.6 - - - +
378A ALA* 1.4 74.9 - - - +
380A HIS* 1.3 57.4 + - - +
383A SER* 3.0 28.6 + - - -
419A PHE* 3.4 43.4 - - + +
422A ARG* 4.1 17.9 - - + -
423A PHE* 3.5 12.6 - - + +
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Residues in contact with HIS 380 (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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25A LEU* 4.4 23.8 + - + +
30A LEU* 3.4 29.8 - - + +
376A THR* 3.0 41.3 + - + +
377A ARG* 3.9 4.2 - - - +
379A ALA* 1.3 76.0 - - + +
381A MET* 1.4 63.5 + - - +
383A SER* 2.6 22.3 + - - -
384A ALA 3.3 5.7 + - - -
422A ARG* 4.3 14.0 + - + +
426A SER* 3.9 22.0 - - - -
429A ARG* 4.5 11.0 + - - -
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Residues in contact with MET 381 (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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25A LEU* 3.8 26.2 - - + -
30A LEU* 4.3 2.9 - - - +
33A VAL* 4.0 27.6 - - + -
266A LEU* 4.1 12.6 - - + -
269A PHE* 3.7 35.2 - - + +
289A TYR* 2.7 30.1 + - + -
292A LEU* 4.1 25.6 - - + -
293A ILE* 4.2 14.8 - - + -
377A ARG* 2.8 32.4 + - + +
378A ALA* 3.9 2.9 - - - +
380A HIS* 1.4 71.9 - - - +
382A CYS* 1.3 55.3 + - - +
384A ALA* 3.4 12.2 + - - +
385A GLY 3.6 1.9 + - - -
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Residues in contact with CYS 382 (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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224A MET* 4.0 15.5 - - - -
226A VAL* 4.0 10.8 - - - -
230A CYS* 3.8 26.9 - - - -
257A TRP* 4.2 4.1 - - - -
289A TYR* 3.4 8.5 + - - -
293A ILE* 3.9 12.2 - - + +
378A ALA 2.9 20.1 + - - +
379A ALA 3.7 4.9 - - - +
381A MET* 1.3 76.4 - - - +
383A SER* 1.3 60.9 + - - +
385A GLY 3.2 10.4 + - - -
386A LEU* 3.2 10.7 + - - +
419A PHE* 4.3 3.8 - - + -
423A PHE* 3.6 20.9 - - + -
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Residues in contact with SER 383 (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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379A ALA 3.0 15.5 + - - -
380A HIS 2.6 17.2 + - - -
382A CYS* 1.3 76.2 - - - +
384A ALA* 1.3 56.1 + - - +
386A LEU 3.5 0.3 + - - -
387A ALA* 2.9 30.8 + - - +
423A PHE* 3.5 12.8 - - - -
426A SER* 2.6 34.0 + - - -
427A VAL* 3.6 23.5 - - - +
430A LEU* 3.8 5.9 - - - +
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Residues in contact with ALA 384 (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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30A LEU* 3.5 31.0 - - + +
33A VAL* 3.8 20.4 - - + -
34A MET* 3.5 19.0 - - - +
37A MET* 4.9 0.2 - - - +
380A HIS 3.3 7.9 + - - +
381A MET 3.6 10.5 - - - +
382A CYS 3.3 0.4 - - - -
383A SER* 1.3 76.7 + - - +
385A GLY* 1.3 59.5 + - - +
387A ALA* 4.4 0.2 - - - -
388A GLY* 3.1 20.6 + - - -
430A LEU* 3.9 11.0 - - + -
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Residues in contact with GLY 385 (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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33A VAL* 5.3 0.2 - - - +
37A MET* 3.9 21.2 - - - +
257A TRP* 3.2 19.4 - - - -
289A TYR* 3.3 21.2 + - - -
382A CYS 3.2 3.4 + - - -
384A ALA* 1.3 76.4 - - - +
386A LEU* 1.4 63.7 + - - +
388A GLY* 3.1 10.9 + - - -
389A VAL* 3.1 12.1 + - - +
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Residues in contact with LEU 386 (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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222A VAL* 3.8 28.0 - - + -
224A MET* 4.0 10.3 - - + -
257A TRP* 3.4 13.8 - - + -
382A CYS 3.2 7.2 + - - +
383A SER 4.0 4.7 - - - +
385A GLY* 1.4 72.9 - - - +
387A ALA* 1.4 58.9 + - - +
389A VAL* 3.3 7.4 + - + -
390A ILE* 2.9 54.0 + - + +
406A VAL* 4.2 8.1 - - + -
423A PHE* 3.6 26.0 - - + -
427A VAL* 3.9 8.1 - - + -
438A PHE* 3.6 31.0 - - + -
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Residues in contact with ALA 387 (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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34A MET* 3.7 10.3 - - - -
383A SER 2.9 19.7 + - - +
384A ALA 3.8 3.1 - - - +
386A LEU* 1.4 75.7 - - - +
388A GLY* 1.3 58.2 + - - +
391A ASN* 2.9 38.1 + - - -
427A VAL* 4.4 4.6 - - + +
430A LEU* 3.5 31.2 - - + -
431A THR* 3.6 19.1 - - + -
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Residues in contact with GLY 388 (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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34A MET* 3.7 13.2 - - - +
37A MET* 5.1 3.1 - - - -
38A GLN* 3.4 26.6 + - - +
41A MET* 4.5 4.0 - - - -
384A ALA 3.1 8.4 + - - -
385A GLY* 3.1 8.5 + - - -
387A ALA* 1.3 75.4 - - - +
389A VAL* 1.3 57.3 + - - +
392A ARG* 3.0 31.6 + - - +
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Residues in contact with VAL 389 (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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41A MET* 3.6 30.2 - - + +
222A VAL* 4.4 15.9 - - + -
232A ALA* 4.9 2.7 - - + -
233A CYS 5.2 0.4 - - - +
234A TYR* 3.8 34.0 - - + -
255A THR* 4.4 8.5 - - + -
257A TRP* 3.7 21.3 - - + -
385A GLY 3.1 13.6 + - - +
386A LEU* 3.6 9.6 - - + +
388A GLY* 1.3 74.5 - - - +
390A ILE* 1.4 57.5 - - - +
392A ARG* 3.3 4.2 + - - +
393A MET* 3.0 37.8 + - - +
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Residues in contact with ILE 390 (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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222A VAL* 4.8 7.4 - - + -
386A LEU* 2.9 49.6 + - + +
387A ALA 4.1 2.5 - - - +
389A VAL* 1.4 72.2 - - - +
391A ASN* 1.4 59.7 + - - +
393A MET* 3.2 7.2 + - - +
394A ARG* 2.9 23.7 + - - +
402A MET* 3.5 23.7 - - + +
404A ILE* 4.3 12.6 - - + -
406A VAL* 4.1 11.9 - - + -
427A VAL* 4.2 3.8 - - + -
431A THR* 3.9 10.8 - - + -
434A CYS* 3.7 21.1 - - + -
436A ILE* 3.8 26.2 - - + -
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Residues in contact with ASN 391 (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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34A MET* 3.3 19.4 - - - +
38A GLN* 3.6 16.4 - - - +
387A ALA 2.9 24.6 + - - +
390A ILE* 1.4 69.0 - - - +
392A ARG* 1.3 63.1 + - - +
394A ARG* 3.3 9.0 - - + +
395A GLU* 3.1 23.7 + - - +
430A LEU 3.0 24.0 + - - -
431A THR* 3.5 21.8 - - - +
432A PRO* 4.8 4.2 - - - +
434A CYS* 4.0 9.0 - - - -
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Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLN* 3.7 16.6 + - + +
41A MET* 3.6 30.1 - - + -
42A ASP* 3.7 39.6 + - - +
45A LEU* 3.5 16.6 - - - +
234A TYR* 3.9 5.0 + - - -
236A GLU* 3.0 33.4 + - - -
240A ASN* 3.8 17.6 - - - +
388A GLY 3.0 20.2 + - - +
389A VAL* 3.4 6.3 - - - +
391A ASN* 1.3 76.1 - - - +
393A MET* 1.4 59.1 + - - +
395A GLU* 3.4 15.2 + - - +
396A SER* 2.9 32.0 + - - -
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Residues in contact with MET 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLU* 4.0 25.6 - - + +
222A VAL* 3.7 22.2 - - - -
234A TYR* 3.8 28.9 - - + -
235A MET 3.7 20.6 - - - +
389A VAL* 3.0 20.2 + - - +
390A ILE* 3.2 9.8 + - - +
392A ARG* 1.4 73.1 - - - +
394A ARG* 1.4 62.3 + - - +
396A SER* 3.4 23.0 + - - +
397A ARG* 3.8 16.8 - - - +
402A MET* 3.9 11.0 - - + -
404A ILE* 3.5 24.7 - - + -
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Residues in contact with ARG 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ILE 2.9 13.2 + - - +
391A ASN* 3.3 16.1 + - + +
393A MET* 1.4 75.2 - - - +
395A GLU* 1.4 63.0 + - - +
397A ARG* 3.0 34.9 + - - +
399A GLU* 2.8 30.9 + - - +
400A ASP 2.6 33.7 + - - -
401A VAL* 3.4 1.4 - - - +
402A MET* 3.8 20.1 - - + +
432A PRO 5.2 0.9 - - - +
433A SER* 3.2 34.8 + - - -
434A CYS* 3.6 22.7 - - - -
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Residues in contact with GLU 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ASN 3.1 9.0 + - - +
392A ARG* 3.5 17.4 + - - +
394A ARG* 1.4 79.7 - - - +
396A SER* 1.3 57.4 + - - +
397A ARG 3.2 8.3 + - - +
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Residues in contact with SER 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLU* 4.7 3.9 + - - -
237A GLU* 4.3 28.3 - - - +
240A ASN* 4.3 14.4 + - - -
392A ARG* 2.9 24.8 + - - -
393A MET* 3.4 7.9 + - - +
394A ARG 3.3 1.2 - - - -
395A GLU* 1.3 76.2 + - - +
397A ARG* 1.4 67.0 + - - +
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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