Contacts of the helix formed by residues 355 - 379 (chain A) in PDB entry 5BUK
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 PHE 355 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A MET* 3.3 30.3 - - + -
305A CYS* 4.1 22.0 - - + -
306A GLY 3.6 18.6 - - - -
309A PHE 4.3 1.1 - - - -
310A LEU* 3.8 18.8 - - + -
340A ASP* 3.2 19.1 - - + +
341A ILE* 3.3 21.3 - - + -
344A ALA* 4.2 9.2 - - + -
350A TYR* 3.4 29.2 - + + -
351A SER 3.7 4.3 - - - -
352A LYS* 2.9 15.7 + - - +
354A ARG* 1.3 91.7 - - + +
356A ASP* 1.3 63.7 + - - +
357A THR 3.2 2.7 - - - -
358A TYR* 3.2 4.3 + - + -
359A GLU* 2.9 24.6 + - - +
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Residues in contact with ASP 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LYS* 4.0 10.2 + - - +
353A LYS* 3.1 36.5 + - - +
354A ARG 3.5 0.8 - - - -
355A PHE* 1.3 77.8 - - - +
357A THR* 1.3 62.0 + - - +
359A GLU* 3.4 17.3 + - - +
360A SER* 3.0 29.8 + - - +
357B THR* 4.8 16.3 + - - +
364B ARG* 6.4 0.4 - - - +
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Residues in contact with THR 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ILE* 5.1 4.7 - - + -
340A ASP* 3.7 16.9 + - - +
354A ARG 5.1 0.4 + - - -
355A PHE 3.2 0.6 - - - -
356A ASP* 1.3 77.3 - - - +
358A TYR* 1.3 67.4 + - - +
360A SER* 3.3 5.3 + - - -
361A MET* 2.9 45.7 + - + +
364B ARG* 3.1 31.3 + - - +
406B ASP* 3.2 23.1 + - + +
407B ASP* 5.3 2.0 - - - +
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Residues in contact with TYR 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A VAL* 4.4 9.2 - - + -
305A CYS* 5.2 1.6 - - + -
310A LEU* 4.1 28.3 - - + -
311A MET 2.6 29.9 + - - -
312A VAL* 3.5 11.3 - - - -
333A SER* 3.4 31.4 - - - -
336A ILE* 3.8 15.7 - - + -
337A ALA* 3.5 28.0 - - + -
340A ASP* 2.8 28.7 + - + +
355A PHE* 3.2 8.5 + - + +
357A THR* 1.3 73.4 - - - +
359A GLU* 1.3 60.3 + - - +
361A MET* 3.9 0.2 - - - -
362A LEU* 2.9 60.6 + - + +
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Residues in contact with GLU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LYS* 5.8 1.7 - - - +
304A VAL* 4.1 26.9 + - + +
305A CYS* 3.7 12.8 - - - -
352A LYS* 3.0 35.7 + - - -
355A PHE 2.9 16.8 + - - +
356A ASP* 3.6 13.4 - - - +
358A TYR* 1.3 78.5 - - - +
360A SER* 1.3 62.7 + - - +
362A LEU* 4.0 2.0 - - - +
363A ARG* 3.1 45.8 + - - +
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Residues in contact with SER 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ASP* 3.0 19.6 + - - +
357A THR* 3.8 5.6 - - - -
359A GLU* 1.3 78.4 + - - +
361A MET* 1.3 63.0 + - - +
363A ARG* 3.4 21.5 + - - +
364A ARG* 2.9 29.7 + - - +
408A GLU* 5.0 1.2 - - - +
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Residues in contact with MET 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ILE* 4.0 25.1 - - + -
357A THR* 2.9 32.4 + - + +
358A TYR 4.0 1.8 - - - +
360A SER* 1.3 75.1 - - - +
362A LEU* 1.3 60.8 + - - +
364A ARG* 3.5 42.6 - - - +
365A GLY* 2.9 27.2 + - - -
405A TYR* 3.9 22.9 - - + +
398B LYS* 5.6 1.8 - - - +
406B ASP* 3.5 39.5 - - + +
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Residues in contact with LEU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A VAL* 4.2 18.4 - - + -
313A GLY 5.8 0.9 - - - +
316A ALA* 3.8 24.5 - - + -
317A ARG* 5.1 6.5 + - + -
329A VAL* 4.5 7.0 - - + -
333A SER* 3.8 28.7 - - - -
358A TYR* 2.9 44.5 + - + +
359A GLU* 4.0 3.4 - - - +
361A MET* 1.3 75.1 - - - +
363A ARG* 1.3 65.6 + - - +
365A GLY* 5.3 0.2 - - - -
366A VAL* 3.0 43.2 + - + +
405A TYR* 5.4 6.5 - - + -
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Residues in contact with ARG 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ARG* 5.0 4.7 - - - +
359A GLU* 3.1 45.5 + - - +
360A SER* 3.6 31.5 + - - +
362A LEU* 1.3 76.7 - - - +
364A ARG* 1.3 57.4 + - - +
367A ASN* 2.9 56.4 + - - +
408A GLU* 5.9 2.7 - - - -
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Residues in contact with ARG 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A SER* 2.9 17.5 + - - +
361A MET* 3.5 35.7 - - - +
363A ARG* 1.3 79.2 - - - +
365A GLY* 1.3 62.9 + - - +
367A ASN* 3.7 4.5 - - - +
368A ASN* 3.0 30.9 + - - +
404A VAL 4.1 0.4 - - - +
405A TYR* 2.9 35.8 + - - +
406A ASP 3.6 14.1 + - - -
407A ASP 3.6 21.1 - - - +
408A GLU* 3.1 33.2 + - - +
110B SER* 3.4 24.9 + - - -
406B ASP* 5.4 2.0 + - - -
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Residues in contact with GLY 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A MET 2.9 20.0 + - - -
364A ARG* 1.3 73.8 - - - +
366A VAL* 1.3 59.6 + - - +
368A ASN* 3.2 6.2 + - - +
369A TRP* 3.1 22.3 + - - -
404A VAL* 3.3 38.7 - - - +
405A TYR* 3.9 10.1 - - - -
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Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ARG* 3.5 42.2 - - + +
319A VAL* 3.7 23.6 - - + -
329A VAL* 4.0 32.3 - - + -
362A LEU* 3.0 30.3 + - + +
365A GLY* 1.3 74.6 - - - +
367A ASN* 1.3 60.5 + - - +
369A TRP* 3.4 6.4 + - + +
370A TYR* 2.9 27.4 + - - +
405A TYR* 5.4 3.1 - - + -
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Residues in contact with ASN 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ARG* 2.7 32.4 + - - +
363A ARG* 2.9 44.1 + - - +
364A ARG* 3.7 5.3 - - - +
366A VAL* 1.3 76.2 - - - +
368A ASN* 1.3 60.4 + - - +
370A TYR* 3.3 4.9 + - - +
371A GLU* 2.9 31.7 + - - +
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Residues in contact with ASN 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ARG* 3.0 17.1 + - - +
365A GLY 3.2 8.9 + - - +
367A ASN* 1.3 75.9 - - - +
369A TRP* 1.3 65.2 + - - +
371A GLU* 4.6 0.7 - - - -
372A PHE* 3.0 24.3 + - - +
399A MET* 4.8 1.8 - - - -
404A VAL* 2.9 33.5 + - + +
407A ASP 2.8 25.5 + - - -
408A GLU 3.8 8.1 - - - +
410A PRO* 3.2 30.5 - - + +
413A LEU* 3.4 17.5 - - + +
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Residues in contact with TRP 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 4.8 1.8 - - + -
319A VAL* 4.3 14.8 - - + -
323A PHE* 3.5 45.8 - + + -
325A SER* 3.5 26.7 - - - -
328A SER* 4.1 8.0 + - - -
329A VAL* 3.5 29.9 - - + +
365A GLY 3.1 22.0 + - - -
366A VAL* 3.6 13.2 - - + +
368A ASN* 1.3 75.9 - - - +
370A TYR* 1.3 58.6 + - - +
372A PHE* 3.3 12.5 + + - +
373A ILE* 2.8 37.0 + - + +
399A MET 3.2 24.5 - - - -
400A LEU* 4.7 4.5 - - - -
402A GLY* 3.5 25.1 + - - -
404A VAL* 3.6 20.2 - - + +
405A TYR* 4.3 2.0 + - - -
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Residues in contact with TYR 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ASP* 2.6 33.3 + - - -
195A PRO* 5.7 0.3 - - - +
197A PHE* 3.4 27.8 - + - -
298A SER* 4.9 6.1 - - - -
317A ARG* 3.4 25.1 - - - +
319A VAL* 4.0 20.0 - - + -
366A VAL 2.9 17.7 + - - +
367A ASN* 3.6 4.9 - - - +
369A TRP* 1.3 76.4 - - - +
371A GLU* 1.3 55.7 + - - +
373A ILE* 3.4 7.9 + - + +
374A SER* 2.7 50.5 + - - -
440A ALA* 4.5 16.9 + - + -
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Residues in contact with GLU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ASN 2.9 16.9 + - - +
368A ASN* 3.8 3.1 - - - +
370A TYR* 1.3 78.1 - - + +
372A PHE* 1.3 66.1 + - - +
374A SER* 3.2 11.7 + - - -
375A ILE* 3.0 37.9 + - + +
413A LEU* 3.8 25.8 - - + +
417A ARG* 3.2 43.6 + - - +
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Residues in contact with PHE 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A PHE* 3.6 17.9 - + + -
368A ASN 3.0 18.9 + - - +
369A TRP* 3.4 13.5 - + - +
371A GLU* 1.3 79.2 - - - +
373A ILE* 1.3 62.2 + - - +
375A ILE* 3.3 4.8 + - + +
376A TYR* 3.0 20.7 + - - +
383A PHE* 3.8 29.6 - + - -
396A VAL* 3.9 17.3 - - + -
399A MET* 3.5 28.5 - - + -
400A LEU* 3.4 34.3 - - + -
413A LEU* 3.9 20.9 - - + -
416A MET* 3.9 20.9 - - + -
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Residues in contact with ILE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 4.1 12.3 - - + -
319A VAL* 3.6 31.4 - - + -
320A ASP* 3.0 36.8 - - + +
322A ILE* 4.0 8.5 - - + -
323A PHE* 3.7 24.9 - - + -
325A SER* 5.0 2.7 - - - +
369A TRP* 2.8 24.1 + - + +
370A TYR* 3.7 6.3 - - + +
372A PHE* 1.3 76.6 - - - +
374A SER* 1.3 61.3 + - - +
376A TYR* 3.2 4.0 + - - +
377A TYR* 3.1 44.0 + - + -
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Residues in contact with SER 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 4.1 17.4 - - - -
370A TYR* 2.7 46.8 + - - -
371A GLU* 3.2 14.7 + - - -
373A ILE* 1.3 74.3 - - - +
375A ILE* 1.3 53.2 + - - +
377A TYR* 3.3 3.5 + - - +
378A ARG* 2.7 38.3 + - - +
438A LEU* 4.7 1.6 - - - +
440A ALA* 4.8 14.4 + - - +
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Residues in contact with ILE 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A GLU* 3.0 37.8 + - + +
372A PHE* 3.6 7.6 - - + +
374A SER* 1.3 74.8 - - - +
376A TYR* 1.3 65.8 + - - +
378A ARG* 4.3 4.9 - - - +
379A LEU 2.9 30.7 + - - +
382A LEU* 4.4 6.3 - - + -
383A PHE* 5.0 4.0 - - + +
413A LEU* 4.1 15.3 - - + +
416A MET* 3.8 49.4 - - + -
417A ARG* 4.2 7.4 - - + +
420A VAL* 4.2 23.3 - - + -
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Residues in contact with TYR 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TRP* 4.0 23.3 - + + +
78A THR 5.1 0.3 + - - -
226A ILE* 3.9 19.1 + - - +
228A PHE* 3.4 42.7 - + + +
235A TRP* 4.6 1.7 - + - +
322A ILE* 3.3 39.3 - - + -
323A PHE* 3.9 10.8 - + + -
372A PHE* 3.0 12.1 + - - +
373A ILE 3.2 8.7 + - - +
375A ILE* 1.3 76.0 - - - +
377A TYR* 1.3 71.2 + + - +
380A ASN* 3.0 56.4 - - - +
383A PHE* 3.9 32.5 - + + +
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Residues in contact with TYR 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 3.6 20.2 - + - -
199A GLN* 3.7 13.2 + - - +
228A PHE* 4.1 24.4 - + - -
233A ASP* 3.8 34.4 + - + +
235A TRP* 3.2 19.7 - + - -
320A ASP* 2.5 29.7 + - - -
322A ILE* 4.4 2.7 - - + -
373A ILE* 3.1 28.2 + - + -
374A SER 3.8 5.8 - - - +
376A TYR* 1.3 94.2 - + - +
378A ARG* 1.3 62.5 + - - +
379A LEU 3.6 0.2 + - - -
380A ASN* 4.5 3.8 + - - +
436A GLY* 3.7 15.8 - - - -
438A LEU* 3.7 37.8 + - + -
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Residues in contact with ARG 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A SER* 2.7 23.5 + - - +
375A ILE* 4.2 3.8 - - - +
377A TYR* 1.3 75.8 - - - +
379A LEU* 1.3 56.0 + - - +
420A VAL* 3.8 23.8 - - + -
424A GLU* 2.7 40.0 + - - +
435A LEU* 3.2 25.1 - - + +
436A GLY 2.7 47.0 + - - +
437A SER* 4.7 3.4 - - - +
438A LEU 4.0 10.1 - - - +
439A LYS* 3.8 34.9 - - + +
440A ALA 6.0 0.7 - - - +
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE* 2.9 17.7 + - - +
378A ARG* 1.3 74.8 - - - +
380A ASN* 1.3 65.6 + - - +
381A ILE* 3.2 18.8 - - + -
382A LEU* 3.0 43.5 + - + +
383A PHE 3.5 3.3 + - - -
419A ILE* 4.8 0.9 - - + -
420A VAL* 4.3 19.1 - - + -
423A VAL* 4.2 28.0 - - + -
431A TRP* 4.1 18.8 - - + +
434A PHE 3.8 26.5 - - - +
435A LEU* 3.8 14.8 - - + +
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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