Contacts of the helix formed by residues 369 - 395 (chain A) in PDB entry 1JQO
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 GLU 369 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A SER* 4.9 8.9 - - - +
332A MET 3.8 10.5 - - - +
361A PHE* 5.3 0.7 - - - -
365A ILE* 3.8 4.5 - - - +
366A PRO* 3.2 33.3 + - + +
367A PRO 3.0 0.6 - - - -
368A ASN* 1.3 89.5 - - + +
370A PRO* 1.3 67.2 - - - +
371A TYR 3.4 2.0 - - - -
372A ARG* 3.0 57.0 + - + +
373A VAL* 3.2 14.4 + - - +
183B ARG* 3.3 26.2 + - - -
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Residues in contact with PRO 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A MET 3.5 12.8 - - - +
333A TRP* 3.4 22.0 - - - +
335A CYS* 3.5 15.9 - - + -
339A LEU* 3.2 27.6 - - + -
340A ARG* 4.1 5.6 - - - +
343A ALA* 4.1 7.9 - - + +
367A PRO 3.6 11.1 - - - +
368A ASN 3.1 13.5 - - - +
369A GLU* 1.3 83.7 - - - +
371A TYR* 1.3 60.4 + - + +
373A VAL* 3.0 28.9 - - + +
374A ILE* 3.4 10.4 + - - +
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Residues in contact with TYR 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 3.7 33.0 - - + +
332A MET* 3.7 37.4 - - + +
333A TRP 4.5 0.2 - - - -
334A ARG 2.9 21.1 + - - -
335A CYS* 3.6 13.0 - - + -
339A LEU* 3.7 15.0 - - + -
369A GLU 3.2 0.4 + - - -
370A PRO* 1.3 69.9 - - + +
372A ARG* 1.3 62.9 + - - +
373A VAL 2.9 5.6 + - - -
374A ILE* 3.2 7.9 + - - +
375A LEU* 2.8 32.9 + - + +
419A CYS* 3.9 17.3 - - + -
422A SER* 2.9 29.2 + - - -
423A LEU* 3.2 38.7 + - + +
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Residues in contact with ARG 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A MET* 3.3 27.8 + - + +
328A PHE* 3.6 20.6 + - - +
330A LEU 3.9 9.6 + - - +
331A SER* 3.5 19.2 - - - -
361A PHE* 3.3 33.4 - - + -
365A ILE* 3.1 29.1 - - + +
369A GLU* 3.0 48.4 + - + +
371A TYR* 1.3 77.5 - - - +
373A VAL* 1.3 56.2 + - - +
375A LEU* 4.3 7.2 - - - -
376A GLY 3.0 21.0 + - - -
183B ARG* 4.7 0.2 - - - +
185B SER* 2.8 36.9 + - - +
1071B SO4 4.0 7.7 + - - -
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Residues in contact with VAL 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ALA* 3.7 30.7 - - + +
346A LEU* 4.2 13.6 - - + +
347A HIS* 4.8 7.4 - - + +
365A ILE* 4.3 15.6 - - + +
366A PRO 3.6 20.4 - - - +
367A PRO* 3.9 13.9 - - + -
369A GLU 3.3 16.4 - - - +
370A PRO* 3.0 12.1 - - + +
371A TYR 2.9 1.0 - - - -
372A ARG* 1.3 75.1 - - - +
374A ILE* 1.3 66.5 + - - +
376A GLY* 3.4 1.7 + - - -
377A HIS* 3.2 20.6 + - - +
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Residues in contact with ILE 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 3.3 48.7 - - + +
342A ARG* 4.6 8.7 - - + +
343A ALA* 4.5 7.4 - - - +
346A LEU* 4.1 22.7 - - + -
370A PRO 3.8 7.0 - - - +
371A TYR* 3.2 4.8 + - - +
373A VAL* 1.3 72.2 - - - +
375A LEU* 1.3 66.5 + - + +
377A HIS* 3.1 6.3 + - + +
378A VAL* 2.9 27.2 + - + +
415A PRO* 4.0 33.4 - - + +
418A LEU* 3.9 17.3 - - + -
419A CYS* 4.6 9.6 - - - -
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ILE* 3.6 16.9 - - + +
326A LEU* 3.9 21.3 - - + +
327A MET* 3.4 46.4 - - + +
330A LEU* 3.9 30.5 - - + -
371A TYR* 2.8 22.9 + - + +
372A ARG* 4.0 1.1 - - - +
374A ILE* 1.3 78.2 - - - +
376A GLY* 1.3 64.2 + - - +
378A VAL* 3.1 9.9 + - + +
379A ARG* 2.8 18.9 + - - +
416A LEU* 4.7 14.6 - - + -
419A CYS* 4.7 14.6 - - - -
436A LEU* 5.9 0.7 - - + -
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Residues in contact with GLY 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A MET* 3.4 26.0 - - - +
365A ILE* 4.5 4.5 - - - -
372A ARG 3.0 14.5 + - - -
373A VAL 3.8 0.9 - - - -
375A LEU* 1.3 76.2 - - - +
377A HIS* 1.3 60.3 + - - +
379A ARG* 2.9 15.0 + - - +
380A ASP* 2.6 27.6 + - - +
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Residues in contact with HIS 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ARG* 4.6 12.9 + - - -
346A LEU* 3.9 39.7 - - + +
373A VAL 3.2 12.1 + - - +
374A ILE* 3.1 11.8 + - + +
376A GLY* 1.3 75.0 - - - +
378A VAL* 1.3 69.5 + - + +
380A ASP* 3.0 19.1 + - - +
381A LYS* 3.0 46.2 + - + +
406A PHE* 6.1 1.0 - + - -
415A PRO* 5.7 4.2 - - + +
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Residues in contact with VAL 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ILE* 4.5 13.9 - - + -
374A ILE* 2.9 19.0 + - + +
375A LEU* 3.3 13.2 - - + +
377A HIS* 1.3 79.5 - - + +
379A ARG* 1.3 61.3 + - - +
381A LYS* 4.7 0.4 - - - -
382A LEU* 3.1 21.2 + - + +
406A PHE* 3.4 16.6 - - + -
412A PHE* 3.3 38.1 - - + +
415A PRO* 3.7 31.9 - - + -
416A LEU* 5.1 5.8 - - + +
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Residues in contact with ARG 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ILE* 4.5 6.7 - - + -
323A ILE* 4.1 16.1 - - + +
324A GLU* 2.8 41.3 + - - +
327A MET* 4.1 17.2 - - - +
358A TYR* 3.0 27.9 - - - -
360A GLU 2.7 25.7 + - - -
361A PHE* 3.1 31.0 + - - +
365A ILE* 5.7 1.2 - - - +
375A LEU 2.8 11.9 + - - +
376A GLY* 2.9 8.7 + - - +
378A VAL* 1.3 75.1 - - - +
380A ASP* 1.3 77.7 + - - +
382A LEU* 2.8 24.1 + - - +
383A TYR* 3.0 29.7 + - + -
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Residues in contact with ASP 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A THR* 5.2 5.2 - - - +
358A TYR* 3.3 29.3 + - - +
376A GLY* 2.6 32.0 + - - +
377A HIS* 3.6 10.2 - - - +
379A ARG* 1.3 86.2 + - - +
381A LYS* 1.3 64.4 + - - +
383A TYR* 2.9 16.2 + - - +
384A ASN* 2.9 16.5 + - - +
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Residues in contact with LYS 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A HIS* 3.0 41.3 + - + +
380A ASP* 1.3 77.2 - - - +
382A LEU* 1.3 54.0 + - - +
384A ASN* 3.3 12.9 + - - +
385A THR* 2.6 30.5 + - - -
403A GLU 3.7 10.9 + - - -
404A SER* 3.1 27.2 - - - +
405A SER* 3.8 10.3 - - - -
406A PHE* 3.3 37.2 - - + -
411A GLU* 3.6 20.7 + - - +
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Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ALA* 4.3 11.2 - - + +
319A TYR* 3.8 20.2 - - + -
320A ILE* 3.8 24.7 - - + +
323A ILE* 3.7 30.3 - - + -
378A VAL 3.1 10.0 + - - +
379A ARG* 2.8 16.3 + - - +
381A LYS* 1.3 74.7 - - - +
383A TYR* 1.3 57.1 + - - +
385A THR* 3.2 9.3 + - + +
386A ARG* 3.0 26.3 + - - +
406A PHE* 3.3 30.5 - - + -
412A PHE* 3.5 22.4 - - + -
448A LEU* 5.9 2.5 - - + -
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Residues in contact with TYR 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ILE* 3.5 25.2 - - + +
324A GLU* 3.0 18.9 + - - -
357A TYR* 5.5 9.2 - + - +
358A TYR* 3.6 33.5 - + - +
379A ARG* 3.0 49.7 + - + -
380A ASP 2.9 8.8 + - - +
382A LEU* 1.3 74.9 - - - +
384A ASN* 1.3 63.9 + - - +
386A ARG* 3.2 30.9 + - - +
387A GLU* 2.8 35.5 + - - +
390B ARG* 5.7 4.9 - - - -
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Residues in contact with ASN 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ASP* 2.9 25.0 + - - +
381A LYS* 3.3 9.1 - - - +
382A LEU 3.3 0.2 - - - -
383A TYR* 1.3 75.6 - - - +
385A THR* 1.3 54.1 + - - +
387A GLU* 4.4 0.4 - - - -
388A ARG* 2.5 42.2 + - - +
400A ILE* 3.5 22.0 - - + +
404A SER* 3.1 41.4 + - - +
405A SER* 4.1 1.1 - - - -
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Residues in contact with THR 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ARG* 5.6 6.6 - - - +
313A MET* 5.3 0.3 - - - -
316A ALA* 4.3 13.3 - - + +
381A LYS 2.6 24.9 + - - -
382A LEU* 3.3 13.9 + - + -
383A TYR 3.1 0.2 - - - -
384A ASN* 1.3 78.8 - - - +
386A ARG* 1.3 61.5 + - - +
388A ARG* 3.7 3.1 - - + +
389A ALA* 3.3 21.7 + - - +
405A SER* 3.8 8.7 - - - -
406A PHE* 3.5 40.7 + - + +
448A LEU* 5.9 4.7 - - + -
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Residues in contact with ARG 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A MET* 3.7 23.8 - - + +
316A ALA* 3.8 15.9 - - + +
317A ASN* 4.0 31.0 + - - +
320A ILE* 3.9 21.9 - - + +
382A LEU 3.0 13.1 + - - +
383A TYR* 3.2 35.5 + - - +
385A THR* 1.3 79.5 - - - +
387A GLU* 1.3 88.1 + - - +
389A ALA* 3.4 4.2 + - - +
390A ARG* 3.0 30.3 + - - +
386B ARG* 6.1 0.8 - - - +
390B ARG* 6.4 0.2 - - - -
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Residues in contact with GLU 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A TYR* 2.8 23.4 + - - +
384A ASN* 4.4 0.7 - - - -
386A ARG* 1.3 104.7 + - - +
388A ARG* 1.3 67.7 + - - +
390A ARG* 2.9 41.8 + - - +
391A HIS* 2.9 33.2 + - + +
400A ILE* 3.5 17.3 - - + -
390B ARG* 3.9 28.2 + - - +
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Residues in contact with ARG 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASN 2.5 26.4 + - - +
385A THR* 3.7 8.3 - - + +
387A GLU* 1.3 73.8 - - - +
389A ALA* 1.3 57.7 + - - +
391A HIS* 3.3 1.7 + - - +
392A LEU* 2.9 57.9 + - + +
397A VAL* 6.3 2.0 - - - -
398A SER* 3.5 24.4 + - - -
400A ILE* 2.7 32.4 + - + +
401A SER 3.5 5.2 + - - -
402A ALA* 3.0 41.6 - - - +
405A SER* 4.3 9.8 + - - +
407A THR* 6.2 1.8 - - - +
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Residues in contact with ALA 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LEU* 4.0 18.3 - - + +
312A ARG* 5.1 3.6 - - + -
313A MET* 3.9 24.5 - - + +
385A THR 3.3 10.4 + - - +
386A ARG 3.6 8.5 - - - +
388A ARG* 1.3 79.5 - - - +
390A ARG* 1.3 54.1 + - - +
392A LEU* 3.2 12.5 + - - +
393A LEU* 2.7 40.1 + - - +
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Residues in contact with ARG 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A MET* 3.9 30.0 - - + +
386A ARG* 3.0 27.9 + - - +
387A GLU* 2.9 41.2 + - - +
389A ALA* 1.3 74.5 - - - +
391A HIS* 1.3 73.9 + - - +
393A LEU* 3.0 4.0 + - - +
394A ALA* 2.5 41.4 + - - +
357B TYR* 3.5 48.6 + - + +
----------------------------------------------------------
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Residues in contact with HIS 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A GLU* 2.9 24.3 + - + +
388A ARG 3.7 0.2 - - - +
390A ARG* 1.3 94.2 + - - +
392A LEU* 1.3 66.1 + - - +
393A LEU 2.9 0.5 + - - -
394A ALA* 2.9 7.7 + - + -
395A SER* 2.7 30.4 + - - +
397A VAL 3.5 10.3 - - - +
398A SER* 2.8 35.9 + - - -
399A GLU* 4.7 5.5 + - + -
400A ILE* 3.8 21.3 - - + +
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Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LEU* 3.4 30.2 - - + +
388A ARG* 2.9 56.5 + - + +
389A ALA* 3.2 13.7 + - - +
391A HIS* 1.3 75.0 - - - +
393A LEU* 1.3 57.7 + - - +
395A SER 2.9 17.2 - - - +
396A GLY 3.9 14.4 - - - +
397A VAL* 3.9 6.7 - - + -
398A SER* 3.4 29.4 - - - +
----------------------------------------------------------
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Residues in contact with LEU 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ASP* 3.9 29.2 - - + +
309A LEU* 3.7 16.6 - - + -
310A LEU* 3.5 26.0 - - + +
313A MET* 3.2 31.9 - - + -
389A ALA 2.7 13.0 + - - +
390A ARG* 3.3 7.4 - - - +
392A LEU* 1.3 75.4 - - - +
394A ALA* 1.3 68.1 + - - +
395A SER 3.8 1.9 - - - +
356B LYS* 3.6 62.3 - - + +
357B TYR* 4.5 4.0 - - + -
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Residues in contact with ALA 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ARG* 2.5 23.2 + - - +
391A HIS* 2.9 8.7 + - + +
393A LEU* 1.3 77.8 - - - +
395A SER* 1.3 61.5 + - - +
356B LYS* 5.3 2.2 - - - -
357B TYR* 3.9 28.8 - - + -
----------------------------------------------------------
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Residues in contact with SER 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A HIS* 2.7 14.5 + - - +
392A LEU 2.9 17.8 - - - +
393A LEU 3.8 1.6 - - - +
394A ALA* 1.3 79.2 - - - +
396A GLY* 1.3 61.2 + - - +
397A VAL 2.8 27.4 + - - -
----------------------------------------------------------
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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