Contacts of the helix formed by residues 377 - 399 (chain A) in PDB entry 2QLU
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 GLN 377 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A PHE* 3.7 5.2 - - - -
375A ASN* 2.5 45.2 + - - +
376A PHE* 1.3 77.6 - - - +
378A ARG* 1.3 68.2 - - - +
379A ASP* 4.5 2.5 - - + +
380A ALA* 3.1 15.0 + - + +
381A PHE* 3.0 21.0 + - - -
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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
----------------------------------------------------------
302A HIS 4.6 2.6 + - - -
304A ASP* 4.3 15.2 - - - +
316A SER* 3.1 30.7 + - - -
346A PHE* 3.5 43.0 - - + -
377A GLN* 1.3 71.8 - - - +
379A ASP* 1.3 93.8 + - - +
381A PHE* 2.9 12.6 + - - -
382A LEU* 3.0 32.9 + - + +
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Residues in contact with ASP 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLN* 3.4 3.1 - - + +
378A ARG* 1.3 107.1 + - - +
380A ALA* 1.3 62.6 + - - +
382A LEU* 3.3 10.1 + - - +
383A ARG* 3.1 57.5 + - - +
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Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A GLU* 4.7 1.6 - - - +
374A ILE* 5.5 0.7 - - + -
375A ASN* 3.4 29.4 - - + +
377A GLN* 3.1 20.5 + - + +
378A ARG 3.0 0.8 - - - -
379A ASP* 1.3 80.2 - - - +
381A PHE* 1.3 61.9 + - + +
383A ARG* 3.7 15.7 + - - +
384A ILE* 3.5 26.5 + - + +
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Residues in contact with PHE 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ALA* 3.5 16.0 - - + +
320A ARG* 3.3 48.9 - - + -
344A VAL* 3.8 22.9 - - + -
346A PHE* 3.6 14.4 - + + -
355A THR* 4.4 4.9 - - + -
356A HIS 5.5 0.4 - - - -
374A ILE* 4.0 19.7 - - + -
375A ASN 3.2 25.4 - - - -
376A PHE* 3.6 26.9 - + + -
377A GLN 3.0 9.4 + - - -
378A ARG 2.9 3.0 + - - +
380A ALA* 1.3 75.4 - - - +
382A LEU* 1.3 68.6 + - - +
384A ILE* 3.0 19.9 + - + +
385A ASP* 3.1 15.9 + - - +
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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
----------------------------------------------------------
302A HIS* 3.6 60.2 - - + +
316A SER* 4.8 2.2 - - - -
317A ILE 4.2 9.9 - - - +
318A ALA* 4.2 12.3 - - + +
346A PHE* 4.9 1.3 - - + -
378A ARG* 3.0 44.1 + - + +
379A ASP* 3.5 13.2 - - - +
381A PHE* 1.3 77.5 - - + +
383A ARG* 1.3 62.2 + - + +
385A ASP* 3.1 7.3 + - - +
386A MET* 3.0 26.2 + - + +
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Residues in contact with ARG 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A GLU* 4.7 0.7 - - - +
379A ASP* 3.1 48.3 + - - +
380A ALA* 3.8 12.6 - - - +
381A PHE 3.2 0.2 - - - -
382A LEU* 1.3 79.3 - - + +
384A ILE* 1.3 61.4 + - - +
386A MET* 3.6 9.9 - - + -
387A TYR 3.3 12.6 + - - -
465A ALA* 3.2 37.0 + - + +
466A GLU* 3.7 37.0 + - - +
468A ARG* 2.9 34.2 + - + +
469A LEU 6.1 0.2 - - - +
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Residues in contact with ILE 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ARG* 6.1 3.6 - - - +
364A TYR 4.9 2.1 - - - +
365A MET* 5.8 0.9 - - - -
366A ALA* 4.3 9.3 - - + +
368A GLU* 3.4 21.3 - - + +
369A VAL* 3.6 34.5 - - + -
374A ILE* 4.2 29.4 - - + -
380A ALA* 3.5 16.1 + - + +
381A PHE* 3.0 17.3 + - + +
383A ARG* 1.3 75.6 - - - +
385A ASP* 1.3 67.2 + - - +
386A MET 3.3 0.3 + - - -
387A TYR* 3.5 5.2 + - - +
388A ALA* 3.4 17.7 + - - +
468A ARG* 4.3 3.1 - - - +
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Residues in contact with ASP 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 4.1 8.4 - - + +
302A HIS* 2.8 27.2 + - + +
318A ALA* 3.5 3.1 - - - +
319A HIS* 2.7 36.0 + - - +
320A ARG* 3.1 25.5 + - - +
322A PHE* 4.4 8.9 + - + +
381A PHE 3.1 13.2 + - - +
382A LEU 3.1 10.0 + - - +
384A ILE* 1.3 78.1 - - - +
386A MET* 1.3 56.6 + - - +
388A ALA* 3.3 8.2 + - - +
389A MET* 2.9 25.6 + - - +
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Residues in contact with MET 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 3.7 21.3 - - - -
302A HIS* 4.2 6.1 - - + +
382A LEU* 3.0 19.8 + - + +
383A ARG* 3.8 10.5 - - + +
384A ILE 3.2 0.6 - - - -
385A ASP* 1.3 72.5 - - - +
387A TYR* 1.3 67.5 + - - +
389A MET* 3.3 15.6 + - - +
390A GLY* 2.9 19.4 + - - -
460A CYS* 3.7 20.8 - - - +
468A ARG* 4.5 9.0 - - + -
469A LEU 3.1 25.4 - - - +
470A SER* 3.7 7.4 - - - +
471A ALA* 3.6 32.8 - - + +
474A VAL* 3.9 16.4 - - + -
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Residues in contact with TYR 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ARG 5.0 0.2 - - - -
364A TYR 3.4 15.9 - - - -
365A MET 3.4 20.3 + - - -
366A ALA* 3.5 15.0 - - + -
367A PRO* 3.9 10.8 - - + -
383A ARG 3.3 4.0 + - - -
384A ILE 3.7 8.3 - - - +
386A MET* 1.3 77.9 - - - +
388A ALA* 1.3 65.3 + - - +
390A GLY* 3.1 12.3 + - - -
391A LEU* 3.3 29.6 + - + +
414A PHE* 3.8 18.2 - - - -
431A VAL* 3.3 23.7 - - + +
437A ARG* 3.7 32.1 + - - -
460A CYS 3.4 10.5 + - - -
461A TRP* 3.7 23.2 - - + +
468A ARG* 3.8 20.0 - - - +
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Residues in contact with ALA 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PHE* 3.4 32.1 - - + +
364A TYR* 3.5 31.2 - - + +
384A ILE 3.4 6.4 + - - +
385A ASP* 3.3 9.5 + - - +
386A MET 3.3 0.4 - - - -
387A TYR* 1.3 78.0 - - - +
389A MET* 1.3 64.9 + - - +
391A LEU* 3.1 6.4 + - - +
392A VAL* 3.1 22.7 + - - +
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Residues in contact with MET 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A MET* 3.1 45.5 - - + +
295A SER* 3.4 22.2 - - - -
298A LEU* 3.1 36.8 - - + -
322A PHE* 3.4 31.7 - - + -
385A ASP 2.9 16.7 + - - +
386A MET* 3.3 21.7 + - + +
388A ALA* 1.3 72.0 - - - +
390A GLY* 1.3 58.0 + - - +
392A VAL* 3.1 0.9 + - - -
393A LEU* 2.9 34.6 + - + +
471A ALA* 5.1 0.2 - - + -
474A VAL* 4.8 6.7 - - - -
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Residues in contact with GLY 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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386A MET 2.9 10.3 + - - -
387A TYR 3.1 7.3 + - - -
389A MET* 1.3 76.9 - - - +
391A LEU* 1.3 59.8 + - - +
393A LEU* 3.4 10.1 + - - +
394A TRP 3.1 17.2 + - - -
457A ILE* 3.5 14.2 - - - +
460A CYS* 3.7 25.4 - - - +
461A TRP* 4.1 7.6 - - - -
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Residues in contact with LEU 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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363A ARG 3.8 8.1 - - - +
364A TYR* 3.6 39.5 - - + -
387A TYR* 3.3 31.3 + - + +
388A ALA* 3.1 6.5 + - - +
390A GLY* 1.3 75.3 - - - +
392A VAL* 1.3 57.5 + - - +
394A TRP* 3.2 9.9 - - - +
395A GLU* 3.1 31.2 + - - +
413A PRO* 3.8 16.2 - - + -
414A PHE* 3.9 12.3 - - + -
437A ARG* 5.2 0.4 - - - -
438A PRO* 3.7 27.1 - - + -
461A TRP* 3.5 22.0 - - + -
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Residues in contact with VAL 392 (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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273A LEU* 3.7 20.6 - - + -
294A MET* 3.5 27.6 - - + -
322A PHE* 3.7 18.4 - - + -
323A LYS* 3.8 7.4 - - - -
324A SER* 3.7 28.5 - - - +
327A VAL* 5.0 0.4 - - + -
364A TYR* 4.1 2.0 - - + -
388A ALA 3.1 14.9 + - - +
389A MET 3.5 6.1 - - - +
391A LEU* 1.3 72.6 - - - +
393A LEU* 1.3 63.6 + - - +
395A GLU* 3.3 14.1 + - - +
396A LEU* 3.1 21.6 + - + +
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Residues in contact with LEU 393 (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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291A ALA* 3.9 25.4 - - + +
294A MET* 3.7 23.1 - - + -
295A SER* 6.1 0.2 - - - -
389A MET* 2.9 25.8 + - + +
390A GLY* 3.5 13.2 - - - +
391A LEU 3.3 0.2 - - - -
392A VAL* 1.3 70.2 - - - +
394A TRP* 1.3 65.7 - - - +
396A LEU* 3.3 10.4 + - + +
397A VAL* 3.0 24.4 + - - +
453A LEU* 4.5 14.5 - - + +
456A THR* 5.1 5.2 - - + -
457A ILE* 3.5 25.1 - - + -
460A CYS* 4.6 10.1 - - - -
474A VAL* 4.2 26.2 - - + -
478A VAL* 5.2 0.2 - - + -
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Residues in contact with TRP 394 (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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390A GLY 3.1 9.8 + - - +
391A LEU* 3.2 11.2 - - - +
393A LEU* 1.3 77.1 - - - +
395A GLU* 1.3 82.3 + - + +
397A VAL* 2.9 5.1 + - - +
398A SER* 2.7 50.5 + - - -
411A MET* 3.5 32.1 - - + -
412A LEU 4.2 6.7 - - - -
413A PRO* 3.9 18.2 - - + -
414A PHE 5.3 0.7 - - - -
416A GLU* 6.5 1.1 - - + -
438A PRO* 3.2 34.6 - - + +
439A THR 2.9 27.4 + - - -
440A ILE* 4.5 5.6 - - + -
444A TRP* 3.7 19.1 - + - -
457A ILE* 3.5 11.9 - - + +
461A TRP* 3.9 22.4 - + + -
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Residues in contact with GLU 395 (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 LEU* 3.7 19.0 - - + +
324A SER* 2.6 21.2 + - - -
364A TYR* 2.8 29.1 + - - -
391A LEU 3.1 10.1 + - - +
392A VAL* 3.4 16.2 - - + +
393A LEU 3.3 0.2 - - - -
394A TRP* 1.3 88.9 - - + +
396A LEU* 1.3 63.6 + - - +
398A SER* 2.5 25.5 + - - -
399A ARG* 3.4 6.2 + - - +
410A TYR* 2.6 35.0 + - + -
413A PRO* 3.4 16.6 - - + +
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Residues in contact with LEU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 3.8 33.7 - - + -
277A LEU* 3.8 8.0 - - + +
282A ILE* 3.8 26.3 - - + +
287A LEU* 4.2 15.7 - - + +
290A VAL* 3.9 26.2 - - + -
291A ALA* 4.3 14.4 - - + +
294A MET* 4.1 20.0 - - + -
392A VAL 3.1 14.6 + - - +
393A LEU* 3.4 12.1 - - + +
395A GLU* 1.3 80.6 - - - +
397A VAL* 1.3 62.8 + - + +
398A SER 3.2 0.3 + - - -
399A ARG* 3.4 9.4 + - - +
400A CYS* 3.4 12.8 + - - +
453A LEU* 5.9 0.4 - - + -
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Residues in contact with VAL 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 4.0 13.7 - - + -
393A LEU 3.0 11.2 + - - +
394A TRP* 2.9 12.9 + - - +
396A LEU* 1.3 72.0 - - - +
398A SER* 1.3 62.8 + - - +
400A CYS* 3.2 18.4 + - - +
444A TRP* 3.2 44.5 + - + -
450A LEU* 4.1 19.9 - - + +
453A LEU* 3.5 34.5 - - + -
454A CYS* 4.1 10.5 - - - -
457A ILE* 3.9 10.8 - - + -
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Residues in contact with SER 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TRP* 2.7 34.0 + - - -
395A GLU* 2.5 28.6 + - - -
397A VAL* 1.3 74.1 - - - +
399A ARG* 1.3 63.2 + - - +
400A CYS 3.6 0.4 - - - -
407A VAL* 3.6 13.4 - - - +
408A ASP* 4.1 10.7 + - - +
410A TYR* 4.9 3.9 - - - -
411A MET 5.0 2.6 + - - -
444A TRP* 3.6 28.0 + - - -
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Residues in contact with ARG 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 2.8 55.3 + - + -
278A LYS 3.8 9.4 + - - -
279A GLY 4.4 0.8 - - - -
280A ASN* 3.2 24.0 + - - +
281A ILE* 3.3 34.9 - - - +
282A ILE* 2.9 25.0 + - - +
395A GLU 3.9 3.6 - - - +
396A LEU 3.4 5.8 + - - -
397A VAL 3.3 0.4 - - - -
398A SER* 1.3 83.4 + - - +
400A CYS* 1.3 57.9 + - - +
407A VAL* 3.6 8.4 + - - -
408A ASP 3.0 27.4 + - - -
409A GLU* 3.9 14.5 + - - +
410A TYR* 3.4 37.0 - - + +
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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