Contacts of the helix formed by residues 387 - 415 (chain A) in PDB entry 2YVX
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 LEU 387 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A VAL* 3.2 35.7 - - + +
378A VAL* 3.3 33.4 - - + +
379A TYR* 3.8 30.7 - - + -
383A HIS 4.9 0.2 - - - +
384A PRO* 3.7 11.2 + - + +
385A LEU 2.6 10.7 + - - +
386A LEU* 1.3 71.0 - - - +
388A PRO* 1.4 65.9 - - + +
389A VAL 3.5 0.9 - - - -
390A VAL* 3.7 9.0 - - + +
391A GLY* 3.7 6.8 + - - -
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Residues in contact with PRO 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A LEU* 3.0 16.8 - - + -
387A LEU* 1.4 89.1 - - + +
389A VAL* 1.3 68.4 + - - +
390A VAL 3.0 3.0 + - - -
391A GLY* 3.2 1.2 + - - +
392A VAL* 2.7 50.0 + - + +
446A LEU* 3.1 33.4 - - + -
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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
----------------------------------------------------------
316A LEU* 5.4 7.4 - - + -
386A LEU* 2.9 52.9 - - + +
388A PRO* 1.3 83.6 - - - +
390A VAL* 1.3 64.7 - - + +
393A SER* 2.2 37.1 + - - -
439A TYR* 4.0 13.8 - - + +
442A VAL* 3.2 28.3 - - - +
443A ALA* 3.5 24.5 - - + -
446A LEU* 4.1 4.9 - - + -
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Residues in contact with VAL 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 5.6 2.9 - - + -
319A TYR* 5.0 10.1 - - + -
323A LEU* 4.0 3.8 - - + +
374A LEU* 3.5 20.4 - - + -
375A VAL* 4.0 3.4 - - + -
378A VAL* 3.1 53.6 - - + -
386A LEU 4.2 1.8 - - - +
387A LEU* 3.7 16.4 - - + +
389A VAL* 1.3 85.3 - - + +
391A GLY* 1.3 61.9 + - - +
393A SER* 2.9 15.9 + - - -
394A LEU* 2.9 20.5 + - - +
439A TYR* 4.4 11.2 - - - +
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Residues in contact with GLY 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A SER* 3.3 12.1 - - - -
375A VAL* 3.2 24.0 - - - +
387A LEU 3.7 3.1 + - - -
388A PRO* 3.2 3.9 + - - -
390A VAL* 1.3 79.4 - - - +
392A VAL* 1.3 63.9 + - - +
393A SER 3.1 1.0 + - - -
394A LEU* 4.7 0.9 - - - -
395A VAL* 3.2 28.7 + - - +
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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
----------------------------------------------------------
388A PRO* 2.7 36.8 + - + +
391A GLY* 1.3 70.0 - - - -
393A SER* 1.3 48.7 + - - +
395A VAL* 5.3 0.9 - - - -
396A LEU* 2.6 60.4 + - + +
442A VAL* 3.7 15.0 - - + -
446A LEU* 5.5 8.1 - - + -
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Residues in contact with SER 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 3.4 1.2 - - - +
389A VAL 2.2 28.0 + - - -
390A VAL 2.9 11.3 + - - -
392A VAL* 1.3 76.8 - - - +
394A LEU* 1.3 66.5 + - - -
395A VAL 3.1 1.3 - - - -
396A LEU* 3.0 3.9 + - - -
397A ILE* 2.6 36.7 + - - +
438A ILE* 4.3 3.6 - - - -
439A TYR* 3.3 30.1 - - - -
442A VAL* 3.6 16.4 - - - -
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Residues in contact with LEU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 3.8 18.9 - - + +
326A THR* 4.6 15.7 - - + -
327A GLY 5.6 0.4 - - - +
367A GLY 4.5 0.4 - - - +
370A LEU* 3.6 10.3 - - + -
371A SER* 3.2 36.6 - - - +
374A LEU* 3.4 37.2 - - + -
390A VAL 2.9 15.8 + - - +
391A GLY* 4.0 1.6 - - - +
393A SER* 1.3 77.8 + - - +
395A VAL* 1.3 56.2 + - + +
397A ILE* 3.4 3.3 - - - +
398A VAL* 2.7 58.7 + - + +
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Residues in contact with VAL 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LEU* 4.8 11.7 - - + +
367A GLY* 2.8 46.9 - - - +
368A LEU* 3.8 20.0 - - + +
371A SER* 3.0 29.4 - - - +
391A GLY 3.2 10.0 + - - +
392A VAL* 4.6 1.1 - - - +
393A SER 3.1 0.4 - - - -
394A LEU* 1.3 71.7 - - - +
396A LEU* 1.3 56.3 + - - +
397A ILE 2.7 14.5 + - - -
398A VAL* 4.3 0.2 - - - +
399A PHE* 3.3 21.7 + - - +
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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
----------------------------------------------------------
392A VAL* 2.6 40.4 + - + +
393A SER* 3.0 4.2 + - - +
395A VAL* 1.3 73.5 - - - +
397A ILE* 1.3 53.4 + - - +
399A PHE* 4.4 3.3 - - - +
400A PHE* 2.6 78.5 + - + +
438A ILE* 4.4 9.0 - - + -
442A VAL* 3.4 28.3 - - + -
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Residues in contact with ILE 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 3.7 25.4 - - + +
324A LEU* 5.7 1.1 - - + -
327A GLY* 4.3 19.3 - - - -
393A SER* 2.6 30.9 + - - +
394A LEU* 3.4 3.4 - - - +
395A VAL 2.7 1.0 + - - -
396A LEU* 1.3 72.5 - - - +
398A VAL* 1.3 69.8 + - - +
399A PHE 2.8 2.0 - - - -
400A PHE* 2.5 18.3 + - + +
401A ALA* 2.6 18.5 + - + +
431A SER 5.4 1.1 - - - +
435A GLY* 3.1 39.9 - - - +
438A ILE* 3.3 35.9 - - + -
439A TYR 4.4 0.7 - - - +
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A THR* 4.6 4.9 - - + -
327A GLY* 4.7 7.2 - - - -
330A THR* 3.2 28.7 - - + +
363A GLY* 4.3 2.7 - - - +
366A LEU* 4.2 9.0 - - + -
367A GLY* 3.9 22.7 - - - +
370A LEU* 3.4 25.1 - - + -
394A LEU* 2.7 46.2 + - + +
395A VAL 4.3 0.2 - - - +
397A ILE* 1.3 73.3 - - - +
399A PHE* 1.3 61.7 + - - +
401A ALA* 4.4 5.4 - - - -
402A ASN* 3.0 20.8 + - - +
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Residues in contact with PHE 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A MET* 3.2 52.5 - - + -
363A GLY* 3.8 17.9 + - - +
364A LEU* 3.3 40.2 - - + +
395A VAL* 3.3 14.4 + - + +
396A LEU* 4.4 3.1 - - - +
397A ILE 2.6 3.8 + - - -
398A VAL* 1.3 77.6 - - - +
400A PHE* 1.3 83.3 + + - +
401A ALA 2.8 6.8 + - - -
402A ASN* 3.1 0.5 + - - -
403A LEU* 3.1 36.2 + - + +
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Residues in contact with PHE 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LEU* 2.6 50.5 + - + +
397A ILE* 2.5 12.9 + - + +
399A PHE* 1.3 95.1 - + - +
401A ALA* 1.3 56.7 + - - +
403A LEU* 3.9 5.9 + - + +
404A VAL* 2.8 27.7 + - - +
434A THR* 6.6 0.2 - - - -
438A ILE* 4.0 18.4 - - + -
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Residues in contact with ALA 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A GLY* 3.0 31.9 - - - +
330A THR* 3.9 2.9 - - + -
331A GLY* 4.0 7.4 - - - +
397A ILE* 2.6 23.1 + - + +
398A VAL 3.6 5.2 - - - +
399A PHE 2.8 1.0 + - - -
400A PHE* 1.3 70.2 - - - +
402A ASN* 1.3 58.1 + - - +
403A LEU 2.9 1.3 - - - -
404A VAL* 2.6 35.7 + - - +
405A GLY 3.3 5.4 + - - -
431A SER* 4.1 8.7 - - - +
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Residues in contact with ASN 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A THR* 3.1 31.3 - - + +
331A GLY* 4.3 0.4 - - - -
334A SER* 3.0 21.1 + - - -
359A GLU* 2.9 43.2 + - - +
362A VAL* 4.7 1.6 - - - +
363A GLY* 4.6 10.1 - - - -
366A LEU* 4.4 2.7 - - - +
398A VAL* 3.0 10.5 + - + +
399A PHE 3.9 2.5 - - - +
401A ALA* 1.3 78.9 - - - +
403A LEU* 1.3 61.7 + - + +
404A VAL 3.3 0.5 + - - -
406A ALA* 2.9 25.6 + - - +
285B ARG* 2.3 31.1 + - - +
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Residues in contact with LEU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A PHE* 3.2 55.9 - - + +
359A GLU* 4.0 15.3 - - + +
360A MET* 3.9 28.3 - - + +
363A GLY* 4.8 0.9 - - - -
399A PHE* 3.1 41.2 + - + +
400A PHE* 4.2 7.6 - - + +
401A ALA 2.9 1.0 - - - -
402A ASN* 1.3 82.2 - - + +
404A VAL* 1.3 60.9 + - - +
406A ALA* 4.1 5.4 - - + -
407A MET* 3.5 25.6 + - + +
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Residues in contact with VAL 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A PHE 2.8 27.6 - - - +
401A ALA* 2.6 17.8 + - - +
403A LEU* 1.3 71.4 - - - +
405A GLY* 1.3 59.7 + - - +
406A ALA 2.9 4.5 + - - -
407A MET* 2.9 3.4 + - - +
408A LEU* 2.8 47.1 + - + +
427A VAL* 6.3 1.8 - - + -
430A LEU* 5.6 13.7 - - + +
434A THR* 5.3 10.3 - - + +
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Residues in contact with GLY 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLY* 3.5 21.2 - - - -
334A SER* 3.0 6.5 - - - -
335A ALA* 2.9 28.4 - - - +
401A ALA 3.3 6.5 + - - -
402A ASN 4.0 0.2 + - - -
404A VAL* 1.3 79.6 - - - +
406A ALA* 1.3 55.9 + - - +
408A LEU* 4.5 5.8 - - - -
409A PRO* 3.0 15.6 - - - +
427A VAL* 4.5 9.4 - - - +
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Residues in contact with ALA 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A SER* 2.6 18.2 + - - +
338A ILE* 3.0 32.8 - - + +
355A VAL* 5.3 3.2 - - + +
356A PHE* 6.5 0.9 - - - -
359A GLU* 4.0 19.3 - - + +
402A ASN 2.9 14.1 + - - +
403A LEU* 4.2 5.2 - - + +
404A VAL 2.9 0.6 - - - -
405A GLY* 1.3 79.5 - - - +
407A MET* 1.3 61.8 + - + +
408A LEU 3.4 0.2 - - - -
409A PRO* 3.8 1.2 - - - +
410A PHE* 3.2 17.7 - - - -
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Residues in contact with MET 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A TRP* 3.2 62.4 - - + +
355A VAL* 5.7 1.3 - - + -
356A PHE* 4.5 32.8 - - + +
403A LEU* 3.5 16.5 + - + +
404A VAL* 2.9 4.6 + - - +
406A ALA* 1.3 80.8 - - + +
408A LEU* 1.3 63.9 + - - +
409A PRO 3.7 0.2 - - - -
410A PHE* 3.9 14.6 + - + +
411A LEU* 3.4 21.2 + - + +
414A ARG* 5.3 4.0 - - - +
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Residues in contact with LEU 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A VAL* 2.8 28.8 + - + +
405A GLY* 4.4 4.3 - - - +
407A MET* 1.3 75.9 - - - +
409A PRO* 1.3 66.8 - - + +
410A PHE 3.0 1.8 - - - -
411A LEU* 2.7 59.0 + - + +
412A LEU* 3.2 10.7 + - + +
422A VAL* 3.9 28.5 - - + -
426A LEU* 4.9 9.2 - - + -
427A VAL* 5.3 5.2 - - + -
430A LEU* 4.7 17.9 - - + -
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Residues in contact with PRO 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ALA* 4.7 2.9 - - + +
338A ILE* 3.8 17.9 - - + -
339A ILE* 4.3 14.1 - - + +
342A LEU* 4.0 13.2 - - + +
405A GLY 3.0 22.7 - - - +
406A ALA 3.8 11.0 - - - +
408A LEU* 1.3 93.3 - - + +
410A PHE* 1.3 65.4 + - - +
412A LEU* 3.2 10.8 + - + +
413A ARG* 3.3 10.0 + - - +
419A PRO* 3.9 26.6 - - + +
422A VAL* 4.3 16.4 - - + -
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Residues in contact with PHE 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ILE* 2.9 36.1 - - + -
342A LEU* 4.2 16.2 - - + -
347A LEU* 4.6 7.4 - - + -
348A ASP 3.1 31.6 - - - -
349A LEU* 4.8 5.6 - - + +
351A ASP* 3.9 3.1 - - + -
352A TRP* 3.5 32.3 - - + -
355A VAL* 3.3 26.7 - - + -
406A ALA 3.2 20.9 - - - -
407A MET* 3.9 15.7 - - + +
408A LEU 3.0 0.6 - - - -
409A PRO* 1.3 77.6 - - + +
411A LEU* 1.3 67.7 + - - +
413A ARG* 2.7 17.2 + - - +
414A ARG* 2.9 22.8 + - + +
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A MET* 3.4 13.9 + - + +
408A LEU* 2.7 41.7 + - + +
410A PHE* 1.3 77.2 - - - +
412A LEU* 1.3 63.5 + - + +
414A ARG* 3.3 26.5 + - + +
415A LEU* 3.5 13.7 + - + +
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Residues in contact with LEU 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A LEU* 3.2 10.5 + - + +
409A PRO 3.6 4.0 - - - +
410A PHE 3.0 0.4 - - - -
411A LEU* 1.3 81.7 - - + +
413A ARG* 1.3 58.0 + - - +
415A LEU* 2.7 23.7 + - - -
416A GLY 2.8 10.4 + - - -
417A VAL* 3.0 34.6 - - + +
418A ASP 3.8 8.1 - - - +
419A PRO* 3.4 21.5 - - + +
421A LEU* 4.1 11.2 - - + -
422A VAL* 3.1 36.3 - - + -
----------------------------------------------------------
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Residues in contact with ARG 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ARG* 5.8 2.6 - - - +
342A LEU* 2.8 69.3 + - + +
343A ALA* 4.5 3.4 - - - +
345A ARG* 6.0 0.4 - - - +
347A LEU 4.9 0.6 + - - -
348A ASP* 3.4 30.6 + - - +
349A LEU* 4.6 23.2 - - + +
409A PRO 3.3 2.7 + - - +
410A PHE* 2.7 14.1 + - - +
412A LEU* 1.3 75.4 - - - +
414A ARG* 1.3 60.6 + - - +
415A LEU 2.9 0.9 + - - -
416A GLY* 3.1 12.3 + - - +
417A VAL 4.1 9.4 + - - +
419A PRO* 4.9 13.8 - - + +
----------------------------------------------------------
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Residues in contact with ARG 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 3.3 35.9 + - + +
352A TRP* 3.4 57.9 - - - +
407A MET* 5.3 3.6 - - - +
410A PHE* 2.9 26.0 + - - +
411A LEU* 3.5 21.1 - - + +
412A LEU 3.1 0.4 - - - -
413A ARG* 1.3 76.1 - - - +
415A LEU* 1.3 61.0 + - + +
416A GLY 3.6 0.2 - - - -
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Residues in contact with LEU 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A LEU* 4.1 12.3 - - + +
412A LEU* 2.7 9.8 + - - +
414A ARG* 1.3 84.7 - - + +
416A GLY* 1.3 64.1 + - - +
417A VAL* 4.2 6.9 - - + +
----------------------------------------------------------
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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