Contacts of the helix formed by residues 379 - 406 (chain A) in PDB entry 3W0A
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 379 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 4.0 32.8 - - + +
325A LEU* 4.0 18.2 - - + -
329A GLU* 3.6 17.5 - - - +
367A ILE* 4.1 20.0 - - + +
371A HIS* 3.4 43.1 - - + +
378A LEU* 1.3 75.3 - - - +
380A TYR* 1.3 61.0 + - - +
382A LYS* 3.2 8.3 + - + +
383A MET* 2.9 41.3 + - + +
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Residues in contact with TYR 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ILE* 5.5 0.2 - - + -
360A SER* 3.7 35.2 + - - -
363A LEU* 4.0 31.0 - - + -
364A GLN* 3.8 43.6 + - + -
367A ILE* 3.8 18.2 - - + +
378A LEU 3.4 0.8 - - - -
379A LEU* 1.3 76.7 - - - +
381A ALA* 1.4 59.6 + - + +
383A MET* 3.2 5.7 + - - +
384A ILE* 2.9 63.3 + - + +
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Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU* 3.4 20.5 + - + +
379A LEU 3.3 0.2 - - - -
380A TYR* 1.4 81.1 - - + +
382A LYS* 1.3 58.5 + - + +
384A ILE* 3.4 8.2 + - - +
385A GLN* 3.0 28.1 + - - +
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Residues in contact with LYS 382 (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 32.8 - - + -
374A PRO 5.7 3.4 + - - -
378A LEU* 3.1 39.8 + - + +
379A LEU* 3.5 11.3 - - + +
381A ALA* 1.3 74.4 - - + +
383A MET* 1.3 62.5 + - - +
385A GLN* 3.3 9.5 + - - +
386A LYS* 3.1 28.6 + - - +
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Residues in contact with MET 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 4.1 4.9 - - + -
325A LEU* 3.8 33.7 - - + -
329A GLU* 3.5 29.8 - - + +
333A LEU* 3.8 28.9 - - + +
363A LEU* 3.7 24.9 - - + -
367A ILE* 3.8 28.0 - - - -
379A LEU* 2.9 21.5 + - + +
380A TYR* 3.2 6.7 + - - +
382A LYS* 1.3 73.7 - - - +
384A ILE* 1.4 65.1 + - + +
386A LYS* 3.1 20.3 + - - +
387A LEU* 3.2 15.1 + - - +
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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
----------------------------------------------------------
333A LEU* 5.6 0.9 - - + -
336A ILE* 5.2 6.3 - - + -
360A SER* 5.5 0.7 - - - +
363A LEU* 5.6 3.1 - - + -
380A TYR* 2.9 61.2 + - + +
381A ALA* 3.7 7.9 - - - +
383A MET* 1.4 73.9 - - + +
385A GLN* 1.4 66.4 + - - +
387A LEU* 3.1 37.2 + - + +
388A ALA* 3.2 12.1 + - + +
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Residues in contact with GLN 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ALA 3.0 14.8 + - - +
382A LYS* 3.5 12.6 - - - +
383A MET 3.3 0.2 - - - -
384A ILE* 1.4 75.7 - - - +
386A LYS* 1.3 61.2 + - - +
388A ALA* 3.1 16.5 + - - +
389A ASP* 2.9 52.6 + - - +
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Residues in contact with LYS 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A PHE* 3.5 34.2 - - + +
319A GLY* 3.4 41.0 + - - -
320A LEU* 3.5 17.3 - - + +
323A LEU* 4.2 17.5 - - + +
333A LEU* 4.9 6.3 - - + -
382A LYS* 3.1 16.1 + - - +
383A MET* 3.1 11.1 + - - +
385A GLN* 1.3 80.5 - - - +
387A LEU* 1.3 56.5 + - - +
389A ASP* 3.3 16.5 + - - +
390A LEU* 2.9 34.3 + - + +
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Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLU* 4.7 1.5 - - - +
333A LEU* 3.8 26.7 - - + -
336A ILE* 3.6 28.0 - - + -
337A CYS* 3.8 33.2 - - + +
340A SER* 6.1 0.7 - - - +
356A GLN* 5.6 1.6 - - - +
383A MET 3.2 4.0 + - - +
384A ILE* 3.1 31.5 + - + +
386A LYS* 1.3 74.8 - - - +
388A ALA* 1.4 61.1 + - - +
390A LEU* 3.4 24.5 + - + +
391A ARG* 3.4 21.9 + - - +
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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
----------------------------------------------------------
384A ILE* 3.2 10.4 + - + +
385A GLN* 3.1 25.2 + - - +
387A LEU* 1.4 74.3 - - - +
389A ASP* 1.4 65.6 + - - +
391A ARG* 3.1 25.5 + - - +
392A SER* 3.6 8.0 + - - -
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Residues in contact with ASP 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LYS* 5.6 4.7 + - - -
316A PHE* 3.9 17.5 - - + -
385A GLN* 2.9 41.8 + - - +
386A LYS* 3.3 31.8 + - - +
388A ALA* 1.4 74.5 - - - +
390A LEU* 1.4 62.0 + - - +
392A SER* 3.3 10.4 + - - -
393A LEU* 3.1 27.5 + - + +
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Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLU* 3.5 47.8 - - + +
272A MET* 3.9 20.0 - - + -
273A LEU* 3.6 35.7 - - + -
316A PHE* 3.7 20.6 - - + -
337A CYS* 4.4 1.6 - - - -
386A LYS 2.9 19.8 + - - +
387A LEU* 3.5 23.6 - - + +
388A ALA 3.2 0.4 - - - -
389A ASP* 1.4 75.7 - - - +
391A ARG* 1.3 51.6 + - - +
393A LEU* 3.3 5.8 + - + +
394A ASN* 2.8 35.5 + - - +
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Residues in contact with ARG 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLU* 3.5 19.3 + - - -
340A SER* 3.5 21.8 + - - -
342A ASP* 2.7 56.1 + - - -
343A ARG* 3.2 21.5 - - - +
387A LEU* 3.5 15.6 + - - +
388A ALA* 3.1 13.1 + - - +
390A LEU* 1.3 75.4 - - - +
392A SER* 1.4 57.0 + - - +
394A ASN* 3.3 4.2 + - - +
395A GLU* 3.0 32.9 + - + +
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Residues in contact with SER 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ALA 3.6 8.0 + - - -
389A ASP* 3.3 11.3 + - - -
391A ARG* 1.4 73.2 - - - +
393A LEU* 1.3 60.4 + - - +
395A GLU* 3.4 8.8 + - - +
396A GLU* 3.0 27.7 + - - +
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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
----------------------------------------------------------
272A MET* 3.8 28.0 - - + -
309A LEU* 3.6 16.9 - - + +
312A PRO* 3.8 18.6 - - + +
313A LEU* 3.7 33.0 - - + +
316A PHE* 3.7 38.6 - - + -
389A ASP* 3.1 21.2 + - + +
390A LEU* 3.7 8.7 - - + +
392A SER* 1.3 76.0 - - - +
394A ASN* 1.4 57.1 + - - +
396A GLU* 3.4 5.1 + - + +
397A HIS* 2.8 31.4 + - - +
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Residues in contact with ASN 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A SER 2.8 28.0 + - - +
268A ILE* 3.5 26.3 - - - +
269A GLU* 2.9 26.2 + - + +
272A MET* 5.3 0.4 - - - -
343A ARG* 4.2 2.6 - - - +
390A LEU 2.8 17.6 + - - +
391A ARG* 3.4 6.3 - - - +
393A LEU* 1.4 75.5 - - - +
395A GLU* 1.3 57.9 + - + +
397A HIS* 3.3 2.6 + - - +
398A SER* 2.9 33.7 + - - -
422A PHE* 5.8 0.9 - - - -
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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
----------------------------------------------------------
391A ARG* 3.0 19.0 + - + +
392A SER* 3.6 10.5 - - - +
394A ASN* 1.3 77.4 - - + +
396A GLU* 1.3 61.2 + - - +
398A SER* 3.5 8.1 + - - -
399A LYS* 3.2 38.3 + - - +
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Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLU* 3.4 46.3 - - - +
309A LEU* 3.9 9.4 - - + -
312A PRO* 6.2 0.7 - - + -
392A SER 3.0 16.5 + - - +
393A LEU* 3.8 6.3 - - + +
395A GLU* 1.3 72.8 - - - +
397A HIS* 1.3 66.5 + - - +
399A LYS* 3.2 24.0 + - - +
400A GLN* 2.7 60.1 + - - +
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Residues in contact with HIS 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ILE* 3.7 27.7 - - + +
272A MET* 4.7 1.6 - - + -
305A HIS* 3.6 21.0 - + - -
309A LEU* 3.8 15.2 - - + +
393A LEU 2.8 18.4 + - - +
394A ASN* 3.3 5.5 + - - +
396A GLU* 1.3 76.1 - - - +
398A SER* 1.3 53.7 + - - +
400A GLN* 3.3 2.6 + - - +
401A TYR* 2.8 37.8 + - + +
422A PHE* 3.5 32.3 - + - -
501A DS5 2.7 56.1 + - + -
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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 ASN* 2.9 22.4 + - - -
395A GLU* 3.7 9.6 - - - -
397A HIS* 1.3 81.2 + - - +
399A LYS* 1.4 61.3 + - - +
401A TYR* 3.4 6.8 + - - +
402A ARG* 3.1 39.0 + - - +
422A PHE* 5.3 7.2 + - - -
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Residues in contact with LYS 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLU* 3.2 27.1 + - - +
396A GLU* 3.5 26.1 + - - +
398A SER* 1.4 74.1 - - - +
400A GLN* 1.3 64.9 + - + +
402A ARG* 3.4 24.2 + - - +
403A CYS* 3.2 19.4 + - - +
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Residues in contact with GLN 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLY 5.1 3.3 - - - +
305A HIS* 3.1 29.5 + - - +
306A SER* 2.8 48.0 + - - -
308A GLU* 3.9 0.8 + - - +
309A LEU* 3.4 28.0 - - - +
396A GLU* 2.7 39.0 + - - +
397A HIS* 3.8 2.7 - - - +
399A LYS* 1.3 76.1 - - + +
401A TYR* 1.3 58.8 + - - +
403A CYS* 3.3 8.3 + - - +
404A LEU* 2.9 28.9 + - - +
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Residues in contact with TYR 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A HIS* 4.4 4.4 - - - -
397A HIS* 2.8 32.1 + - + +
398A SER* 3.7 7.4 - - - +
400A GLN* 1.3 69.7 - - - +
402A ARG* 1.3 59.5 - - - +
404A LEU* 3.2 9.9 + - + +
405A SER* 2.8 44.2 + - - -
414A LEU* 3.5 31.3 - - + +
418A VAL* 4.0 3.3 + - + -
419A LEU* 3.6 25.6 + - - +
422A PHE* 3.5 45.3 - + + -
423A GLY* 3.9 7.0 + - - -
501A DS5 3.5 39.0 - - - -
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Residues in contact with ARG 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A SER* 3.1 27.3 + - - +
399A LYS* 3.4 35.2 - - - +
401A TYR* 1.3 78.6 - - + +
403A CYS* 1.4 60.1 + - - +
405A SER* 2.7 25.3 + - - +
406A PHE* 3.5 32.4 + - + -
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Residues in contact with CYS 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 4.9 20.8 - - - +
304A GLY 5.3 5.2 - - - -
399A LYS 3.2 12.4 + - - +
400A GLN* 3.3 10.7 + - - +
402A ARG* 1.4 69.2 - - - +
404A LEU* 1.3 68.9 + - - +
406A PHE* 3.0 33.8 + - + +
407A GLN* 3.9 3.5 + - - +
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Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 4.8 9.0 - - + -
224A LEU* 3.6 34.3 - - + -
227A LEU* 3.9 8.3 - - + -
303A ALA 3.7 16.6 - - - +
304A GLY* 4.4 11.0 - - - +
305A HIS* 4.8 5.6 - - + +
400A GLN 2.9 17.6 + - - +
401A TYR* 3.2 12.5 + - + +
403A CYS* 1.3 77.8 - - - +
405A SER* 1.3 57.1 + - - +
407A GLN* 3.0 28.1 + - - +
410A CYS* 3.5 21.5 - - - -
414A LEU* 4.7 0.7 - - + -
501A DS5 3.4 33.7 - - - +
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Residues in contact with SER 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A TYR* 2.8 34.7 + - - -
402A ARG* 2.7 20.6 + - - +
404A LEU* 1.3 75.1 - - - +
406A PHE* 1.4 66.5 + - - +
407A GLN 3.2 6.5 + - - +
410A CYS* 4.3 12.1 - - - +
414A LEU* 5.7 1.6 - - - -
419A LEU* 6.4 1.1 - - - -
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Residues in contact with PHE 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ARG* 3.7 39.0 - - + -
403A CYS* 3.0 23.9 + - + +
405A SER* 1.4 80.1 + - - +
407A GLN* 1.3 64.4 + - - +
408A PRO* 3.3 9.9 - - - +
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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