Contacts of the helix formed by residues 388 - 418 (chain A) in PDB entry 5A86
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 388 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ALA 5.1 1.4 + - - -
386A HIS 3.2 0.4 - - - -
387A ARG* 1.3 121.9 - - + +
389A LEU* 1.3 64.5 + - - +
390A PHE* 3.3 2.5 - - - -
391A LEU* 3.1 34.4 + - + +
392A LYS* 2.9 39.7 + - + +
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Residues in contact with LEU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LEU* 4.2 27.1 - - + +
335A LEU* 4.0 20.0 - - + -
339A GLU* 4.0 7.0 - - - +
377A ILE* 4.0 13.5 - - + -
381A ARG* 3.5 46.2 - - - +
385A ALA 5.5 0.4 + - - +
386A HIS* 3.1 31.6 + - + +
387A ARG 3.5 0.2 - - - -
388A PHE* 1.3 76.1 - - - +
390A PHE* 1.3 64.7 + - - +
392A LYS* 3.1 12.8 + - + +
393A ILE* 2.9 34.2 + - + +
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Residues in contact with PHE 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ALA* 3.4 35.2 - - + -
373A LEU* 3.9 15.3 - - + -
374A LYS* 3.8 55.6 - - + +
377A ILE* 3.7 22.0 - - + +
386A HIS 4.8 0.2 + - - -
387A ARG 5.3 1.7 + - - +
388A PHE 3.3 0.6 - - - -
389A LEU* 1.3 76.5 - - - +
391A LEU* 1.3 72.6 + - + +
393A ILE* 3.2 6.1 + - - +
394A MET* 3.0 65.7 + - + +
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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
----------------------------------------------------------
374A LYS* 5.5 5.2 - - - +
388A PHE* 3.1 41.5 + - + +
390A PHE* 1.3 92.5 - - + +
392A LYS* 1.3 60.3 + - + +
394A MET* 3.4 8.1 + - + +
395A ALA* 2.9 29.6 + - - +
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Residues in contact with LYS 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LEU* 4.3 31.7 - - + +
385A ALA 4.4 14.3 + - - -
388A PHE* 2.9 35.6 + - + +
389A LEU* 3.4 12.6 - - - +
391A LEU* 1.3 73.9 - - - +
393A ILE* 1.3 58.7 + - - +
395A ALA* 3.2 7.2 + - - +
396A MET* 3.0 35.9 + - + +
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Residues in contact with ILE 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 5.7 0.4 - - + -
333A LEU* 4.5 5.4 - - + -
335A LEU* 3.8 34.8 - - + -
339A GLU* 4.7 3.6 - - + -
343A MET* 3.4 33.4 - - + +
373A LEU* 3.9 24.9 - - + -
377A ILE* 4.0 22.7 - - + -
389A LEU* 2.9 25.1 + - + +
390A PHE* 3.5 7.6 - - - +
392A LYS* 1.3 75.2 - - - +
394A MET* 1.3 61.7 + - - +
396A MET* 3.1 10.1 + - - +
397A LEU* 3.0 27.7 + - + +
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Residues in contact with MET 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ILE* 4.0 34.1 - - + -
366A GLN* 5.9 2.7 - - + -
370A ALA* 4.4 10.5 - - + -
373A LEU* 4.9 2.5 - - - -
390A PHE* 3.0 58.7 + - + +
391A LEU* 3.8 9.9 - - + +
393A ILE* 1.3 75.8 - - - +
395A ALA* 1.3 61.4 + - - +
397A LEU* 3.3 15.0 + - + +
398A THR* 3.2 25.1 + - - -
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Residues in contact with ALA 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A LEU 2.9 17.7 + - - +
392A LYS* 3.5 8.1 - - - +
393A ILE 3.2 0.2 - - - -
394A MET* 1.3 76.3 - - - +
396A MET* 1.3 64.0 + - + +
398A THR* 3.3 9.0 + - - +
399A GLU* 3.1 22.1 + - - +
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Residues in contact with MET 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LYS* 6.4 0.2 - - - +
326A PHE* 3.3 53.9 - - + +
329A MET* 3.9 39.0 - - + -
330A LEU* 4.0 23.8 - - + -
333A LEU* 4.3 11.7 - - + -
343A MET* 4.9 6.7 - - + -
392A LYS* 3.0 18.2 + - + +
393A ILE* 3.4 10.3 - - - +
395A ALA* 1.3 78.2 - - + +
397A LEU* 1.3 55.5 + - - +
399A GLU* 3.2 8.7 + - + +
400A LEU 2.9 24.9 + - - -
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Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLU* 4.8 4.1 - - - +
286A LEU* 4.3 13.5 - - + -
343A MET* 3.7 48.0 - - + +
346A ILE* 3.8 36.1 - - + -
347A SER* 4.4 11.4 - - - +
393A ILE* 3.0 18.9 + - + +
394A MET* 3.6 20.6 - - + +
395A ALA 3.3 0.4 - - - -
396A MET* 1.3 74.1 - - - +
398A THR* 1.3 61.5 + - - +
400A LEU* 3.4 11.1 + - + +
401A ARG* 3.1 22.3 + - - +
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Residues in contact with THR 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A MET 3.2 14.1 + - - -
395A ALA* 3.3 11.5 + - - -
397A LEU* 1.3 75.3 - - - +
399A GLU* 1.3 63.1 + - - +
401A ARG* 3.3 16.7 + - - +
402A SER* 3.3 12.0 + - - -
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Residues in contact with GLU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PRO* 4.3 5.0 - - - +
325A LYS* 3.4 25.5 + - - +
326A PHE* 4.7 7.6 - - + -
395A ALA 3.1 12.6 + - - +
396A MET* 3.2 15.5 + - + +
398A THR* 1.3 74.7 - - - +
400A LEU* 1.3 59.5 + - - +
402A SER* 2.9 16.1 + - - +
403A ILE* 2.9 56.7 + - - +
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Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 4.4 8.3 - - + -
282A GLU* 3.7 39.5 - - + +
285A GLN* 4.2 9.2 - - + -
286A LEU* 4.0 15.9 - - + -
323A MET* 4.0 32.8 - - + -
326A PHE* 3.8 25.9 - - + -
396A MET 2.9 15.5 + - - +
397A LEU* 3.6 14.1 - - + +
398A THR 3.4 0.2 - - - -
399A GLU* 1.3 75.5 - - - +
401A ARG* 1.3 57.4 + - - +
403A ILE* 3.2 6.0 + - + +
404A ASN* 2.8 29.0 + - - +
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Residues in contact with ARG 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLU* 3.5 22.2 + - - +
350A SER* 4.3 9.6 + - - -
352A ASP* 2.6 69.3 + - - +
353A ARG* 3.4 27.1 - - - +
354A PRO* 4.9 3.6 - - - +
397A LEU 3.1 13.8 + - - +
398A THR* 3.4 13.0 - - + +
399A GLU 3.2 0.2 - - - -
400A LEU* 1.3 76.0 - - - +
402A SER* 1.3 60.3 + - - +
404A ASN* 3.4 3.3 + - + +
405A ALA* 3.3 21.1 + - - +
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Residues in contact with SER 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A THR 3.3 7.6 + - - -
399A GLU* 2.9 19.3 + - - -
401A ARG* 1.3 76.0 - - - +
403A ILE* 1.3 66.5 + - - +
405A ALA* 3.4 7.2 + - - +
406A GLN* 3.2 30.4 + - - +
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Residues in contact with ILE 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 4.2 7.2 - - + -
322A PRO* 3.6 34.8 - - + +
323A MET* 3.5 35.9 - - + +
326A PHE* 4.0 15.7 - - + -
399A GLU* 2.9 46.0 + - - +
400A LEU* 3.6 8.5 - - + +
402A SER* 1.3 77.2 - - - +
404A ASN* 1.3 56.1 + - - +
406A GLN* 3.2 13.5 + - + +
407A HIS* 2.9 30.0 + - + +
410A ARG* 6.1 2.5 - - - +
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Residues in contact with ASN 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LYS 5.3 1.6 + - - -
278A GLY* 3.0 28.3 + - - -
281A PHE* 3.3 42.4 - - + +
282A GLU* 3.0 18.2 + - - +
353A ARG* 4.4 1.4 - - - +
400A LEU 2.8 17.2 + - - +
401A ARG* 3.4 7.5 + - - +
402A SER 3.2 0.2 - - - -
403A ILE* 1.3 76.9 - - - +
405A ALA* 1.3 56.5 + - - +
407A HIS* 3.3 1.4 + - - +
408A THR* 2.9 45.7 + - - -
429A PHE* 4.9 2.4 - - - -
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Residues in contact with ALA 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ARG 3.3 9.7 + - - +
402A SER* 3.7 11.0 - - - +
403A ILE 3.3 0.2 - - - -
404A ASN* 1.3 78.9 - - - +
406A GLN* 1.3 61.4 + - - +
408A THR* 3.5 6.3 + - - -
409A GLN* 3.1 34.5 + - - +
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Residues in contact with GLN 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PRO* 4.6 24.2 - - - +
402A SER* 3.2 19.8 + - - +
403A ILE* 3.4 16.4 - - + +
405A ALA* 1.3 76.2 - - - +
407A HIS* 1.3 64.5 + - - +
409A GLN* 3.3 18.9 + - - +
410A ARG* 3.2 40.7 + - + +
413A ARG* 5.3 0.3 + - - -
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Residues in contact with HIS 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 4.6 21.1 - - + +
243A MET* 5.1 16.7 - - + +
281A PHE* 3.4 36.9 - + + -
403A ILE* 2.9 21.9 + - + +
404A ASN 3.9 2.5 - - - +
406A GLN* 1.3 69.3 - - - +
408A THR* 1.3 64.2 + - - +
410A ARG* 3.1 22.5 + - + +
411A LEU* 2.9 37.1 + - + +
429A PHE* 5.8 6.0 - + - -
1433A D7E 3.8 26.9 - + + +
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Residues in contact with THR 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ASN* 2.9 36.3 + - - -
405A ALA* 3.7 7.0 - - - -
407A HIS* 1.3 80.1 - - - +
409A GLN* 1.3 63.0 + - + +
411A LEU* 3.2 8.9 + - - +
412A LEU* 3.1 34.2 + - + +
429A PHE* 4.0 37.3 - - + +
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Residues in contact with GLN 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A ALA* 3.1 18.6 + - - +
406A GLN* 3.5 22.9 - - - +
407A HIS 3.2 0.4 - - - -
408A THR* 1.3 77.2 - - + +
410A ARG* 1.3 62.6 + - - +
412A LEU* 3.3 10.5 + - + +
413A ARG* 3.1 48.3 + - - +
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Residues in contact with ARG 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LYS 5.2 0.8 + - - -
205A ASP* 3.9 31.4 + - + +
208A SER* 2.9 28.3 + - - -
209A LEU* 4.8 8.6 - - + +
321A GLU* 3.0 26.9 + - - -
322A PRO* 5.5 0.6 - - - +
323A MET* 5.8 5.3 - - - +
403A ILE* 6.1 2.8 - - - +
406A GLN* 3.3 27.8 + - + +
407A HIS* 3.1 30.4 + - + +
409A GLN* 1.3 77.4 - - - +
411A LEU* 1.3 62.6 + - - +
413A ARG* 3.2 22.7 + - - +
414A ILE* 3.1 31.4 + - + +
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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
----------------------------------------------------------
243A MET* 5.1 4.5 - - + -
407A HIS* 2.9 23.9 + - + +
408A THR* 3.2 11.2 + - - +
410A ARG* 1.3 76.3 - - - +
412A LEU* 1.3 52.1 + - + +
414A ILE* 3.2 9.4 + - - +
415A GLN* 2.8 36.5 + - + +
420A PHE* 3.5 31.6 - - + -
421A ALA* 5.0 2.0 - - + -
425A MET* 4.0 15.9 - - + -
429A PHE* 3.4 49.4 - - + -
431A ILE* 4.2 17.7 - - + -
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Residues in contact with LEU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A THR* 3.1 27.3 + - + +
409A GLN* 3.7 10.1 - - - +
411A LEU* 1.3 72.4 - - + +
413A ARG* 1.3 60.7 + - + +
415A GLN* 3.3 5.1 + - + +
416A ASP* 2.8 31.9 + - - +
429A PHE* 3.8 19.3 - - + +
430A GLY 4.7 5.2 - - - +
431A ILE* 3.6 33.9 - - + -
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Residues in contact with ARG 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LYS 5.8 0.2 - - - -
201A GLN* 3.5 28.5 + - - +
202A VAL* 3.6 15.0 - - + +
205A ASP* 2.8 51.3 + - - +
409A GLN* 3.1 38.9 + - - +
410A ARG* 3.5 26.8 - - - +
412A LEU* 1.3 76.7 - - + +
414A ILE* 1.4 62.3 + - - +
416A ASP* 3.3 19.8 + - - +
417A ILE* 3.5 6.1 + - - +
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Residues in contact with ILE 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A VAL* 4.0 17.5 - - + -
205A ASP* 4.3 12.3 - - + +
206A LEU* 3.7 24.9 - - + -
209A LEU* 3.9 18.2 - - + -
237A PHE* 4.1 14.6 - - + -
240A LEU* 3.6 31.9 - - + -
410A ARG* 3.1 21.7 + - + +
411A LEU* 3.7 8.1 - - - +
413A ARG* 1.4 71.1 - - - +
415A GLN* 1.3 58.6 + - - +
417A ILE* 3.1 2.8 + - - +
418A HIS* 2.7 35.8 + - - +
420A PHE* 3.8 12.3 - - + -
----------------------------------------------------------
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Residues in contact with GLN 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A LEU* 2.8 17.7 + - + +
412A LEU* 3.5 9.4 - - + +
414A ILE* 1.3 76.8 - - - +
416A ASP* 1.3 61.9 + - - +
418A HIS 3.8 4.9 - - - -
419A PRO* 3.2 50.4 - - - +
420A PHE* 3.0 13.1 + - + +
421A ALA* 3.0 41.5 + - - +
426A GLN* 4.9 5.3 - - - +
431A ILE* 3.7 38.9 - - + +
----------------------------------------------------------
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Residues in contact with ASP 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LYS* 2.8 39.7 + - - +
412A LEU 2.8 14.0 + - - +
413A ARG* 3.3 14.4 - - - +
415A GLN* 1.3 78.1 - - - +
417A ILE* 1.3 57.9 + - + +
419A PRO* 4.9 3.1 - - - +
----------------------------------------------------------
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Residues in contact with ILE 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLU* 4.8 6.7 - - - +
198A LYS* 3.2 56.8 - - + -
199A TRP* 3.5 51.5 - - + +
202A VAL* 3.7 16.8 - - + -
237A PHE* 4.2 14.4 - - + -
413A ARG 3.5 4.7 + - - +
414A ILE 3.1 5.2 + - - +
416A ASP* 1.3 79.0 - - - +
418A HIS* 1.3 61.5 + - + +
419A PRO* 3.9 6.3 - - - +
----------------------------------------------------------
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Residues in contact with HIS 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A TRP* 5.9 0.6 - - - -
234A LYS* 3.7 32.3 - - - +
237A PHE* 3.3 59.0 + + + +
240A LEU* 4.2 9.6 - - + +
241A PRO* 5.9 3.6 - - - +
414A ILE* 2.7 22.7 + - + +
417A ILE* 1.3 75.1 + - - +
419A PRO* 1.4 78.7 + - + +
420A PHE* 3.3 17.6 + - + +
----------------------------------------------------------
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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