Contacts of the helix formed by residues 395 - 416 (chain A) in PDB entry 4BGG
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 CYS 395 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LEU* 4.9 0.2 - - - -
392A GLN* 3.0 35.2 + - - +
394A ASP* 1.3 77.9 - - - +
396A PHE* 1.3 64.6 + - - +
397A ASP* 4.2 8.5 - - + +
398A SER* 3.1 30.9 + - - +
399A TYR* 3.7 8.9 - - - -
401A ARG* 5.9 2.2 - - - +
392C GLN* 4.1 2.5 - - - +
394C ASP 5.2 0.2 - - - -
395C CYS* 2.1 52.3 - - - -
397C ASP* 4.6 3.1 - - - -
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Residues in contact with PHE 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ALA* 3.6 40.4 - - + -
332A ILE 3.9 4.3 - - - -
333A ALA* 4.0 9.2 - - + -
359A VAL* 3.7 31.9 - - + -
360A MET 4.1 0.2 - - - -
361A HIS* 3.4 36.1 - + + -
368A LEU* 3.6 25.0 - - + +
394A ASP 4.0 0.8 + - - -
395A CYS* 1.3 71.7 - - - +
397A ASP* 1.3 66.5 + - - +
399A TYR* 3.0 20.1 + - - +
400A LYS* 3.6 35.8 + - + -
392C GLN* 3.4 21.8 + - - +
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Residues in contact with ASP 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A CYS* 3.1 6.0 - - + +
396A PHE* 1.3 78.2 - - - +
398A SER* 1.3 65.6 + - - +
400A LYS* 3.0 35.8 + - - +
401A ARG* 3.0 52.2 + - - +
392C GLN* 5.2 4.1 - - - +
401C ARG* 2.9 35.1 + - - +
483C SER* 3.5 18.7 + - - -
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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
----------------------------------------------------------
385A GLU* 4.7 1.4 - - - +
391A ILE* 3.9 18.7 - - - +
392A GLN* 2.9 39.2 + - - +
395A CYS* 3.1 17.1 + - - +
396A PHE 3.1 0.4 - - - -
397A ASP* 1.3 78.8 - - - +
399A TYR* 1.3 63.7 + - - +
401A ARG* 3.4 14.3 + - - +
402A VAL* 3.2 27.9 + - - +
482A PRO* 6.1 1.6 - - - -
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Residues in contact with TYR 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ALA* 3.7 21.5 - - + +
335A ARG* 4.1 36.0 - - + +
359A VAL* 4.0 15.5 - - + -
368A LEU* 4.5 11.4 - - + -
370A VAL* 4.5 19.7 - - + +
391A ILE* 4.3 19.1 - - + -
392A GLN 5.0 0.2 - - - -
393A VAL* 2.8 51.4 + - + +
395A CYS 3.7 14.6 - - - -
396A PHE* 3.0 14.1 + + - +
398A SER* 1.3 74.8 - - - +
400A LYS* 1.3 65.0 + - - +
402A VAL* 3.4 10.2 + - + +
403A ASP* 3.3 22.3 + - - +
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Residues in contact with LYS 400 (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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320A HIS* 3.6 56.9 + - + +
331A ALA* 5.5 0.4 - - - +
333A ALA* 4.5 2.2 - - + -
396A PHE* 3.6 37.0 + - + +
397A ASP* 3.0 35.8 + - - +
399A TYR* 1.3 77.1 - - - +
401A ARG* 1.3 61.4 + - + +
403A ASP* 3.0 17.3 + - - +
404A ILE* 3.1 18.1 + - + +
483C SER* 4.9 8.3 + - - -
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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
----------------------------------------------------------
385A GLU* 4.6 0.4 - - - +
392A GLN* 5.4 8.1 - - - +
395A CYS* 5.9 2.2 - - - +
397A ASP* 3.0 36.8 + - - +
398A SER* 3.8 11.2 + - - +
400A LYS* 1.3 77.6 - - + +
402A VAL* 1.3 62.4 + - - +
404A ILE* 3.3 11.5 + - + +
405A TRP 3.2 14.4 + - - -
482A PRO* 3.4 38.9 + - + +
483A SER* 4.0 29.0 + - - +
485A ARG* 3.1 30.6 + - + +
486A LEU 5.9 0.7 - - - +
397C ASP* 5.7 4.9 - - - +
401C ARG* 3.6 25.3 - - - +
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Residues in contact with VAL 402 (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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335A ARG* 5.1 15.5 - - + +
381A TYR 5.2 1.6 - - - +
382A MET* 6.0 1.6 - - - -
383A ALA* 4.2 12.3 - - + +
385A GLU* 3.7 17.0 - - - +
386A VAL* 3.8 19.1 - - + -
391A ILE* 3.8 21.1 - - + -
398A SER 3.2 15.9 + - - +
399A TYR* 3.5 12.8 - - + +
401A ARG* 1.3 75.6 - - - +
403A ASP* 1.3 67.2 + - - +
405A TRP* 3.5 5.5 + - - +
406A ALA* 3.3 19.9 + - - +
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Residues in contact with ASP 403 (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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316A LEU* 3.9 10.2 - - + +
320A HIS* 2.9 27.2 + - + +
333A ALA* 3.6 2.3 - - - -
334A HIS* 2.8 33.0 + - - +
335A ARG* 2.8 30.2 + - - -
336A ASP 4.6 0.3 + - - -
337A LEU* 3.7 9.6 + - + +
399A TYR 3.3 10.4 + - - +
400A LYS 3.0 10.5 + - - +
402A VAL* 1.3 81.5 - - - +
404A ILE* 1.3 57.6 + - - +
406A ALA* 3.3 6.8 + - - +
407A PHE* 2.9 29.4 + - - +
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Residues in contact with ILE 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 4.3 11.2 - - + -
320A HIS* 4.4 4.3 - - + -
400A LYS* 3.1 17.2 + - + +
401A ARG* 3.6 12.3 - - + +
402A VAL 3.3 0.2 - - - -
403A ASP* 1.3 73.8 - - - +
405A TRP* 1.3 66.4 + - - +
407A PHE* 3.2 4.8 + - + +
408A GLY 3.1 17.5 + - - -
477A CYS* 3.5 34.1 - - + +
485A ARG* 4.2 8.5 - - + -
486A LEU 3.4 23.3 - - - +
487A THR* 4.0 2.0 - - - -
488A ALA* 3.6 39.3 - - + +
491A ILE* 4.1 9.0 - - + -
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Residues in contact with TRP 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ARG 5.3 0.2 + - - -
381A TYR 3.3 23.3 + - - -
382A MET 3.4 12.9 + - - -
383A ALA* 3.7 17.5 - - + -
384A PRO* 3.5 31.9 - - + -
401A ARG 3.2 11.8 + - - +
402A VAL 3.6 8.5 - - - +
404A ILE* 1.3 76.2 - - - +
406A ALA* 1.3 63.0 + - - +
408A GLY* 3.1 11.4 + - - -
409A LEU* 3.3 29.5 + - + +
431A PHE* 4.5 17.4 - + - -
448A VAL* 4.1 12.6 - - + -
453A GLN 5.0 0.7 - - - -
454A ARG* 3.5 31.9 - - - -
455A PRO* 6.2 0.7 - - + -
477A CYS 3.6 12.5 + - - -
478A TRP* 3.4 47.3 + + + -
485A ARG* 4.0 10.5 - - - +
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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
----------------------------------------------------------
337A LEU* 3.6 33.2 - - + +
381A TYR* 4.1 16.9 - - + +
402A VAL 3.3 9.2 + - - +
403A ASP* 3.3 8.4 + - - +
404A ILE 3.3 0.6 - - - -
405A TRP* 1.3 81.4 - - - +
407A PHE* 1.3 66.0 + - - +
409A LEU* 3.2 10.0 + - - +
410A VAL* 3.1 26.2 + - - +
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Residues in contact with PHE 407 (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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309A VAL* 4.2 7.6 - - + -
312A ILE* 3.5 39.9 - - + -
313A ALA* 4.0 15.3 - - + -
316A LEU* 4.2 14.8 - - + -
337A LEU* 4.0 12.0 - - + +
403A ASP 2.9 17.2 + - - +
404A ILE* 3.5 8.3 - - - +
406A ALA* 1.3 77.1 - - - +
408A GLY* 1.3 58.8 + - - +
410A VAL* 3.1 9.1 + - + +
411A LEU* 2.9 56.6 + - + +
477A CYS* 4.2 3.4 - - - -
491A ILE* 3.5 47.6 - - + -
495A LEU* 4.6 2.9 - - + -
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Residues in contact with GLY 408 (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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404A ILE 3.1 11.3 + - - -
405A TRP 3.1 5.1 + - - -
407A PHE* 1.3 75.6 - - - +
409A LEU* 1.3 62.4 + - - +
411A LEU* 3.3 10.8 - - - +
412A TRP* 3.1 17.0 + - - +
474A MET* 3.8 4.2 - - - +
477A CYS* 3.9 17.9 - - - -
478A TRP* 3.5 24.4 - - - -
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Residues in contact with LEU 409 (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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380A ARG 3.9 8.3 - - - +
381A TYR* 3.8 38.6 - - + +
405A TRP* 3.3 36.4 + - + +
406A ALA* 3.2 7.1 + - - +
408A GLY* 1.3 77.6 - - - +
410A VAL* 1.3 58.0 + - - +
412A TRP* 3.2 7.9 + - - +
413A GLU* 3.0 31.0 + - - +
430A PRO* 4.0 17.5 - - + -
431A PHE* 4.1 11.9 - - + -
455A PRO* 3.7 30.5 - - + -
478A TRP* 3.9 13.5 - - + +
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Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU* 4.1 17.9 - - + -
309A VAL* 6.3 0.2 - - + -
312A ILE* 4.2 12.3 - - + -
337A LEU* 5.0 2.9 - - + -
338A LYS* 4.0 8.5 - - - +
339A SER* 4.0 17.7 - - - +
342A ILE* 4.1 22.0 - - + -
381A TYR* 4.0 7.4 - - + -
406A ALA 3.1 14.3 + - - +
407A PHE* 3.1 13.7 + - + +
409A LEU* 1.3 73.1 - - - +
411A LEU* 1.3 67.3 + - - +
413A GLU* 3.1 21.3 + - + +
414A VAL* 3.0 23.0 + - + +
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Residues in contact with LEU 411 (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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309A VAL* 3.5 35.2 - - + -
407A PHE* 2.9 45.2 + - + +
408A GLY* 3.3 13.2 - - - +
410A VAL* 1.3 77.3 - - - +
412A TRP* 1.3 57.2 + - - +
414A VAL* 3.3 2.1 + - - +
415A ALA* 2.9 32.0 + - - +
470A LEU* 4.2 25.8 - - + +
473A LEU* 4.3 28.0 - - + -
474A MET* 4.0 16.2 - - + +
477A CYS* 5.0 1.1 - - - -
495A LEU* 5.4 1.6 - - + -
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Residues in contact with TRP 412 (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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408A GLY 3.1 7.5 + - - +
409A LEU* 3.3 10.8 - - - +
411A LEU* 1.3 75.8 - - - +
413A GLU* 1.3 88.0 + - + +
415A ALA* 4.0 2.0 - - - +
416A ARG* 3.3 56.2 + - - +
428A LYS* 3.5 20.9 - - + -
429A PRO 3.8 0.4 - - - -
430A PRO* 3.7 26.0 - - + -
431A PHE 5.0 0.9 - - - -
432A TYR* 4.0 28.7 - + - -
455A PRO* 3.5 24.6 - - + +
456A ASN* 3.0 29.2 + - + -
458A PRO* 4.9 0.6 - - - +
461A TRP* 4.0 12.5 - + - -
474A MET* 3.3 36.5 - - + -
478A TRP* 4.2 4.3 - + + -
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Residues in contact with GLU 413 (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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295A LEU* 4.2 8.7 - - + +
339A SER* 2.7 23.8 + - - -
381A TYR* 2.4 35.8 + - - -
409A LEU 3.0 13.0 + - - +
410A VAL* 3.3 18.6 - - + +
412A TRP* 1.3 86.9 - - + +
414A VAL* 1.3 62.4 + - + +
416A ARG* 3.6 13.8 - - - +
417A ARG* 3.9 10.2 - - - +
427A TYR* 2.5 37.5 + - + -
428A LYS 3.9 11.0 - - - +
430A PRO* 3.7 17.8 - - + +
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Residues in contact with VAL 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU* 3.9 28.0 - - + -
295A LEU* 4.0 14.4 - - + -
300A LEU* 3.8 23.2 - - + +
305A CYS* 4.0 10.1 - - - +
308A ILE* 4.1 17.5 - - + -
309A VAL* 3.9 24.2 - - + -
312A ILE* 5.2 0.4 - - + -
410A VAL* 3.0 18.5 + - + +
411A LEU 3.8 3.8 - - - +
412A TRP 3.2 0.2 - - - -
413A GLU* 1.3 75.0 - - + +
415A ALA* 1.3 61.3 + - - +
417A ARG* 2.9 25.1 + - - +
418A MET* 3.7 3.5 + - - +
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Residues in contact with ALA 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A CYS* 4.5 8.7 - - - -
411A LEU 2.9 18.4 + - - +
414A VAL* 1.3 73.7 - - - +
416A ARG* 1.3 65.8 + - - +
417A ARG 3.0 1.2 + - - -
418A MET* 3.1 16.1 + - - +
460A ARG* 3.8 5.0 + - - -
461A TRP* 3.7 26.1 - - + -
467A LEU* 3.6 24.3 - - + +
470A LEU* 4.3 16.6 - - + -
474A MET* 5.1 0.7 - - - -
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Residues in contact with ARG 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A TRP* 3.3 54.6 + - + +
413A GLU* 3.6 12.1 - - - +
415A ALA* 1.3 78.7 - - - +
417A ARG* 1.3 59.7 + - + +
418A MET 3.3 0.9 - - - -
424A VAL* 3.4 0.7 - - - +
425A GLU* 3.2 61.4 + - + +
426A ASP* 2.9 40.2 + - - +
427A TYR* 5.8 0.2 - - - -
428A LYS* 3.4 27.9 - - - +
432A TYR* 4.5 12.1 + - - -
456A ASN 5.5 0.6 + - - -
458A PRO* 5.0 7.0 - - + +
460A ARG* 3.3 3.6 + - - -
461A TRP* 3.6 14.1 - - + -
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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