Contacts of the helix formed by residues 395 - 416 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B GLN* 3.0 32.4 + - + +
394B ASP* 1.3 83.4 - - - +
396B PHE* 1.3 66.5 - - - +
397B ASP* 4.3 8.1 - - + +
398B SER* 3.1 32.6 + - - +
399B TYR* 3.6 8.9 - - - -
401B ARG* 6.2 0.4 - - - +
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Residues in contact with PHE 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ALA* 3.6 39.7 - - + -
332B ILE 3.9 4.3 - - - -
333B ALA* 4.0 9.4 - - + -
359B VAL* 3.6 31.6 - - + -
361B HIS* 3.5 44.2 - + + +
368B LEU* 3.6 24.2 - - + +
394B ASP 4.0 2.8 + - - -
395B CYS* 1.3 71.4 - - - +
397B ASP* 1.3 66.0 + - - +
399B TYR* 3.0 18.4 + + - +
400B LYS* 3.5 40.6 + - + -
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Residues in contact with ASP 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B CYS* 3.2 5.9 - - + +
396B PHE* 1.3 78.4 - - - +
398B SER* 1.3 65.2 + - - +
400B LYS* 3.2 32.0 + - - +
401B ARG* 3.0 57.8 + - - +
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Residues in contact with SER 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B GLU* 4.7 1.4 - - - +
391B ILE* 3.9 19.7 - - - +
392B GLN* 2.9 40.3 + - - +
395B CYS* 3.1 16.3 + - - +
397B ASP* 1.3 77.8 - - - +
399B TYR* 1.3 64.8 + - - +
401B ARG* 3.5 13.8 + - - +
402B VAL* 3.2 28.1 + - - +
482B PRO* 6.0 1.6 - - - -
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Residues in contact with TYR 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ALA* 3.7 21.1 - - + +
335B ARG* 4.0 36.2 + - + +
359B VAL* 3.9 15.9 - - + -
368B LEU* 4.5 5.8 - - + -
370B VAL* 4.3 25.6 - - + +
391B ILE* 4.3 19.7 - - + -
392B GLN 4.9 0.4 - - - -
393B VAL* 2.7 51.2 + - + +
395B CYS 3.6 15.5 - - - -
396B PHE* 3.0 14.3 + + + +
398B SER* 1.3 75.9 - - - +
400B LYS* 1.3 64.4 + - - +
402B VAL* 3.4 9.2 + - + +
403B ASP* 3.3 22.5 + - - +
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Residues in contact with LYS 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B HIS* 3.6 56.8 + - + +
333B ALA* 4.5 2.0 - - + -
396B PHE* 3.5 35.9 + - + +
397B ASP* 3.2 34.7 + - - +
399B TYR* 1.3 76.8 - - - +
401B ARG* 1.3 64.6 + - + +
403B ASP* 3.0 14.2 + - - +
404B ILE* 3.1 18.5 + - + +
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Residues in contact with ARG 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B GLU* 4.6 0.7 - - - +
392B GLN* 5.4 6.9 - - - +
395B CYS* 6.2 1.0 - - - +
397B ASP* 3.0 46.6 + - - +
398B SER* 3.8 10.9 + - - +
399B TYR 3.3 0.2 - - - -
400B LYS* 1.3 76.5 - - + +
402B VAL* 1.3 63.6 + - - +
404B ILE* 3.3 11.1 + - + +
405B TRP 3.1 13.9 + - - -
482B PRO* 3.4 37.2 + - + +
483B SER* 4.0 28.9 + - - +
485B ARG* 3.1 31.9 + - + +
486B LEU 5.9 0.9 - - - +
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Residues in contact with VAL 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ARG* 5.0 15.9 - - + +
381B TYR 5.2 1.8 - - - +
382B MET* 6.1 0.9 - - - -
383B ALA* 4.2 12.8 - - + +
385B GLU* 3.8 16.8 - - - +
386B VAL* 3.9 19.3 - - + -
391B ILE* 3.8 21.5 - - + -
398B SER 3.2 15.6 + - - +
399B TYR* 3.5 13.0 - - + +
401B ARG* 1.3 76.9 - - - +
403B ASP* 1.3 67.5 + - - +
405B TRP* 3.5 5.5 + - - +
406B ALA* 3.3 19.5 + - + +
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Residues in contact with ASP 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 3.9 11.2 - - + +
320B HIS* 2.9 27.8 + - + +
333B ALA* 3.5 2.4 - - - -
334B HIS* 2.8 33.1 + - - +
335B ARG* 2.8 30.0 + - - -
336B ASP 4.5 0.5 + - - -
337B LEU* 3.7 10.0 + - + +
399B TYR 3.3 10.0 + - - +
400B LYS 3.0 10.5 + - - +
402B VAL* 1.3 80.6 - - - +
404B ILE* 1.3 58.7 + - - +
406B ALA* 3.3 6.6 + - - +
407B PHE* 2.9 28.6 + - - +
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Residues in contact with ILE 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 4.3 10.8 - - + -
320B HIS* 4.4 3.6 - - + -
400B LYS* 3.1 18.1 + - + +
401B ARG* 3.6 11.9 - - + +
402B VAL 3.2 0.2 - - - -
403B ASP* 1.3 74.5 - - - +
405B TRP* 1.3 66.3 + - - +
407B PHE* 3.3 5.2 + - + +
408B GLY 3.0 18.4 + - - -
477B CYS* 3.5 33.0 - - + +
485B ARG* 4.1 9.0 - - + -
486B LEU 3.4 23.1 - - - +
487B THR* 3.9 1.6 - - - -
488B ALA* 3.5 39.3 - - + +
491B ILE* 4.1 8.7 - - + -
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Residues in contact with TRP 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ARG 5.3 0.2 + - - -
381B TYR 3.2 23.1 + - - -
382B MET 3.3 13.4 + - - -
383B ALA* 3.6 19.1 - - + -
384B PRO* 3.5 31.2 - - + -
401B ARG 3.1 10.7 + - - +
402B VAL 3.6 8.7 - - - +
404B ILE* 1.3 76.4 - - - +
406B ALA* 1.3 62.7 + - - +
408B GLY* 3.2 11.3 + - - -
409B LEU* 3.3 29.0 + - + +
431B PHE* 4.6 12.5 - + - -
448B VAL* 4.0 17.0 - - + -
453B GLN 5.0 0.9 - - - -
454B ARG* 3.4 33.4 - - - -
455B PRO* 6.2 0.2 - - + -
477B CYS 3.6 12.0 + - - +
478B TRP* 3.4 50.1 + + + -
485B ARG* 4.0 10.5 - - - +
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Residues in contact with ALA 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B LEU* 3.6 34.1 - - + +
381B TYR* 4.1 17.1 - - + +
402B VAL* 3.3 9.2 + - + +
403B ASP* 3.3 10.1 + - - +
405B TRP* 1.3 81.7 - - - +
407B PHE* 1.3 66.7 + - - +
409B LEU* 3.1 10.0 + - - +
410B VAL* 3.1 26.4 + - - +
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Residues in contact with PHE 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B VAL* 4.2 7.9 - - + -
312B ILE* 3.5 38.6 - - + -
313B ALA* 3.9 17.5 - - + -
316B LEU* 4.2 14.8 - - + -
337B LEU* 4.0 11.8 - - + +
403B ASP 2.9 16.8 + - - +
404B ILE* 3.5 7.4 - - - +
406B ALA* 1.3 76.9 - - - +
408B GLY* 1.3 64.4 + - - +
410B VAL* 3.1 9.0 + - + +
411B LEU* 2.9 51.8 + - + +
477B CYS* 4.2 2.7 - - - -
491B ILE* 3.5 47.3 - - + -
495B LEU* 4.6 3.6 - - + -
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Residues in contact with GLY 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B ILE 3.0 11.3 + - - -
405B TRP 3.2 4.4 + - - -
407B PHE* 1.3 77.6 - - - +
409B LEU* 1.3 60.7 + - - +
411B LEU* 3.3 10.8 - - - +
412B TRP 3.1 17.0 + - - -
474B MET* 3.8 3.9 - - - +
477B CYS* 3.8 19.3 - - - -
478B TRP* 3.5 26.1 - - - -
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Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ARG 3.9 7.6 - - - +
381B TYR* 3.8 38.8 - - + -
405B TRP* 3.3 36.8 + - + +
406B ALA* 3.1 7.3 + - - +
408B GLY* 1.3 75.7 - - - +
410B VAL* 1.3 64.3 + - - +
412B TRP* 3.2 7.5 + - - +
413B GLU* 3.0 26.3 + - - +
430B PRO* 4.0 16.6 - - + -
431B PHE* 4.1 11.4 - - + -
455B PRO* 3.7 30.1 - - + -
478B TRP* 3.6 14.1 - - + +
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Residues in contact with VAL 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LEU* 4.1 17.9 - - + -
309B VAL* 6.3 0.2 - - + -
312B ILE* 4.2 12.1 - - + -
337B LEU* 5.0 2.7 - - + -
338B LYS* 4.0 18.2 - - - +
339B SER* 4.0 5.2 - - - +
342B ILE* 4.1 21.8 - - + -
381B TYR* 4.0 10.8 - - + -
406B ALA 3.1 15.9 + - - +
407B PHE* 3.1 12.1 + - + +
409B LEU* 1.3 72.6 - - - +
411B LEU* 1.3 67.7 + - - +
413B GLU* 3.1 21.5 + - + +
414B VAL* 3.0 22.8 + - + +
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Residues in contact with LEU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B VAL* 3.5 34.8 - - + -
407B PHE* 2.9 44.7 + - + +
408B GLY* 3.3 12.8 - - - +
410B VAL* 1.3 78.2 - - - +
412B TRP* 1.3 57.0 + - - +
414B VAL* 3.3 2.1 + - - +
415B ALA* 2.9 32.5 + - - +
470B LEU* 4.2 26.2 - - + +
473B LEU* 4.2 24.5 - - + -
474B MET* 4.0 19.3 - - + +
477B CYS* 5.0 1.3 - - - -
495B LEU* 5.4 1.6 - - + -
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Residues in contact with TRP 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408B GLY 3.1 6.3 + - - +
409B LEU* 3.3 9.9 - - - +
410B VAL 3.2 0.2 - - - -
411B LEU* 1.3 76.5 - - - +
413B GLU* 1.3 84.1 + - + +
414B VAL 3.3 0.3 + - - -
415B ALA* 3.4 2.2 + - - +
416B ARG* 3.3 61.2 + - - +
428B LYS 3.6 21.1 - - - -
429B PRO 4.1 0.4 - - - -
430B PRO* 3.7 25.1 - - + -
431B PHE 5.0 0.9 - - - -
432B TYR* 3.8 29.8 - + - -
455B PRO* 3.5 26.2 - - + +
456B ASN 3.0 28.5 + - - -
458B PRO* 5.0 0.6 - - - +
461B TRP* 4.0 10.9 - + - -
474B MET* 3.3 38.5 - - + -
478B TRP* 4.2 4.3 - + + -
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Residues in contact with GLU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 4.2 9.1 - - + +
339B SER* 2.7 23.1 + - - -
381B TYR* 2.4 36.3 + - - -
409B LEU 3.0 12.6 + - - +
410B VAL* 3.1 18.4 + - + +
412B TRP* 1.3 85.2 - - + +
414B VAL* 1.3 64.3 + - + +
416B ARG* 3.6 13.1 - - - +
417B ARG* 3.9 10.6 - - - +
427B TYR* 2.5 37.0 + - + -
428B LYS 4.0 11.2 - - - +
430B PRO* 3.7 17.9 - - + +
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Residues in contact with VAL 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LEU* 3.8 28.7 - - + -
295B LEU* 4.0 15.3 - - + -
300B LEU* 3.8 23.0 - - + +
305B CYS* 4.0 11.0 - - - +
308B ILE* 4.1 16.8 - - + -
309B VAL* 3.9 23.8 - - + -
312B ILE* 5.2 0.2 - - + -
410B VAL* 3.0 21.5 + - + +
411B LEU 3.8 3.6 - - - +
413B GLU* 1.3 76.1 - - + +
415B ALA* 1.3 59.6 + - - +
417B ARG* 2.9 25.5 + - - +
418B MET* 3.7 3.5 + - - +
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Residues in contact with ALA 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B CYS* 4.5 9.6 - - - -
309B VAL* 5.8 0.2 - - - +
411B LEU 2.9 16.7 + - - +
412B TRP 3.4 0.6 + - - +
414B VAL* 1.3 74.7 - - - +
416B ARG* 1.3 66.2 + - - +
418B MET* 3.0 17.7 + - - +
460B ARG* 3.8 5.2 + - - -
461B TRP* 3.7 25.3 - - + -
467B LEU* 3.6 25.0 - - + +
470B LEU* 4.3 16.6 - - + -
474B MET* 5.1 1.1 - - - -
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Residues in contact with ARG 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B TRP* 3.3 55.6 + - + +
413B GLU 3.6 11.7 - - - +
415B ALA* 1.3 76.9 - - - +
417B ARG* 1.3 60.3 + - + +
418B MET 3.3 0.4 - - - -
424B VAL* 3.4 0.9 - - - +
425B GLU* 3.2 64.5 + - + +
426B ASP* 2.9 31.8 + - - +
427B TYR* 5.9 0.4 - - - -
428B LYS* 3.4 31.7 - - - +
432B TYR* 4.1 15.0 + - - -
456B ASN 5.5 0.8 + - - -
458B PRO* 5.1 6.4 - - + +
460B ARG* 3.3 4.7 + - - -
461B TRP* 3.7 13.8 - - + -
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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