Contacts of the helix formed by residues 403 - 426 (chain F) in PDB entry 4YJL
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 HIS 403 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401F HIS* 3.1 4.0 - - - +
402F HIS* 1.3 116.4 + + + +
404F HIS* 1.3 62.8 + - - +
405F HIS 3.4 2.7 - - - -
406F MET* 3.3 6.4 + - + -
407F LEU* 3.0 26.8 + - + +
461F GLU 5.3 1.0 + - - -
462F HIS* 5.4 4.5 - + - -
465F ALA* 3.3 33.9 - - + +
469F LEU* 4.6 15.0 - - + +
802F EDO 3.7 22.7 - - - +
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Residues in contact with HIS 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D GLU* 2.8 25.0 + - - +
400F HIS* 3.8 26.5 - - + +
401F HIS* 3.0 37.2 + - + +
402F HIS* 3.4 9.9 + - - -
403F HIS* 1.3 75.6 - - - +
405F HIS* 1.3 98.5 + + - +
407F LEU* 3.4 9.0 + - - +
408F HIS* 2.9 24.9 + - - +
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Residues in contact with HIS 405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D GLU* 2.6 32.5 + - - +
421D TRP* 3.4 67.8 + + + -
403F HIS 3.4 0.6 - - - -
404F HIS* 1.3 102.8 + + - +
406F MET* 1.3 63.3 + - - +
408F HIS* 3.2 4.7 + - - +
409F LEU* 3.1 27.7 + - - +
802F EDO 3.5 21.0 + - - +
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Residues in contact with MET 406 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403F HIS* 3.3 7.1 + - + +
405F HIS* 1.3 75.7 - - - +
407F LEU* 1.3 62.8 + - - +
409F LEU* 3.3 9.7 + - - +
410F LEU* 3.1 36.9 + - + +
453F LEU* 4.6 7.9 - - + -
456F LEU* 4.3 4.9 - - + -
462F HIS* 3.4 43.7 - - + +
465F ALA* 3.6 18.2 - - + +
466F MET* 3.3 45.1 - - + -
469F LEU* 4.1 8.1 - - + -
802F EDO 3.0 24.1 + - - +
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Residues in contact with LEU 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401F HIS* 5.2 17.5 - - + -
403F HIS* 3.0 19.6 + - + +
404F HIS* 3.6 9.0 - - - +
406F MET* 1.3 77.4 - - - +
408F HIS* 1.3 61.9 + - - +
410F LEU* 3.4 3.1 + - - +
411F GLU* 2.9 71.3 + - + +
414F ARG* 5.2 1.5 + - - +
469F LEU* 4.4 21.2 - - + +
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Residues in contact with HIS 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415D ALA* 3.9 23.3 - - + +
418D GLU* 3.4 43.5 - - + +
419D THR* 4.2 12.7 + - - -
421D TRP* 6.1 1.1 - + - -
422D GLU* 3.5 11.0 + - + -
404F HIS 2.9 14.3 + - - +
405F HIS 3.2 7.6 + - - +
407F LEU* 1.3 78.9 - - - +
409F LEU* 1.3 61.4 + - + +
411F GLU* 3.9 6.5 - - - +
412F GLN* 2.9 60.6 + - + +
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Residues in contact with LEU 409 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421D TRP* 4.2 10.1 - - + -
422D GLU* 3.5 35.9 - - + +
405F HIS 3.1 19.2 + - - +
406F MET* 3.6 7.9 - - - +
408F HIS* 1.3 79.5 - - + +
410F LEU* 1.3 61.8 + - - +
412F GLN* 3.4 6.2 - - - +
413F ILE* 3.2 27.5 + - - +
449F ALA* 3.9 17.6 - - + +
452F VAL* 3.7 19.1 - - + -
453F LEU* 3.7 24.0 - - + -
456F LEU* 3.7 31.0 - - + -
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Residues in contact with LEU 410 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406F MET* 3.1 30.2 + - + +
407F LEU* 4.1 2.7 - - - +
409F LEU* 1.3 73.4 - - - +
411F GLU* 1.3 60.7 + - - +
413F ILE* 3.4 13.9 - - + +
414F ARG* 3.0 50.7 + - - +
453F LEU* 3.8 28.7 - - + -
466F MET* 4.4 4.3 - - + +
469F LEU* 3.5 39.0 - - + +
471F GLY* 3.8 28.5 - - - +
474F ALA* 4.3 4.0 - - + -
475F ILE* 4.6 2.0 - - + -
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Residues in contact with GLU 411 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407F LEU* 2.9 48.3 + - + +
408F HIS* 3.9 5.1 - - - +
410F LEU* 1.3 74.6 - - - +
412F GLN* 1.3 57.2 + - - +
414F ARG* 3.8 22.7 + - - +
415F ALA* 2.8 32.7 + - - +
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Residues in contact with GLN 412 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422D GLU* 2.5 33.7 + - - +
408F HIS* 2.9 38.2 + - + +
409F LEU* 3.4 6.2 - - - +
410F LEU 3.3 0.2 - - - -
411F GLU* 1.3 76.8 - - - +
413F ILE* 1.3 57.6 + - - +
415F ALA* 3.4 4.8 + - - +
416F TYR* 3.1 26.7 + - - +
444F HIS* 3.1 19.4 - - + +
445F GLN* 2.9 32.3 + - - +
446F ILE* 4.7 2.2 - - + -
449F ALA* 3.5 12.3 - - + +
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Residues in contact with ILE 413 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409F LEU 3.2 12.5 + - - +
410F LEU* 3.4 13.5 - - + +
412F GLN* 1.3 74.1 - - - +
414F ARG* 1.3 67.2 + - - +
416F TYR* 3.4 7.5 + - - +
417F CYS* 3.1 28.4 + - - -
446F ILE* 4.3 6.5 - - + -
449F ALA* 3.9 22.7 - - + -
450F VAL* 4.4 4.7 - - + -
453F LEU* 3.9 11.9 - - + -
474F ALA* 3.7 37.2 - - + +
475F ILE* 3.7 22.0 - - + +
478F LEU* 4.0 29.0 - - + +
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Residues in contact with ARG 414 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A HIS 5.5 10.4 - - - +
407F LEU* 5.2 1.6 + - - +
410F LEU* 3.0 36.6 + - - +
411F GLU* 3.8 24.6 + - - +
413F ILE* 1.3 74.3 - - - +
415F ALA* 1.3 63.6 + - - +
417F CYS* 3.2 9.2 + - - +
418F GLU* 3.1 27.1 + - + +
469F LEU* 3.3 28.1 + - - +
470F GLY* 4.2 4.4 + - - -
474F ALA* 3.8 30.9 - - + +
477F GLU* 6.0 2.0 - - - +
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Residues in contact with ALA 415 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A HIS* 4.0 11.7 - - + +
411F GLU 2.8 18.8 + - - +
412F GLN* 3.8 5.8 - - - +
413F ILE 3.4 0.2 - - - -
414F ARG* 1.3 73.5 - - - +
416F TYR* 1.3 60.5 + - - +
418F GLU* 3.2 11.4 + - - +
419F THR* 2.9 31.7 + - - -
444F HIS* 6.2 0.4 - - - -
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Residues in contact with TYR 416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412F GLN 3.1 9.7 + - - +
413F ILE 3.7 5.8 - - - +
414F ARG 3.2 0.2 - - - -
415F ALA* 1.3 76.5 - - - +
417F CYS* 1.3 62.0 + - - +
419F THR* 3.1 8.0 + - - -
420F CYS* 3.0 43.2 + - - -
439F PRO* 3.5 25.8 + - + -
440F ALA 3.4 3.3 - - - -
441F PRO* 3.2 44.1 - - + +
444F HIS* 3.5 41.5 - + + -
446F ILE* 3.6 23.3 - - + -
478F LEU* 3.6 26.0 - - + -
481F VAL* 4.6 6.5 - - + -
482F ASP* 4.9 6.1 + - + -
485F MET* 4.5 4.4 - - - +
486F TYR* 4.7 0.5 - - - -
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Residues in contact with CYS 417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413F ILE 3.1 19.6 + - - +
414F ARG* 3.2 11.4 + - - +
416F TYR* 1.3 76.8 - - - +
418F GLU* 1.3 57.7 + - - +
420F CYS* 3.5 7.5 + - - +
421F TRP* 3.0 27.8 + - - +
474F ALA 5.0 1.6 - - - -
477F GLU* 3.9 13.0 - - + +
478F LEU* 3.5 41.3 - - - -
481F VAL* 3.8 22.5 - - + +
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Residues in contact with GLU 418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A HIS* 2.8 34.6 + - - +
405A HIS* 2.8 34.1 - - - -
408A HIS* 3.4 45.1 + - + +
414F ARG* 3.1 20.2 + - + +
415F ALA* 3.2 6.0 + - - +
417F CYS* 1.3 73.6 - - + +
419F THR* 1.3 56.3 + - - +
421F TRP* 3.3 9.3 + - - +
422F GLU* 2.8 35.2 + - - +
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Residues in contact with THR 419 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A HIS* 4.2 10.7 + - - -
445A GLN* 3.1 41.3 + - + +
415F ALA* 2.9 16.4 + - - +
416F TYR* 3.1 13.6 + - - -
418F GLU* 1.3 76.7 - - - +
420F CYS* 1.3 56.2 + - - +
422F GLU* 3.4 2.1 + - - +
423F TRP* 3.0 23.6 + - - +
439F PRO* 3.8 19.5 - - + -
444F HIS* 4.2 24.9 + - + +
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Residues in contact with CYS 420 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416F TYR* 3.0 50.3 + - - -
417F CYS 3.7 6.5 - - - +
419F THR* 1.3 74.5 - - - +
421F TRP* 1.3 63.9 + - - +
423F TRP* 3.3 10.4 + - + +
424F GLN* 2.9 21.9 + - - +
439F PRO* 4.0 10.1 - - - -
481F VAL* 3.7 13.2 - - + -
485F MET* 3.3 36.8 - - + -
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Residues in contact with TRP 421 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A HIS* 3.4 64.1 - + + +
408A HIS* 6.1 1.1 - + - -
409A LEU* 4.1 16.6 - - + -
452A VAL* 3.6 30.1 - - + -
456A LEU* 4.9 6.7 - - + -
803A EDO 4.3 8.1 - - - -
417F CYS 3.0 17.4 + - - +
418F GLU* 3.5 11.0 - - - +
420F CYS* 1.3 76.0 - - - +
422F GLU* 1.3 74.7 + - + +
424F GLN* 3.2 18.6 + - - +
425F GLU* 2.9 54.9 + - + +
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Residues in contact with GLU 422 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A HIS* 3.6 7.0 + - + -
409A LEU* 3.5 14.4 - - + +
412A GLN* 2.5 31.2 + - - +
445A GLN* 2.9 32.1 - - - +
448A PRO* 3.9 16.2 - - + +
449A ALA* 2.9 26.9 + - - -
452A VAL* 3.7 4.4 - - + +
418F GLU 2.8 18.9 + - - +
419F THR 3.5 4.7 - - - +
421F TRP* 1.3 84.7 - - + +
423F TRP* 1.3 66.1 + - - +
425F GLU 3.2 1.4 + - - -
426F ALA* 3.0 26.2 + - - +
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Residues in contact with TRP 423 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLN* 3.9 5.1 - - - +
419F THR 3.0 11.1 + - - +
420F CYS 3.4 17.9 - - - +
422F GLU* 1.3 76.3 - - - +
424F GLN* 1.3 72.9 + - + +
426F ALA 3.2 3.8 + - - -
427F HIS* 2.9 46.0 + + - -
436F ASN* 3.0 55.1 + - - +
437F PRO 3.5 9.4 - - - +
438F MET* 3.5 42.6 - - + +
439F PRO* 3.5 20.2 - - + -
485F MET* 4.0 31.2 - - + -
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Residues in contact with GLN 424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420F CYS 2.9 13.2 + - - +
421F TRP* 3.2 21.9 + - - +
423F TRP* 1.3 89.2 - - + +
425F GLU* 1.3 83.5 + - - +
427F HIS* 3.2 26.4 + - + +
484F GLU* 5.9 1.6 + - - -
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Residues in contact with GLU 425 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A VAL* 3.8 24.5 - - + +
455A LYS* 2.7 43.4 + - - +
421F TRP* 2.9 48.9 + - + +
422F GLU 3.7 0.2 - - - -
424F GLN* 1.3 105.7 - - - +
426F ALA* 1.3 55.4 + - - +
427F HIS 3.4 1.8 - - - -
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Residues in contact with ALA 426 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A PRO* 3.8 35.0 - - + +
451A CYS* 4.0 11.8 - - - -
452A VAL* 4.1 1.3 - - + -
422F GLU 3.0 15.8 + - - +
423F TRP 3.2 1.2 + - - -
425F GLU* 1.3 78.0 - - - +
427F HIS* 1.3 57.0 + - - +
428F GLU* 2.9 11.7 + - - +
431F MET* 3.4 22.3 - - + +
436F ASN* 3.6 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