Contacts of the helix formed by residues 401 - 426 (chain A) in PDB entry 3QHE
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 ARG 401 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A ARG* 1.3 113.9 + - - +
403A GLU* 3.8 29.5 + - + +
404A ILE* 3.2 36.5 - - + +
405A ARG* 3.2 11.3 + - - +
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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
----------------------------------------------------------
401A ARG* 1.3 113.9 - - - +
403A GLU* 1.3 61.6 + - + +
405A ARG* 3.2 8.1 + - - +
406A VAL* 2.8 33.8 + - - +
461A GLU* 3.3 52.2 + - - +
462A HIS* 3.5 44.0 - - + +
465A ALA* 5.0 6.2 - - + +
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Residues in contact with GLU 403 (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 22.6 + - + +
402A ARG* 1.3 78.1 - - + +
404A ILE* 1.3 57.6 + - - +
406A VAL* 3.3 1.8 + - - +
407A LEU* 2.8 31.7 + - - +
464A HIS* 5.9 0.9 + - - -
465A ALA* 4.1 26.2 - - + +
468A GLU* 5.0 11.6 - - - +
469A LEU* 3.9 10.6 - - + +
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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
----------------------------------------------------------
401A ARG* 3.2 38.6 - - + +
403A GLU* 1.3 76.9 - - - +
405A ARG* 1.3 57.5 + - + +
407A LEU* 3.4 19.2 + - + +
408A HIS* 2.9 32.3 + - + +
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Residues in contact with ARG 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ARG 3.5 9.0 - - - +
402A ARG* 3.2 12.6 + - - +
404A ILE* 1.3 84.0 - - + +
406A VAL* 1.3 62.4 + - + +
408A HIS* 3.5 10.6 + - + +
409A LEU* 3.2 33.3 + - + +
452A VAL* 4.0 26.4 - - - +
456A LEU* 3.7 30.5 - - - +
462A HIS* 4.9 7.7 + - - +
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Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ARG 2.8 23.0 + - - +
403A GLU 3.3 3.6 + - - +
405A ARG* 1.3 70.5 - - - +
407A LEU* 1.3 67.0 + - - +
409A LEU* 3.3 8.0 + - - +
410A LEU* 2.9 36.9 + - + +
453A LEU* 4.7 3.8 - - + -
456A LEU* 4.6 8.5 - - + -
462A HIS* 4.1 26.9 - - + +
465A ALA* 4.2 17.9 - - + -
466A MET* 3.7 38.6 - - + +
469A LEU* 4.5 2.9 - - + -
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Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A GLU 2.8 18.1 + - - +
404A ILE* 3.7 20.4 - - + +
406A VAL* 1.3 76.3 - - - +
408A HIS* 1.3 54.9 + - - +
410A LEU* 3.0 4.9 + - + +
411A GLU* 2.8 67.7 + - + +
414A ARG* 5.0 9.4 - - - +
469A LEU* 4.0 31.3 - - + +
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Residues in contact with HIS 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ILE* 2.9 23.7 + - + +
405A ARG* 3.5 14.6 - - + +
407A LEU* 1.3 75.1 - - - +
409A LEU* 1.3 72.3 + - + +
411A GLU* 3.4 11.6 + - - +
412A GLN* 3.0 50.6 + - + +
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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
----------------------------------------------------------
405A ARG* 3.2 23.1 + - + +
406A VAL* 3.7 3.1 - - - +
408A HIS* 1.3 86.8 - - + +
410A LEU* 1.3 62.9 + - - +
412A GLN* 3.1 29.4 + - - +
413A ILE* 3.2 13.1 + - - +
449A ALA* 3.8 34.1 - - + +
452A VAL* 3.5 34.3 - - + -
453A LEU* 3.6 31.6 - - + -
456A LEU* 4.1 10.5 - - + -
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Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A VAL* 2.9 32.4 + - + +
407A LEU* 3.6 4.7 - - + +
409A LEU* 1.3 72.3 - - - +
411A GLU* 1.3 65.2 + - - +
413A ILE* 3.3 7.2 + - + +
414A ARG* 3.0 44.3 + - - +
453A LEU* 3.9 30.1 - - + -
466A MET* 4.5 2.2 - - + +
469A LEU* 3.5 41.7 - - + +
471A GLY* 3.7 29.4 - - - +
474A ALA* 4.4 10.5 - - + -
475A ILE* 4.7 1.6 - - + -
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Residues in contact with GLU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A LEU* 2.8 53.3 + - + +
408A HIS* 3.7 10.3 - - - +
410A LEU* 1.3 71.9 - - - +
412A GLN* 1.3 62.5 + - - +
414A ARG* 3.3 14.3 + - - +
415A ALA* 3.0 26.9 + - - +
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Residues in contact with GLN 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 HIS* 3.0 51.0 + - + +
409A LEU* 3.1 18.6 + - - +
411A GLU* 1.3 76.1 - - - +
413A ILE* 1.3 61.9 + - + +
415A ALA* 3.5 5.1 + - - +
416A TYR* 3.3 21.0 + - - +
444A HIS 4.7 6.2 + - - +
445A GLN* 4.2 14.3 + - - +
446A ILE* 4.1 8.0 - - + +
449A ALA* 3.9 23.1 - - + +
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Residues in contact with ILE 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A LEU 3.2 11.3 + - - +
410A LEU* 3.4 15.5 - - + +
412A GLN* 1.3 74.6 - - - +
414A ARG* 1.3 61.1 + - - +
416A TYR* 3.4 7.2 + - - +
417A CYS* 3.0 32.9 + - - -
446A ILE* 4.6 8.5 - - + -
449A ALA* 4.4 18.4 - - + -
450A VAL* 4.5 6.7 - - + -
453A LEU* 4.2 12.8 - - + -
474A ALA* 3.5 39.3 - - + +
475A ILE* 3.7 19.7 - - + +
478A LEU* 4.1 28.9 - - + -
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Residues in contact with ARG 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A LEU* 5.0 7.3 - - - +
410A LEU* 3.0 43.0 + - - +
411A GLU* 3.6 15.5 - - - +
413A ILE* 1.3 75.2 - - - +
415A ALA* 1.3 58.7 + - - +
417A CYS* 3.3 8.1 + - - +
418A GLU* 2.9 35.8 + - + +
421A TRP* 5.0 1.4 - - - -
469A LEU* 2.7 29.5 + - - +
470A GLY* 3.5 16.6 + - - -
474A ALA* 4.2 20.5 - - + +
477A GLU* 5.5 4.5 + - - +
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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
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411A GLU 3.0 17.5 + - - +
412A GLN* 3.8 5.8 - - - +
414A ARG* 1.3 74.9 - - - +
416A TYR* 1.3 62.8 + - - +
418A GLU* 3.5 9.6 + - - +
419A THR* 3.1 24.9 + - - -
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Residues in contact with TYR 416 (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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412A GLN 3.3 4.4 + - - +
413A ILE 3.7 5.4 - - - +
414A ARG 3.2 0.2 - - - -
415A ALA* 1.3 76.6 - - - +
417A CYS* 1.3 66.4 + - - +
419A THR* 3.1 9.7 + - - -
420A CYS* 3.0 47.6 + - - -
439A PRO* 4.6 4.0 - - + -
440A ALA 3.8 10.1 - - - -
441A PRO* 3.2 47.4 - - + +
444A HIS* 3.9 23.3 - + + -
446A ILE* 3.6 35.9 - - + -
478A LEU* 3.6 31.6 - - + -
481A VAL* 4.8 4.0 - - + -
482A ASP* 4.7 6.0 + - + -
485A MET* 4.1 9.4 - - - +
497A LEU* 5.5 1.1 - - + -
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Residues in contact with CYS 417 (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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413A ILE 3.0 26.3 + - - +
414A ARG* 3.6 7.2 - - - +
416A TYR* 1.3 75.3 - - - +
418A GLU* 1.3 54.4 + - - +
420A CYS* 3.0 9.0 + - - +
421A TRP* 2.8 63.0 + - + +
474A ALA 4.6 2.0 - - - -
477A GLU* 3.9 11.2 - - - -
478A LEU* 3.6 42.8 - - - -
481A VAL* 4.2 5.8 - - - -
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Residues in contact with GLU 418 (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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414A ARG* 2.9 23.7 + - + +
415A ALA* 3.5 10.3 - - - +
416A TYR 3.2 0.2 - - - -
417A CYS* 1.3 76.9 - - - +
419A THR* 1.3 61.8 + - - +
421A TRP* 3.5 27.2 + - + +
422A GLU* 3.0 41.1 + - - +
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Residues in contact with THR 419 (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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415A ALA 3.1 14.7 + - - -
416A TYR* 3.3 13.7 - - + -
418A GLU* 1.3 76.7 - - - +
420A CYS* 1.3 55.4 + - - +
422A GLU* 3.2 15.7 + - - +
423A TRP* 3.0 26.5 + - - +
439A PRO* 3.4 30.0 - - + +
444A HIS* 5.0 13.7 + - + +
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Residues in contact with CYS 420 (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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416A TYR* 3.0 53.4 + - - +
417A CYS 3.4 7.6 - - - +
419A THR* 1.3 77.4 - - - +
421A TRP* 1.3 58.6 + - - +
423A TRP* 3.2 7.0 + - - +
424A GLN* 3.0 30.8 + - - +
439A PRO* 4.4 10.8 - - - -
481A VAL* 3.7 22.9 - - + -
485A MET* 3.5 27.1 - - - -
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Residues in contact with TRP 421 (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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414A ARG* 5.0 1.8 - - - -
417A CYS* 2.8 43.8 + - + +
418A GLU* 3.8 37.7 - - + +
420A CYS* 1.3 71.7 - - - +
422A GLU* 1.3 58.7 + - + +
424A GLN* 3.2 25.6 + - - +
425A GLU* 2.9 42.8 + - - +
477A GLU* 3.8 43.4 + - + -
480A GLN* 6.0 3.8 - - - +
481A VAL* 3.6 21.0 - - + +
484A GLU* 5.8 0.4 + - - -
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Residues in contact with GLU 422 (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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418A GLU* 3.0 33.0 + - - +
419A THR* 3.2 18.3 + - - +
421A TRP* 1.3 76.2 - - - +
423A TRP* 1.3 61.5 + - - +
425A GLU* 3.4 24.0 + - + +
426A ALA* 3.8 4.7 + - - +
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Residues in contact with TRP 423 (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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419A THR 3.0 9.3 + - - +
420A CYS 3.5 8.3 - - - +
422A GLU* 1.3 74.5 - - - +
424A GLN* 1.3 103.4 + - + +
426A ALA* 3.1 28.9 + - + +
436A ASN 3.8 11.2 + - - -
437A PRO* 3.3 26.6 - - - +
438A MET* 3.4 45.3 - - + +
439A PRO* 3.7 19.1 - - + -
485A MET* 4.2 19.5 - - + -
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Residues in contact with GLN 424 (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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420A CYS 3.0 12.6 + - - +
421A TRP* 3.2 35.3 - - - +
423A TRP* 1.3 97.4 - - + +
425A GLU* 1.3 65.0 + - - +
426A ALA 3.2 8.0 + - - +
427A HIS 4.1 8.8 - - - +
481A VAL* 3.8 13.4 + - + +
484A GLU* 2.9 41.6 + - - +
485A MET* 4.9 3.8 - - + +
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Residues in contact with GLU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A TRP* 2.9 31.6 + - - +
422A GLU* 3.5 17.8 - - + +
423A TRP 3.2 0.2 - - - -
424A GLN* 1.3 76.7 - - - +
426A ALA* 1.3 57.9 + - - +
427A HIS* 2.8 12.1 + - - -
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Residues in contact with ALA 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A GLU 3.8 4.9 + - - +
423A TRP* 3.1 22.2 + - + +
424A GLN 3.8 3.4 - - - +
425A GLU* 1.3 72.5 - - - +
427A HIS* 1.3 72.5 + - - +
436A ASN* 5.3 19.5 - - + +
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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) + - + + + + + -
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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