Contacts of the helix formed by residues 403 - 427 (chain C) 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 GLU 403 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402C ARG* 1.3 73.0 - - + +
404C ILE* 1.3 62.7 + - - +
405C ARG 3.1 2.5 - - - -
406C VAL* 3.3 10.3 + - - +
407C LEU* 3.1 20.4 + - - +
462C HIS* 6.1 1.6 - - - -
465C ALA* 3.6 30.3 - - + -
469C LEU* 4.2 6.8 - - + +
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Residues in contact with ILE 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C ARG* 3.9 23.8 - - + +
403C GLU* 1.3 75.8 - - - +
405C ARG* 1.3 71.4 + - + +
407C LEU* 3.3 19.8 + - + +
408C HIS* 3.1 52.8 + - + +
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Residues in contact with ARG 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C ARG 3.6 11.1 + - - +
403C GLU 3.1 0.6 - - - -
404C ILE* 1.3 85.8 - - + +
406C VAL* 1.3 62.0 + - + +
408C HIS* 3.5 7.8 + - - +
409C LEU* 3.3 29.8 + - + +
452C VAL* 3.4 34.0 - - - +
456C LEU* 4.1 25.0 - - + +
462C HIS* 5.4 8.5 - - + -
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Residues in contact with VAL 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C GLU* 3.3 11.0 + - - +
405C ARG* 1.3 74.0 - - + +
407C LEU* 1.3 66.6 + - - +
409C LEU* 3.1 12.4 + - + +
410C LEU* 3.1 30.9 + - + +
453C LEU* 6.0 2.5 - - + -
456C LEU* 4.1 15.3 - - + -
462C HIS* 4.0 30.3 - - + +
465C ALA* 4.4 13.9 - - + -
466C MET* 3.7 30.5 - - + +
469C LEU* 4.0 14.6 - - + -
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Residues in contact with LEU 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C GLU 3.1 12.6 + - - +
404C ILE* 3.4 27.6 - - + +
406C VAL* 1.3 78.4 - - - +
408C HIS* 1.3 61.7 + - + +
410C LEU* 3.3 3.8 + - + +
411C GLU* 3.0 56.0 + - + +
414C ARG* 5.3 7.9 - - - +
469C LEU* 3.9 32.5 - - + +
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Residues in contact with HIS 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C ILE* 3.1 49.0 + - + +
405C ARG* 3.9 7.9 - - - +
406C VAL 3.3 0.2 - - - -
407C LEU* 1.3 78.1 - - + +
409C LEU* 1.3 62.2 + - + +
411C GLU* 3.4 23.9 + - - +
412C GLN* 3.2 23.9 + - - +
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Residues in contact with LEU 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C ARG* 3.3 21.7 + - + +
406C VAL* 3.1 11.3 + - + +
408C HIS* 1.3 76.4 - - + +
410C LEU* 1.3 64.4 + - - +
412C GLN* 3.2 18.0 + - - +
413C ILE* 3.2 25.6 + - - +
449C ALA* 4.1 26.7 - - + +
452C VAL* 3.9 33.2 - - + -
453C LEU* 4.4 22.4 - - + +
456C LEU* 4.2 15.5 - - + -
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Residues in contact with LEU 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C VAL* 3.1 29.7 + - + +
407C LEU* 3.8 5.8 - - - +
409C LEU* 1.3 71.9 - - - +
411C GLU* 1.3 60.5 + - - +
413C ILE* 3.3 9.1 - - + +
414C ARG* 2.9 50.6 + - - +
453C LEU* 3.7 27.6 - - + -
466C MET* 4.7 1.6 - - + +
469C LEU* 3.8 35.7 - - + +
470C GLY 4.7 0.4 - - - -
471C GLY* 3.8 32.5 - - - +
474C ALA* 4.1 13.9 - - + -
475C ILE* 4.8 0.2 - - + -
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Residues in contact with GLU 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C LEU* 3.0 42.9 + - + +
408C HIS* 3.4 30.2 + - - +
410C LEU* 1.3 74.5 - - - +
412C GLN* 1.3 56.7 + - - +
414C ARG* 3.7 10.9 - - - +
415C ALA* 2.9 32.2 + - - +
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Residues in contact with GLN 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C HIS 3.2 11.1 + - - +
409C LEU* 3.3 21.7 - - - +
411C GLU* 1.3 79.5 - - - +
413C ILE* 1.3 60.5 + - - +
415C ALA* 3.9 4.9 - - - +
416C TYR* 3.2 21.1 + - - +
444C HIS 4.3 5.5 + - - +
445C GLN* 3.3 29.9 + - - +
446C ILE* 4.1 8.7 - - + +
449C ALA* 3.6 23.0 - - + +
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Residues in contact with ILE 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C LEU 3.2 13.1 + - - +
410C LEU* 3.3 22.4 - - + +
412C GLN* 1.3 73.4 - - - +
414C ARG* 1.3 58.1 + - - +
416C TYR* 3.2 8.3 + - - +
417C CYS* 2.7 38.4 + - - -
446C ILE* 4.4 9.2 - - + -
449C ALA* 4.1 21.1 - - + -
450C VAL* 4.6 5.4 - - + +
453C LEU* 4.7 5.8 - - + -
474C ALA* 3.6 42.8 - - + +
475C ILE* 3.9 12.1 - - + +
478C LEU* 4.2 26.2 - - + -
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Residues in contact with ARG 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C LEU* 5.3 8.1 - - - +
410C LEU* 2.9 37.2 + - - +
411C GLU* 3.7 9.5 - - - +
413C ILE* 1.3 75.0 - - - +
415C ALA* 1.3 59.5 + - - +
417C CYS* 3.1 8.9 + - + +
418C GLU* 2.9 39.1 + - + +
421C TRP* 4.9 4.8 - - + -
469C LEU* 2.7 32.1 + - - +
470C GLY* 3.6 15.2 + - - -
474C ALA* 4.1 19.8 - - + +
477C GLU* 5.1 8.1 + - - +
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Residues in contact with ALA 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C GLU 2.9 18.0 + - - +
412C GLN* 3.9 6.3 - - - +
414C ARG* 1.3 74.7 - - - +
416C TYR* 1.3 62.4 + - - +
418C GLU* 3.5 11.0 + - - +
419C THR* 3.4 22.2 + - - -
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Residues in contact with TYR 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412C GLN 3.2 5.6 + - - +
413C ILE 3.5 6.1 - - - +
414C ARG 3.2 0.4 - - - -
415C ALA* 1.3 77.6 - - - +
417C CYS* 1.3 64.1 + - - +
419C THR* 3.2 11.4 + - - -
420C CYS* 3.1 46.1 + - - -
439C PRO* 3.5 17.1 + - + -
440C ALA* 3.2 6.5 - - - -
441C PRO* 2.9 44.6 - - + +
444C HIS* 3.9 31.4 - + + -
446C ILE* 3.5 32.5 - - + -
478C LEU* 3.7 30.5 - - + -
481C VAL* 5.3 1.3 - - + -
482C ASP* 5.2 3.0 + - + -
485C MET* 4.7 2.3 - - - +
486C TYR* 5.0 0.2 - - - -
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Residues in contact with CYS 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C ILE* 2.7 27.7 + - - +
414C ARG* 3.5 8.1 - - - +
416C TYR* 1.3 73.0 - - - +
418C GLU* 1.3 53.3 + - - +
420C CYS* 3.0 9.8 + - - +
421C TRP* 2.7 61.2 + - + +
474C ALA* 4.6 3.1 - - - -
477C GLU* 4.1 11.9 - - - -
478C LEU* 3.7 44.6 - - - -
481C VAL* 4.4 4.0 - - - -
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Residues in contact with GLU 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C ARG* 2.9 33.2 + - - +
415C ALA* 3.6 10.8 - - - +
416C TYR 3.3 0.2 - - - -
417C CYS* 1.3 74.7 - - - +
419C THR* 1.3 56.8 + - - +
421C TRP* 3.3 31.5 - - - +
422C GLU* 3.0 30.5 + - - +
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Residues in contact with THR 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415C ALA 3.4 10.5 + - - -
416C TYR* 3.2 17.5 + - + +
417C CYS 3.2 0.2 - - - -
418C GLU* 1.3 79.3 - - - +
420C CYS* 1.3 59.3 + - - +
422C GLU* 3.7 9.1 + - - +
423C TRP* 3.2 21.3 + - - +
439C PRO* 3.4 28.9 - - + +
444C HIS* 5.5 7.0 - - + +
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Residues in contact with CYS 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C TYR* 3.1 53.5 + - - -
417C CYS 3.0 7.2 + - - +
419C THR* 1.3 75.8 - - - +
421C TRP* 1.3 58.8 + - - +
423C TRP* 3.2 3.1 + - - +
424C GLN* 2.8 33.4 + - - +
439C PRO* 3.8 13.2 - - - -
481C VAL* 3.6 21.5 - - + -
485C MET* 3.6 28.9 - - - +
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Residues in contact with TRP 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414C ARG* 4.9 6.1 - - + -
417C CYS* 2.7 37.6 + - + +
418C GLU* 3.3 43.5 - - + +
420C CYS* 1.3 69.2 - - - +
422C GLU* 1.3 57.7 + - - +
424C GLN* 3.2 4.1 + - - -
425C GLU* 2.7 67.1 + - - +
477C GLU* 3.6 47.8 + - + +
481C VAL* 3.9 25.9 - - + +
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Residues in contact with GLU 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418C GLU 3.0 17.7 + - - +
419C THR* 3.8 8.6 - - - +
421C TRP* 1.3 75.3 - - - +
423C TRP* 1.3 63.7 + - - +
425C GLU* 5.1 0.9 - - - -
426C ALA* 2.9 37.3 + - + +
427C HIS* 3.8 3.5 + - - +
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Residues in contact with TRP 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C THR 3.2 12.8 + - - +
420C CYS 3.2 6.9 + - - +
422C GLU* 1.3 77.6 - - - +
424C GLN* 1.3 81.9 + - + +
427C HIS* 3.2 69.1 + + - +
429C PRO* 6.2 2.0 - - + -
437C PRO* 3.3 50.9 - - + -
438C MET* 3.4 31.5 - - + +
439C PRO* 3.7 12.8 - - + -
485C MET* 4.5 11.0 - - + -
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Residues in contact with GLN 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420C CYS 2.8 22.3 + - - +
421C TRP* 3.9 4.9 - - - +
423C TRP* 1.3 90.0 - - + +
425C GLU* 1.3 66.2 + - + +
427C HIS 4.9 4.2 - - - +
481C VAL* 3.8 11.9 - - - +
484C GLU* 3.0 54.3 + - - +
485C MET* 3.5 23.1 + - + +
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Residues in contact with GLU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C TRP* 2.7 54.3 + - - +
422C GLU* 5.1 0.4 - - - -
424C GLN* 1.3 82.3 + - + +
426C ALA* 1.3 60.0 + - + +
427C HIS 3.8 0.7 - - - -
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Residues in contact with ALA 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C GLU* 2.9 24.8 + - + +
425C GLU* 1.3 79.2 - - + +
427C HIS* 1.3 61.5 + - - +
428C GLU* 4.2 7.3 - - - +
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Residues in contact with HIS 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C GLU* 4.0 5.6 - - + +
423C TRP* 3.2 62.1 + + - +
424C GLN 4.9 3.1 - - - +
425C GLU 3.8 1.4 - - - -
426C ALA* 1.3 79.1 - - - +
428C GLU* 1.3 79.1 + - - +
429C PRO* 3.9 9.6 - - + +
438C MET* 5.0 11.8 - - - +
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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) + - + + + + + -
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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