Contacts of the helix formed by residues 400 - 422 (chain C) in PDB entry 5YD6
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 THR 400 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399C ASP* 1.3 76.7 + - - +
401C GLN* 1.3 75.5 + - - +
403C ILE* 3.3 3.8 + - - +
404C GLN* 2.9 31.3 + - + +
582C VAL* 3.8 36.7 - - + +
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Residues in contact with GLN 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C ASP* 3.4 11.3 + - - +
400C THR* 1.3 95.4 - - - +
402C HIS* 1.3 61.7 + - + +
404C GLN* 3.7 13.0 - - - +
405C GLN* 3.0 29.7 + - - +
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Residues in contact with HIS 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C ASP* 3.3 18.6 + - + +
400C THR 3.3 0.6 - - - -
401C GLN* 1.3 78.1 - - + +
403C ILE* 1.3 60.1 + - - +
405C GLN* 3.5 20.4 + - - +
406C PHE* 2.9 27.4 + - - +
474C GLN* 3.4 29.3 + - - +
477C ARG* 3.8 45.2 + - + +
478C GLY* 3.4 21.8 - - - +
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Residues in contact with ILE 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C ASP 3.3 25.1 + - - +
400C THR 3.3 5.8 + - - +
402C HIS* 1.3 73.9 - - - +
404C GLN* 1.3 59.7 + - - +
406C PHE* 3.3 8.8 + - - +
407C TYR* 2.9 59.6 + - + +
477C ARG 4.3 5.2 - - - +
478C GLY* 4.3 1.1 - - - +
572C ARG* 4.0 17.5 - - - +
576C LEU* 3.8 33.4 - - + -
579C GLU* 4.9 5.8 - - - +
582C VAL* 3.9 23.1 - - + -
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Residues in contact with GLN 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C THR* 2.9 19.6 + - + +
401C GLN* 3.7 17.0 - - - +
403C ILE* 1.3 75.6 - - - +
405C GLN* 1.3 56.0 + - - +
407C TYR* 3.2 20.6 + - - +
408C ASP* 2.9 65.0 + - - +
582C VAL* 4.5 11.7 - - + +
583C PRO 5.2 2.4 - - - +
585C PRO* 5.7 3.9 - - - +
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Residues in contact with GLN 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C ARG* 3.5 30.8 + - - +
401C GLN 3.0 18.2 + - - +
402C HIS* 3.5 28.3 + - - +
404C GLN* 1.3 73.3 - - - +
406C PHE* 1.3 63.6 + - - +
408C ASP* 3.3 11.2 + - - +
409C LEU* 3.0 37.6 + - + +
470C LEU* 4.1 20.8 - - - +
474C GLN* 4.0 18.9 + - - +
475C CYS* 4.9 5.3 - - - +
478C GLY* 5.2 1.4 - - - -
479C PHE* 5.2 2.8 - - - -
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Residues in contact with PHE 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C HIS 2.9 18.4 + - - +
403C ILE 3.4 8.3 - - - +
405C GLN* 1.3 76.7 - - - +
407C TYR* 1.3 70.9 + + - +
409C LEU* 3.4 3.9 + - - +
410C LEU* 3.3 46.8 + - + +
478C GLY* 3.7 20.6 - - - -
479C PHE* 3.6 56.3 - + + +
482C TRP* 3.9 17.9 - + - -
572C ARG* 4.3 13.2 - - + -
573C ILE* 4.3 15.9 - - + -
576C LEU* 4.0 23.3 - - + -
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Residues in contact with TYR 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ILE* 2.9 35.2 + - + +
404C GLN* 3.4 20.0 - - - +
406C PHE* 1.3 87.0 - + - +
408C ASP* 1.3 53.5 + - - +
410C LEU* 3.1 6.9 + - + +
411C THR* 2.8 37.6 + - - +
573C ILE* 5.3 5.4 - - + -
576C LEU* 3.3 35.9 - - + +
582C VAL* 2.9 30.7 + - + -
583C PRO 3.7 3.4 - - - -
584C PRO* 3.6 30.2 - - + +
585C PRO* 3.6 24.0 - - + -
588C ILE* 3.6 20.9 - - + -
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Residues in contact with ASP 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C ARG* 6.3 1.3 - - - +
404C GLN* 2.9 50.6 + - - +
405C GLN* 3.3 11.1 + - - +
407C TYR* 1.3 71.8 - - - +
409C LEU* 1.3 57.9 + - - +
411C THR* 3.3 9.7 + - - +
412C GLY* 2.7 34.1 + - - -
585C PRO* 6.0 1.2 - - - +
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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
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386C ARG* 4.7 15.5 - - - +
405C GLN* 3.0 27.6 + - + +
406C PHE 3.7 4.7 - - - +
408C ASP* 1.3 75.7 - - - +
410C LEU* 1.3 62.2 + - - +
412C GLY* 4.3 1.3 - - - -
413C SER* 3.2 21.1 + - - -
447C PHE* 3.7 9.9 - - + -
464C PHE* 3.5 64.5 - - + +
465C CYS* 5.3 1.2 - - - -
466C ASN* 4.3 11.0 - - - +
468C VAL* 4.8 3.8 - - + -
470C LEU* 4.0 14.4 - - + -
479C PHE* 4.0 15.9 - - + -
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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 PHE* 3.3 45.9 + - + +
407C TYR* 3.1 7.4 + - - +
409C LEU* 1.3 74.7 - - - +
411C THR* 1.3 64.5 + - - +
413C SER* 3.1 10.6 + - - -
414C MET* 3.3 3.3 - - - +
443C PHE* 3.3 31.3 - - + -
444C LEU* 3.8 20.0 - - + -
447C PHE* 3.7 35.4 - - + -
482C TRP* 5.1 0.7 - - + -
573C ILE* 4.2 16.8 - - + -
588C ILE* 4.1 22.7 - - + -
601C 8SU 4.4 4.0 - - + -
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Residues in contact with THR 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C TYR 2.8 22.2 + - - +
408C ASP* 3.3 15.3 + - - +
410C LEU* 1.3 65.9 - - - +
412C GLY* 1.3 59.0 + - - +
413C SER 2.9 9.8 + - - -
414C MET* 3.0 24.6 + - - +
415C GLU* 4.3 2.8 + - - +
585C PRO* 3.8 22.0 - - + -
587C ILE* 3.5 31.0 - - + -
588C ILE* 3.8 9.9 - - + -
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Residues in contact with GLY 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C ASP 2.7 21.5 + - - -
409C LEU* 4.3 1.6 - - - -
411C THR* 1.3 71.4 + - - +
413C SER* 1.3 58.1 + - - +
414C MET 3.5 0.2 - - - -
415C GLU* 4.9 2.5 + - - +
416C ILE* 3.8 20.4 + - - +
465C CYS* 4.0 4.8 - - - -
466C ASN* 6.0 1.4 - - - +
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Residues in contact with SER 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C LEU 3.2 19.2 + - - -
410C LEU 3.3 7.0 - - - -
411C THR 2.9 0.6 + - - -
412C GLY* 1.3 81.0 - - - +
414C MET* 1.3 62.1 + - - +
415C GLU 3.6 0.7 - - - -
416C ILE* 3.6 3.6 + - - +
417C ILE* 3.2 42.3 + - - +
443C PHE* 4.1 2.1 - - - -
447C PHE* 3.6 18.3 - - - -
465C CYS* 3.7 24.2 - - - +
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Residues in contact with MET 414 (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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410C LEU 3.3 14.6 - - - +
411C THR* 3.0 24.0 + - - +
413C SER* 1.3 78.6 - - - +
415C GLU* 1.3 65.9 + - + +
417C ILE 3.4 0.7 + - - -
418C ARG* 2.9 30.1 + - - +
439C PHE* 3.6 15.6 - - + -
443C PHE* 3.4 26.5 - - + -
587C ILE* 3.2 46.0 - - + +
588C ILE* 5.1 4.7 - - - -
591C LEU* 3.9 29.2 - - + -
601C 8SU 5.9 0.7 - - - -
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Residues in contact with GLU 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C THR 4.3 2.9 + - - +
412C GLY 4.9 2.3 + - - +
414C MET* 1.3 83.4 - - + +
416C ILE* 1.3 61.3 + - + +
418C ARG* 3.3 40.7 + - - +
419C GLY* 2.8 27.2 + - - -
439C PHE* 6.0 0.2 - - - -
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Residues in contact with ILE 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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380A THR* 3.8 27.6 - - + +
375C SER* 3.2 34.4 - - - +
412C GLY 3.8 12.0 + - - +
413C SER 3.6 8.9 + - - +
414C MET 3.3 0.4 - - - -
415C GLU* 1.3 78.8 - - + +
417C ILE* 1.3 56.2 + - - +
419C GLY* 3.2 3.4 + - - -
420C TRP* 2.9 26.3 + - - +
450C ARG* 3.3 14.1 - - - +
465C CYS* 3.7 36.8 - - + +
466C ASN* 5.1 4.7 - - + +
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Residues in contact with ILE 417 (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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413C SER* 3.2 35.7 + - - +
414C MET 4.1 2.5 - - - +
416C ILE* 1.3 71.5 - - - +
418C ARG* 1.3 61.2 - - - +
420C TRP* 3.2 25.4 + - + +
421C ALA* 2.9 25.5 + - - +
439C PHE* 4.0 18.4 - - + -
443C PHE* 3.7 20.4 - - + -
446C LEU* 4.1 16.4 - - + -
447C PHE* 3.9 24.0 - - - +
450C ARG* 3.6 27.4 - - - +
511C MET* 5.9 0.4 - - - -
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Residues in contact with ARG 418 (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 MET* 2.9 16.8 + - - +
415C GLU* 3.3 38.2 + - - +
417C ILE* 1.3 77.1 - - - +
419C GLY* 1.3 60.1 + - - +
421C ALA* 3.2 6.7 + - + +
422C GLU* 3.1 50.3 + - - +
432C LYS* 4.1 21.0 - - - +
436C ASP* 4.7 4.9 + - - -
439C PHE* 3.6 45.3 - - + -
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Residues in contact with GLY 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C SER* 5.4 0.9 - - - -
415C GLU 2.8 18.5 + - - -
416C ILE 3.2 4.5 + - - -
418C ARG* 1.3 70.7 - - - +
420C TRP* 1.3 62.3 + - - +
422C GLU* 3.5 11.6 + - - +
423C LYS* 3.4 32.6 + - - +
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Residues in contact with TRP 420 (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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368C LEU* 4.8 3.2 + - - +
371C ALA* 3.5 36.9 - - + +
372C HIS* 3.7 10.9 - - - +
375C SER* 3.5 22.8 - - - +
416C ILE 2.9 10.9 + - - +
417C ILE* 3.2 26.0 + - + +
419C GLY* 1.3 73.5 - - - +
421C ALA* 1.3 76.2 + - + +
423C LYS* 3.1 16.6 + - - +
424C ILE* 3.5 30.8 + - + +
446C LEU* 3.8 20.9 - - + -
450C ARG* 4.1 12.0 - - - +
504C SER* 4.9 3.5 + - - +
507C ALA* 3.3 47.1 - - + +
508C ALA* 3.6 7.4 - - + -
511C MET* 3.9 27.6 - - + -
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Residues in contact with ALA 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C ILE 2.9 12.8 + - - +
418C ARG* 3.2 13.6 + - + +
420C TRP* 1.3 83.4 - - + +
422C GLU* 1.3 57.2 + - - +
424C ILE* 3.0 30.7 + - - +
427C PHE* 3.5 24.5 - - + +
439C PHE* 5.2 4.5 - - + -
511C MET* 3.6 30.5 - - + -
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Residues in contact with GLU 422 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C ARG* 3.1 50.3 + - - +
419C GLY* 3.5 9.3 + - - +
420C TRP 3.3 0.2 - - - -
421C ALA* 1.3 73.0 - - - +
423C LYS* 1.3 62.8 + - + +
424C ILE 3.4 4.2 - - - +
427C PHE* 4.3 9.9 - - + -
428C ALA* 4.6 16.6 - - + +
432C LYS* 5.7 0.7 + - - -
435C GLN* 4.4 21.4 + - - +
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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