Contacts of the helix formed by residues 452 - 472 (chain C) in PDB entry 5Y3R
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 LYS 452 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C ARG* 3.4 35.4 - - - +
450C SER* 3.2 11.8 + - - +
451C PRO* 1.3 81.2 - - - +
453C MET* 1.3 74.9 + - + +
454C GLN 2.7 12.2 + - - -
455C LEU* 3.7 10.9 + - - +
456C VAL* 4.2 9.0 + - - +
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Residues in contact with MET 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C LYS* 6.2 7.2 - - + -
408C TYR* 5.1 20.0 - - + -
449C TYR* 4.9 3.6 - - + -
450C SER* 2.9 33.2 + - - +
452C LYS* 1.3 98.6 - - + +
454C GLN* 1.3 58.3 + - + +
455C LEU 3.5 0.4 - - - -
456C VAL* 3.1 30.6 - - + +
457C CYS* 2.9 32.1 + - - -
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Residues in contact with GLN 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C PHE* 5.4 1.8 - - - -
449C TYR* 3.0 52.4 + - + +
450C SER 2.9 22.5 + - - +
451C PRO* 3.0 24.5 - - - +
452C LYS 2.7 4.6 + - - -
453C MET* 1.3 73.0 - - - +
455C LEU* 1.3 60.3 + - + +
457C CYS* 3.0 13.2 - - - +
458C CYS* 2.9 29.7 + - - -
532C ARG* 5.8 4.2 - - - +
533C HIS* 4.1 7.0 + - + -
536C SER* 5.3 3.4 - - - +
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Residues in contact with LEU 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C PRO 5.7 1.6 - - - +
452C LYS 3.7 7.6 + - - +
454C GLN* 1.3 74.9 - - + +
456C VAL* 1.3 67.4 + - + +
458C CYS* 3.0 10.1 - - - +
459C ARG* 3.0 27.4 + - - +
532C ARG* 6.0 3.1 - - - +
536C SER* 3.6 22.0 - - - +
539C GLN* 6.5 0.9 - - + -
540C MET* 3.6 36.0 - - + +
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Residues in contact with VAL 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C TYR* 5.9 2.9 - - - +
411C PRO* 6.0 5.6 - - + -
415C GLN* 3.9 9.5 + - - +
452C LYS* 4.2 7.4 - - + +
453C MET* 3.1 45.1 - - + +
455C LEU* 1.3 77.5 - - + +
457C CYS* 1.3 62.2 + - - +
459C ARG* 3.0 37.0 + - - +
460C ALA* 2.9 21.2 + - + +
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Residues in contact with CYS 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C TYR* 6.2 1.1 - - - -
411C PRO* 4.9 16.4 - - + -
442C GLN* 5.2 3.1 - - - +
449C TYR* 3.9 30.5 - - - -
453C MET* 2.9 30.5 + - - -
454C GLN* 3.0 18.8 - - - +
456C VAL* 1.3 74.9 - - - +
458C CYS* 1.3 63.7 + - - +
460C ALA* 2.9 22.4 - - - +
461C ILE* 3.0 17.1 + - + +
533C HIS* 3.3 18.2 - - + +
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Residues in contact with CYS 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C GLN 2.9 17.4 + - - -
455C LEU* 3.0 20.2 + - - +
457C CYS* 1.3 77.4 - - - +
459C ARG* 1.3 66.8 + - - +
460C ALA 2.8 1.6 + - - -
461C ILE* 2.9 15.0 + - - +
462C VAL* 2.9 18.1 + - + +
533C HIS* 4.7 4.5 - - - -
536C SER* 2.3 50.7 - - - +
537C SER* 4.4 7.9 - - - +
540C MET* 4.5 14.4 - - + -
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Residues in contact with ARG 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C GLN* 3.1 16.9 + - - +
455C LEU* 3.0 10.4 + - - +
456C VAL* 3.2 49.5 - - - +
458C CYS* 1.3 78.2 - - - +
460C ALA* 1.3 65.2 + - - +
462C VAL* 3.1 10.4 - - - +
463C LYS* 3.0 23.9 + - - +
540C MET* 4.7 6.3 - - + +
541C MET* 3.4 42.7 - - + +
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Residues in contact with ALA 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C PRO* 3.8 19.5 - - + -
414C LEU* 3.4 23.2 - - + +
415C GLN* 3.0 24.8 - - + +
456C VAL* 2.9 11.7 + - + +
457C CYS 2.9 13.5 - - - +
458C CYS 2.8 0.6 + - - -
459C ARG* 1.3 80.7 - - - +
461C ILE* 1.3 66.1 - - + +
463C LYS* 2.9 9.7 + - - +
464C VAL 3.0 8.7 + - - -
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Residues in contact with ILE 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C LEU* 3.4 9.0 - - + -
439C VAL* 4.3 5.6 - - + -
442C GLN* 3.0 30.7 - - - +
443C ILE* 3.4 40.2 - - + -
457C CYS 3.0 25.1 - - - +
458C CYS* 2.9 8.5 + - - +
460C ALA* 1.3 71.6 - - - +
462C VAL* 1.3 56.0 + - - +
464C VAL* 2.2 50.0 + - + +
465C PHE* 2.9 30.0 - - + -
533C HIS* 4.2 8.3 - - + +
537C SER* 6.2 5.4 - - - -
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Residues in contact with VAL 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C CYS 2.9 21.6 + - - +
459C ARG* 3.1 17.9 - - + +
461C ILE* 1.3 75.1 - - - +
463C LYS* 1.3 64.6 + - - +
465C PHE* 2.7 35.8 + - + +
466C LEU* 3.0 11.4 + - + +
537C SER 5.4 6.5 - - - +
540C MET* 5.8 2.9 - - + +
541C MET* 5.5 12.8 - - + -
542C ASP* 6.1 0.9 - - - +
543C SER 5.0 5.6 - - - +
545C LEU* 4.7 11.0 - - + -
548C GLU* 3.8 29.8 - - - +
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Residues in contact with LYS 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C GLN* 3.3 46.4 - - + +
418C ALA* 3.6 10.3 - - + -
419C SER* 2.8 32.0 + - - +
422C LEU* 5.0 10.8 - - + +
459C ARG 3.0 19.1 + - - +
460C ALA 2.9 7.5 + - - +
462C VAL* 1.3 77.9 - - + +
464C VAL* 1.3 62.5 + - - +
465C PHE 2.9 0.7 + - - -
466C LEU* 3.1 12.3 + - + +
467C ALA* 3.0 20.8 + - - +
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Residues in contact with VAL 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C LEU* 3.8 26.2 - - + -
417C VAL* 5.9 3.8 - - + -
418C ALA* 4.6 9.3 - - + +
435C LEU* 5.3 9.0 - - + -
439C VAL* 4.8 11.4 - - + -
460C ALA 3.0 5.9 + - - -
461C ILE* 2.2 41.8 + - + +
463C LYS* 1.3 68.8 - - - +
465C PHE* 1.3 86.1 + - + +
467C ALA* 3.1 10.0 - - + +
468C LEU* 2.8 42.1 + - + +
479C ILE* 5.7 4.7 - - + -
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Residues in contact with PHE 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C VAL* 6.4 0.2 - - + -
443C ILE* 5.4 1.8 - - + -
461C ILE* 2.9 53.8 - - + -
462C VAL* 2.7 27.7 + - + +
464C VAL* 1.3 79.2 - - + +
466C LEU* 1.3 60.3 + - - +
468C LEU* 2.7 41.6 + - + +
469C ALA* 2.8 11.6 + - - +
476C ARG* 5.4 6.7 - - + -
479C ILE* 6.0 6.7 - - + -
480C SER* 5.9 7.6 - - - -
548C GLU* 4.7 30.1 - - + +
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Residues in contact with LEU 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C LEU* 4.3 26.7 - - + -
462C VAL* 3.0 11.2 + - + +
463C LYS* 3.1 12.8 + - + +
465C PHE* 1.3 74.9 - - - +
467C ALA* 1.3 64.9 + - - +
469C ALA* 2.8 27.1 + - + +
470C ALA* 3.0 14.1 + - + +
543C SER* 5.5 14.8 - - - +
548C GLU* 5.9 0.2 + - - -
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Residues in contact with ALA 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C ALA* 4.4 23.8 - - - +
421C LEU* 5.2 5.5 - - + -
422C LEU* 4.3 22.8 - - + +
463C LYS 3.0 11.6 + - - +
464C VAL* 3.1 15.0 - - + +
466C LEU* 1.3 78.0 - - - +
468C LEU* 1.3 54.8 + - + +
469C ALA 3.0 0.3 + - - -
470C ALA* 3.2 1.0 + - - +
471C LYS* 2.5 38.5 + - - +
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Residues in contact with LEU 468 (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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435C LEU* 5.6 2.9 - - + -
464C VAL* 2.8 27.1 - - + +
465C PHE* 2.7 48.3 + - + +
467C ALA* 1.3 74.1 - - + +
469C ALA* 1.3 57.2 + - - +
471C LYS* 3.1 54.5 + - + +
472C GLY 3.4 3.1 + - - -
473C PRO* 4.4 1.6 - - - +
475C LEU* 5.0 7.0 - - + -
476C ARG* 3.5 37.1 - - + +
479C ILE* 5.5 8.3 - - + -
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Residues in contact with ALA 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C PHE 2.8 9.6 + - - +
466C LEU* 2.8 23.0 + - + +
468C LEU* 1.3 74.1 - - - +
470C ALA* 1.3 65.1 + - - +
471C LYS 3.0 1.9 + - - -
472C GLY* 3.0 9.4 + - - -
473C PRO* 4.5 2.6 - - - +
1552C HIS* 2.9 21.7 - - + -
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Residues in contact with ALA 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C LEU* 3.4 38.1 - - + +
424C LEU 5.8 0.2 - - - -
425C ASP* 2.9 29.3 - - - +
466C LEU* 3.0 5.4 + - + +
467C ALA 3.8 2.0 - - - +
469C ALA* 1.3 78.7 - - - +
471C LYS* 1.3 63.8 + - - +
472C GLY* 3.4 0.5 + - - -
1552C HIS* 3.5 19.7 + - + +
1555C HIS* 5.9 0.5 - - - -
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Residues in contact with LYS 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C LEU 6.2 0.2 - - - -
424C LEU 5.5 4.0 - - - -
425C ASP* 4.8 5.0 - - - +
467C ALA 2.5 23.1 + - - +
468C LEU* 3.1 48.9 + - + +
470C ALA* 1.3 74.9 - - - +
472C GLY* 1.3 61.9 + - - +
473C PRO 3.6 0.4 - - - -
474C VAL* 2.6 47.8 - - + +
475C LEU* 3.1 21.4 - - + +
476C ARG* 3.6 6.6 - - - +
1556C GLY* 5.1 2.6 - - - -
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Residues in contact with GLY 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C LEU 3.4 0.4 + - - -
469C ALA 3.0 10.6 + - - -
470C ALA 4.3 1.1 - - - -
471C LYS* 1.3 81.8 + - - +
473C PRO* 1.3 66.0 - - - -
474C VAL* 2.7 36.0 + - - +
1552C HIS* 4.7 3.8 - - - -
1556C GLY* 4.3 16.2 - - - -
1561C SER* 3.9 3.9 + - - -
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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