Contacts of the helix formed by residues 463 - 474 (chain C) in PDB entry 6DBT
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 463 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447A LYS* 3.3 25.0 + - - +
458C LEU* 3.3 19.4 + - - +
461C GLY* 2.9 31.7 - - - +
462C ASN* 1.3 69.1 - - - +
464C HIS* 1.3 57.8 + - - +
465C LYS* 3.1 4.5 - - + -
466C GLN* 2.9 49.8 + - + +
467C ALA* 3.6 2.8 + - - +
22H A 4.9 8.3 - - - -
23H G 5.1 2.5 - - - -
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Residues in contact with HIS 464 (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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459C ARG* 2.7 73.4 + - + +
462C ASN* 3.0 38.7 + - - +
463C GLU* 1.3 71.4 - - - +
465C LYS* 1.3 64.8 + - - +
466C GLN 3.2 0.2 - - - -
467C ALA* 3.6 4.7 - - - +
468C ASP* 2.8 35.3 + - - +
42G G 4.5 24.5 + - + +
43G C 4.6 6.3 + - - -
23H G 4.9 4.2 + - - -
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Residues in contact with LYS 465 (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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463C GLU 3.1 1.8 - - - +
464C HIS* 1.3 76.1 - - - +
466C GLN* 1.3 60.7 + - + +
468C ASP* 3.2 10.4 + - - +
469C GLU* 2.9 43.9 + - - +
23H G 3.0 48.7 + - - +
24H A 5.5 1.6 + - - -
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Residues in contact with GLN 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LYS* 4.3 1.8 + - - +
473A MET* 3.7 13.7 - - + +
474A MET* 3.8 26.3 - - - +
477A ARG* 2.8 34.6 + - - +
458C LEU* 3.3 35.2 - - + +
463C GLU* 2.9 28.8 + - + +
465C LYS* 1.3 77.6 - - + +
467C ALA* 1.3 58.5 + - - +
469C GLU* 3.3 20.1 - - - +
470C LEU* 2.9 29.3 + - - +
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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
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455C LEU* 4.2 11.7 - - + +
458C LEU* 3.7 19.5 - - + +
459C ARG* 3.2 48.6 + - + +
463C GLU 3.6 3.0 + - - +
464C HIS* 3.2 6.6 + - - +
466C GLN* 1.3 78.9 - - - +
468C ASP* 1.3 55.3 + - - +
470C LEU* 3.3 4.4 + - - +
471C GLU* 2.9 29.5 + - - +
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Residues in contact with ASP 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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459C ARG* 2.6 36.3 + - - +
464C HIS* 2.8 19.3 + - - +
465C LYS* 3.6 8.6 - - - +
467C ALA* 1.3 77.0 - - - +
469C GLU* 1.3 57.3 + - + +
471C GLU* 3.4 6.0 + - - +
472C ALA* 2.9 28.6 + - - +
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Residues in contact with GLU 469 (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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473A MET* 3.4 26.1 - - + +
479A PHE* 5.9 6.1 - - - -
465C LYS* 2.9 40.9 + - - +
466C GLN* 3.3 17.3 + - - +
467C ALA 3.3 0.2 - - - -
468C ASP* 1.3 76.1 - - + +
470C LEU* 1.3 56.4 + - - +
472C ALA* 3.1 10.3 + - - +
473C MET* 2.9 25.6 + - - +
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Residues in contact with LEU 470 (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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454A PHE* 5.1 4.7 - - + -
470A LEU* 3.7 33.2 - - + -
473A MET* 4.6 6.2 - - + -
451C LEU* 4.1 16.6 - - + -
454C PHE* 3.5 30.1 - - + -
455C LEU* 3.7 29.6 - - + +
458C LEU* 5.1 3.4 - - + -
466C GLN 2.9 18.5 + - - +
467C ALA* 3.6 5.6 - - - +
469C GLU* 1.3 76.8 - - - +
471C GLU* 1.3 57.6 + - - +
473C MET* 2.8 32.5 + - + +
474C MET* 3.1 15.0 + - + +
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Residues in contact with GLU 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C LEU* 4.3 19.9 - - + +
459C ARG* 5.4 5.4 + - - +
467C ALA 2.9 17.5 + - - +
468C ASP* 3.8 6.7 - - - +
470C LEU* 1.3 76.3 - - - +
472C ALA* 1.3 57.1 + - - +
474C MET* 2.8 28.1 - - - +
476C GLY* 4.5 0.9 + - - -
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Residues in contact with ALA 472 (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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468C ASP 2.9 14.5 + - - +
469C GLU* 3.1 15.0 + - - +
471C GLU* 1.3 76.3 - - - +
473C MET* 1.3 57.5 + - - +
476C GLY* 3.2 26.4 - - - -
477C ARG* 3.3 33.8 + - - +
478C GLY* 3.9 2.3 + - - -
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Residues in contact with MET 473 (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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454A PHE* 5.8 2.0 - - + -
458A LEU* 5.4 2.2 - - + -
466A GLN* 3.6 49.6 - - + +
469A GLU* 4.8 5.8 - - + +
470A LEU* 4.7 13.2 - - - -
469C GLU 2.9 10.8 + - - +
470C LEU* 2.8 23.2 + - + +
472C ALA* 1.3 75.9 - - - +
474C MET* 1.3 94.1 + - + +
475C GLN 3.4 3.1 + - - -
476C GLY 3.5 5.4 + - - +
478C GLY* 3.3 43.4 + - - +
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Residues in contact with MET 474 (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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416A LEU* 5.4 5.4 - - + -
454A PHE* 4.2 15.0 - - + -
466A GLN* 4.6 5.6 - - - +
447C LYS* 3.6 34.1 - - + +
448C SER* 5.8 1.3 - - - +
451C LEU* 3.6 46.0 - - + -
470C LEU* 3.1 12.6 + - + +
471C GLU* 2.8 25.0 - - - +
473C MET* 1.3 91.5 - - + +
475C GLN* 1.3 67.3 + - + +
476C GLY 2.9 6.4 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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