Contacts of the helix formed by residues 463 - 479 (chain O) in PDB entry 5KHR
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 463 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462O ASN* 3.9 27.6 - - - +
464O GLU* 3.8 28.3 - - - +
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Residues in contact with GLU 464 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463O THR* 3.8 25.4 - - - +
465O SER* 3.8 28.9 - - - +
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Residues in contact with SER 465 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464O GLU* 3.8 28.9 - - - +
466O PHE* 3.8 28.3 - - - +
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Residues in contact with PHE 466 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465O SER* 3.8 25.6 - - - +
467O ALA* 3.8 29.4 - - - +
469O ALA* 4.7 15.9 - - - +
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Residues in contact with ALA 467 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466O PHE* 3.8 29.2 - - - +
468O VAL* 3.8 26.5 - - - +
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Residues in contact with VAL 468 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467O ALA* 3.8 29.2 - - - +
469O ALA* 3.8 24.7 - - - +
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Residues in contact with ALA 469 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466O PHE* 4.7 16.2 - - - +
468O VAL* 3.8 29.2 - - - +
470O LEU* 3.8 28.0 - - - +
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Residues in contact with LEU 470 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469O ALA* 3.8 25.1 - - - +
471O CYS* 3.7 29.6 - - - +
473O LEU* 4.5 16.4 - - - +
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Residues in contact with CYS 471 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470O LEU* 3.7 27.1 - - - +
472O HIS* 3.7 29.6 - - - +
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Residues in contact with HIS 472 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471O CYS* 3.7 29.8 - - - +
473O LEU* 3.8 24.9 - - - +
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Residues in contact with LEU 473 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470O LEU* 4.5 16.4 - - - +
472O HIS* 3.8 28.9 - - - +
474O ALA* 3.8 26.2 - - - +
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Residues in contact with ALA 474 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473O LEU* 3.8 26.0 - - - +
475O GLU* 3.8 28.5 - - - +
486O ALA* 4.5 22.0 - - - +
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Residues in contact with GLU 475 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474O ALA* 3.8 29.2 - - - +
476O LEU* 3.8 27.6 - - - +
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Residues in contact with LEU 476 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475O GLU* 3.8 25.1 - - - +
477O HIS* 3.8 28.9 - - - +
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Residues in contact with HIS 477 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476O LEU* 3.8 27.1 - - - +
478O ALA* 3.8 28.9 - - - +
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Residues in contact with ALA 478 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477O HIS* 3.8 24.9 - - - +
479O GLU* 3.8 29.2 - - - +
483O PHE* 4.5 23.1 - - - +
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Residues in contact with GLU 479 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478O ALA* 3.8 28.7 - - - +
480O GLN* 3.8 27.1 - - - +
656O ALA* 4.6 16.6 - - - +
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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