Contacts of the helix formed by residues 452 - 477 (chain H) 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 PHE 452 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451H ALA* 3.8 26.5 - - - +
453H ASN* 3.8 28.7 - - - +
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Residues in contact with ASN 453 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452H PHE* 3.8 28.5 - - - +
454H LEU* 3.8 26.0 - - - +
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Residues in contact with LEU 454 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453H ASN* 3.8 26.2 - - - +
455H GLN* 3.8 28.5 - - - +
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Residues in contact with GLN 455 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454H LEU* 3.8 28.7 - - - +
456H LYS* 3.9 26.2 - - - +
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Residues in contact with LYS 456 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455H GLN* 3.9 28.3 - - - +
457H ALA* 3.9 25.6 - - - +
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Residues in contact with ALA 457 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456H LYS* 3.9 26.7 - - - +
458H ALA* 3.9 28.5 - - - +
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Residues in contact with ALA 458 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457H ALA* 3.9 26.0 - - - +
459H ALA* 3.8 28.9 - - - +
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Residues in contact with ALA 459 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458H ALA* 3.8 28.9 - - - +
460H GLU* 3.8 26.0 - - - +
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Residues in contact with GLU 460 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459H ALA* 3.8 24.7 - - - +
461H GLY* 3.8 28.9 - - - +
463H MET* 4.7 16.8 - - - +
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Residues in contact with GLY 461 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460H GLU* 3.8 25.8 - - - +
462H LEU* 3.8 29.6 - - - +
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Residues in contact with LEU 462 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461H GLY* 3.8 28.9 - - - +
463H MET* 3.8 26.9 - - - +
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Residues in contact with MET 463 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460H GLU* 4.7 15.3 - - - +
462H LEU* 3.8 28.7 - - - +
464H SER* 3.8 25.4 - - - +
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Residues in contact with SER 464 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463H MET* 3.8 26.2 - - - +
465H LEU* 3.8 28.9 - - - +
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Residues in contact with LEU 465 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464H SER* 3.8 29.4 - - - +
466H LEU* 3.8 26.7 - - - +
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Residues in contact with LEU 466 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465H LEU* 3.8 28.0 - - - +
467H ARG* 3.8 25.8 - - - +
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Residues in contact with ARG 467 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466H LEU* 3.8 26.2 - - - +
468H GLU* 3.8 29.6 - - - +
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Residues in contact with GLU 468 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467H ARG* 3.8 26.5 - - - +
469H MET* 3.8 28.7 - - - +
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Residues in contact with MET 469 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468H GLU* 3.8 27.1 - - - +
470H GLY* 3.8 29.2 - - - +
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Residues in contact with GLY 470 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469H MET* 3.8 28.7 - - - +
471H LYS* 3.8 26.5 - - - +
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Residues in contact with LYS 471 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470H GLY* 3.8 24.7 - - - +
472H GLY* 3.8 29.6 - - - +
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Residues in contact with GLY 472 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471H LYS* 3.8 29.6 - - - +
473H TYR* 3.8 27.1 - - - +
484H ALA* 4.5 22.0 - - - +
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Residues in contact with TYR 473 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472H GLY* 3.8 28.9 - - - +
474H LEU* 3.8 25.6 - - - +
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Residues in contact with LEU 474 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473H TYR* 3.8 25.6 - - - +
475H ALA* 3.8 28.5 - - - +
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Residues in contact with ALA 475 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474H LEU* 3.8 25.6 - - - +
476H LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 476 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475H ALA* 3.8 26.7 - - - +
477H CYS* 3.8 29.8 - - - +
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Residues in contact with CYS 477 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476H LEU* 3.8 29.4 - - - +
478H SER* 3.8 24.7 - - - +
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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