Contacts of the helix formed by residues 504 - 522 (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 ALA 504 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503O HIS* 3.8 28.9 - - - +
505O GLN* 3.8 21.5 - - - +
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Residues in contact with GLN 505 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503O HIS* 4.6 7.6 - - - +
504O ALA* 3.8 26.7 - - - +
506O LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 506 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505O GLN* 3.8 29.8 - - - +
507O TRP* 3.8 27.4 - - - +
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Residues in contact with TRP 507 (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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506O LEU* 3.8 29.2 - - - +
508O MET* 3.8 25.6 - - - +
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Residues in contact with MET 508 (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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507O TRP* 3.8 24.9 - - - +
509O LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 509 (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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508O MET* 3.8 29.4 - - - +
510O CYS* 3.8 25.8 - - - +
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Residues in contact with CYS 510 (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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509O LEU* 3.8 28.9 - - - +
511O ASP* 3.9 25.8 - - - +
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Residues in contact with ASP 511 (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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510O CYS* 3.9 25.8 - - - +
512O GLN* 3.7 29.8 - - - +
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Residues in contact with GLN 512 (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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511O ASP* 3.7 29.4 - - - +
513O LYS* 3.9 26.0 - - - +
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Residues in contact with LYS 513 (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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512O GLN* 3.9 25.1 - - - +
514O ILE* 3.8 28.7 - - - +
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Residues in contact with ILE 514 (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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513O LYS* 3.8 26.5 - - - +
515O GLN* 3.8 28.9 - - - +
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Residues in contact with GLN 515 (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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514O ILE* 3.8 29.4 - - - +
516O PHE* 3.8 26.0 - - - +
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Residues in contact with PHE 516 (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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515O GLN* 3.8 26.5 - - - +
517O ASP* 3.7 30.3 - - - +
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Residues in contact with ASP 517 (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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516O PHE* 3.7 29.6 - - - +
518O ARG* 3.8 26.5 - - - +
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Residues in contact with ARG 518 (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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517O ASP* 3.8 25.6 - - - +
519O ALA* 3.8 28.7 - - - +
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Residues in contact with ALA 519 (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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518O ARG* 3.8 28.9 - - - +
520O MET* 3.9 25.6 - - - +
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Residues in contact with MET 520 (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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519O ALA* 3.9 27.1 - - - +
521O ASN* 3.8 29.2 - - - +
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Residues in contact with ASN 521 (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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520O MET* 3.8 29.4 - - - +
522O ASP* 3.8 25.8 - - - +
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Residues in contact with ASP 522 (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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521O ASN* 3.8 24.7 - - - +
523O GLY* 3.8 28.5 - - - +
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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