Contacts of the helix formed by residues 597 - 614 (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 PRO 597 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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596O SER* 3.8 26.0 - - - -
598O THR* 3.8 29.2 - - - -
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Residues in contact with THR 598 (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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597O PRO* 3.8 28.0 - - - -
599O ILE* 3.8 26.2 - - - +
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Residues in contact with ILE 599 (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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598O THR* 3.8 29.4 - - - +
600O ALA* 3.9 24.5 - - - +
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Residues in contact with ALA 600 (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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599O ILE* 3.9 27.4 - - - +
601O LEU* 3.8 28.7 - - - +
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Residues in contact with LEU 601 (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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600O ALA* 3.8 28.0 - - - +
602O PRO* 3.9 27.8 - - - -
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Residues in contact with PRO 602 (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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601O LEU* 3.9 26.2 - - - -
603O MET* 3.8 29.2 - - - -
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Residues in contact with MET 603 (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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602O PRO* 3.8 28.7 - - - -
604O LEU* 3.8 27.6 - - - +
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Residues in contact with LEU 604 (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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603O MET* 3.8 25.8 - - - +
605O LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 605 (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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604O LEU* 3.8 29.4 - - - +
606O GLN* 3.8 26.2 - - - +
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Residues in contact with GLN 606 (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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605O LEU* 3.8 24.0 - - - +
607O ALA* 3.8 28.9 - - - +
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Residues in contact with ALA 607 (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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606O GLN* 3.8 28.7 - - - +
608O LEU* 3.8 27.6 - - - +
610O LEU* 4.7 16.2 - - - +
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Residues in contact with LEU 608 (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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607O ALA* 3.8 26.0 - - - +
609O ALA* 3.8 28.9 - - - +
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Residues in contact with ALA 609 (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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608O LEU* 3.8 25.6 - - - +
610O LEU* 3.8 29.6 - - - +
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Residues in contact with LEU 610 (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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607O ALA* 4.7 16.8 - - - +
609O ALA* 3.8 29.2 - - - +
611O SER* 3.9 26.2 - - - +
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Residues in contact with SER 611 (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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610O LEU* 3.9 24.5 - - - +
612O LYS* 3.8 29.2 - - - +
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Residues in contact with LYS 612 (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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611O SER* 3.8 29.4 - - - +
613O GLU* 3.8 24.7 - - - +
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Residues in contact with GLU 613 (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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612O LYS* 3.8 26.7 - - - +
614O TYR* 3.8 29.2 - - - +
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Residues in contact with TYR 614 (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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613O GLU* 3.8 28.7 - - - +
615O ARG* 3.8 27.6 - - - +
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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