Contacts of the helix formed by residues 688 - 696 (chain H) in PDB entry 5KRA
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 LYS 688 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542F GLU* 3.5 21.2 + - - +
687H HIS* 1.3 77.0 - - - +
689H ILE* 1.3 84.6 + - - +
690H LEU 3.2 1.3 - - - -
691H HIS* 3.4 15.1 - - + +
692H ARG* 2.7 46.4 + - + +
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Residues in contact with ILE 689 (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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538F ASP* 3.8 29.4 - - + +
539F LEU* 3.6 33.4 - - + +
542F GLU* 3.2 22.8 + - - +
688H LYS* 1.3 100.7 - - - +
690H LEU* 1.3 63.8 + - - +
692H ARG* 3.2 19.5 + - - +
693H LEU* 3.0 34.2 + - + +
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Residues in contact with LEU 690 (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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358F ILE* 3.6 26.7 - - + -
376F VAL* 3.5 41.3 - - + +
379F LEU* 3.7 26.0 - - + -
380F GLU* 3.6 20.0 - - + +
539F LEU* 4.1 7.9 - - + +
542F GLU* 4.5 1.0 + - - -
543F MET* 3.7 26.7 - - + -
687H HIS* 5.1 5.6 - - + +
688H LYS* 4.2 0.4 - - - +
689H ILE* 1.3 78.1 - - - +
691H HIS* 1.3 64.4 + - - +
693H LEU* 4.0 2.8 - - - -
694H LEU* 3.1 30.7 + - + +
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Residues in contact with HIS 691 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372F LEU* 3.3 27.1 + - + +
373F HIS* 5.9 1.7 - - - -
376F VAL* 4.0 18.9 - - + +
687H HIS 3.6 9.1 + - - +
688H LYS* 3.4 27.4 - - + +
690H LEU* 1.3 80.2 - - - +
692H ARG* 1.3 61.8 + - + +
694H LEU* 3.9 3.5 - - - +
695H GLN* 3.3 47.8 + - - +
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Residues in contact with ARG 692 (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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688H LYS* 2.7 27.1 + - + +
689H ILE* 3.3 28.1 + - - +
690H LEU 3.2 0.2 - - - -
691H HIS* 1.3 72.2 - - + +
693H LEU* 1.3 82.9 + - - +
694H LEU 3.0 1.6 - - - -
695H GLN* 2.8 30.8 + - - +
696H ASP* 3.1 39.5 + - - +
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Residues in contact with LEU 693 (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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355F VAL* 4.6 20.4 - - + -
358F ILE* 3.6 38.1 - - + +
359F ASN* 4.6 7.1 + - - +
362F LYS* 3.0 22.5 + - - -
539F LEU* 4.0 18.4 - - + -
689H ILE* 3.0 24.2 + - + +
690H LEU 3.5 2.4 + - - +
692H ARG* 1.3 102.0 - - - +
694H LEU* 1.3 56.4 + - - +
696H ASP* 3.9 10.7 + - - +
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Residues in contact with LEU 694 (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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358F ILE* 3.6 27.1 - - + +
362F LYS* 3.4 31.2 + - + +
367F PHE* 4.5 4.3 - - + -
372F LEU* 3.8 14.0 - - + +
375F GLN* 3.4 45.0 - - + +
376F VAL* 4.0 17.0 - - + +
379F LEU* 3.8 22.2 - - + -
690H LEU* 3.1 20.9 + - + +
691H HIS 3.9 0.7 - - - +
692H ARG 3.0 0.8 - - - -
693H LEU* 1.3 77.3 - - - +
695H GLN* 1.3 63.6 + - - +
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Residues in contact with GLN 695 (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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372F LEU* 3.6 19.7 - - + +
691H HIS* 3.3 39.7 + - - +
692H ARG* 2.8 18.7 + - - +
694H LEU* 1.3 80.2 - - - +
696H ASP* 1.3 69.5 + - - +
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Residues in contact with ASP 696 (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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362F LYS* 3.6 20.4 - - - -
692H ARG* 3.1 39.6 + - - +
693H LEU* 3.9 8.8 + - - +
694H LEU 3.6 0.6 - - - -
695H GLN* 1.3 85.0 - - - +
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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