Contacts of the helix formed by residues 723 - 732 (chain N) in PDB entry 1CZA
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 723 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476N HIS* 3.7 39.9 - - + +
477N PHE* 3.4 24.0 - - + -
721N ILE 4.0 2.2 - - - +
722N ARG* 1.3 76.4 - - - +
724N HIS* 1.3 65.3 + - - +
725N TYR* 3.3 9.4 + - - -
726N ASP* 2.8 35.1 + - - +
727N ARG* 3.0 28.7 + - - +
829N ARG* 3.9 10.8 - - - +
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Residues in contact with HIS 724 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723N THR* 1.3 74.1 - - - +
725N TYR* 1.3 86.2 + + + +
727N ARG* 3.3 29.0 + - - +
728N LEU* 3.0 63.9 + - + +
760N ASP* 5.7 2.1 - - - -
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Residues in contact with TYR 725 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473N THR* 3.5 32.0 + - + +
476N HIS* 6.0 2.2 - - - -
477N PHE* 3.8 22.0 - + + -
723N THR* 3.2 15.7 - - - +
724N HIS* 1.3 98.5 - + + +
726N ASP* 1.3 58.9 + - - +
728N LEU* 3.7 6.8 - - + +
729N VAL* 3.1 33.6 + - - +
753N ILE* 4.1 14.6 - - + +
756N ASN* 3.7 26.7 + - + -
757N ILE* 3.7 27.3 - - + -
760N ASP* 2.4 35.1 + - + +
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Residues in contact with ASP 726 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477N PHE* 4.9 0.7 - - - -
722N ARG* 3.5 22.6 + - + +
723N THR* 2.8 33.1 + - - +
725N TYR* 1.3 72.2 - - - +
727N ARG* 1.3 68.5 + - - +
729N VAL* 3.2 7.5 + - - +
730N ASP* 3.0 24.8 + - - +
743N LYS* 4.7 2.1 - - - +
744N MET* 3.8 15.0 - - + +
753N ILE* 3.6 13.9 - - - +
829N ARG* 2.8 46.1 + - - -
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Residues in contact with ARG 727 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719N ASP 5.0 4.0 + - - -
722N ARG* 3.3 53.1 + - + +
723N THR* 3.0 10.2 + - - +
724N HIS* 3.3 40.5 + - - +
726N ASP* 1.3 78.4 - - - +
728N LEU* 1.3 55.0 + - - +
730N ASP* 3.7 2.0 - - - +
731N GLU* 2.8 34.0 + - - +
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Residues in contact with LEU 728 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724N HIS* 3.0 52.4 + - + +
725N TYR* 3.7 9.6 - - + +
726N ASP 3.3 0.2 - - - -
727N ARG* 1.3 72.3 - - - +
729N VAL* 1.3 65.7 + - - +
731N GLU* 3.3 18.3 + - - +
732N TYR* 3.0 46.0 + - + +
756N ASN* 4.0 34.1 - - + +
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Residues in contact with VAL 729 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725N TYR 3.1 15.0 + - - +
726N ASP* 3.2 8.0 + - - +
728N LEU* 1.3 76.8 - - - +
730N ASP* 1.3 63.5 + - - +
732N TYR* 3.5 4.2 + - - +
733N SER* 3.2 20.4 + - - -
743N LYS* 4.9 10.3 - - + +
749N TYR* 4.1 33.0 - - + +
752N GLU* 3.8 15.5 - - + -
753N ILE* 3.8 28.5 - - + +
756N ASN* 3.7 20.6 - - - +
779N ARG* 5.7 1.1 + - - +
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Residues in contact with ASP 730 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722N ARG* 3.4 24.6 + - - +
726N ASP 3.0 7.2 + - - +
727N ARG* 3.7 2.9 - - - +
729N VAL* 1.3 76.3 - - - +
731N GLU* 1.3 64.7 + - - +
733N SER* 2.7 25.1 + - - -
736N ALA* 3.3 8.1 - - - +
737N GLY* 2.7 28.1 + - - -
738N LYS 3.9 0.3 + - - -
740N ARG* 3.3 26.7 + - - -
743N LYS* 2.7 40.5 + - + +
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Residues in contact with GLU 731 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727N ARG 2.8 17.6 + - - +
728N LEU* 3.3 20.9 + - - +
730N ASP* 1.3 78.4 - - - +
732N TYR* 1.3 74.5 + - + +
733N SER 3.5 2.1 + - - +
736N ALA* 4.1 14.6 - - - +
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Residues in contact with TYR 732 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728N LEU* 3.0 46.4 + - + +
729N VAL* 3.8 4.5 - - - +
731N GLU* 1.3 93.3 - - + +
733N SER* 1.3 62.1 + - - +
756N ASN* 6.3 0.2 - - - -
779N ARG* 3.3 34.5 + - - +
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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