Contacts of the helix formed by residues 724 - 733 (chain A) in PDB entry 4N78
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 ASP 724 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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722A LEU 3.4 4.8 + - - -
723A LEU* 1.3 78.1 - - - +
725A LYS* 1.3 64.9 + - - +
726A ARG* 3.1 14.3 + - - +
727A LEU* 2.8 42.9 + - + +
728A ARG* 3.3 20.4 + - - +
898A TYR* 5.6 0.2 - - - -
901A ILE* 5.0 6.8 - - + +
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Residues in contact with LYS 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720A SER 4.8 4.8 + - - -
721A LEU* 4.0 19.8 + - - +
723A LEU 4.1 10.7 + - - +
724A ASP* 1.3 72.7 + - - +
726A ARG* 1.3 65.9 + - - +
728A ARG* 3.0 31.9 + - - +
729A SER* 3.1 13.2 + - - -
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Residues in contact with ARG 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724A ASP* 3.1 12.1 + - - +
725A LYS* 1.3 78.2 - - - +
727A LEU* 1.3 57.7 + - - +
729A SER* 2.7 27.1 + - - -
730A GLU* 2.9 50.5 + - + +
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Residues in contact with LEU 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723A LEU* 4.2 11.7 - - + -
724A ASP* 2.8 24.4 + - + +
726A ARG* 1.3 76.8 - - - +
728A ARG* 1.3 63.0 + - - +
730A GLU* 3.3 7.7 + - + +
731A CYS* 2.9 40.8 + - - -
738A ILE* 4.9 3.4 - - + -
897A ALA* 4.8 10.1 - - + +
901A ILE* 3.6 38.6 - - + -
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Residues in contact with ARG 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720A SER* 3.3 47.3 + - - +
723A LEU* 3.9 29.9 + - + +
724A ASP 3.3 11.2 + - - +
725A LYS* 3.0 29.2 + - + +
727A LEU* 1.3 80.2 - - - +
729A SER* 1.3 62.3 + - - +
731A CYS* 3.2 7.0 + - - +
732A LYS* 3.0 23.5 + - - +
737A THR* 5.4 0.5 - - - +
738A ILE* 3.2 43.6 + - + +
739A HIS 4.5 2.8 + - - -
740A LEU* 3.3 28.1 - - - +
741A PRO* 5.1 0.8 - - - +
894A LEU* 4.9 2.4 - - - +
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Residues in contact with SER 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725A LYS 3.1 6.5 + - - -
726A ARG* 2.7 35.0 + - - -
728A ARG* 1.3 78.5 - - - +
730A GLU* 1.3 58.7 + - - +
732A LYS* 3.2 11.7 + - - +
733A ASN* 2.9 41.5 + - - +
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Residues in contact with GLU 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726A ARG* 2.9 54.4 + - + +
727A LEU* 3.8 11.4 - - + +
728A ARG 3.2 0.2 - - - -
729A SER* 1.3 81.3 + - - +
731A CYS* 1.3 61.1 + - - +
733A ASN* 3.3 21.2 + - - +
734A GLN* 3.2 39.2 + - - +
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Residues in contact with CYS 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727A LEU* 2.9 38.7 + - - +
728A ARG 3.2 4.0 + - - +
730A GLU* 1.3 75.2 - - - +
732A LYS* 1.3 62.9 + - - +
734A GLN* 3.2 9.8 + - - -
736A ALA* 2.8 51.1 + - + +
738A ILE* 4.0 26.0 - - + +
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Residues in contact with LYS 732 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728A ARG 3.0 13.6 + - - +
729A SER* 3.4 15.0 - - - +
731A CYS* 1.3 73.5 - - - +
733A ASN* 1.3 67.6 + - - +
734A GLN 3.0 9.9 + - - -
735A GLY* 3.0 14.6 + - - -
737A THR* 3.4 40.0 + - + +
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Residues in contact with ASN 733 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729A SER* 2.9 22.9 + - - +
730A GLU* 3.3 24.5 + - - +
731A CYS 3.4 0.2 - - - -
732A LYS* 1.3 85.0 - - - +
734A GLN* 1.3 60.3 + - + +
735A GLY 3.4 1.9 + - - -
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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