Contacts of the helix formed by residues 774 - 785 (chain A) in PDB entry 2ZNS
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 GLY 774 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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771A GLN* 2.7 16.3 + - - -
772A GLU 3.1 2.4 + - - -
773A GLU* 1.3 76.6 - - - +
775A LYS* 1.3 62.3 + - - +
776A LEU 3.4 2.7 - - - -
777A HIS* 3.1 22.9 + - - +
778A MET* 3.2 23.0 + - - +
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Residues in contact with LYS 775 (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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455A GLU* 3.3 32.9 + - - +
770A LEU* 2.9 26.1 + - + +
773A GLU* 3.1 38.7 + - + +
774A GLY* 1.3 74.7 - - - +
776A LEU* 1.3 57.8 + - - +
778A MET* 3.4 17.6 + - + +
779A MET* 2.9 41.3 + - + +
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Residues in contact with LEU 776 (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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448A TYR* 4.0 16.9 + - - +
452A LEU* 4.2 13.0 - - + -
517A PRO 5.1 1.1 - - - +
518A PHE* 3.7 25.6 - - + +
767A ILE* 3.9 20.2 - - + +
770A LEU* 3.5 12.4 + - + -
771A GLN* 3.6 47.6 - - + +
774A GLY 3.4 0.6 - - - -
775A LYS* 1.3 77.8 - - - +
777A HIS* 1.3 57.7 + - - +
779A MET* 3.5 23.7 + - + +
780A LYS* 3.1 27.0 + - - +
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Residues in contact with HIS 777 (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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771A GLN* 5.1 3.4 + - - +
774A GLY* 3.1 16.2 + - - +
776A LEU* 1.3 77.3 - - - +
778A MET* 1.3 66.8 + - + +
780A LYS* 3.3 8.0 + - - +
781A GLU* 2.9 57.3 + - + +
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Residues in contact with MET 778 (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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773A GLU 3.9 22.2 - - - +
774A GLY* 3.2 12.5 + - - +
775A LYS* 3.4 18.6 + - + +
777A HIS* 1.3 82.8 - - + +
779A MET* 1.3 58.2 + - + +
781A GLU* 3.7 6.0 - - - +
782A LYS* 2.8 31.0 + - - +
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Residues in contact with MET 779 (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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448A TYR* 3.5 19.9 - - + +
451A ASP* 4.0 17.0 - - + +
452A LEU* 3.9 38.8 - - + -
455A GLU* 4.3 12.6 - - + +
770A LEU* 4.5 7.0 - - + -
775A LYS* 2.9 35.8 + - + +
776A LEU* 3.5 30.7 - - + +
778A MET* 1.3 73.4 - - + +
780A LYS* 1.3 66.4 + - - +
782A LYS* 3.5 6.0 + - + -
783A TRP* 3.1 34.2 + - + -
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Residues in contact with LYS 780 (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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448A TYR* 3.6 7.7 - - + -
519A MET* 3.7 35.2 - - + -
725A THR* 4.0 14.2 - - - +
728A GLU* 2.9 28.7 + - - -
776A LEU 3.1 11.6 + - - +
777A HIS* 3.3 11.0 + - - +
779A MET* 1.3 79.8 - - - +
781A GLU* 1.3 56.9 + - - +
783A TRP 3.2 1.0 + - - -
784A TRP* 2.8 52.5 + - + +
785A ARG* 3.4 25.5 - - - +
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Residues in contact with GLU 781 (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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777A HIS* 2.9 50.8 + - + +
778A MET* 3.7 6.5 - - - +
780A LYS* 1.3 72.4 - - - +
782A LYS* 1.3 64.0 + - - +
785A ARG* 2.1 76.9 + - - +
786A GLY* 3.2 8.3 + - - -
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Residues in contact with LYS 782 (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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451A ASP* 2.9 33.7 + - - +
778A MET 2.8 21.5 + - - +
779A MET* 3.5 8.7 - - + +
781A GLU* 1.3 73.3 - - - +
783A TRP* 1.3 71.6 + - + +
786A GLY* 3.0 34.4 - - - +
787A ASN* 3.2 2.6 - - - -
788A GLY 3.5 12.7 + - - +
789A CYS* 3.2 35.4 - - - +
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Residues in contact with TRP 783 (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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428A PRO* 4.0 8.7 - - + -
431A MET* 3.6 26.2 - - + -
446A GLU* 4.0 18.4 - - + -
447A GLY* 3.4 27.8 - - - -
448A TYR* 3.4 24.0 - + + +
451A ASP* 2.7 30.6 + - - -
729A TYR* 3.4 8.5 - - - -
779A MET* 3.1 25.4 + - + +
782A LYS* 1.3 100.4 - - + +
784A TRP* 1.3 82.9 + - + +
787A ASN* 2.7 56.3 + - - +
788A GLY* 3.7 13.5 - - - -
789A CYS* 4.0 12.6 - - - -
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Residues in contact with TRP 784 (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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428A PRO* 3.6 26.2 - - + -
429A TYR* 3.5 44.0 - + - -
448A TYR* 3.8 24.5 - + - -
519A MET* 3.8 11.0 - - + -
725A THR* 2.8 30.9 + - - -
728A GLU* 3.8 25.6 + - - -
729A TYR* 3.7 21.4 - + + +
732A GLN* 3.0 14.6 - - - +
733A ARG* 2.6 27.1 + - - -
780A LYS* 2.8 36.8 + - + +
783A TRP* 1.3 86.5 - - + +
785A ARG* 1.3 78.5 + - - +
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Residues in contact with ARG 785 (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 GLU* 2.3 33.1 + - - -
732A GLN* 3.3 28.9 - - - +
733A ARG* 4.7 1.6 + - - -
780A LYS* 3.4 34.4 - - - +
781A GLU* 2.1 61.5 + - - +
784A TRP* 1.3 90.0 - - - +
786A GLY* 1.3 60.9 + - - +
787A ASN 3.5 2.6 + - - -
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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