Contacts of the helix formed by residues 1913 - 1928 (chain C) in PDB entry 5Y3R
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 LYS1913 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1735C ARG* 5.8 4.5 - - - +
1876C ILE* 5.2 1.8 - - - +
1877C LEU* 3.8 14.3 - - - +
1911C LEU* 3.0 42.2 + - + +
1912C THR* 1.3 77.2 - - - +
1914C THR* 1.3 52.7 + - - +
1915C LEU* 2.9 11.2 - - + +
1916C ILE* 3.5 40.6 - - + +
1917C LYS* 2.6 38.9 + - - +
1952C ILE* 4.9 3.1 - - - +
1953C CYS* 6.1 0.7 - - - -
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Residues in contact with THR1914 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1912C THR 3.9 3.7 + - - +
1913C LYS* 1.3 70.8 - - - +
1915C LEU* 1.3 72.5 + - - +
1917C LYS* 3.0 18.1 - - - +
1918C LEU* 2.9 36.5 + - - +
1953C CYS* 4.4 25.7 - - + -
1957C ASN* 5.9 0.7 - - - -
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Residues in contact with LEU1915 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1913C LYS* 2.9 6.9 - - + -
1914C THR* 1.3 87.6 - - - +
1916C ILE* 1.3 67.4 + - + +
1917C LYS 3.0 0.9 - - - -
1918C LEU* 2.8 27.8 + - + +
1919C CYS* 2.8 18.7 + - - -
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Residues in contact with ILE1916 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1735C ARG* 5.2 5.8 - - - +
1877C LEU* 3.1 32.3 - - + +
1878C ASP* 3.8 14.8 - - - +
1879C VAL 5.6 0.2 - - - +
1911C LEU* 3.4 13.0 - - + -
1913C LYS* 3.2 33.6 + - + +
1915C LEU* 1.3 79.5 - - + +
1917C LYS* 1.3 69.8 + - - +
1919C CYS* 2.8 21.7 + - + -
1920C TYR* 3.0 37.2 + - + +
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Residues in contact with LYS1917 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1911C LEU* 4.8 2.3 - - - +
1913C LYS 2.6 23.7 + - - +
1914C THR* 3.0 27.6 - - - +
1916C ILE* 1.3 74.5 - - - +
1918C LEU* 1.3 78.7 + - - +
1920C TYR* 3.0 5.6 + - - +
1921C ASP* 2.8 47.1 + - - +
1949C ILE* 4.5 0.6 - - + +
1952C ILE* 3.6 35.4 - - + -
1953C CYS* 3.8 21.8 - - + +
1955C VAL 2.8 27.5 + - - -
1956C PHE* 3.2 13.9 - - + +
1957C ASN* 3.2 2.4 - - - +
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Residues in contact with LEU1918 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1914C THR* 3.2 18.8 - - - +
1915C LEU* 2.8 14.7 + - + +
1917C LYS* 1.3 90.6 - - - +
1919C CYS* 1.3 56.8 + - - +
1921C ASP* 3.0 27.0 - - + +
1922C ALA* 2.9 30.3 + - - +
1956C PHE 3.1 18.6 - - - +
1957C ASN* 3.5 29.2 - - + +
1958C GLU 4.9 0.2 - - - +
1959C LEU* 4.5 4.7 - - + +
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Residues in contact with CYS1919 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1879C VAL* 4.4 4.6 - - + +
1915C LEU* 2.8 27.2 + - - -
1916C ILE* 2.8 31.8 + - + +
1918C LEU* 1.3 77.9 - - - +
1920C TYR* 1.3 63.2 + - + +
1922C ALA* 4.4 1.8 - - - +
1923C PHE* 2.8 27.4 + - - +
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Residues in contact with TYR1920 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1875C LYS 5.9 0.2 - - - -
1877C LEU 2.2 36.7 + - - -
1878C ASP* 2.8 8.1 + - - -
1879C VAL* 3.2 40.4 - - + -
1882C SER* 3.5 21.8 - - - +
1907C GLU* 3.7 23.0 + - - -
1911C LEU* 4.4 2.9 - - + -
1916C ILE* 3.0 31.8 + - + -
1917C LYS* 3.9 4.9 - - - +
1919C CYS* 1.3 77.6 - - + +
1921C ASP* 1.3 60.9 + - - +
1922C ALA 3.3 0.4 - - - -
1923C PHE* 3.5 4.5 - + - -
1924C THR* 2.2 48.4 + - + -
1945C TYR* 4.5 4.5 - - + -
1949C ILE* 6.5 0.2 - - + -
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Residues in contact with ASP1921 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1917C LYS* 2.8 35.9 + - - +
1918C LEU* 3.0 34.3 + - + +
1920C TYR* 1.3 76.0 - - - +
1922C ALA* 1.3 51.5 + - - +
1924C THR* 3.4 0.9 + - - -
1925C GLU* 2.3 41.1 + - - +
1945C TYR* 3.9 4.7 + - - -
1949C ILE* 3.2 25.7 - - - +
1956C PHE* 4.0 0.3 - - - -
1959C LEU* 3.2 39.5 - - + +
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Residues in contact with ALA1922 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1918C LEU 2.9 15.5 + - - +
1919C CYS* 4.4 2.2 - - - +
1921C ASP* 1.3 73.5 - - - +
1923C PHE* 1.3 71.2 + - - +
1925C GLU* 2.8 23.4 + - - +
1926C ASN* 2.9 16.9 + - - +
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Residues in contact with PHE1923 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1879C VAL* 3.2 26.9 - - + -
1882C SER* 3.5 22.4 - - - -
1883C ARG* 3.7 42.4 - - + -
1886C LYS* 5.6 8.5 - - + -
1919C CYS 2.8 24.1 + - - +
1920C TYR* 3.3 6.0 + + - -
1922C ALA* 1.3 76.3 - - - +
1924C THR* 1.3 78.5 + - + +
1927C MET* 2.8 66.4 + - + +
1941C HIS* 5.9 0.4 - + - -
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Residues in contact with THR1924 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1882C SER* 5.1 1.8 - - - +
1886C LYS* 5.5 7.0 - - - -
1920C TYR* 2.2 34.4 + - + +
1921C ASP 3.4 0.3 + - - -
1923C PHE* 1.3 92.4 - - + +
1925C GLU* 1.3 68.4 + - - +
1927C MET* 2.9 2.9 + - - -
1928C ALA* 2.9 19.9 + - - +
1941C HIS* 2.9 34.1 + - + +
1945C TYR* 2.9 39.5 - - + -
1990C PHE* 4.9 2.6 - - - -
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Residues in contact with GLU1925 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1921C ASP 2.3 31.1 + - - +
1922C ALA* 2.8 22.1 + - - +
1924C THR* 1.3 79.4 + - - +
1926C ASN* 1.3 63.3 + - - +
1928C ALA* 3.1 21.8 - - - +
1945C TYR* 5.9 0.7 - - - -
1959C LEU* 3.1 42.6 + - + +
1962C TYR* 2.9 19.7 - - + +
1963C GLN* 2.2 43.1 + - - +
1966C LEU* 4.8 4.9 - - - +
1990C PHE* 5.9 2.0 - - - -
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Residues in contact with ASN1926 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1922C ALA* 2.9 12.3 + - - +
1923C PHE 3.8 0.7 - - - -
1925C GLU* 1.3 79.1 - - - +
1927C MET* 1.3 52.9 + - - +
1928C ALA 2.8 5.3 - - - -
1929C GLY* 2.5 30.6 + - - +
1931C ASN* 3.8 3.6 + - - +
1962C TYR* 3.1 47.7 + - - -
1966C LEU* 3.8 4.9 - - - +
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Residues in contact with MET1927 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1883C ARG* 5.7 6.5 - - + -
1886C LYS* 6.0 6.1 - - + -
1923C PHE* 2.8 57.8 + - + +
1924C THR* 3.1 12.6 - - - +
1926C ASN* 1.3 76.4 - - - +
1928C ALA* 1.3 54.9 + - - +
1929C GLY 3.1 0.2 - - - -
1931C ASN* 2.9 21.9 - - - +
1933C LEU* 3.0 37.4 - - + +
1937C ARG* 5.1 6.3 - - - +
1941C HIS* 3.2 18.2 - - + +
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Residues in contact with ALA1928 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1924C THR 2.9 4.8 + - - +
1925C GLU 3.1 17.5 - - - +
1926C ASN* 2.8 0.8 - - - -
1927C MET* 1.3 72.8 - - - +
1929C GLY* 1.3 64.1 - - - +
1938C ARG* 3.0 32.4 + - - +
1941C HIS* 3.2 0.9 - - - -
1966C LEU* 6.2 0.9 - - + -
1969C GLU* 4.7 4.7 - - - +
1987C ARG* 3.7 14.7 - - + +
1990C PHE* 3.7 28.9 - - + -
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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