Contacts of the helix formed by residues 1934 - 1951 (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 LEU1934 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1890C HIS* 4.4 15.9 - - + +
1932C GLN 3.6 1.8 + - - +
1933C LEU* 1.3 74.7 - - - +
1935C GLU* 1.3 77.8 + - + +
1936C ARG* 3.2 41.7 - - + +
1937C ARG* 3.2 31.3 - - + +
1938C ARG* 3.0 23.2 + - - +
1979C GLU* 4.9 2.5 - - - -
1982C ILE* 4.6 5.6 - - + -
1983C ASP* 3.7 11.2 - - - +
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Residues in contact with GLU1935 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1934C LEU* 1.3 75.3 - - + +
1936C ARG* 1.3 62.0 + - + +
1937C ARG 2.9 1.1 - - - -
1938C ARG* 2.7 23.7 + - - -
1939C LEU 3.0 7.1 + - - -
1982C ILE* 3.7 34.2 - - + +
1986C ARG* 3.0 45.7 + - - +
2036C LEU* 4.0 20.5 - - + +
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Residues in contact with ARG1936 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1759C LEU* 3.3 27.4 - - - +
1889C VAL 4.8 1.6 - - - -
1890C HIS* 2.8 44.0 + - + +
1891C ALA 4.5 0.8 + - - -
1893C GLU* 2.8 55.8 + - - +
1934C LEU* 3.2 18.6 - - + +
1935C GLU* 1.3 84.2 - - + +
1937C ARG* 1.3 55.1 + - - +
1939C LEU* 2.5 33.4 + - + -
1940C TYR* 3.0 19.3 + - + -
1986C ARG* 4.3 1.5 - - - +
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Residues in contact with ARG1937 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1886C LYS 4.5 8.1 + - - -
1887C ASP* 4.6 10.5 + - - +
1890C HIS* 3.0 47.5 - - + +
1891C ALA* 5.2 1.8 - - - +
1927C MET* 5.1 6.3 - - - +
1932C GLN* 4.6 3.7 + - - +
1933C LEU* 3.1 38.1 - - + +
1934C LEU* 3.2 48.4 - - + +
1935C GLU 2.9 0.6 - - - -
1936C ARG* 1.3 79.0 - - - +
1938C ARG* 1.3 56.8 + - - +
1941C HIS* 3.1 13.2 + - - +
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Residues in contact with ARG1938 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1928C ALA* 3.0 45.3 + - - +
1929C GLY 3.4 8.3 + - - -
1930C GLU* 5.5 0.4 - - - +
1931C ASN* 5.2 3.0 + - - +
1933C LEU* 3.3 25.6 - - + +
1934C LEU 3.0 5.8 + - - +
1935C GLU 2.7 14.5 + - - +
1937C ARG* 1.3 74.4 - - - +
1939C LEU* 1.3 65.1 + - - +
1941C HIS* 3.6 7.3 + - - -
1942C CYS* 3.0 4.7 + - - +
1983C ASP* 2.9 35.3 + - - +
1986C ARG* 3.1 40.4 - - - -
1987C ARG* 3.3 24.3 - - - +
1990C PHE* 2.8 35.1 - - + -
1993C GLU* 4.4 0.7 - - - +
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Residues in contact with LEU1939 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1935C GLU 3.0 6.0 + - - +
1936C ARG* 2.5 30.7 + - + +
1938C ARG* 1.3 74.6 - - - +
1940C TYR* 1.3 77.5 + - + +
1942C CYS 3.3 0.5 + - - -
1943C ALA* 2.7 39.9 + - + +
1986C ARG* 4.2 14.1 - - - +
1993C GLU* 3.8 16.8 - - - +
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Residues in contact with TYR1940 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1886C LYS* 3.7 5.7 - - - -
1889C VAL* 3.3 24.0 - - + -
1890C HIS* 3.0 34.5 - + + +
1893C GLU* 2.4 35.8 + - + -
1897C ASN* 2.7 35.9 + - + -
1900C PHE* 4.2 10.1 - + + -
1936C ARG* 3.0 23.5 + - + -
1939C LEU* 1.3 93.3 - - + +
1941C HIS* 1.3 65.8 + - - +
1943C ALA* 3.6 9.6 - - + -
1944C ALA* 2.9 28.1 + - + +
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Residues in contact with HIS1941 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1886C LYS* 4.3 15.6 - - + +
1890C HIS* 3.6 8.0 - + + -
1923C PHE* 5.9 0.4 - + - -
1924C THR* 2.9 51.9 + - + -
1927C MET* 3.2 25.8 + - + +
1928C ALA* 3.2 18.8 - - - -
1933C LEU* 4.5 3.8 - - + +
1937C ARG 3.1 22.2 + - - +
1938C ARG* 3.3 13.3 + - - +
1939C LEU 3.0 0.2 - - - -
1940C TYR* 1.3 81.3 - - - +
1942C CYS* 1.3 51.4 + - - +
1945C TYR* 2.4 35.9 + - + +
1990C PHE* 3.0 21.2 - + + -
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Residues in contact with CYS1942 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1938C ARG 3.0 3.4 + - - +
1941C HIS* 1.3 79.6 - - - +
1943C ALA* 1.3 56.5 + - - +
1945C TYR* 3.3 7.3 - - - +
1946C ASN* 2.9 25.3 + - - +
1990C PHE* 2.9 45.0 - - + -
1993C GLU* 3.1 30.3 - - - +
1994C VAL* 3.1 33.9 - - - -
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Residues in contact with ALA1943 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1939C LEU* 2.7 35.2 + - + +
1940C TYR* 3.6 10.5 - - + -
1941C HIS 3.0 2.2 + - - -
1942C CYS* 1.3 73.7 - - - +
1944C ALA* 1.3 59.4 + - - +
1945C TYR 3.0 0.2 - - - -
1946C ASN* 2.6 27.7 + - - +
1947C CYS* 2.8 16.1 + - - -
1993C GLU* 4.7 3.8 - - - +
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Residues in contact with ALA1944 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1886C LYS* 3.3 24.5 - - - +
1900C PHE* 4.2 21.8 - - + -
1904C CYS* 3.4 19.9 - - - +
1940C TYR* 2.9 15.8 + - + +
1943C ALA* 1.3 75.3 - - - +
1945C TYR* 1.3 63.1 + - - +
1947C CYS* 3.0 15.1 + - - +
1948C ALA* 3.0 21.1 + - - +
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Residues in contact with TYR1945 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1886C LYS* 4.0 5.8 - - - +
1920C TYR* 3.9 9.9 - - + -
1921C ASP* 3.9 8.4 + - - -
1924C THR* 2.9 42.2 - - + -
1925C GLU* 5.7 1.3 - - - -
1940C TYR 3.5 0.2 + - - -
1941C HIS* 2.4 32.9 + + - +
1942C CYS* 3.3 10.1 - - - +
1944C ALA* 1.3 77.5 - - - +
1946C ASN* 1.3 61.0 + - - +
1948C ALA* 3.3 5.3 + - - +
1949C ILE* 2.9 38.6 + - + +
1959C LEU* 3.2 41.8 - - + +
1990C PHE* 5.9 2.5 - + - -
1994C VAL* 3.3 39.7 - - + -
1998C MET* 4.8 0.9 - - - -
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Residues in contact with ASN1946 (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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1942C CYS 2.9 17.5 + - - +
1943C ALA* 2.6 12.2 + - - +
1945C TYR* 1.3 70.0 - - - +
1947C CYS* 1.3 58.2 + - - +
1949C ILE* 2.7 14.5 + - - +
1950C SER* 2.0 67.7 + - - -
1993C GLU 3.8 2.6 + - - -
1994C VAL* 3.2 39.6 + - + +
1997C PRO* 3.7 14.6 - - - +
1998C MET* 3.2 1.4 - - - +
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Residues in contact with CYS1947 (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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1900C PHE* 5.0 1.1 - - - +
1901C HIS* 4.1 25.4 - - - +
1904C CYS* 3.6 9.4 - - + -
1905C ILE* 3.1 41.8 - - + +
1943C ALA* 2.8 20.4 + - - -
1944C ALA* 3.0 18.1 + - - +
1946C ASN* 1.3 77.2 - - - +
1948C ALA* 1.3 64.2 + - - +
1950C SER* 4.1 3.0 + - - -
1951C VAL* 3.6 6.9 + - - +
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Residues in contact with ALA1948 (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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1904C CYS* 3.2 36.4 - - + +
1907C GLU* 4.8 4.5 - - + +
1908C GLY* 3.0 27.8 - - - +
1944C ALA 3.0 7.5 + - - +
1945C TYR* 3.8 7.0 - - - +
1947C CYS* 1.3 77.4 - - - +
1949C ILE* 1.3 62.6 + - + +
1951C VAL* 3.0 12.8 + - - +
1952C ILE* 3.5 5.1 + - + +
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Residues in contact with ILE1949 (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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1917C LYS* 4.5 3.4 - - + +
1921C ASP* 3.2 27.8 - - - +
1945C TYR* 2.9 25.0 + - + +
1946C ASN* 2.7 29.1 + - - +
1948C ALA* 1.3 71.5 - - + +
1950C SER* 1.3 67.8 + - - +
1951C VAL 3.1 2.2 - - - -
1952C ILE* 3.1 26.7 + - + +
1956C PHE* 3.4 36.3 - - + -
1994C VAL* 3.3 23.8 - - + -
1998C MET* 3.4 16.6 - - + -
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Residues in contact with SER1950 (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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1946C ASN* 2.0 48.7 + - - -
1947C CYS* 4.8 2.0 - - - -
1949C ILE* 1.3 73.6 - - - +
1951C VAL* 1.3 57.1 + - - +
1952C ILE 3.7 3.5 + - - +
1956C PHE* 5.5 0.5 - - - -
1997C PRO* 4.2 3.3 - - - +
1998C MET* 3.1 33.9 + - - +
1999C GLU* 4.4 6.1 - - - +
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Residues in contact with VAL1951 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1905C ILE* 3.0 41.7 - - + +
1909C ASN* 3.2 40.4 + - + +
1947C CYS 3.6 9.8 + - - +
1948C ALA 3.0 15.3 - - - +
1950C SER* 1.3 77.7 - - - +
1952C ILE* 1.3 60.1 + - - +
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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
------------------------------------------------------------
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