Contacts of the helix formed by residues 1908 - 1925 (chain B) in PDB entry 2H02
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 VAL1908 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B 2UN 3.3 27.2 + - + +
1736B ILE* 3.6 32.5 - - + -
1904B CYS* 3.7 1.8 - - - -
1906B ALA* 4.2 0.9 - - + -
1907B GLY* 1.3 78.4 - - - +
1909B GLY* 1.3 65.3 + - - +
1910B ARG 3.8 0.2 - - - -
1912B GLY 3.0 20.1 + - - -
1943B ARG* 3.8 4.7 - - - +
1944B VAL* 3.1 13.7 - - + +
1945B HIS* 3.5 24.0 - - + +
1946B MET* 2.9 31.9 - - + -
1947B VAL 3.0 14.7 + - - -
1948B GLN* 4.1 3.4 - - + -
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Residues in contact with GLY1909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B 2UN 2.9 20.9 + - - -
1908B VAL* 1.3 73.6 - - - +
1910B ARG* 1.3 58.6 + - - +
1913B THR* 2.7 34.7 + - - -
1947B VAL* 4.0 0.9 - - - -
1948B GLN* 3.5 26.7 - - - -
1952B GLN* 3.6 13.2 - - - +
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Residues in contact with ARG1910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B 2UN 2.9 35.3 + - - +
1801B VAL* 3.6 24.1 + - + +
1802B THR* 2.7 32.5 + - - +
1806B GLU* 3.0 18.0 + - - -
1811B LYS* 4.7 0.8 - - - +
1868B TRP* 2.7 76.2 + - + +
1869B PRO 3.7 7.2 - - - +
1870B ASP* 3.3 27.1 + - - +
1904B CYS* 4.0 2.4 - - + +
1905B SER* 3.7 7.1 - - - +
1909B GLY* 1.3 69.6 - - - -
1911B THR* 1.3 60.7 + - - +
1914B PHE* 2.9 27.4 + - - +
1952B GLN* 4.0 8.7 - - - +
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Residues in contact with THR1911 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1774B VAL* 3.2 44.9 - - + -
1801B VAL* 3.9 1.5 - - - +
1902B VAL* 3.7 17.4 - - + +
1903B HIS* 3.0 35.7 + - - -
1904B CYS* 3.1 15.1 + - - -
1907B GLY* 3.9 9.8 - - - +
1909B GLY 3.3 0.2 - - - -
1910B ARG* 1.3 79.7 - - - +
1912B GLY* 1.3 63.6 + - - +
1914B PHE* 3.2 5.0 + - - +
1915B ILE* 3.1 23.0 + - + +
1946B MET* 4.9 0.7 - - - -
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Residues in contact with GLY1912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1908B VAL 3.0 21.8 + - - -
1911B THR* 1.3 81.8 - - - +
1913B THR* 1.3 56.7 + - - +
1915B ILE* 4.4 2.5 - - - -
1916B ALA* 2.8 26.5 + - - +
1939B LEU* 3.1 24.2 - - - +
1946B MET* 4.4 7.6 - - - -
1947B VAL* 3.6 11.2 - - - -
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Residues in contact with THR1913 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1868B TRP* 3.6 25.8 - - + -
1880B LEU* 4.9 2.7 - - + -
1909B GLY 2.7 21.5 + - - -
1912B GLY* 1.3 75.1 - - - +
1914B PHE* 1.3 64.5 + - - +
1916B ALA* 3.3 1.5 + - - -
1917B LEU* 3.0 22.5 + - - +
1947B VAL* 3.7 11.3 - - - +
1952B GLN* 3.4 30.6 + - + +
1955B TYR* 4.6 12.1 - - + -
1956B LEU* 3.7 23.1 - - + +
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Residues in contact with PHE1914 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1772B TYR* 5.3 2.2 - + - -
1799B VAL* 3.9 23.6 - - + -
1801B VAL* 4.3 6.1 - - + -
1868B TRP* 3.7 10.8 - - + -
1880B LEU* 4.4 6.3 - - + -
1883B PHE* 3.4 33.9 - + - -
1884B VAL* 3.6 33.2 - - + +
1887B VAL* 3.9 23.1 - - + -
1891B ILE* 5.8 1.3 - - + -
1900B THR* 5.8 1.1 - - + -
1902B VAL* 4.0 23.8 - - + -
1910B ARG 2.9 15.8 + - - +
1911B THR 3.2 8.5 + - - +
1913B THR* 1.3 76.0 - - - +
1915B ILE* 1.3 59.4 + - + +
1917B LEU* 3.2 6.2 + - - +
1918B ASP* 2.8 44.8 + - + +
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Residues in contact with ILE1915 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1763B ILE* 4.5 6.5 - - + -
1772B TYR* 3.6 48.0 - - + -
1774B VAL* 3.2 35.7 - - + -
1902B VAL* 4.2 11.2 - - + -
1911B THR* 3.1 20.3 + - + +
1912B GLY* 3.9 6.1 - - - +
1914B PHE* 1.3 78.3 - - + +
1916B ALA* 1.3 67.2 + - - +
1918B ASP* 3.2 5.9 + - - +
1919B ARG* 3.0 26.2 + - - +
1939B LEU* 3.6 26.0 - - + -
1946B MET* 6.0 0.7 - - - -
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Residues in contact with ALA1916 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1912B GLY 2.8 19.5 + - - +
1913B THR* 3.7 4.0 - - - +
1915B ILE* 1.3 80.4 - - - +
1917B LEU* 1.3 60.0 + - - +
1919B ARG* 3.3 3.7 + - - +
1920B ILE* 3.1 32.3 + - + +
1932B ILE* 6.0 0.2 - - + -
1935B ALA* 4.4 18.2 - - + -
1936B VAL* 4.5 1.8 - - + -
1939B LEU* 4.1 11.4 - - + -
1947B VAL* 4.4 2.7 - - + -
1956B LEU* 3.7 26.7 - - + -
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Residues in contact with LEU1917 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1880B LEU* 3.7 28.5 - - + -
1881B ILE* 4.1 13.9 - - + +
1884B VAL* 3.9 14.1 - - + -
1913B THR 3.0 13.2 + - - +
1914B PHE* 3.5 8.1 - - - +
1916B ALA* 1.3 72.8 - - - +
1918B ASP* 1.3 67.1 + - - +
1920B ILE* 3.2 27.1 + - + -
1921B LEU* 3.0 47.7 + - + +
1955B TYR* 5.0 0.7 - - + -
1956B LEU* 3.9 7.6 - - + +
1959B CYS* 3.7 37.2 - - + -
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Residues in contact with ASP1918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1772B TYR* 2.5 30.0 + - - +
1884B VAL* 3.4 25.1 - - + +
1888B ARG* 2.7 42.0 + - - +
1891B ILE* 4.7 3.8 - - - +
1914B PHE* 2.8 26.7 + - + +
1915B ILE* 3.2 9.8 + - - +
1917B LEU* 1.3 77.1 - - - +
1919B ARG* 1.3 58.3 + - - +
1921B LEU* 4.2 1.7 - - - +
1922B GLN* 2.9 28.6 + - - +
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Residues in contact with ARG1919 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1764B PRO 3.4 14.7 + - - -
1765B GLY* 3.7 24.5 + - - -
1766B ASN* 3.2 39.6 + - + +
1772B TYR* 3.7 15.0 - - - +
1915B ILE* 3.0 20.8 + - - +
1916B ALA 3.6 6.5 - - - +
1918B ASP* 1.3 73.9 - - - +
1920B ILE* 1.3 61.9 + - + +
1921B LEU 3.2 2.2 - - - -
1922B GLN* 3.2 8.4 + - - +
1923B GLN* 3.1 31.9 + - - +
1934B GLY 5.6 0.8 + - - -
1935B ALA* 4.7 20.9 + - + +
1938B ASP* 3.2 35.8 + - - +
1939B LEU* 4.5 9.0 - - - +
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Residues in contact with ILE1920 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1916B ALA* 3.1 18.0 + - + +
1917B LEU* 3.2 34.0 + - + +
1919B ARG* 1.3 75.9 - - + +
1921B LEU* 1.3 63.9 + - + +
1922B GLN 3.2 0.2 - - - -
1923B GLN* 3.5 12.2 + - - +
1924B LEU* 3.1 31.1 + - + +
1930B VAL* 3.8 12.8 - - + +
1931B ASP 4.3 6.1 - - - +
1932B ILE* 4.1 22.7 - - + -
1935B ALA* 4.3 17.9 - - + -
1956B LEU* 4.2 14.8 - - + +
1960B VAL* 3.7 26.2 - - + -
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Residues in contact with LEU1921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1881B ILE* 4.3 15.7 - - + +
1884B VAL* 3.9 23.6 - - + -
1885B ARG* 4.3 20.4 - - + +
1917B LEU* 3.0 49.2 + - + +
1918B ASP* 4.2 4.3 - - - +
1920B ILE* 1.3 77.9 - - + +
1922B GLN* 1.3 66.3 + - + +
1924B LEU* 3.5 24.4 + - + +
1925B ASP* 3.4 25.3 + - - +
1959B CYS* 5.5 1.1 - - + +
1960B VAL 5.9 0.4 - - - +
1963B VAL* 4.1 18.6 - - + -
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Residues in contact with GLN1922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1766B ASN* 3.6 15.6 - - - +
1767B ASN* 3.0 29.2 + - - +
1772B TYR* 4.2 3.2 + - - -
1888B ARG* 3.5 45.0 + - + +
1892B ASN* 5.5 0.2 - - - +
1918B ASP* 2.9 26.2 + - - +
1919B ARG* 3.4 13.5 - - - +
1920B ILE 3.2 0.2 - - - -
1921B LEU* 1.3 76.8 - - + +
1923B GLN* 1.3 61.1 + - - +
1925B ASP* 2.8 26.2 + - - +
1926B SER* 3.1 14.0 + - - -
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Residues in contact with GLN1923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1766B ASN* 3.6 23.9 + - - +
1919B ARG* 3.1 25.2 + - - +
1920B ILE* 3.7 12.2 - - - +
1922B GLN* 1.3 74.6 - - - +
1924B LEU* 1.3 62.2 + - - +
1926B SER* 3.9 6.3 - - - -
1927B LYS* 3.0 58.2 + - + +
1929B SER 3.7 5.5 - - - +
1930B VAL* 3.4 9.4 - - + +
1931B ASP* 2.8 45.0 + - - +
1935B ALA* 5.5 1.6 - - - +
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Residues in contact with LEU1924 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1685B ILE* 4.1 23.9 - - + +
1920B ILE 3.1 17.8 + - - +
1921B LEU* 3.6 26.0 - - + +
1922B GLN 3.1 0.4 - - - -
1923B GLN* 1.3 77.6 - - - +
1925B ASP* 1.3 59.9 + - - +
1926B SER 3.3 4.2 + - - -
1927B LYS 3.9 9.5 - - - +
1930B VAL* 4.3 6.5 - - + -
1960B VAL* 3.9 31.9 - - + +
1963B VAL* 3.4 35.7 - - + -
1964B LEU* 4.2 14.6 - - + -
1967B ARG* 3.6 28.1 + - - +
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Residues in contact with ASP1925 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1921B LEU 3.4 14.1 + - - +
1922B GLN* 2.8 13.8 + - - +
1924B LEU* 1.3 79.3 - - - +
1926B SER* 1.3 60.8 + - - -
1967B ARG* 3.7 14.4 + - - +
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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
------------------------------------------------------------
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