Contacts of the helix formed by residues 1911 - 1930 (chain B) in PDB entry 3AU5
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 MET1911 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1912B TRP* 1.3 54.6 + - - +
1913B ILE* 2.9 10.5 - - - +
1914B LYS* 3.8 13.2 - - - +
1915B GLU* 2.5 46.9 + - + +
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Residues in contact with TRP1912 (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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1860B LEU* 5.9 2.4 - - - +
1911B MET* 1.3 78.1 - - - +
1913B ILE* 1.3 60.0 + - - +
1915B GLU* 4.2 6.4 - - - +
1916B GLU* 4.1 20.4 + - - +
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Residues in contact with ILE1913 (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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1860B LEU* 6.1 4.9 - - - -
1911B MET 2.9 5.6 - - - +
1912B TRP* 1.3 78.7 - - - +
1914B LYS* 1.3 65.0 + - - +
1915B GLU 3.2 1.1 + - - -
1916B GLU* 4.7 0.5 - - - +
1917B VAL* 3.1 33.3 + - + +
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Residues in contact with LYS1914 (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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1911B MET* 3.2 14.0 + - - +
1913B ILE* 1.3 75.3 - - - +
1915B GLU* 1.3 68.9 + - - +
1917B VAL* 3.9 7.7 - - - +
1918B SER* 3.3 19.8 + - - -
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Residues in contact with GLU1915 (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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1911B MET* 2.5 28.8 + - + +
1912B TRP* 4.2 6.7 - - - +
1914B LYS* 1.3 76.3 - - - +
1916B GLU* 1.3 76.4 + - + +
1918B SER* 3.3 15.6 - - - -
1919B SER* 3.5 4.7 + - - -
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Residues in contact with GLU1916 (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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1860B LEU* 5.2 9.9 - - - +
1912B TRP 4.1 13.0 + - - +
1913B ILE 3.7 2.4 + - - +
1914B LYS 3.5 0.2 - - - -
1915B GLU* 1.3 89.4 - - + +
1917B VAL* 1.3 56.9 + - - +
1918B SER 2.9 2.5 - - - -
1919B SER* 2.8 13.1 + - - -
1920B ALA* 2.7 36.4 + - + +
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Residues in contact with VAL1917 (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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1851B LEU* 3.6 22.5 - - + +
1857B LEU* 3.8 31.9 - - + -
1913B ILE* 3.1 30.6 + - + +
1914B LYS* 3.9 8.3 - - - +
1915B GLU 3.4 0.4 - - - -
1916B GLU* 1.3 76.5 - - - +
1918B SER* 1.3 59.0 + - - +
1920B ALA* 4.6 2.5 - - - -
1921B ARG* 3.1 30.7 + - + +
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Residues in contact with SER1918 (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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1914B LYS 3.3 8.9 + - - -
1915B GLU* 3.3 12.6 - - - -
1916B GLU 2.9 0.2 - - - -
1917B VAL* 1.3 79.5 - - - +
1919B SER* 1.3 59.0 + - - +
1921B ARG* 3.6 7.9 + - - +
1922B ALA* 3.0 30.2 + - - +
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Residues in contact with SER1919 (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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1915B GLU* 3.5 3.2 + - - -
1916B GLU* 2.8 22.8 + - - -
1918B SER* 1.3 77.4 - - - +
1920B ALA* 1.3 65.0 + - - -
1922B ALA* 3.2 7.3 + - - +
1923B SER* 3.0 25.0 + - - -
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Residues in contact with ALA1920 (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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1824B GLU* 5.5 0.2 - - - +
1828B GLN* 5.4 5.2 - - - +
1851B LEU* 4.6 2.9 - - + -
1855B TYR* 3.5 42.6 - - + +
1857B LEU* 5.6 0.4 - - + -
1916B GLU* 2.7 18.2 + - + +
1917B VAL* 4.2 4.3 - - - +
1919B SER* 1.3 72.9 - - - +
1921B ARG* 1.3 64.7 + - - +
1923B SER* 3.0 7.8 + - - -
1924B ILE* 2.9 30.1 + - - +
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Residues in contact with ARG1921 (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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1846B ALA 5.1 4.8 + - - -
1847B ALA* 5.6 1.2 - - - +
1848B ILE* 3.5 45.2 + - + +
1851B LEU* 4.4 23.7 - - + +
1917B VAL* 3.1 22.1 + - - +
1918B SER* 3.7 7.2 - - - +
1920B ALA* 1.3 78.4 - - - +
1922B ALA* 1.3 62.2 + - - +
1924B ILE* 3.5 3.3 + - - +
1925B ILE* 3.2 45.0 + - - +
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Residues in contact with ALA1922 (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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1918B SER 3.0 19.5 + - - +
1919B SER* 3.4 7.2 - - - +
1920B ALA 3.1 0.2 - - - -
1921B ARG* 1.3 77.5 - - - +
1923B SER* 1.3 57.6 + - - +
1925B ILE* 3.5 7.7 + - - +
1926B ASP* 3.0 27.8 + - - +
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Residues in contact with SER1923 (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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1828B GLN* 3.0 27.6 + - - -
1919B SER* 3.0 16.0 + - - -
1920B ALA* 3.6 4.7 - - - -
1922B ALA* 1.3 74.8 - - - +
1924B ILE* 1.3 62.7 - - - +
1926B ASP* 3.5 7.7 + - - +
1927B LYS* 3.2 36.9 + - - +
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Residues in contact with ILE1924 (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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1828B GLN* 3.7 20.9 - - + +
1831B ALA* 3.4 37.2 - - + -
1832B ALA* 3.5 17.0 - - - +
1835B LEU* 4.0 13.5 - - + -
1851B LEU* 3.8 20.0 - - + -
1854B VAL* 5.0 1.8 - - + -
1855B TYR* 3.8 26.7 - - + -
1920B ALA 2.9 19.6 + - - +
1921B ARG 3.9 3.4 - - - +
1923B SER* 1.3 72.7 - - - +
1925B ILE* 1.3 62.5 + - + +
1926B ASP 3.0 1.3 - - - -
1927B LYS* 3.1 3.1 + - - -
1928B TRP* 2.8 29.3 + - - +
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Residues in contact with ILE1925 (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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1835B LEU* 5.1 2.9 - - + -
1842B TYR* 3.4 30.2 - - + -
1846B ALA 5.6 4.3 - - - +
1848B ILE* 3.8 24.9 - - + -
1921B ARG* 3.2 45.8 + - + +
1922B ALA* 3.8 6.1 - - - +
1924B ILE* 1.3 77.3 - - + +
1926B ASP* 1.3 63.1 + - - +
1928B TRP* 3.2 17.7 + - + +
1929B ARG* 3.0 28.5 + - + +
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Residues in contact with ASP1926 (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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1922B ALA 3.0 18.6 + - - +
1923B SER* 3.5 10.5 - - - +
1925B ILE* 1.3 78.4 - - - +
1927B LYS* 1.3 61.6 + - - +
1929B ARG* 3.2 43.6 + - - +
1930B LYS* 3.1 28.6 + - - +
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Residues in contact with LYS1927 (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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1825B GLU* 3.2 33.9 + - - -
1828B GLN* 2.7 36.9 + - - +
1829B VAL* 3.6 31.2 - - + +
1832B ALA* 3.9 10.5 - - + -
1923B SER* 3.2 20.6 + - - +
1924B ILE 3.1 6.3 + - - +
1926B ASP* 1.3 75.6 - - - +
1928B TRP* 1.3 66.0 + - - +
1930B LYS* 3.0 35.0 + - + +
1931B PHE* 3.6 17.3 - - + -
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Residues in contact with TRP1928 (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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1832B ALA* 3.6 28.4 - - + +
1835B LEU* 3.9 22.0 - - + -
1836B GLN* 3.0 31.9 + - + +
1839B GLN* 3.3 38.6 - - + -
1840B GLY 3.1 15.8 + - - -
1841B ASP 4.0 2.9 - - - -
1842B TYR* 3.5 48.6 + + + +
1846B ALA* 4.0 14.1 - - + -
1848B ILE* 3.5 21.8 - - + -
1924B ILE 2.8 16.9 + - - +
1925B ILE* 3.4 13.5 - - + +
1926B ASP 3.2 0.2 - - - -
1927B LYS* 1.3 74.7 - - - +
1929B ARG* 1.3 65.0 + - - +
1931B PHE* 3.1 14.5 + - - +
1932B GLN 4.2 0.3 + - - -
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Residues in contact with ARG1929 (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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1842B TYR* 3.5 52.2 + - + -
1925B ILE* 3.0 13.8 + - - +
1926B ASP* 3.2 36.9 + - - +
1928B TRP* 1.3 77.4 - - - +
1930B LYS* 1.3 67.9 + - - +
1931B PHE 3.1 1.0 + - - -
1932B GLN* 3.4 21.0 + - - +
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Residues in contact with LYS1930 (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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1926B ASP* 3.1 39.7 + - - +
1927B LYS* 3.0 21.9 + - + +
1929B ARG* 1.3 85.6 - - + +
1931B PHE* 1.3 65.6 + - + +
1932B GLN* 3.3 5.6 + - - +
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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