Contacts of the helix formed by residues 1913 - 1930 (chain A) 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 ILE1913 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1857A LEU* 6.4 0.9 - - + -
1860A LEU* 3.5 44.2 - - + -
1861A LYS* 4.6 24.0 - - + -
1914A LYS* 1.3 67.5 + - - +
1915A GLU* 3.1 4.6 + - - -
1916A GLU* 3.2 17.2 + - + +
1917A VAL* 3.3 21.0 + - + +
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Residues in contact with LYS1914 (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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1913A ILE* 1.3 78.3 - - - +
1915A GLU* 1.3 66.9 + - + +
1917A VAL* 4.1 7.4 - - - +
1918A SER* 3.2 27.8 + - - -
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Residues in contact with GLU1915 (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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1913A ILE 3.1 1.2 + - - -
1914A LYS* 1.3 81.9 - - + +
1916A GLU* 1.3 68.1 + - - +
1918A SER* 3.3 10.4 + - - -
1919A SER* 2.8 25.1 + - - -
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Residues in contact with GLU1916 (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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1860A LEU* 3.2 40.5 - - + +
1913A ILE* 3.2 10.0 + - + +
1915A GLU* 1.3 78.3 - - + +
1917A VAL* 1.3 64.4 + - - +
1919A SER* 2.9 10.5 + - - -
1920A ALA* 2.9 24.7 + - - +
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Residues in contact with VAL1917 (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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1851A LEU* 3.5 29.5 - - + +
1855A TYR* 6.3 0.4 - - - -
1857A LEU* 6.2 4.0 - - + -
1860A LEU* 4.3 13.9 - - + +
1913A ILE* 3.3 26.7 - - + +
1914A LYS* 4.1 7.4 - - - +
1915A GLU 3.4 0.2 - - - -
1916A GLU* 1.3 74.8 - - - +
1918A SER* 1.3 53.2 + - - +
1920A ALA* 3.1 5.9 + - - +
1921A ARG* 2.7 43.0 + - + +
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Residues in contact with SER1918 (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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1914A LYS* 3.2 17.7 + - - +
1915A GLU* 3.6 13.3 + - - -
1917A VAL* 1.3 78.5 - - - +
1919A SER* 1.3 58.3 + - - +
1921A ARG* 3.6 9.5 - - - +
1922A ALA* 2.8 30.5 + - - +
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Residues in contact with SER1919 (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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1915A GLU 2.8 14.0 + - - -
1916A GLU* 3.4 12.1 - - - -
1918A SER* 1.3 75.4 - - - +
1920A ALA* 1.3 60.3 + - - +
1922A ALA* 3.2 6.3 + - - +
1923A SER* 2.9 29.4 + - - -
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Residues in contact with ALA1920 (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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1828A GLN* 3.7 13.7 - - - +
1851A LEU* 5.1 1.1 - - + -
1855A TYR* 3.8 37.5 - - + +
1916A GLU 2.9 14.2 + - - +
1917A VAL* 3.6 10.1 - - - +
1919A SER* 1.3 71.8 - - - +
1921A ARG* 1.3 57.2 + - - +
1923A SER* 3.0 3.7 + - - -
1924A ILE* 2.9 37.3 + - + +
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Residues in contact with ARG1921 (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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1848A ILE* 3.5 34.1 - - + +
1851A LEU* 4.2 35.2 - - + +
1917A VAL* 2.7 24.3 + - - +
1918A SER* 3.6 10.5 - - - +
1920A ALA* 1.3 75.2 - - - +
1922A ALA* 1.3 62.3 + - - +
1923A SER 3.2 0.9 + - - -
1924A ILE* 3.4 2.2 + - - +
1925A ILE* 3.2 41.8 + - + +
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Residues in contact with ALA1922 (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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1918A SER 2.8 22.1 + - - +
1919A SER* 3.7 6.5 - - - +
1921A ARG* 1.3 74.7 - - - +
1923A SER* 1.3 59.3 + - - +
1925A ILE* 4.2 7.8 - - - +
1926A ASP* 3.4 20.7 + - - +
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Residues in contact with SER1923 (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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1828A GLN* 2.5 34.4 + - - -
1919A SER 2.9 12.6 + - - -
1920A ALA* 3.3 7.9 - - - -
1921A ARG 3.0 0.2 - - - -
1922A ALA* 1.3 78.2 - - - +
1924A ILE* 1.3 64.7 + - - +
1926A ASP* 3.3 7.9 + - - +
1927A LYS* 3.1 31.9 + - - +
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Residues in contact with ILE1924 (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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1828A GLN* 3.8 24.5 - - + +
1831A ALA* 3.7 9.6 - - + -
1832A ALA* 3.5 23.4 - - - +
1835A LEU* 3.8 20.9 - - + -
1851A LEU* 3.9 18.6 - - + -
1854A VAL* 5.0 1.8 - - + -
1855A TYR* 3.7 37.0 - - + -
1920A ALA* 2.9 21.4 + - + +
1921A ARG* 3.4 3.8 + - - +
1923A SER* 1.3 77.6 - - - +
1925A ILE* 1.3 52.4 + - + +
1927A LYS* 3.0 9.9 + - - +
1928A TRP* 2.8 32.6 + - - +
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Residues in contact with ILE1925 (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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1835A LEU* 5.2 3.8 - - + -
1842A TYR* 4.0 25.0 - - + -
1848A ILE* 3.7 35.2 - - + -
1921A ARG* 3.2 36.6 + - + +
1922A ALA* 4.4 6.3 - - - +
1924A ILE* 1.3 74.6 - - + +
1926A ASP* 1.3 66.2 + - - +
1928A TRP* 3.7 18.1 - - + +
1929A ARG* 3.1 21.8 + - - +
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Residues in contact with ASP1926 (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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1922A ALA 3.4 14.3 + - - +
1923A SER* 3.3 12.1 + - - +
1924A ILE 3.1 0.2 - - - -
1925A ILE* 1.3 82.3 - - - +
1927A LYS* 1.3 62.8 + - - +
1929A ARG* 2.6 45.9 + - - +
1930A LYS* 2.9 32.2 + - - +
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Residues in contact with LYS1927 (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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1825A GLU* 3.2 37.1 + - - -
1828A GLN* 3.8 26.1 - - + +
1829A VAL* 3.8 24.9 - - + +
1832A ALA* 3.6 11.0 - - + -
1923A SER* 3.1 28.6 + - - +
1924A ILE* 3.0 8.6 + - - +
1926A ASP* 1.3 76.7 + - - +
1928A TRP* 1.3 64.2 + - - +
1929A ARG 3.1 1.8 - - - -
1930A LYS* 3.1 33.7 + - - +
1931A PHE* 3.5 20.0 - - + -
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Residues in contact with TRP1928 (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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1832A ALA* 3.5 17.0 - - + +
1835A LEU* 4.1 18.4 - - + -
1836A GLN* 2.9 48.9 + - + +
1839A GLN* 3.2 33.9 - - + -
1840A GLY 3.0 19.6 + - - -
1841A ASP 4.0 3.1 - - - -
1842A TYR* 3.5 45.6 + + + +
1846A ALA* 4.0 17.3 - - + -
1848A ILE* 3.6 24.5 - - + -
1924A ILE 2.8 14.3 + - - +
1925A ILE* 3.7 13.0 - - + +
1927A LYS* 1.3 76.7 - - - +
1929A ARG* 1.3 63.4 + - - +
1931A PHE* 3.0 18.3 + - + +
1932A GLN 4.1 0.3 + - - -
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Residues in contact with ARG1929 (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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1842A TYR* 3.6 45.9 - - + +
1925A ILE 3.1 13.7 + - - +
1926A ASP* 2.6 57.2 + - - +
1928A TRP* 1.3 78.0 - - - +
1930A LYS* 1.3 85.2 + - - +
1931A PHE 3.3 0.9 + - - -
1932A GLN* 3.6 17.3 + - - +
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Residues in contact with LYS1930 (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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1926A ASP* 2.9 37.0 + - - +
1927A LYS* 3.1 26.9 + - - +
1929A ARG* 1.3 97.9 - - - +
1931A PHE* 1.3 66.7 + - + +
1932A GLN* 3.3 4.8 + - - +
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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