Contacts of the helix formed by residues 1916 - 1930 (chain B) in PDB entry 5WBY
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 TRP1916 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1874B SER* 4.4 19.5 - - - -
1877B LEU* 3.7 27.1 - - + -
1878B LEU* 3.7 43.7 - - + -
1881B THR* 4.2 3.1 - - - -
1913B TYR* 3.1 39.8 + + + +
1914B GLY 3.6 1.7 - - - +
1915B HIS* 1.3 108.9 + + - +
1917B PRO* 1.4 67.6 - - + +
1918B ASP 3.4 0.7 - - - -
1919B VAL* 3.2 26.2 + - + +
1920B ASN 2.9 23.7 + - - -
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Residues in contact with PRO1917 (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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1878B LEU* 5.9 2.0 - - + -
1915B HIS 3.5 6.0 - - - +
1916B TRP* 1.4 85.2 - - + +
1918B ASP* 1.3 65.9 + - - +
1920B ASN* 3.3 1.9 + - - +
1921B GLU* 3.0 37.1 + - - +
1952B LEU* 4.1 17.3 - - + -
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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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1878B LEU* 4.0 32.3 - - + +
1882B VAL* 3.7 20.5 - - + +
1916B TRP* 3.4 1.4 - - - +
1917B PRO* 1.3 85.6 - - - +
1919B VAL* 1.3 61.9 + - - +
1921B GLU* 3.7 16.5 + - - +
1922B ALA* 3.4 16.3 + - - +
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Residues in contact with VAL1919 (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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1878B LEU* 4.9 3.6 - - + -
1881B THR* 3.5 33.4 - - + -
1882B VAL* 3.9 17.0 - - + -
1885B VAL* 4.2 11.4 - - + -
1909B LEU 4.3 2.5 - - - +
1913B TYR* 3.4 33.0 - - + +
1916B TRP* 3.2 23.3 + - + +
1918B ASP* 1.3 73.8 - - - +
1920B ASN* 1.3 60.5 - - - +
1922B ALA* 3.3 5.3 + - - +
1923B LEU* 3.0 38.5 + - + +
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Residues in contact with ASN1920 (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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1910B TRP* 5.2 0.7 + - - -
1914B GLY* 3.5 14.3 + - - +
1916B TRP 2.9 6.4 + - - +
1917B PRO* 3.3 6.0 + - + +
1919B VAL* 1.3 74.3 - - - +
1921B GLU* 1.3 60.8 + - - +
1923B LEU* 3.1 8.8 + - - +
1924B VAL* 2.8 43.1 + - - +
1952B LEU* 3.4 59.0 + - + +
1953B VAL* 5.0 0.9 - - - -
1956B LEU* 4.1 14.3 - - - +
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Residues in contact with GLU1921 (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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1917B PRO* 3.0 22.4 + - - +
1918B ASP* 3.8 18.0 - - - +
1919B VAL 3.3 0.2 - - - -
1920B ASN* 1.3 79.3 - - + +
1922B ALA* 1.3 56.0 + - - +
1924B VAL* 4.0 5.5 - - - +
1925B GLU* 3.0 33.6 + - - +
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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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1882B VAL* 4.2 21.5 - - + +
1885B VAL* 3.9 19.7 - - + +
1886B GLN* 4.5 11.6 - - + +
1889B PHE* 4.0 5.5 - - - -
1918B ASP 3.4 10.7 + - - +
1919B VAL* 3.3 10.2 + - - +
1920B ASN 3.2 0.4 - - - -
1921B GLU* 1.3 77.3 - - - +
1923B LEU* 1.3 59.2 + - - +
1925B GLU* 3.4 7.5 - - - +
1926B GLY* 2.9 25.1 + - - -
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Residues in contact with LEU1923 (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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1885B VAL* 4.0 18.8 - - + -
1889B PHE* 3.9 8.3 - - + -
1906B VAL* 4.1 20.4 - - + +
1910B TRP* 3.7 44.2 - - + +
1914B GLY* 3.8 28.9 - - - +
1919B VAL* 3.0 26.9 + - + +
1920B ASN* 3.1 9.6 + - - +
1922B ALA* 1.3 74.7 - - - +
1924B VAL* 1.3 59.3 + - - +
1926B GLY* 3.3 1.0 + - - -
1927B VAL* 2.9 34.3 + - + +
1956B LEU* 4.0 13.2 - - + -
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Residues in contact with VAL1924 (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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1920B ASN* 2.8 38.7 + - - +
1921B GLU* 4.0 5.4 - - - +
1923B LEU* 1.3 68.1 - - - +
1925B GLU* 1.3 66.6 + - - +
1927B VAL* 3.4 4.5 + - - +
1928B LYS* 3.1 45.0 + - + +
1956B LEU* 3.8 27.8 - - + -
1959B GLN* 6.1 0.4 - - - +
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Residues in contact with GLU1925 (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 GLU 3.0 20.8 + - - +
1922B ALA* 3.4 9.4 - - - +
1924B VAL* 1.3 78.3 - - - +
1926B GLY* 1.3 61.8 + - - +
1928B LYS* 3.5 18.7 + - - +
1929B ALA* 3.3 21.5 + - - +
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Residues in contact with GLY1926 (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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1889B PHE* 3.6 38.3 - - - -
1922B ALA 2.9 10.9 + - - -
1923B LEU 3.6 3.1 - - - -
1924B VAL 3.2 0.2 - - - -
1925B GLU* 1.3 73.7 - - - +
1927B VAL* 1.3 64.1 + - - +
1929B ALA* 3.0 6.3 + - - +
1930B ILE* 3.0 26.9 + - - +
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Residues in contact with VAL1927 (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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1889B PHE* 3.9 3.3 - - + -
1910B TRP* 4.7 4.9 - - + -
1923B LEU* 2.9 20.7 + - + +
1924B VAL 3.4 3.6 + - - +
1926B GLY* 1.3 72.8 - - - +
1928B LYS* 1.3 63.7 + - + +
1930B ILE* 3.4 21.3 - - - +
1935B TRP* 3.8 24.9 + - + +
1956B LEU* 4.4 28.3 - - + -
1959B GLN* 4.7 8.1 - - - +
1960B LEU* 3.9 30.3 - - + -
1963B ASP* 5.4 2.9 - - - +
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Residues in contact with LYS1928 (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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1924B VAL* 3.1 35.0 + - + +
1925B GLU* 3.5 21.4 + - - +
1927B VAL* 1.3 80.0 - - + +
1929B ALA* 1.3 61.2 + - + +
1930B ILE 3.9 3.1 - - - +
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Residues in contact with ALA1929 (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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1889B PHE* 6.5 0.4 - - + -
1893B SER* 6.0 1.1 - - - -
1925B GLU 3.3 8.5 + - - +
1926B GLY* 3.0 9.6 + - - +
1928B LYS* 1.3 77.9 - - - +
1930B ILE* 1.3 68.7 + - - +
1931B GLN* 3.8 5.7 + - - -
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Residues in contact with ILE1930 (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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1889B PHE* 4.4 16.4 - - + +
1892B ILE* 3.4 36.6 - - + -
1893B SER* 5.3 13.7 - - - +
1903B THR* 5.9 0.2 - - + -
1926B GLY 3.0 19.7 + - - +
1927B VAL* 3.4 24.2 - - - +
1928B LYS 3.9 2.9 - - - +
1929B ALA* 1.3 82.9 - - - +
1931B GLN* 1.3 64.1 + - - +
1932B ILE* 3.7 2.1 + - - +
1934B THR* 3.4 27.6 - - + +
1935B TRP* 3.8 29.2 - - + +
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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