Contacts of the helix formed by residues 1899 - 1914 (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 ASN1899 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1787B TYR* 5.6 0.2 - - - -
1892B ILE* 3.3 31.8 - - + +
1895B SER* 3.6 14.1 - - - +
1896B ARG* 3.2 26.8 + - - -
1897B GLY 3.8 6.1 + - - +
1898B ASN* 1.3 75.2 - - - +
1900B LEU* 1.3 62.6 + - - +
1901B GLN* 3.3 2.5 - - - -
1902B ASP* 3.6 9.8 + - - +
1903B THR* 2.7 35.5 + - - -
1934B THR* 3.9 10.8 + - - +
1937B GLN* 3.0 30.9 + - - +
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Residues in contact with LEU1900 (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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1898B ASN* 3.9 4.5 + - - +
1899B ASN* 1.3 76.7 - - - +
1901B GLN* 1.3 62.4 + - - +
1903B THR* 3.6 1.1 + - - -
1904B LEU* 3.0 51.4 + - + +
1937B GLN* 3.3 47.9 - - + +
1938B VAL* 5.1 2.7 - - + -
2200B GLN* 4.3 17.5 - - + +
2204B LEU* 3.9 34.5 - - + +
2417B VAL* 3.8 21.3 - - + -
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Residues in contact with GLN1901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1787B TYR* 5.6 1.6 + - - +
1791B HIS* 3.7 30.8 + - + -
1795B VAL* 4.6 7.3 - - - +
1899B ASN 3.3 0.4 - - - -
1900B LEU* 1.3 75.2 - - - +
1902B ASP* 1.3 63.7 + - - +
1904B LEU* 3.0 6.3 + - - +
1905B ARG* 2.9 49.6 + - + +
2204B LEU* 6.3 0.2 - - - +
2412B ASP* 3.6 26.4 + - - +
2413B SER* 3.2 36.1 + - - +
2416B ALA* 3.6 27.8 - - + -
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Residues in contact with ASP1902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1787B TYR* 3.1 29.1 + - - -
1791B HIS* 2.6 31.2 + - - -
1888B PHE* 3.4 18.1 - - + +
1891B SER* 3.1 18.2 + - - +
1892B ILE* 3.4 22.9 - - + -
1895B SER* 4.3 4.2 + - - -
1899B ASN* 3.6 9.7 + - + +
1900B LEU 3.5 0.2 - - - -
1901B GLN* 1.3 79.6 - - - +
1903B THR* 1.3 57.4 + - - +
1905B ARG* 3.2 5.3 + - - +
1906B VAL* 3.0 31.2 + - - +
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Residues in contact with THR1903 (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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1892B ILE* 3.7 13.8 - - + +
1899B ASN* 2.7 23.2 + - - -
1900B LEU* 3.8 4.7 - - - -
1902B ASP* 1.3 77.1 - - - +
1904B LEU* 1.3 61.5 + - - +
1906B VAL* 3.3 6.8 + - - +
1907B LEU* 3.2 20.8 + - - +
1934B THR* 3.2 34.8 - - + +
1935B TRP* 4.1 14.6 - - + -
1937B GLN* 3.6 7.4 + - - +
1938B VAL* 3.8 30.7 - - + -
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Residues in contact with LEU1904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1900B LEU* 3.0 40.7 + - + +
1901B GLN 3.0 5.6 + - - +
1903B THR* 1.3 75.3 - - - +
1905B ARG* 1.3 61.0 + - - +
1907B LEU* 3.2 11.6 + - + +
1908B THR* 3.1 23.4 + - - -
1938B VAL* 3.3 24.9 - - + -
1941B GLN* 4.0 12.8 - - + +
2200B GLN* 5.2 1.3 - - - +
2416B ALA* 3.8 15.5 - - + +
2417B VAL* 3.7 36.1 - - + +
2420B ALA* 3.8 21.5 - - + -
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Residues in contact with ARG1905 (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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1798B PHE* 3.7 41.7 - - + -
1888B PHE* 3.7 32.3 - - + -
1901B GLN* 2.9 34.2 + - - +
1902B ASP 3.2 7.8 + - - +
1904B LEU* 1.3 73.0 - - - +
1906B VAL* 1.3 65.8 - - - +
1908B THR* 3.2 23.3 + - - +
1909B LEU* 3.3 18.5 + - - +
2412B ASP* 3.9 11.3 + - - +
2415B MET* 4.4 3.4 - - - +
2416B ALA* 3.8 31.7 - - - +
2419B GLU* 2.8 35.3 + - - +
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Residues in contact with VAL1906 (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* 4.6 5.3 - - + +
1888B PHE* 3.5 23.3 - - + -
1889B PHE* 3.5 39.0 - - + +
1892B ILE* 3.7 15.3 - - + -
1902B ASP 3.0 18.3 + - - +
1903B THR* 3.3 9.2 + - - +
1905B ARG* 1.3 76.0 - - - +
1907B LEU* 1.3 59.5 + - - +
1909B LEU* 3.4 8.5 + - - +
1910B TRP* 2.9 29.1 + - + +
1923B LEU* 4.1 11.6 - - + +
1935B TRP* 4.3 14.1 - - + -
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Residues in contact with LEU1907 (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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1903B THR 3.2 10.4 + - - +
1904B LEU* 3.4 11.2 - - + +
1905B ARG 3.2 0.6 - - - -
1906B VAL* 1.3 75.1 - - - +
1908B THR* 1.3 59.0 + - - +
1910B TRP* 3.6 30.5 - - + -
1911B PHE* 2.8 55.9 + - + -
1935B TRP* 4.0 14.4 - - + -
1938B VAL* 3.3 36.3 - - + +
1941B GLN* 3.8 19.3 - - + -
1942B LEU* 3.8 18.2 - - + -
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Residues in contact with THR1908 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1798B PHE* 4.6 18.8 - - + -
1904B LEU 3.1 15.4 + - - -
1905B ARG* 3.2 20.7 + - - +
1907B LEU* 1.3 75.2 - - - +
1909B LEU* 1.3 57.6 + - - +
1911B PHE* 4.9 3.4 - - - -
1912B ASP* 2.9 54.3 + - - +
1913B TYR* 5.7 0.4 - - + -
2419B GLU* 6.1 0.4 - - - +
2423B TYR* 6.4 2.2 - - + -
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Residues in contact with LEU1909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1798B PHE* 3.9 22.0 - - + -
1801B VAL* 5.0 5.6 - - + -
1881B THR* 4.1 15.0 - - + +
1884B ALA* 3.9 23.1 - - + -
1885B VAL* 3.8 29.6 - - + -
1888B PHE* 4.0 19.3 - - + -
1905B ARG 3.3 15.2 + - - +
1906B VAL* 3.9 4.7 - - - +
1908B THR* 1.3 72.6 - - - +
1910B TRP* 1.3 59.0 + - - +
1913B TYR* 2.8 57.5 + - + +
1914B GLY* 3.2 5.5 + - - -
1919B VAL* 4.3 1.8 - - - +
1923B LEU* 5.0 1.8 - - - -
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Residues in contact with TRP1910 (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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1906B VAL* 2.9 18.9 + - + +
1907B LEU* 3.5 26.5 - - + +
1909B LEU* 1.3 75.4 - - - +
1911B PHE* 1.3 64.8 + + + +
1914B GLY* 2.7 30.2 + - - -
1920B ASN* 5.2 1.0 + - - -
1923B LEU* 3.7 36.5 - - + +
1927B VAL* 4.7 4.0 - - + -
1935B TRP* 4.2 11.7 - + - -
1942B LEU* 3.9 11.4 - - + -
1953B VAL* 3.6 34.7 + - + +
1956B LEU* 3.8 28.1 - - + +
1957B ILE* 3.4 38.6 - - + -
1960B LEU* 3.6 33.0 - - + -
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Residues in contact with PHE1911 (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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1907B LEU* 2.8 62.8 + - + +
1908B THR* 4.3 3.8 - - - +
1910B TRP* 1.3 86.4 - + + +
1912B ASP* 1.3 62.3 + - - +
1914B GLY 4.8 0.2 + - - -
1941B GLN* 3.8 17.9 - - + -
1942B LEU* 4.3 7.0 - - + -
1945B ARG* 3.5 61.0 + - + +
1948B THR* 5.7 3.1 - - + +
1950B ARG* 3.0 21.8 + - - -
1953B VAL* 4.5 8.8 - - + +
1957B ILE* 3.8 29.2 - - + -
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Residues in contact with ASP1912 (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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1805B LYS* 4.2 16.6 + - - -
1908B THR* 2.9 37.2 + - - +
1911B PHE* 1.3 83.6 - - - +
1913B TYR* 1.3 83.7 + - + +
1915B HIS* 3.4 8.1 - - - -
1945B ARG* 5.3 6.2 + - - -
1950B ARG* 2.8 22.0 + - - +
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Residues in contact with TYR1913 (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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1798B PHE* 6.3 0.7 - + - -
1801B VAL* 3.7 26.8 - - + +
1802B LEU* 6.3 0.7 - - + -
1805B LYS* 3.3 36.1 + - + +
1877B LEU* 4.5 10.4 - - + +
1881B THR* 3.9 20.4 - - + -
1908B THR* 5.7 0.7 - - + -
1909B LEU* 2.8 42.2 + - + +
1912B ASP* 1.3 99.0 - - + +
1914B GLY* 1.3 61.2 + - - +
1915B HIS* 3.2 8.5 - + - -
1916B TRP* 3.1 53.2 + + + +
1919B VAL* 3.4 12.9 - - - +
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Residues in contact with GLY1914 (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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1909B LEU 3.2 1.4 + - - -
1910B TRP* 2.7 28.0 + - - -
1912B ASP 3.8 0.6 - - - -
1913B TYR* 1.3 72.6 - - - +
1915B HIS* 1.3 60.8 + - - +
1916B TRP 3.2 1.1 - - - -
1919B VAL* 4.1 1.8 - - - -
1920B ASN* 3.5 29.6 - - - +
1923B LEU* 3.8 22.2 - - - -
1952B LEU* 3.9 2.3 - - - +
1953B VAL* 3.4 10.1 - - - +
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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