Contacts of the helix formed by residues 1928 - 1946 (chain B) in PDB entry 4JKE
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 SER1928 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1924B LEU* 3.9 0.9 - - - -
1927B ILE* 1.3 79.2 - - - +
1929B SER* 1.3 64.3 + - - +
1930B TYR* 3.5 17.3 + - - +
1931B THR* 3.1 27.3 + - - -
1932B ALA* 3.0 21.0 + - - +
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Residues in contact with SER1929 (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 PHE* 3.6 18.3 + - - +
1812B PRO 3.9 3.7 - - - +
1813B ARG* 3.3 39.8 - - - +
1924B LEU* 3.7 16.0 - - - +
1928B SER* 1.3 72.7 - - - +
1930B TYR* 1.3 72.2 + - - +
1932B ALA* 3.4 2.1 + - - +
1933B PHE* 2.9 30.5 + - - +
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Residues in contact with TYR1930 (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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1770B GLU* 3.0 32.2 + - - +
1771B LEU* 3.4 15.5 + - + -
1772B PHE* 3.0 65.0 + + + +
1928B SER* 3.1 16.0 - - - +
1929B SER* 1.3 83.2 - - - +
1931B THR* 1.3 59.0 + - - +
1933B PHE* 3.3 5.0 + - - +
1934B SER* 3.0 30.9 + - - -
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Residues in contact with THR1931 (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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1927B ILE* 4.0 25.8 - - + -
1928B SER* 3.1 19.9 + - - -
1930B TYR* 1.3 76.9 - - - +
1932B ALA* 1.3 64.3 + - - +
1934B SER* 3.3 9.1 + - - -
1935B ARG* 3.0 26.1 + - - +
1980B GLU* 5.7 5.4 - - - +
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Residues in contact with ALA1932 (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 TYR* 3.7 33.4 - - + -
1923B TRP* 3.6 16.9 - - + -
1924B LEU* 3.9 9.0 - - + -
1927B ILE* 3.6 12.9 - - + +
1928B SER 3.0 14.1 + - - +
1929B SER 3.6 7.4 - - - +
1931B THR* 1.3 73.6 - - - +
1933B PHE* 1.3 64.4 + - - +
1935B ARG* 3.2 3.9 + - - +
1936B LEU* 2.9 22.3 + - - +
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Residues in contact with PHE1933 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1772B PHE* 3.7 29.8 - + + -
1779B PHE* 3.9 27.8 - + - -
1810B PHE* 3.8 22.7 - + - -
1812B PRO* 4.1 4.0 - - + -
1889B LEU* 4.1 7.0 - - + -
1891B LEU* 3.9 25.8 - - + -
1920B TYR* 3.3 22.1 + - - +
1929B SER 2.9 14.3 + - - +
1930B TYR 3.5 5.4 - - - +
1932B ALA* 1.3 76.0 - - - +
1934B SER* 1.3 62.7 + - - +
1936B LEU* 3.2 5.6 + - + +
1937B ILE* 3.0 49.1 + - + +
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Residues in contact with SER1934 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1930B TYR 3.0 13.5 + - - -
1931B THR* 3.3 12.9 + - - -
1933B PHE* 1.3 76.1 - - - +
1935B ARG* 1.3 61.5 + - - +
1937B ILE* 3.3 13.8 + - - +
1938B LEU* 3.1 29.3 + - - +
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Residues in contact with ARG1935 (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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1923B TRP* 3.4 53.7 - - + +
1927B ILE* 3.7 21.9 - - - +
1931B THR* 3.0 16.5 + - - +
1932B ALA 3.2 8.3 + - - +
1934B SER* 1.3 75.2 - - - +
1936B LEU* 1.3 64.1 + - - +
1938B LEU* 3.2 7.6 + - - +
1939B ILE* 3.0 33.9 + - + +
1973B ASP* 3.4 23.2 + - - -
1976B TRP* 3.4 50.0 - - + +
1980B GLU* 2.9 34.0 + - + +
1983B LEU* 6.3 0.4 - - + -
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Residues in contact with LEU1936 (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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1810B PHE* 3.4 41.3 - - + -
1891B LEU* 5.4 1.6 - - + -
1893B PHE* 4.9 2.0 - - + -
1919B LEU* 4.0 19.5 - - + +
1920B TYR* 4.0 10.1 - - + -
1923B TRP* 4.1 5.3 - - + -
1932B ALA 2.9 14.0 + - - +
1933B PHE* 3.6 10.8 - - + +
1935B ARG* 1.3 77.4 - - - +
1937B ILE* 1.3 63.2 + - - +
1939B ILE* 3.2 4.9 + - + +
1940B LEU* 2.9 44.1 + - + +
1968B TRP* 3.8 36.8 - - + +
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Residues in contact with ILE1937 (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 LEU* 4.5 15.7 - - + -
1890B GLN 4.2 3.1 - - - +
1891B LEU* 4.0 23.6 - - + -
1933B PHE* 3.0 52.4 + - + +
1934B SER* 3.6 13.2 - - - +
1936B LEU* 1.3 75.3 - - - +
1938B LEU* 1.3 66.1 + - + +
1940B LEU* 4.0 0.9 - - - +
1941B ARG* 2.9 65.9 + - - +
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Residues in contact with LEU1938 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1934B SER* 3.1 19.6 + - - +
1935B ARG* 3.5 8.1 - - - +
1937B ILE* 1.3 81.5 - - + +
1939B ILE* 1.3 62.9 + - - +
1941B ARG* 5.3 6.1 - - - +
1942B ALA* 2.9 26.9 + - - +
1980B GLU* 3.8 46.2 - - + +
1983B LEU* 4.2 13.2 - - + +
1984B LYS* 3.9 31.2 - - + -
1987B ILE* 3.7 22.0 - - + +
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Residues in contact with ILE1939 (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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1923B TRP* 3.8 26.9 - - + -
1935B ARG* 3.0 22.6 + - + +
1936B LEU* 3.7 7.6 - - - +
1938B LEU* 1.3 76.6 - - - +
1940B LEU* 1.3 58.6 + - - +
1942B ALA* 3.3 3.0 + - - +
1943B LEU* 3.0 37.0 + - + +
1950B ALA* 5.4 0.2 - - - +
1954B LEU* 4.4 14.5 - - + +
1968B TRP* 3.5 46.0 - - + -
1976B TRP* 4.0 20.9 - - + -
1983B LEU* 4.0 21.8 - - + -
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Residues in contact with LEU1940 (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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1891B LEU* 3.8 24.0 - - + -
1892B PRO* 3.8 21.5 - - + +
1893B PHE* 4.1 23.8 - - + -
1895B ALA* 3.4 10.1 - - + +
1896B CYS* 3.9 33.2 - - - +
1919B LEU* 5.4 0.2 - - + -
1936B LEU* 2.9 34.0 + - + +
1937B ILE 4.1 2.0 - - - +
1939B ILE* 1.3 75.0 - - - +
1941B ARG* 1.3 57.6 + - - +
1943B LEU* 3.4 4.2 + - + -
1944B HIS* 2.9 30.3 + - - +
1968B TRP* 4.3 21.5 - - + -
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Residues in contact with ARG1941 (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 LEU* 3.4 25.3 - - - +
1890B GLN* 2.7 43.2 + - + +
1892B PRO* 3.8 23.1 - - + +
1937B ILE* 2.9 37.9 + - - +
1938B LEU* 5.3 6.8 - - - +
1940B LEU* 1.3 75.2 - - - +
1942B ALA* 1.3 61.7 + - - +
1944B HIS* 3.4 3.2 + - - +
1945B VAL* 3.1 29.2 + - + +
1987B ILE* 3.7 32.1 - - + +
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Residues in contact with ALA1942 (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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1938B LEU 2.9 18.8 + - - +
1939B ILE 3.7 3.6 - - - +
1941B ARG* 1.3 74.3 - - - +
1943B LEU* 1.3 60.7 + - - +
1945B VAL 3.3 0.7 + - - -
1946B ASN 2.9 32.6 + - - +
1950B ALA* 3.9 5.4 - - + -
1983B LEU* 3.7 32.3 - - + -
1986B LEU* 3.7 25.5 - - + +
1987B ILE* 4.0 4.4 - - + +
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Residues in contact with LEU1943 (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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1895B ALA* 3.8 15.3 - - + +
1898B LYS* 3.0 23.1 + - + +
1899B VAL* 3.9 24.5 - - + -
1939B ILE* 3.0 40.0 + - + +
1940B LEU* 3.8 8.3 - - + +
1942B ALA* 1.3 76.7 - - - +
1944B HIS* 1.3 63.4 + - - +
1947B ASN* 3.3 35.7 + - - +
1950B ALA* 3.9 19.3 - - + -
1951B LYS* 3.8 18.4 - - + +
1954B LEU* 4.7 7.6 - - + -
1968B TRP* 4.0 7.2 - - + -
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Residues in contact with HIS1944 (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 PRO* 3.7 24.7 - - + +
1894B GLN* 3.4 37.4 + - + +
1895B ALA* 3.8 7.1 - - + +
1898B LYS* 3.2 21.7 + - - +
1940B LEU 2.9 18.2 + - - +
1941B ARG* 3.4 6.1 - - - +
1942B ALA 3.2 0.2 - - - -
1943B LEU* 1.3 77.6 - - - +
1945B VAL* 1.3 72.4 + - + +
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Residues in contact with VAL1945 (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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1941B ARG* 3.1 18.3 + - + +
1944B HIS* 1.3 94.5 - - + +
1946B ASN* 1.3 60.6 + - + +
1986B LEU* 3.4 28.9 - - + +
1987B ILE* 4.5 15.5 - - + +
1989B ALA 6.5 0.4 - - - -
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Residues in contact with ASN1946 (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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1942B ALA 2.9 8.6 + - - +
1945B VAL* 1.3 81.8 + - - +
1947B ASN* 1.3 64.8 + - - +
1948B ASP* 3.6 7.3 + - - +
1949B ARG* 3.0 32.9 + - - +
1950B ALA* 2.9 21.0 + - - +
1986B LEU* 3.8 19.3 - - + +
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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