Contacts of the helix formed by residues 1925 - 1944 (chain A) in PDB entry 5PED
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 ASN1925 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1923A TYR* 3.2 7.6 - - - +
1924A PRO* 1.3 87.1 + - - +
1926A LEU* 1.3 64.5 + - + +
1927A GLU* 2.9 25.0 + - + +
1928A THR* 2.8 41.7 + - - +
1929A PHE* 3.4 4.6 + - - +
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Residues in contact with LEU1926 (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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1864A ARG* 3.5 26.2 - - - +
1869A ASP* 3.2 35.4 + - + +
1873A CYS* 3.4 20.4 - - - -
1925A ASN* 1.3 73.9 - - + +
1927A GLU* 1.3 78.3 + - + +
1929A PHE* 3.1 10.9 + - - +
1930A ALA 3.1 16.5 + - - -
1965A TRP* 3.4 19.7 - - + -
1969A PHE* 3.3 43.5 - - + -
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Residues in contact with GLU1927 (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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1925A ASN* 2.9 11.7 + - + +
1926A LEU* 1.3 92.2 - - + +
1928A THR* 1.3 61.8 + - + +
1930A ALA* 3.2 8.1 + - - +
1931A LEU* 3.0 36.8 + - + +
1934A ARG* 4.7 6.2 + - - -
1965A TRP* 4.2 20.3 + - - -
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Residues in contact with THR1928 (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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1923A TYR* 3.5 18.9 - - - -
1924A PRO* 3.4 33.3 - - + +
1925A ASN* 2.8 43.4 + - - +
1927A GLU* 1.3 77.9 - - + +
1929A PHE* 1.3 60.9 + - - +
1931A LEU* 3.5 15.7 + - + +
1932A ASP* 3.4 17.2 + - - +
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Residues in contact with PHE1929 (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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1873A CYS* 3.5 53.4 - - + -
1876A ILE* 5.0 3.8 - - + -
1877A LEU* 4.2 13.2 - - + -
1880A MET* 5.1 0.2 - - + -
1914A ILE* 3.5 31.4 - - + -
1918A LEU* 4.1 18.2 - - + -
1923A TYR* 3.7 26.2 - + + -
1925A ASN 3.4 5.8 + - - +
1926A LEU 3.1 9.3 + - - +
1928A THR* 1.3 80.7 + - - +
1930A ALA* 1.3 65.5 + - - +
1932A ASP* 3.2 5.9 + - - +
1933A VAL* 3.1 38.4 + - + +
1961A PHE* 4.3 7.9 - + - -
1965A TRP* 3.7 16.8 - + - -
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Residues in contact with ALA1930 (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 LEU 3.1 6.3 + - - -
1927A GLU* 3.2 9.6 + - - +
1929A PHE* 1.3 78.6 - - - +
1931A LEU* 1.3 57.5 + - - +
1933A VAL* 3.3 2.1 + - - +
1934A ARG* 2.9 59.0 + - - +
1961A PHE* 4.1 14.8 - - + -
1965A TRP* 3.6 32.5 - - + -
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Residues in contact with LEU1931 (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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1927A GLU* 3.0 23.4 + - + +
1928A THR* 3.7 17.7 - - + +
1929A PHE 3.2 0.2 - - - -
1930A ALA* 1.3 76.5 - - - +
1932A ASP* 1.3 58.4 + - - +
1934A ARG* 3.5 16.8 + - + +
1935A LEU* 2.9 28.1 + - - +
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Residues in contact with ASP1932 (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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1907A LYS* 5.9 0.9 - - - -
1909A MET* 3.5 24.8 - - - +
1914A ILE* 3.9 9.0 - - + -
1917A LYS* 2.8 25.4 + - - -
1923A TYR* 2.6 35.1 + - - +
1928A THR 3.4 5.3 + - - +
1929A PHE 3.2 7.4 + - - +
1931A LEU* 1.3 78.4 - - - +
1933A VAL* 1.3 64.6 + - - +
1935A LEU* 3.3 16.4 + - - +
1936A VAL* 3.2 24.1 + - - +
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Residues in contact with VAL1933 (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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1880A MET* 3.7 24.9 - - + -
1911A PHE* 5.0 2.0 - - + -
1914A ILE* 3.8 19.1 - - + -
1929A PHE* 3.1 42.7 + - + +
1930A ALA 3.3 5.8 + - - +
1932A ASP* 1.3 75.5 - - - +
1934A ARG* 1.3 63.7 + - - +
1936A VAL* 3.1 19.7 + - - +
1937A PHE* 3.5 28.8 - - + -
1961A PHE* 3.7 22.4 - - + -
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Residues in contact with ARG1934 (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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1927A GLU* 4.7 7.7 + - - -
1930A ALA* 2.9 38.0 + - - +
1931A LEU* 3.9 17.3 - - + +
1933A VAL* 1.3 77.1 - - - +
1935A LEU* 1.3 51.3 + - - +
1937A PHE* 3.0 11.5 + - + +
1938A ASP* 2.8 44.2 + - - +
1958A ARG* 4.5 11.7 - - - +
1961A PHE* 4.0 9.8 - - + -
1962A GLU* 2.7 41.3 + - - +
1965A TRP* 3.7 24.4 - - - +
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Residues in contact with LEU1935 (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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1907A LYS* 3.4 50.5 - - + +
1909A MET* 3.7 19.3 - - + -
1931A LEU 2.9 17.6 + - - +
1932A ASP* 3.4 20.6 - - - +
1934A ARG* 1.3 74.6 - - - +
1936A VAL* 1.3 56.2 + - - +
1938A ASP* 4.3 9.4 + - + -
1939A ASN* 2.8 60.0 + - - +
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Residues in contact with VAL1936 (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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1889A PHE* 3.6 39.3 - - + -
1909A MET* 3.7 39.5 - - + +
1910A ASP* 3.8 7.2 - - - +
1911A PHE* 4.1 6.1 - - + -
1914A ILE* 3.8 13.2 - - + -
1932A ASP 3.2 15.5 + - - +
1933A VAL 3.1 11.1 + - - +
1935A LEU* 1.3 76.1 - - - +
1937A PHE* 1.3 68.0 + - + +
1939A ASN* 3.7 3.9 - - - +
1940A CYS* 3.1 25.6 + - - +
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Residues in contact with PHE1937 (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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1880A MET* 4.4 2.5 - - - -
1889A PHE* 4.3 8.5 - + - -
1911A PHE* 3.9 25.4 - + - -
1933A VAL* 3.5 36.3 + - + -
1934A ARG* 3.0 7.6 + - + +
1936A VAL* 1.3 91.9 - - + +
1938A ASP* 1.3 58.2 + - - +
1940A CYS* 3.3 5.5 + - - +
1941A GLU* 2.9 28.4 + - - +
1954A GLY* 3.8 20.3 - - - +
1957A MET* 3.4 32.8 - - + -
1958A ARG* 3.4 56.4 + - + +
1961A PHE* 4.3 5.2 - + + -
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Residues in contact with ASP1938 (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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1934A ARG* 2.8 24.6 + - - +
1935A LEU* 3.9 10.8 + - + +
1937A PHE* 1.3 70.7 - - - +
1939A ASN* 1.3 68.5 + - - +
1941A GLU* 3.3 5.7 + - - +
1942A THR* 3.0 27.2 + - - -
1958A ARG* 2.7 38.2 + - - +
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Residues in contact with ASN1939 (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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1901A TYR* 3.6 17.5 + - - +
1905A ILE* 3.4 34.2 - - + +
1907A LYS 2.8 25.6 + - - +
1908A PRO* 3.6 0.4 - - - +
1909A MET* 3.6 18.7 + - - +
1935A LEU* 2.8 35.9 + - - +
1936A VAL* 3.7 4.7 - - - +
1938A ASP* 1.3 77.3 - - - +
1940A CYS* 1.3 61.5 + - - +
1942A THR* 3.2 5.8 + - - -
1943A PHE* 3.1 21.3 + - - +
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Residues in contact with CYS1940 (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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1889A PHE* 3.7 27.6 - - + -
1901A TYR* 5.4 0.9 - - - -
1936A VAL 3.1 12.8 + - - +
1937A PHE* 3.3 11.2 + - - +
1939A ASN* 1.3 80.0 - - - +
1941A GLU* 1.3 59.5 + - - +
1943A PHE 3.3 0.5 + - - -
1944A ASN* 2.9 42.5 + - - +
1950A ILE* 3.5 39.0 - - - -
1951A GLY* 4.4 5.2 - - - -
1954A GLY* 4.0 9.6 - - - -
2001A EDO 4.9 3.1 - - - -
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Residues in contact with GLU1941 (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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1937A PHE 2.9 18.0 + - - +
1938A ASP* 3.7 5.4 - - - +
1939A ASN 3.3 0.2 - - - -
1940A CYS* 1.3 78.8 - - + +
1942A THR* 1.3 63.3 + - - +
1943A PHE 3.5 0.2 + - - -
1944A ASN* 3.5 16.0 - - - +
1946A ASP* 4.7 7.8 - - - +
1951A GLY* 5.9 2.0 - - - +
1954A GLY* 6.2 2.0 - - - -
1955A HIS* 3.5 37.9 + - + +
1958A ARG* 3.0 27.2 + - - +
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Residues in contact with THR1942 (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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1904A VAL* 4.0 18.2 - - + +
1905A ILE* 3.7 20.6 - - + -
1938A ASP 3.0 16.9 + - - -
1939A ASN* 3.2 9.7 + - - -
1941A GLU* 1.3 78.7 - - - +
1943A PHE* 1.3 58.9 + - - +
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Residues in contact with PHE1943 (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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1898A VAL* 3.9 15.3 - - + -
1899A PRO 3.4 23.6 - - - -
1900A GLY* 3.8 21.3 - - - -
1901A TYR* 3.7 40.2 - + + -
1904A VAL* 4.3 22.4 - - + -
1905A ILE* 4.3 3.4 - - + -
1939A ASN 3.1 14.9 + - - +
1942A THR* 1.3 78.9 - - - +
1944A ASN* 1.3 64.5 + - - +
1945A GLU 4.3 0.2 + - - -
2001A EDO 3.8 18.8 - - - -
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Residues in contact with ASN1944 (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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1940A CYS* 2.9 28.6 + - - +
1941A GLU* 3.5 16.5 - - - +
1942A THR 3.7 0.2 - - - -
1943A PHE* 1.3 85.7 - - - +
1945A GLU* 1.3 66.5 + - - +
1946A ASP* 3.5 4.0 + - - +
1948A SER* 3.9 12.6 + - - +
1950A ILE* 3.3 26.4 - - + +
1951A GLY* 4.1 12.4 - - - +
2001A EDO 2.9 40.6 + - - -
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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
------------------------------------------------------------
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