Contacts of the helix formed by residues 1924 - 1937 (chain B) in PDB entry 4ASI
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 ASP1924 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1878B VAL* 3.7 14.1 - - - -
1922B VAL* 3.3 8.3 - - - +
1923B CYS* 1.3 93.9 - - - +
1925B ASP* 1.3 64.3 + - - +
1926B PHE* 3.7 13.4 - - - +
1927B GLU* 2.7 27.2 + - - +
1928B GLY 3.1 15.2 + - - -
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Residues in contact with ASP1925 (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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1631B GLY 4.7 2.7 - - - +
1632B THR* 3.5 5.0 - - - -
1633B THR* 2.7 37.8 + - - +
1638B ILE* 5.7 2.2 - - + -
1641B MET* 3.8 10.1 - - + -
1856B LEU* 4.2 4.5 - - + +
1858B THR* 2.9 41.9 + - - +
1878B VAL* 3.5 19.0 - - - +
1924B ASP* 1.3 72.5 - - - +
1926B PHE* 1.3 66.5 + - - +
1928B GLY* 2.9 12.6 + - - +
1929B VAL* 3.0 16.7 + - + +
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Residues in contact with PHE1926 (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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1641B MET* 3.6 24.6 - - + +
1644B GLN* 3.7 30.5 - - + -
1645B SER* 3.7 29.4 + - - -
1648B LYS* 3.8 33.4 - - + -
1924B ASP* 3.3 14.8 + - - +
1925B ASP* 1.3 77.4 - - - +
1927B GLU* 1.3 61.5 + - + +
1929B VAL* 3.2 2.1 + - - -
1930B PHE* 3.0 27.5 + - + -
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Residues in contact with GLU1927 (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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1648B LYS* 4.9 13.7 - - - +
1921B THR 4.7 1.9 - - - +
1922B VAL* 3.8 16.0 - - + +
1923B CYS* 2.8 44.7 + - - +
1924B ASP* 2.7 22.9 + - - +
1926B PHE* 1.3 77.0 - - + +
1928B GLY* 1.3 61.0 + - - +
1930B PHE* 3.6 8.0 - - + +
1931B THR* 2.8 35.6 + - - +
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Residues in contact with GLY1928 (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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1856B LEU* 3.6 21.8 - - - -
1876B ILE* 3.7 2.4 - - - +
1922B VAL* 3.8 20.6 - - - +
1924B ASP 3.1 8.0 + - - -
1925B ASP 2.9 8.4 + - - -
1927B GLU* 1.3 74.2 - - - +
1929B VAL* 1.3 65.4 + - - +
1931B THR* 3.0 13.7 + - - -
1932B VAL* 3.0 15.1 + - - +
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Residues in contact with VAL1929 (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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1638B ILE* 4.9 9.0 - - + -
1641B MET* 3.9 22.7 - - + +
1642B PHE* 3.6 53.8 - - + -
1645B SER* 3.7 18.2 - - - +
1753B VAL* 5.8 2.2 - - + -
1856B LEU* 4.3 10.3 - - + -
1925B ASP* 3.0 13.6 + - + +
1926B PHE 3.8 2.5 - - - +
1928B GLY* 1.3 74.4 - - - +
1930B PHE* 1.3 64.5 + - - +
1932B VAL* 3.1 9.9 + - - +
1933B LEU* 3.1 19.8 + - - +
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Residues in contact with PHE1930 (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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1645B SER* 3.7 26.8 + - - -
1648B LYS* 3.7 39.9 - - + +
1649B LEU* 3.7 36.3 - - + -
1652B SER* 3.9 19.5 - - - -
1926B PHE* 3.0 17.5 + - + +
1927B GLU* 3.6 15.3 - - + +
1929B VAL* 1.3 77.3 - - - +
1931B THR* 1.3 57.3 + - - +
1933B LEU* 3.1 5.6 + - + +
1934B HIS* 2.7 52.2 + + + +
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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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1876B ILE* 3.5 26.7 - - + -
1920B CYS* 4.5 10.1 - - + -
1922B VAL* 3.5 11.4 - - - +
1927B GLU* 2.8 21.7 + - - +
1928B GLY 3.0 8.7 + - - -
1930B PHE* 1.3 80.3 - - - +
1932B VAL* 1.3 64.3 + - - +
1934B HIS* 3.1 11.3 + - + +
1935B TRP* 2.8 48.7 + - + +
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Residues in contact with VAL1932 (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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1642B PHE* 4.6 10.5 - - + -
1751B ILE* 3.8 44.4 - - + -
1854B ILE* 4.0 16.8 - - + +
1856B LEU* 4.8 10.5 - - + -
1876B ILE* 3.5 22.0 - - + -
1928B GLY 3.0 14.2 + - - +
1929B VAL* 3.1 13.2 + - - +
1931B THR* 1.3 77.8 - - - +
1933B LEU* 1.3 62.6 + - - +
1935B TRP* 3.2 5.1 + - - +
1936B LEU* 2.9 31.3 + - + +
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Residues in contact with LEU1933 (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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1642B PHE* 3.9 35.2 - - + +
1645B SER* 3.9 11.0 - - - -
1646B LEU* 3.6 42.8 - - + +
1649B LEU* 3.7 22.5 - - + +
1703B PHE* 3.7 35.4 - - + -
1707B GLU* 4.9 1.2 - - - +
1929B VAL 3.1 9.7 + - - +
1930B PHE* 3.6 7.2 - - + +
1932B VAL* 1.3 80.1 - - - +
1934B HIS* 1.3 62.2 + - - +
1936B LEU* 3.4 12.8 + - + +
1937B SER* 3.2 16.5 + - - -
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Residues in contact with HIS1934 (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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1649B LEU* 4.2 16.2 - - + +
1653B MET* 6.1 1.8 - - - +
1930B PHE* 2.7 37.1 + + + +
1931B THR* 3.1 12.8 + - + +
1933B LEU* 1.3 70.9 - - - +
1935B TRP* 1.3 76.5 + + - +
1937B SER* 2.6 27.7 + - - -
1938B TYR* 3.4 31.2 + + - -
1998B SER* 3.0 30.4 + - - -
2014B ARG* 5.9 0.4 - - - -
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Residues in contact with TRP1935 (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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1854B ILE* 4.0 26.5 - - + -
1874B ARG* 4.0 21.5 - - + -
1875B THR 3.9 7.4 - - - -
1876B ILE* 3.5 29.6 - - + -
1919B HIS* 3.7 28.7 - - + -
1920B CYS* 3.8 27.8 - - + -
1931B THR* 2.8 32.3 + - + +
1932B VAL* 3.5 3.1 - - - +
1934B HIS* 1.3 90.2 - + - +
1936B LEU* 1.3 62.9 + - - +
1937B SER 2.9 1.7 + - - -
1938B TYR* 3.0 21.1 + + - -
1939B MET* 3.4 25.8 - - + +
1998B SER* 4.5 6.3 + - - -
2000B ILE* 4.1 10.5 - - + +
2012B ARG* 3.7 27.9 - - - +
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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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1703B PHE* 4.6 4.5 - - + -
1707B GLU* 5.1 0.9 - - - +
1712B ARG* 2.8 37.2 + - - +
1714B ILE* 4.2 21.1 - - + -
1749B PRO* 3.7 34.1 - - + -
1751B ILE* 4.2 4.3 - - + -
1852B ILE* 4.7 1.3 - - + -
1854B ILE* 4.0 15.5 - - + -
1932B VAL* 2.9 36.8 + - + +
1933B LEU* 3.8 20.0 - - + +
1935B TRP* 1.3 76.3 - - - +
1937B SER* 1.3 56.9 + - - +
1938B TYR 3.1 0.9 - - - -
1939B MET* 2.8 31.3 + - - +
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Residues in contact with SER1937 (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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1649B LEU* 4.7 1.6 - - - -
1653B MET* 4.0 17.0 - - - -
1707B GLU* 3.6 41.8 - - - +
1933B LEU 3.2 11.2 + - - -
1934B HIS* 2.6 25.0 + - - -
1935B TRP 2.9 2.0 + - - -
1936B LEU* 1.3 76.5 - - - +
1938B TYR* 1.3 62.2 + - - +
1939B MET 3.3 0.2 - - - -
1948B PRO* 3.9 5.9 - - - +
2014B ARG* 2.8 31.1 + - - -
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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
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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