Contacts of the helix formed by residues 1931 - 1943 (chain A) in PDB entry 2H04
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 ASP1931 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1680A SER* 3.2 20.0 + - - -
1681A CYS 2.8 32.4 + - - +
1682A PRO* 3.9 13.4 - - + +
1920A ILE* 4.8 1.6 - - - -
1923A GLN* 2.8 22.5 + - - +
1927A LYS* 4.9 5.6 - - - +
1930A VAL* 1.3 75.2 - - - +
1932A ILE* 1.3 64.0 + - - +
1933A TYR 3.8 0.5 + - - -
1934A GLY* 3.0 24.5 + - - -
1935A ALA* 3.1 17.8 + - - +
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Residues in contact with ILE1932 (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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1681A CYS 4.7 2.2 + - - -
1683A ILE* 5.4 4.6 - - + +
1688A PHE* 3.9 12.3 - - + -
1916A ALA* 6.0 0.4 - - + -
1920A ILE* 4.0 24.9 - - + -
1930A VAL* 3.9 6.8 + - + -
1931A ASP* 1.3 70.7 - - - +
1933A TYR* 1.3 63.4 + - - +
1935A ALA* 3.3 2.9 + - + +
1936A VAL* 3.2 22.4 + - + +
1953A TYR* 4.1 10.5 - - + -
1956A LEU* 3.9 25.4 - - + +
1957A HIS* 3.6 60.3 - - + +
1960A VAL* 3.8 23.1 - - + -
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Residues in contact with TYR1933 (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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1678A LYS* 3.1 50.1 + - + +
1679A THR* 3.7 10.1 - - - -
1680A SER* 3.6 14.8 - - - -
1681A CYS* 3.8 26.5 + - + +
1706A GLU* 3.7 32.8 - - + +
1709A GLU* 3.9 18.8 + - + +
1710A LEU* 3.6 30.5 - - + +
1713A VAL* 5.3 0.7 - - - +
1931A ASP* 3.3 0.8 + - - -
1932A ILE* 1.3 77.0 - - - +
1934A GLY* 1.3 59.9 + - - +
1936A VAL* 3.2 3.6 + - - +
1937A HIS* 2.9 28.8 + + - +
1953A TYR* 3.6 25.8 + - - +
1957A HIS* 5.6 0.2 - - - -
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Residues in contact with GLY1934 (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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1679A THR 3.4 18.7 - - - +
1680A SER* 4.6 0.4 - - - -
1919A ARG* 5.6 1.6 - - - -
1931A ASP* 3.0 29.7 + - - -
1933A TYR* 1.3 77.7 - - - +
1935A ALA* 1.3 61.6 + - - +
1937A HIS* 3.4 2.1 + - - +
1938A ASP* 3.0 25.7 + - - +
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Residues in contact with ALA1935 (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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1916A ALA* 4.5 16.4 - - + -
1919A ARG* 4.3 29.3 + - + +
1920A ILE* 4.4 17.9 - - + -
1923A GLN* 5.1 3.1 - - - +
1931A ASP* 3.1 15.1 + - - +
1932A ILE 3.3 8.9 + - - +
1934A GLY* 1.3 73.6 - - - +
1936A VAL* 1.3 62.5 + - - +
1938A ASP* 3.3 4.0 + - - +
1939A LEU* 3.0 28.1 + - - +
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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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1707A TYR* 5.4 0.4 - - + -
1710A LEU* 3.9 22.0 - - + -
1916A ALA* 4.3 5.4 - - + -
1932A ILE 3.2 14.8 + - - +
1933A TYR 3.2 4.9 + - - +
1935A ALA* 1.3 73.5 - - - +
1937A HIS* 1.3 66.3 + - - +
1939A LEU* 3.1 8.7 + - - +
1940A ARG* 3.0 37.7 + - + +
1946A MET 3.6 22.2 - - - +
1947A VAL* 3.8 23.8 - - + -
1953A TYR* 4.0 17.9 - - + -
1956A LEU* 4.1 11.9 - - + -
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Residues in contact with HIS1937 (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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1678A LYS 3.7 20.5 + - - -
1679A THR* 3.6 42.3 + - + +
1710A LEU* 3.8 13.6 - - + +
1713A VAL* 3.6 28.7 - - + +
1933A TYR* 2.9 21.8 + + + +
1934A GLY 3.4 6.0 + - - +
1936A VAL* 1.3 75.3 - - - +
1938A ASP* 1.3 63.6 + - - +
1940A ARG* 3.1 17.0 + - - +
1941A LEU* 3.1 44.3 + - + +
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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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1764A PRO* 3.8 17.0 - - - +
1765A GLY 5.5 0.3 - - - +
1919A ARG* 3.1 28.2 + - - +
1934A GLY 3.0 19.6 + - - +
1935A ALA 3.6 5.4 - - - +
1936A VAL 3.3 0.2 - - - -
1937A HIS* 1.3 74.1 + - - +
1939A LEU* 1.3 64.1 + - + +
1940A ARG 3.2 0.5 + - - -
1941A LEU* 3.2 15.8 + - - +
1942A HIS* 2.7 42.2 + - - -
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Residues in contact with LEU1939 (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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1763A ILE* 3.5 29.8 - - + +
1764A PRO* 4.5 5.8 - - + +
1912A GLY* 3.3 38.4 - - - +
1915A ILE* 3.8 15.5 - - + -
1916A ALA* 4.1 16.8 - - + +
1919A ARG* 4.8 8.1 - - - +
1935A ALA 3.0 20.9 + - - +
1936A VAL* 3.1 6.2 + - - +
1938A ASP* 1.3 76.2 - - - +
1940A ARG* 1.3 56.9 + - - +
1942A HIS* 3.1 9.6 + - - +
1943A ARG* 3.0 23.6 + - - +
1946A MET* 3.5 26.7 - - + +
1947A VAL* 4.3 5.6 - - + -
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Residues in contact with ARG1940 (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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1707A TYR* 3.4 24.5 + - - -
1710A LEU* 3.1 39.2 + - + +
1711A LYS* 3.9 13.1 + - - +
1713A VAL* 3.5 35.1 + - + +
1714A GLY* 3.6 5.4 - - - -
1739A TYR* 3.8 5.0 + - - -
1936A VAL* 3.0 24.5 + - + +
1937A HIS* 3.1 8.7 + - - +
1939A LEU* 1.3 73.0 - - - +
1941A LEU* 1.3 61.8 + - - +
1942A HIS 2.9 6.5 + - - -
1943A ARG 3.5 12.5 + - - +
1944A VAL* 4.4 0.8 - - - +
1945A HIS* 3.7 29.8 + - - +
1946A MET 2.9 24.8 + - - +
1947A VAL 3.0 24.4 + - - -
1948A GLN* 5.0 0.4 - - - +
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Residues in contact with LEU1941 (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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1713A VAL* 3.7 18.6 - - + -
1714A GLY* 4.2 12.3 - - - +
1717A GLN* 2.9 28.5 + - - +
1739A TYR* 4.1 0.5 - - - -
1742A THR* 4.7 3.1 - - - +
1937A HIS* 3.1 37.2 + - + +
1938A ASP* 3.2 22.6 + - - +
1940A ARG* 1.3 76.5 - - - +
1942A HIS* 1.3 68.2 - - + +
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Residues in contact with HIS1942 (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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1739A TYR* 3.6 9.8 + - - +
1742A THR* 2.8 44.8 + - + -
1761A SER* 4.0 6.4 + - - -
1762A TYR* 3.8 6.7 - - + +
1763A ILE* 3.7 18.2 - - + -
1764A PRO* 3.2 40.5 - - + +
1769A ARG* 6.2 1.4 - - - +
1938A ASP* 2.7 34.5 + - - -
1939A LEU* 3.1 7.3 + - - +
1940A ARG 2.9 0.6 - - - -
1941A LEU* 1.3 91.2 - - + +
1943A ARG* 1.3 61.7 + - - +
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Residues in contact with ARG1943 (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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1736A ILE* 3.9 8.7 - - - +
1737A LEU 5.0 3.8 - - - +
1738A PRO* 4.1 10.4 - - + +
1739A TYR* 4.0 10.8 - - - +
1759A ASN* 2.8 30.9 + - - -
1760A ALA 4.1 8.3 - - - +
1761A SER* 2.9 34.1 + - - +
1763A ILE* 4.2 5.8 - - + -
1774A VAL* 3.4 30.0 - - - +
1776A GLN 3.9 10.1 - - - +
1906A ALA 2.9 24.4 + - - -
1907A GLY* 3.0 18.7 + - - -
1908A VAL* 3.5 6.8 - - + +
1939A LEU 3.0 4.0 + - - -
1940A ARG* 3.5 15.8 + - - -
1942A HIS* 1.3 79.0 - - - +
1944A VAL* 1.3 75.7 + - + +
1946A MET* 3.3 24.6 - - + +
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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
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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