Contacts of the helix formed by residues 1876 - 1893 (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 THR1876 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1840A GLU* 5.0 2.0 + - - +
1874A PRO* 3.8 7.4 - - - +
1875A GLU* 1.3 90.7 - - + +
1877A THR* 1.3 56.5 + - - +
1878A GLN* 3.5 10.2 + - - +
1879A SER* 3.2 31.3 + - - -
1955A TYR* 2.7 27.6 + - - -
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Residues in contact with THR1877 (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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1876A THR* 1.3 72.4 - - - +
1878A GLN* 1.3 67.8 + - - +
1879A SER 3.2 0.4 + - - -
1880A LEU* 3.3 1.9 + - - +
1881A ILE* 3.0 41.9 + - - +
1955A TYR* 3.6 15.4 + - + -
1958A GLN* 3.7 14.1 - - + +
1959A CYS* 3.6 30.3 - - - +
1961A ARG* 5.5 0.4 - - - +
1962A ASP* 2.7 32.9 + - - +
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Residues in contact with GLN1878 (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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1876A THR* 3.3 9.8 - - - +
1877A THR* 1.3 82.7 + - - +
1879A SER* 1.3 57.5 + - - +
1881A ILE* 3.6 9.2 + - + +
1882A GLN* 3.0 38.4 + - + +
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Residues in contact with SER1879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1840A GLU* 2.8 37.0 + - - +
1841A TRP* 3.6 7.9 - - - -
1865A TYR* 2.8 26.9 + - - -
1874A PRO* 5.1 0.2 - - - -
1876A THR* 3.2 20.9 + - - -
1878A GLN* 1.3 81.4 + - - +
1880A LEU* 1.3 57.6 + - - +
1882A GLN* 3.3 3.3 + - - +
1883A PHE* 3.0 27.2 + - - +
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Residues in contact with LEU1880 (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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1801A VAL* 5.2 0.2 - - + -
1865A TYR* 4.0 22.2 - - + +
1868A TRP* 3.6 47.1 - - + -
1874A PRO* 4.1 4.5 - - + -
1876A THR 4.2 0.4 + - - -
1877A THR 3.3 3.4 + - - -
1879A SER* 1.3 76.4 - - - +
1881A ILE* 1.3 68.1 + - - +
1883A PHE* 4.1 18.2 - - + -
1884A VAL* 2.8 34.5 + - + +
1913A THR* 5.1 1.3 - - + -
1914A PHE* 4.7 7.9 - - + +
1917A LEU* 3.5 28.0 - - + -
1955A TYR* 3.3 30.3 - - + +
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Residues in contact with ILE1881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1877A THR* 3.0 42.1 + - - +
1878A GLN* 3.8 8.3 - - + +
1880A LEU* 1.3 79.2 - - - +
1882A GLN* 1.3 62.5 + - + +
1884A VAL* 3.7 2.4 - - - +
1885A ARG* 3.0 59.9 + - - +
1917A LEU* 4.1 9.4 - - + +
1921A LEU* 4.0 13.0 - - + +
1959A CYS* 3.9 22.9 - - + +
1962A ASP* 5.1 3.1 - - + -
1963A VAL* 3.9 24.5 - - + -
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Residues in contact with GLN1882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1841A TRP* 3.3 31.2 - - + -
1878A GLN* 3.0 28.4 + - + +
1879A SER* 3.9 0.9 - - - +
1880A LEU 3.1 0.2 - - - -
1881A ILE* 1.3 79.4 - - + +
1883A PHE* 1.3 52.3 + - - +
1885A ARG* 3.4 8.4 + - - +
1886A THR* 2.5 46.8 + - - -
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Residues in contact with PHE1883 (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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1799A VAL* 3.9 9.4 - - + -
1801A VAL* 4.3 1.6 - - + -
1841A TRP* 3.5 52.9 - + + -
1863A PHE* 3.7 40.8 - + + -
1865A TYR* 3.7 31.4 - + + -
1879A SER 3.0 16.3 + - - +
1880A LEU* 3.7 10.8 - - + +
1882A GLN* 1.3 75.5 - - - +
1884A VAL* 1.3 67.6 + - - +
1886A THR* 3.3 8.6 + - - -
1887A VAL* 3.0 34.2 + - + +
1914A PHE* 3.6 28.3 - + - -
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Residues in contact with VAL1884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1880A LEU* 2.8 27.9 + - + +
1881A ILE 3.7 3.6 - - - +
1883A PHE* 1.3 73.1 - - - +
1885A ARG* 1.3 62.0 + - + +
1887A VAL* 3.6 2.8 + - - +
1888A ARG* 3.1 21.8 + - + +
1914A PHE* 3.7 37.3 - - + +
1917A LEU* 3.8 21.1 - - + -
1918A ASP* 3.6 39.7 - - + +
1921A LEU* 3.8 17.0 - - + -
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Residues in contact with ARG1885 (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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1881A ILE* 3.0 42.8 + - - +
1882A GLN* 3.8 8.0 - - - +
1883A PHE 3.2 0.2 - - - -
1884A VAL* 1.3 73.1 - - + +
1886A THR* 1.3 65.6 + - - +
1888A ARG* 3.5 6.0 + - - +
1889A ASP* 3.0 24.4 + - - +
1921A LEU* 4.2 20.6 + - + +
1924A LEU* 6.3 0.2 - - - +
1925A ASP* 5.1 12.1 + - - -
1963A VAL* 4.1 28.9 - - - +
1967A ARG* 5.3 1.8 - - - +
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Residues in contact with THR1886 (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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1841A TRP* 4.5 9.1 - - - +
1843A ILE* 4.7 15.0 - - + -
1863A PHE* 5.0 2.2 - - + -
1882A GLN* 2.5 34.4 + - - +
1883A PHE* 3.4 12.5 - - + -
1885A ARG* 1.3 73.1 - - - +
1887A VAL* 1.3 68.0 + - - +
1889A ASP* 3.1 21.8 - - + +
1890A TYR* 3.2 31.2 + - + -
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Residues in contact with VAL1887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1797A ASN* 5.6 0.2 - - + -
1799A VAL* 3.8 21.3 - - + -
1863A PHE* 3.9 39.2 - - + -
1883A PHE* 3.0 40.4 + - + +
1884A VAL 3.8 4.5 - - - +
1886A THR* 1.3 73.3 - - - +
1888A ARG* 1.3 58.7 + - - +
1890A TYR* 3.0 5.4 + - - +
1891A ILE* 2.8 45.0 + - + +
1900A THR* 4.9 2.7 - - + -
1914A PHE* 4.2 15.7 - - + -
1918A ASP* 6.1 0.7 - - - +
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Residues in contact with ARG1888 (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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1767A ASN* 3.7 17.6 - - - +
1771A GLU* 3.6 17.6 + - - +
1772A TYR* 3.8 5.5 + - - -
1884A VAL* 3.1 15.8 + - + +
1885A ARG* 3.9 6.5 - - - +
1886A THR 3.2 0.4 - - - -
1887A VAL* 1.3 75.8 - - - +
1889A ASP* 1.3 61.8 + - - +
1891A ILE* 3.1 46.0 + - - +
1892A ASN* 2.8 48.7 + - - +
1918A ASP* 2.7 38.7 + - - +
1922A GLN* 3.6 29.2 + - - +
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Residues in contact with ASP1889 (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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1885A ARG 3.0 14.7 + - - +
1886A THR* 3.1 16.8 - - + +
1888A ARG* 1.3 78.1 - - - +
1890A TYR* 1.3 57.6 + - + +
1892A ASN* 3.4 14.1 + - - +
1893A ARG* 2.9 60.9 + - - +
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Residues in contact with TYR1890 (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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1797A ASN* 4.4 4.7 - - - +
1843A ILE* 4.9 11.0 - - + +
1845A GLU* 5.5 0.7 + - - -
1861A ARG* 3.5 47.2 + - - -
1863A PHE* 3.4 35.7 - + + -
1886A THR* 3.2 29.0 + - + -
1887A VAL 3.0 9.4 + - - +
1889A ASP* 1.3 77.5 - - + +
1891A ILE* 1.3 60.7 + - - +
1893A ARG* 3.0 47.7 + - + +
1894A SER* 2.6 27.4 + - - -
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Residues in contact with ILE1891 (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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1768A PHE* 6.4 2.0 - - + -
1772A TYR* 5.4 1.6 - - + -
1797A ASN* 4.0 17.5 - - - +
1887A VAL* 2.8 38.0 + - + +
1888A ARG* 3.1 48.0 + - - +
1890A TYR* 1.3 76.3 - - - +
1892A ASN* 1.3 59.2 + - - +
1894A SER* 2.9 26.3 + - - +
1897A ALA* 5.6 3.3 - - + +
1900A THR* 3.6 31.4 - - + +
1914A PHE* 6.4 0.4 - - + -
1918A ASP* 4.8 3.1 - - - +
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Residues in contact with ASN1892 (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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1888A ARG* 2.8 42.0 + - - +
1889A ASP* 3.4 16.1 + - - +
1891A ILE* 1.3 75.2 - - - +
1893A ARG* 1.3 59.5 + - + +
1894A SER 3.1 4.5 + - - -
1895A PRO* 4.9 3.3 - - - +
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Residues in contact with ARG1893 (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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1861A ARG* 5.2 8.0 + - - +
1889A ASP* 2.9 37.5 + - - +
1890A TYR* 3.0 62.5 + - + +
1892A ASN* 1.3 80.7 - - + +
1894A SER* 1.3 56.6 + - - +
1895A PRO* 3.0 15.8 - - - +
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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
------------------------------------------------------------
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