Contacts of the helix formed by residues 1876 - 1893 (chain B) in PDB entry 2H02
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1874B PRO* 3.7 8.6 - - - +
1875B GLU* 1.3 88.7 - - + +
1877B THR* 1.3 55.9 + - - +
1878B GLN* 3.6 6.8 + - - +
1879B SER* 3.2 30.6 + - - -
1955B TYR* 2.6 28.2 + - - -
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Residues in contact with THR1877 (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 THR* 1.3 73.3 - - - +
1878B GLN* 1.3 68.5 + - - +
1879B SER 3.3 0.2 + - - -
1880B LEU 3.5 1.7 + - - -
1881B ILE* 2.8 40.1 + - - +
1955B TYR* 3.3 22.5 + - + -
1958B GLN* 4.0 31.0 - - + +
1959B CYS* 3.8 8.3 - - - +
1962B ASP* 2.7 37.3 + - - +
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Residues in contact with GLN1878 (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 THR* 3.4 7.0 + - - +
1877B THR* 1.3 84.4 + - - +
1879B SER* 1.3 57.5 + - - +
1881B ILE* 3.5 31.7 - - - +
1882B GLN* 3.0 38.8 + - + +
1885B ARG* 3.8 13.1 - - - +
1962B ASP* 5.3 6.2 - - - +
1963B VAL* 5.3 4.2 - - - +
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Residues in contact with SER1879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1840B GLU* 2.7 31.5 + - - +
1841B TRP* 3.5 13.1 - - - -
1865B TYR* 2.5 31.9 + - - -
1867B VAL* 4.3 1.8 - - - +
1874B PRO* 5.0 1.3 - - - -
1876B THR* 3.2 22.8 + - - -
1877B THR 3.2 0.6 - - - -
1878B GLN* 1.3 77.7 - - - +
1880B LEU* 1.3 63.0 + - - +
1882B GLN* 3.4 1.1 + - - -
1883B PHE* 3.1 17.3 + - - +
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Residues in contact with LEU1880 (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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1865B TYR* 4.2 10.3 - - + -
1868B TRP* 3.4 48.5 - - + -
1874B PRO* 4.1 7.0 - - + -
1876B THR 4.1 1.0 + - - -
1877B THR 3.5 1.6 + - - +
1878B GLN 3.4 0.2 - - - -
1879B SER* 1.3 75.8 + - - +
1881B ILE* 1.3 58.7 + - - +
1883B PHE* 3.0 23.6 + - + -
1884B VAL* 2.7 42.4 + - + +
1913B THR* 4.9 2.9 - - + -
1914B PHE* 4.4 9.2 - - + -
1917B LEU* 3.7 25.4 - - + -
1955B TYR* 3.3 31.6 - - + +
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Residues in contact with ILE1881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1877B THR* 2.8 37.7 + - - +
1878B GLN* 3.5 28.9 - - - +
1880B LEU* 1.3 76.0 - - - +
1882B GLN* 1.3 57.5 + - - +
1884B VAL* 3.4 1.4 + - - +
1885B ARG* 2.9 63.5 + - + +
1917B LEU* 4.1 10.9 - - + +
1921B LEU* 4.3 8.7 - - + +
1959B CYS* 3.5 44.2 - - + +
1962B ASP* 5.2 0.9 - - + -
1963B VAL* 4.0 12.1 - - + -
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Residues in contact with GLN1882 (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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1841B TRP* 3.7 22.7 - - + -
1878B GLN* 3.0 34.7 + - + +
1879B SER* 3.9 0.9 - - - +
1881B ILE* 1.3 73.9 - - - +
1883B PHE* 1.3 53.0 + - - +
1885B ARG* 4.1 19.7 + - - +
1886B THR* 2.6 46.4 + - - +
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Residues in contact with PHE1883 (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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1799B VAL* 3.8 9.0 - - + -
1801B VAL* 4.1 1.3 - - + -
1841B TRP* 3.5 50.9 - + + -
1863B PHE* 3.6 43.1 - + + -
1865B TYR* 3.5 36.6 - + + -
1879B SER 3.1 16.1 + - - +
1880B LEU* 3.0 8.8 + - + +
1882B GLN* 1.3 74.0 - - - +
1884B VAL* 1.3 65.5 + - - +
1886B THR* 2.9 6.7 + - - -
1887B VAL* 2.9 30.3 + - + +
1914B PHE* 3.4 33.7 - + - -
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Residues in contact with VAL1884 (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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1880B LEU* 2.7 27.6 + - + +
1883B PHE* 1.3 73.6 - - - +
1885B ARG* 1.3 56.5 + - - +
1887B VAL* 3.8 0.9 - - - +
1888B ARG* 2.8 29.4 + - + +
1914B PHE* 3.6 38.6 - - + +
1917B LEU* 3.9 17.9 - - + -
1918B ASP* 3.4 41.7 - - + +
1921B LEU* 3.9 18.4 - - + -
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Residues in contact with ARG1885 (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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1878B GLN* 3.8 12.3 - - - +
1881B ILE* 2.9 42.3 + - + +
1882B GLN* 3.8 23.5 + - - +
1884B VAL* 1.3 76.1 - - - +
1886B THR* 1.3 56.6 + - - +
1888B ARG* 3.9 5.3 - - - +
1889B ASP* 3.0 29.8 + - - +
1921B LEU* 4.3 19.1 - - + +
1963B VAL* 3.6 39.8 - - - +
1967B ARG* 5.4 2.2 - - - +
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Residues in contact with THR1886 (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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1841B TRP* 4.2 16.6 - - + +
1843B ILE* 4.5 16.6 - - + -
1863B PHE* 4.7 3.6 - - + -
1882B GLN* 2.6 30.1 + - - +
1883B PHE* 2.9 11.5 + - + -
1885B ARG* 1.3 73.4 - - - +
1887B VAL* 1.3 67.9 + - - +
1888B ARG 3.4 0.2 + - - -
1889B ASP* 3.4 8.0 + - - +
1890B TYR* 3.2 43.1 + - + -
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Residues in contact with VAL1887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1797B ASN* 5.5 0.7 - - + -
1799B VAL* 3.4 26.5 - - + -
1863B PHE* 3.8 42.4 - - + -
1883B PHE* 2.9 38.7 + - + +
1884B VAL 3.9 0.9 - - - +
1886B THR* 1.3 72.8 - - - +
1888B ARG* 1.3 57.4 + - - +
1890B TYR* 3.1 4.0 + - - +
1891B ILE* 2.9 43.3 + - + +
1900B THR* 5.2 0.4 - - + -
1914B PHE* 3.9 14.8 - - + -
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Residues in contact with ARG1888 (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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1767B ASN* 4.6 3.6 - - - +
1768B PHE* 6.2 0.8 - - - -
1771B GLU* 3.5 21.0 + - - +
1772B TYR* 3.6 3.8 + - - -
1884B VAL* 2.8 23.4 + - + +
1885B ARG* 3.9 5.8 - - - +
1887B VAL* 1.3 71.5 - - - +
1889B ASP* 1.3 57.8 + - - +
1891B ILE* 3.0 44.0 + - - +
1892B ASN* 2.8 56.7 + - - +
1918B ASP* 2.7 41.4 + - - +
1922B GLN* 3.5 33.6 + - + +
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Residues in contact with ASP1889 (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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1885B ARG 3.0 16.3 + - - +
1886B THR* 3.6 7.1 - - - +
1887B VAL 3.3 0.2 - - - -
1888B ARG* 1.3 76.8 - - - +
1890B TYR* 1.3 61.3 + - - +
1892B ASN* 3.4 9.1 + - - +
1893B ARG* 2.8 60.3 + - - +
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Residues in contact with TYR1890 (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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1797B ASN* 4.4 4.7 - - - +
1843B ILE* 4.7 13.5 - - + +
1861B ARG* 3.1 41.3 - - - -
1863B PHE* 3.4 34.3 - + + -
1886B THR* 3.2 34.9 + - + -
1887B VAL 3.1 5.7 + - - +
1889B ASP* 1.3 76.6 - - - +
1891B ILE* 1.3 61.7 + - - +
1892B ASN 3.2 0.9 - - - -
1893B ARG* 3.4 43.3 + - + +
1894B SER* 2.7 33.4 + - - -
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Residues in contact with ILE1891 (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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1768B PHE* 6.2 4.5 - - + -
1771B GLU* 6.5 1.1 - - + -
1772B TYR* 5.2 2.0 - - + -
1797B ASN* 3.9 16.6 + - - +
1887B VAL* 2.9 33.0 + - + +
1888B ARG* 3.0 50.5 - - - +
1890B TYR* 1.3 75.2 - - - +
1892B ASN* 1.3 59.2 + - - +
1894B SER* 2.9 23.7 + - - +
1900B THR* 3.3 39.7 - - + +
1914B PHE* 5.8 1.8 - - + -
1918B ASP* 4.7 5.6 - - - +
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Residues in contact with ASN1892 (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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1888B ARG* 2.8 57.4 + - - +
1889B ASP* 3.6 8.3 - - - +
1890B TYR 3.2 0.2 - - - -
1891B ILE* 1.3 74.1 - - - +
1893B ARG* 1.3 55.3 + - - +
1894B SER 3.3 4.4 + - - -
1895B PRO* 5.0 1.6 - - - +
1922B GLN* 5.5 0.3 - - - +
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Residues in contact with ARG1893 (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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1861B ARG* 5.0 6.1 - - - +
1889B ASP* 2.8 55.1 + - - +
1890B TYR* 3.5 46.0 + - + +
1891B ILE 3.2 0.4 - - - -
1892B ASN* 1.3 72.3 - - - +
1894B SER* 1.3 55.3 + - - +
1895B PRO* 2.7 20.0 - - - +
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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