Contacts of the helix formed by residues 1884 - 1895 (chain B) in PDB entry 1GZH
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 PHE1884 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1876B LEU* 3.3 26.7 - - + -
1877B VAL 4.0 3.6 - - - -
1878B SER* 3.3 28.5 - - - +
1880B GLN* 3.2 15.7 + - + +
1882B GLN 3.1 1.8 - - - -
1883B ASN* 1.3 80.7 - - - +
1885B LEU* 1.3 65.7 + - + +
1886B GLU 3.3 0.7 - - - -
1887B LEU 3.8 0.2 - - - -
1888B TRP* 2.8 57.3 + + - +
1921B VAL* 3.7 15.9 - - + -
1922B THR* 3.6 32.8 - - - -
1923B ASP* 3.7 20.4 - - + -
1944B GLN* 3.8 20.2 - - + -
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Residues in contact with LEU1885 (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 LEU* 3.4 45.7 - - + +
1878B SER* 3.6 27.8 - - - +
1880B GLN 3.2 7.1 + - - +
1881B GLN* 3.5 43.3 - - + +
1884B PHE* 1.3 81.1 - - + +
1886B GLU* 1.3 58.9 + - - +
1889B SER* 2.9 28.1 + - - -
1902B GLN* 3.7 19.3 - - + +
1903B HIS 3.6 21.3 - - - +
1904B HIS* 4.3 4.5 - - + +
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Residues in contact with GLU1886 (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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1881B GLN* 3.7 17.2 + - - +
1882B GLN* 3.5 36.8 + - - +
1884B PHE 3.3 0.4 - - - -
1885B LEU* 1.3 79.9 - - - +
1887B LEU* 1.3 63.3 + - - +
1889B SER* 3.7 3.8 - - - -
1890B GLU* 3.4 24.8 + - - +
1902B GLN* 4.5 7.8 + - - +
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Residues in contact with LEU1887 (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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1813B ARG* 3.7 40.3 - - + +
1816B PHE* 5.5 1.3 - - + -
1882B GLN 3.4 13.1 + - - +
1883B ASN* 3.9 21.3 - - + +
1884B PHE 3.2 1.4 + - - +
1886B GLU* 1.3 81.6 - - - +
1888B TRP* 1.3 94.6 + - + +
1890B GLU* 3.8 3.7 + - - +
1891B ILE* 3.1 51.4 + - + +
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Residues in contact with TRP1888 (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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1816B PHE* 3.9 17.3 - + - -
1876B LEU* 3.9 17.9 - - + -
1883B ASN 4.2 5.2 + - - -
1884B PHE* 2.8 55.8 + + - +
1887B LEU* 1.3 87.9 - - + +
1889B SER* 1.3 60.8 + - - +
1890B GLU 3.4 0.2 - - - -
1891B ILE* 3.8 21.0 - - + +
1892B LEU* 2.8 38.4 + - + +
1921B VAL* 5.4 3.1 - - + -
1944B GLN* 3.2 48.2 + - + +
1947B VAL* 3.8 27.6 - - + -
1948B ILE* 3.4 34.5 - - + -
1951B LEU* 5.3 0.4 - - + -
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Residues in contact with SER1889 (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 LEU* 3.4 12.0 - - - +
1885B LEU 2.9 24.1 + - - -
1886B GLU 3.7 4.0 - - - -
1887B LEU 3.3 0.6 - - - -
1888B TRP* 1.3 78.9 - - - +
1890B GLU* 1.3 64.1 + - - +
1892B LEU* 3.7 1.2 - - - +
1893B MET* 3.0 31.9 + - - +
1900B VAL* 3.8 20.0 + - - +
1902B GLN* 3.0 24.7 + - - -
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Residues in contact with GLU1890 (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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1790B ASP* 5.3 1.2 - - - +
1791B PHE* 4.5 17.7 - - - +
1792B ASN 5.6 1.2 - - - -
1813B ARG* 2.6 34.0 + - - -
1817B LEU* 3.8 17.2 - - + +
1886B GLU 3.4 13.6 + - - +
1887B LEU* 4.2 3.0 - - - +
1889B SER* 1.3 79.1 - - - +
1891B ILE* 1.3 61.7 + - - +
1893B MET* 3.9 4.0 - - - +
1894B THR* 2.7 39.8 + - + +
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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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1813B ARG* 4.6 8.7 - - + -
1816B PHE* 4.2 17.0 - - + +
1817B LEU* 3.6 26.9 - - + -
1820B ALA* 3.8 7.6 - - + +
1869B PHE* 4.4 1.5 - - + -
1887B LEU* 3.1 47.0 + - + +
1888B TRP* 3.8 22.4 - - + +
1889B SER 3.2 0.8 - - - -
1890B GLU* 1.3 76.6 - - + +
1892B LEU* 1.3 64.7 + - - +
1894B THR* 3.6 3.1 + - - -
1895B GLY* 3.1 19.8 + - - -
1947B VAL* 4.6 4.3 - - + -
1951B LEU* 3.8 29.6 - - + -
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Residues in contact with LEU1892 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1869B PHE* 3.6 41.1 - - + -
1872B LEU* 4.8 2.7 - - + -
1874B VAL* 3.4 43.5 - - + -
1876B LEU* 4.4 9.9 - - + -
1888B TRP* 2.8 30.2 + - + +
1889B SER 3.7 2.7 - - - +
1891B ILE* 1.3 72.9 - - - +
1893B MET* 1.3 60.3 + - - +
1895B GLY* 3.2 10.6 + - - -
1897B ALA* 3.1 24.2 + - + +
1900B VAL* 3.8 18.4 - - + -
1921B VAL* 4.7 7.2 - - + -
1946B TRP* 5.5 1.1 - - + -
1947B VAL* 4.3 18.6 - - + -
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Residues in contact with MET1893 (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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1889B SER* 3.0 25.1 + - - +
1890B GLU* 3.9 5.2 - - - +
1892B LEU* 1.3 71.9 - - - +
1894B THR* 1.3 56.1 + - + +
1895B GLY 2.8 4.7 - - - -
1896B GLY* 2.7 26.5 + - - -
1897B ALA* 3.5 21.3 + - - +
1898B ALA 4.2 4.7 - - - +
1899B SER* 3.7 21.8 - - - -
1900B VAL* 3.6 27.1 - - + +
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Residues in contact with THR1894 (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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1791B PHE* 4.6 13.7 - - + -
1817B LEU* 4.1 16.0 + - + +
1820B ALA* 3.1 29.6 - - - +
1821B SER* 4.1 12.8 - - - -
1867B ASN* 4.6 3.6 + - - -
1890B GLU* 2.7 33.8 + - + +
1891B ILE 3.7 1.9 + - - -
1893B MET* 1.3 76.1 - - + +
1895B GLY* 1.3 57.7 + - - +
1896B GLY 3.1 3.5 + - - -
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Residues in contact with GLY1895 (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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1820B ALA* 3.6 17.5 - - - -
1867B ASN* 3.5 14.5 - - - +
1868B PRO* 3.9 2.6 - - - -
1869B PHE* 3.1 35.8 + - - +
1891B ILE 3.1 14.1 + - - -
1892B LEU 3.2 10.5 + - - -
1893B MET 2.8 2.2 - - - -
1894B THR* 1.3 77.1 - - - +
1896B GLY* 1.3 55.1 + - - +
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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