Contacts of the helix formed by residues 1812 - 1822 (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 THR1812 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1737B THR* 3.0 25.8 + - - +
1738B MET 3.6 18.6 - - - +
1740B THR* 3.7 16.8 - - + -
1810B CYS* 3.5 12.2 + - + -
1811B ARG* 1.3 77.8 - - - +
1813B ARG* 1.3 65.8 + - - +
1814B LYS 3.6 2.8 + - - -
1815B TYR* 2.9 30.7 + - - +
1816B PHE* 2.9 18.6 + - - -
2972B SO4 4.1 11.0 - - - +
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Residues in contact with ARG1813 (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* 2.4 45.3 + - - -
1791B PHE* 4.5 0.6 - - - +
1812B THR* 1.3 72.1 - - - +
1814B LYS* 1.3 62.9 + - + +
1816B PHE* 3.4 9.5 + - - +
1817B LEU* 2.9 52.5 + - + +
1887B LEU* 3.7 41.9 + - + +
1890B GLU* 2.6 30.5 + - - -
1891B ILE* 4.6 4.4 - - + +
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Residues in contact with LYS1814 (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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1735B LEU* 4.1 24.9 - - + -
1736B LEU 3.1 33.3 + - - +
1737B THR* 4.2 6.5 - - - +
1773B LYS* 3.7 10.9 - - - +
1788B LEU 4.7 2.6 + - - -
1789B GLU* 3.2 29.7 + - - +
1790B ASP* 4.6 11.9 - - - +
1791B PHE* 5.5 2.0 - - + +
1804B LEU* 4.0 6.1 - - + -
1812B THR* 3.2 3.2 + - - +
1813B ARG* 1.3 85.4 - - + +
1815B TYR* 1.3 64.2 + - - +
1817B LEU* 3.4 8.4 + - + +
1818B CYS* 3.1 29.3 + - - -
2972B SO4 3.3 32.2 + - - +
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Residues in contact with TYR1815 (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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1737B THR* 4.2 2.0 - - + -
1804B LEU* 3.4 35.8 - - + +
1806B ALA* 4.6 0.2 - - + -
1808B GLN 4.2 5.8 - - - -
1809B HIS* 3.6 10.0 - - - -
1810B CYS* 3.1 47.3 - - - +
1812B THR* 2.9 19.1 + - - +
1814B LYS* 1.3 77.9 - - - +
1816B PHE* 1.3 63.7 + + + +
1818B CYS* 3.0 4.9 + - - +
1819B LEU* 3.0 40.4 + - + +
1825B CYS* 3.5 17.2 - - + +
1848B LEU* 3.4 19.6 - - + +
1849B PRO 2.7 22.4 + - - -
1850B ALA 3.4 22.2 - - - -
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Residues in contact with PHE1816 (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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1810B CYS 4.2 3.1 - - - -
1811B ARG* 3.3 52.0 - - + -
1812B THR 2.9 18.2 + - - +
1813B ARG* 3.8 4.7 - - - +
1815B TYR* 1.3 78.3 - + + +
1817B LEU* 1.3 57.8 + - - +
1819B LEU* 3.3 18.0 + - + +
1820B ALA* 2.9 30.5 + - - +
1887B LEU* 5.5 1.1 - - + -
1888B TRP* 3.9 20.0 - + - -
1891B ILE* 4.2 14.6 - - + -
1948B ILE* 3.7 44.4 - - + -
1951B LEU* 3.9 17.5 - - + +
1952B ILE* 4.4 5.8 - - + -
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Residues in contact with LEU1817 (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* 3.7 37.1 - - + -
1813B ARG* 2.9 55.5 + - + +
1814B LYS* 3.8 7.0 - - + +
1816B PHE* 1.3 77.5 - - - +
1818B CYS* 1.3 53.1 + - - +
1820B ALA* 3.4 3.9 + - - +
1821B SER* 2.6 37.7 + - - -
1890B GLU* 3.8 22.4 - - + +
1891B ILE* 3.6 30.7 - - + -
1894B THR* 4.1 15.3 + - + +
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Residues in contact with CYS1818 (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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1735B LEU* 3.6 28.0 - - - -
1791B PHE* 4.5 3.4 - - - -
1804B LEU* 3.5 28.0 - - + -
1814B LYS 3.1 18.2 + - - +
1815B TYR 3.0 5.6 + - - +
1817B LEU* 1.3 76.7 - - - +
1819B LEU* 1.3 59.4 + - - +
1821B SER* 3.6 5.4 - - - -
1822B GLY* 2.9 26.7 + - - -
1823B ILE* 3.2 36.7 + - - +
1825B CYS* 4.2 5.6 - - - -
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Residues in contact with LEU1819 (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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1815B TYR* 3.0 43.2 + - + +
1816B PHE* 3.3 13.0 + - + +
1818B CYS* 1.3 78.5 - - - +
1820B ALA* 1.3 62.3 + - - +
1822B GLY* 3.8 4.9 + - - -
1825B CYS* 4.6 9.4 - - - -
1850B ALA* 4.1 13.2 - - + +
1862B TRP* 4.0 29.2 + - + +
1865B ARG* 3.9 21.4 + - - +
1868B PRO* 5.6 1.2 - - - +
1951B LEU* 3.9 40.1 - - + +
1952B ILE* 4.1 17.7 - - + +
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Residues in contact with ALA1820 (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 2.9 18.6 + - - +
1817B LEU* 3.6 4.3 - - - +
1819B LEU* 1.3 79.0 - - - +
1821B SER* 1.3 57.7 + - - +
1822B GLY 4.0 0.2 + - - -
1867B ASN* 4.0 11.4 + - - -
1868B PRO* 5.1 4.0 - - - +
1891B ILE* 3.8 19.1 - - + +
1894B THR* 3.1 31.3 - - - +
1895B GLY* 3.6 10.9 - - - -
1951B LEU* 3.5 19.9 - - + +
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Residues in contact with SER1821 (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* 3.1 32.9 - - - -
1817B LEU 2.6 21.9 + - - -
1818B CYS* 3.2 6.1 + - - -
1820B ALA* 1.3 78.0 - - - +
1822B GLY* 1.3 59.2 + - - +
1823B ILE* 3.5 8.6 + - - +
1867B ASN* 5.7 2.2 - - - +
1894B THR* 4.1 13.2 - - - -
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Residues in contact with GLY1822 (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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1818B CYS 2.9 6.9 + - - -
1819B LEU 3.8 5.0 + - - -
1820B ALA 3.6 2.2 + - - -
1821B SER* 1.3 77.4 - - - +
1823B ILE* 1.3 61.2 + - - +
1824B PRO* 3.1 16.7 - - - +
1862B TRP* 5.4 15.2 - - - -
1865B ARG* 6.1 2.9 - - - -
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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