Contacts of the helix formed by residues 1823 - 1840 (chain B) in PDB entry 3AU5
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 PRO1823 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1822B ALA* 1.3 88.4 - - + +
1824B GLU* 1.3 69.5 + - - +
1825B GLU* 4.6 7.2 - - + +
1826B ASN* 2.6 43.7 + - + +
1827B LEU 3.4 1.8 + - - -
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Residues in contact with GLU1824 (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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1822B ALA 3.5 3.4 + - - -
1823B PRO* 1.3 68.4 - - - +
1825B GLU* 1.3 66.8 + - - +
1827B LEU* 2.9 26.4 + - - +
1828B GLN* 2.6 42.2 + - - +
1855B TYR* 2.4 34.2 + - - -
1859B ARG* 5.0 11.6 - - - +
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Residues in contact with GLU1825 (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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1823B PRO* 2.9 9.1 + - + +
1824B GLU* 1.3 77.4 - - - +
1826B ASN* 1.3 70.6 + - - +
1828B GLN* 3.2 10.3 + - - +
1829B VAL* 3.1 35.3 + - + +
1927B LYS* 3.2 29.5 + - - -
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Residues in contact with ASN1826 (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 HIS* 5.6 2.0 + - - -
1822B ALA* 3.9 21.1 - - + +
1823B PRO* 2.6 33.6 + - + +
1825B GLU* 1.3 81.9 - - - +
1827B LEU* 1.3 62.9 + - + +
1829B VAL* 3.3 7.9 + - - +
1830B LEU* 3.0 29.9 + - + +
1946B LEU* 3.1 39.4 + - + +
1949B GLU* 4.1 12.0 + - - +
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Residues in contact with LEU1827 (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 VAL* 4.3 21.0 - - + +
1820B HIS* 4.0 23.6 - - + +
1822B ALA* 4.0 36.3 - - + +
1823B PRO 4.3 0.4 - - - +
1824B GLU* 2.9 23.2 + - - +
1826B ASN* 1.3 74.8 - - - +
1828B GLN* 1.3 58.2 + - - +
1830B LEU* 3.4 7.6 + - + +
1831B ALA* 3.0 26.3 + - - +
1854B VAL 4.9 0.7 - - - +
1855B TYR* 4.3 20.6 - - + -
1856B SER* 5.5 13.5 - - - +
1859B ARG* 6.3 3.6 - - + -
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Residues in contact with GLN1828 (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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1824B GLU* 2.6 50.9 + - - +
1825B GLU* 3.7 5.2 - - - +
1827B LEU* 1.3 72.4 - - - +
1829B VAL* 1.3 66.2 + - - +
1831B ALA* 3.1 9.5 + - - +
1832B ALA* 2.9 22.7 + - - +
1855B TYR* 3.9 12.6 + - + +
1920B ALA* 5.0 5.6 - - - +
1923B SER* 3.0 20.2 + - - -
1924B ILE* 3.7 18.9 - - + +
1927B LYS* 2.7 39.3 + - + +
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Residues in contact with VAL1829 (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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1825B GLU* 3.1 30.6 + - + +
1826B ASN* 3.6 7.6 - - - +
1828B GLN* 1.3 76.0 - - - +
1830B LEU* 1.3 57.5 + - - +
1832B ALA* 3.1 6.5 + - - +
1833B LEU* 2.9 31.8 + - + +
1927B LYS* 3.6 21.5 - - + -
1931B PHE* 4.0 19.7 - - + -
1946B LEU* 3.6 20.6 - - + -
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Residues in contact with LEU1830 (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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1812B HIS* 5.9 0.2 - - - -
1815B VAL* 4.5 10.1 - - + -
1820B HIS* 4.2 16.2 - - + +
1826B ASN* 3.0 26.2 + - + +
1827B LEU* 3.6 13.7 - - + +
1829B VAL* 1.3 77.3 - - - +
1831B ALA* 1.3 61.6 + - - +
1833B LEU* 3.4 2.6 + - + +
1834B ARG* 3.1 19.4 + - - +
1854B VAL 5.0 0.7 - - - -
1943B TYR* 3.3 62.2 - - + +
1946B LEU* 3.4 26.5 - - + -
1947B ILE* 3.8 22.4 - - + -
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Residues in contact with ALA1831 (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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1827B LEU 3.0 13.4 + - - +
1828B GLN 3.1 9.4 + - - +
1830B LEU* 1.3 76.7 - - - +
1832B ALA* 1.3 58.2 + - - +
1834B ARG* 3.3 4.5 + - - +
1835B LEU* 2.9 32.2 + - - +
1854B VAL* 3.3 32.5 + - + +
1855B TYR* 4.4 2.0 - - + -
1924B ILE* 3.4 31.6 - - + -
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Residues in contact with ALA1832 (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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1828B GLN 2.9 11.6 + - - +
1829B VAL 3.4 4.3 - - - +
1831B ALA* 1.3 79.3 - - - +
1833B LEU* 1.3 56.4 + - - +
1835B LEU* 3.3 8.1 - - - +
1836B GLN* 2.8 27.9 + - - +
1924B ILE* 3.5 27.3 - - - +
1927B LYS* 3.9 6.1 - - + -
1928B TRP* 3.6 15.7 - - - +
1931B PHE* 3.4 21.9 - - + -
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Residues in contact with LEU1833 (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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1808B PHE* 5.9 0.4 - - - -
1829B VAL* 2.9 29.0 + - + +
1830B LEU 3.8 4.9 - - - +
1831B ALA 3.3 0.2 - - - -
1832B ALA* 1.3 73.1 - - - +
1834B ARG* 1.3 55.5 + - - +
1836B GLN* 3.0 5.5 + - - +
1837B TYR* 2.7 37.2 + - - +
1931B PHE* 3.3 31.0 - - + -
1934B MET* 3.8 24.7 - - + -
1939B ALA* 4.0 9.3 - - - +
1942B LYS* 3.8 15.3 - - + +
1943B TYR* 3.5 44.2 - - + +
1946B LEU* 4.5 7.2 - - + -
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Residues in contact with ARG1834 (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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1708B GLY* 4.5 8.5 - - - -
1808B PHE* 3.3 28.1 - - - -
1809B GLU* 2.8 43.7 + - - -
1812B HIS* 3.3 53.5 + - + +
1830B LEU 3.1 13.1 + - - +
1831B ALA* 3.5 9.4 - - - +
1833B LEU* 1.3 75.0 - - - +
1835B LEU* 1.3 54.4 + - - +
1837B TYR* 3.2 5.9 + - - +
1838B LEU* 2.7 76.5 + - + +
1853B GLU 5.3 0.2 + - - -
1854B VAL* 4.1 7.9 - - + -
1943B TYR* 4.4 6.0 - - + -
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Residues in contact with LEU1835 (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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1831B ALA 2.9 8.0 + - - +
1832B ALA 3.3 9.0 - - - +
1833B LEU 3.1 0.2 - - - -
1834B ARG* 1.3 77.8 - - - +
1836B GLN* 1.3 61.4 + - - +
1838B LEU* 4.6 4.9 - - + -
1839B GLN* 3.1 32.1 + - - +
1840B GLY 3.9 0.7 - - - +
1848B ILE* 4.1 23.1 - - + -
1849B PRO* 4.3 20.4 - - + -
1854B VAL* 3.6 35.0 - - + -
1924B ILE* 4.0 27.1 - - + -
1925B ILE* 5.1 2.2 - - + -
1928B TRP* 3.8 38.4 + - + -
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Residues in contact with GLN1836 (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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1832B ALA 2.8 17.3 + - - +
1833B LEU* 3.3 12.3 - - - +
1835B LEU* 1.3 74.4 - - - +
1837B TYR* 1.3 57.4 + - - +
1840B GLY* 3.1 45.4 + - - +
1841B ASP* 3.3 19.0 + - - +
1928B TRP* 3.0 29.1 + - + +
1931B PHE* 3.3 33.8 + - + +
1934B MET* 2.9 41.8 + - + +
1936B GLN* 5.1 4.2 + - - +
1939B ALA* 4.4 3.1 - - + +
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Residues in contact with TYR1837 (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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1808B PHE* 3.6 28.7 - + + -
1809B GLU* 4.1 13.8 + - - -
1833B LEU 2.7 17.7 + - - +
1834B ARG* 3.6 6.7 - - - +
1836B GLN* 1.3 74.4 - - - +
1838B LEU* 1.3 84.3 + - + +
1840B GLY 4.6 1.1 + - - -
1936B GLN* 2.7 80.8 + - + +
1939B ALA* 4.0 12.6 - - + -
1940B MET* 3.5 32.7 - - + +
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Residues in contact with LEU1838 (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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1834B ARG* 2.7 65.5 + - + +
1835B LEU* 4.1 5.8 - - + +
1837B TYR* 1.3 92.6 - - + +
1839B GLN* 1.3 66.7 + - + +
1840B GLY 3.8 0.2 - - - -
1849B PRO* 5.3 10.3 - - + -
1853B GLU 5.7 0.7 - - - +
1854B VAL* 4.5 12.1 - - + -
1936B GLN* 5.0 1.7 + - - -
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Residues in contact with GLN1839 (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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1835B LEU* 3.1 15.2 + - - +
1838B LEU* 1.3 81.4 - - + +
1840B GLY* 1.3 64.0 + - - +
1841B ASP 3.8 5.2 + - - +
1846B ALA* 4.4 5.3 - - - +
1847B ALA 2.9 25.2 + - - +
1848B ILE* 4.7 1.6 - - - -
1849B PRO* 3.4 30.0 - - - +
1928B TRP* 3.3 29.9 - - + -
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Residues in contact with GLY1840 (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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1836B GLN* 3.1 39.2 + - - +
1837B TYR 4.6 1.0 + - - -
1838B LEU 3.8 1.2 - - - -
1839B GLN* 1.3 78.4 - - - +
1841B ASP* 1.3 61.1 + - - -
1928B TRP* 3.1 14.6 + - - -
1934B MET 5.5 0.4 - - - -
1936B GLN* 6.3 0.2 - - - +
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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