Contacts of the helix formed by residues 1823 - 1840 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1822A ALA* 1.3 91.4 - - + +
1824A GLU* 1.3 57.2 + - - +
1825A GLU* 3.0 8.3 - - + +
1826A ASN* 2.8 44.9 + - - +
1827A LEU* 3.1 7.4 + - - +
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Residues in contact with GLU1824 (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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1822A ALA 3.4 2.7 + - - -
1823A PRO* 1.3 70.9 - - - +
1825A GLU* 1.3 62.4 + - - +
1827A LEU* 3.2 17.7 + - - +
1828A GLN* 3.0 37.8 + - - +
1855A TYR* 2.3 47.4 + - - +
1859A ARG* 4.5 15.1 - - - +
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Residues in contact with GLU1825 (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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1823A PRO* 4.2 6.9 - - + +
1824A GLU* 1.3 79.0 - - - +
1826A ASN* 1.3 71.0 + - - +
1828A GLN* 3.0 20.5 + - - +
1829A VAL* 3.2 20.9 + - + +
1927A LYS* 3.2 33.4 + - - -
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Residues in contact with ASN1826 (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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1822A ALA* 3.8 17.2 - - + +
1823A PRO* 2.8 37.8 + - - +
1825A GLU* 1.3 78.0 - - - +
1827A LEU* 1.3 59.5 + - - +
1829A VAL* 3.6 2.8 + - - -
1830A LEU* 3.1 32.6 + - + +
1946A LEU* 3.3 39.3 + - + +
1949A GLU* 4.1 10.9 + - - +
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Residues in contact with LEU1827 (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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1815A VAL* 3.7 31.7 - - + +
1820A HIS* 4.1 23.6 - - + +
1822A ALA* 4.0 15.7 - - + +
1823A PRO 3.1 11.6 + - - +
1824A GLU* 3.5 31.6 - - - +
1825A GLU 3.1 0.2 - - - -
1826A ASN* 1.3 77.0 - - - +
1828A GLN* 1.3 65.2 + - - +
1830A LEU* 3.7 13.8 + - + +
1831A ALA* 3.2 20.4 + - - +
1854A VAL 4.7 1.2 - - - +
1855A TYR* 3.8 12.8 - - + -
1856A SER* 5.6 10.5 - - - +
1859A ARG* 5.4 10.1 - - + -
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Residues in contact with GLN1828 (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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1824A GLU* 3.0 24.1 - - - +
1825A GLU* 3.0 12.3 + - - +
1827A LEU* 1.3 77.6 - - - +
1829A VAL* 1.3 60.1 + - - +
1831A ALA* 3.1 4.2 + - - +
1832A ALA* 2.8 28.4 + - - +
1855A TYR* 3.8 15.3 + - + -
1920A ALA* 3.7 26.0 - - - +
1923A SER* 2.5 35.4 + - - -
1924A ILE* 3.8 17.7 - - + +
1927A LYS* 3.8 20.3 - - + +
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Residues in contact with VAL1829 (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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1825A GLU* 3.2 20.7 + - + +
1826A ASN* 3.9 7.4 - - - +
1828A GLN* 1.3 77.3 - - - +
1830A LEU* 1.3 52.1 + - - +
1832A ALA* 3.0 5.1 + - - +
1833A LEU* 2.7 57.4 + - + +
1927A LYS* 3.8 23.6 - - + -
1931A PHE* 4.0 13.2 - - + -
1946A LEU* 3.8 14.8 - - + -
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Residues in contact with LEU1830 (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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1812A HIS* 5.8 0.2 - - - -
1815A VAL* 4.1 14.4 - - + -
1820A HIS* 4.2 7.2 - - + +
1826A ASN* 3.1 23.4 + - + +
1827A LEU* 3.8 25.4 - - + +
1829A VAL* 1.3 78.9 - - - +
1831A ALA* 1.3 57.4 + - - +
1833A LEU* 3.5 1.5 + - + -
1834A ARG* 3.0 24.8 + - - +
1854A VAL 4.8 0.9 - - - -
1943A TYR* 3.1 60.9 - - + +
1946A LEU* 3.5 25.4 - - + -
1947A ILE* 3.7 22.2 - - + -
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Residues in contact with ALA1831 (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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1827A LEU 3.2 11.2 + - - +
1828A GLN 3.1 8.7 + - - +
1830A LEU* 1.3 80.6 - - - +
1832A ALA* 1.3 56.8 + - - +
1834A ARG* 3.2 4.1 + - - +
1835A LEU* 3.0 29.8 + - - +
1854A VAL* 3.2 36.9 + - + +
1855A TYR* 4.3 1.6 - - + -
1924A ILE* 3.7 28.9 - - + -
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Residues in contact with ALA1832 (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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1828A GLN 2.8 13.5 + - - +
1829A VAL 3.5 7.0 - - - +
1831A ALA* 1.3 77.2 - - - +
1833A LEU* 1.3 55.7 + - - +
1835A LEU* 3.2 5.2 + - - +
1836A GLN* 2.9 27.7 + - - +
1924A ILE* 3.5 28.0 - - - +
1927A LYS* 3.6 7.6 - - + -
1928A TRP* 3.5 23.1 - - - +
1931A PHE* 3.6 13.5 - - + -
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Residues in contact with LEU1833 (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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1808A PHE* 5.5 0.6 - - - -
1829A VAL* 2.7 40.7 + - + +
1830A LEU* 3.8 7.0 - - - +
1832A ALA* 1.3 72.7 - - - +
1834A ARG* 1.3 57.7 + - - +
1836A GLN* 3.3 5.2 + - - +
1837A TYR* 2.9 28.6 + - - +
1931A PHE* 3.3 32.8 - - + -
1934A MET* 3.8 24.9 - - + -
1939A ALA* 3.9 11.4 - - - +
1942A LYS* 4.0 17.5 - - + +
1943A TYR* 4.0 35.2 - - + +
1946A LEU* 4.8 2.9 - - + -
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Residues in contact with ARG1834 (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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1708A GLY* 5.8 1.0 - - - -
1808A PHE* 3.4 27.4 - - - -
1809A GLU* 3.1 41.6 + - - -
1812A HIS* 3.3 54.4 + - + +
1830A LEU 3.0 18.6 + - - +
1831A ALA* 3.4 6.7 - - - +
1832A ALA 3.2 0.2 - - - -
1833A LEU* 1.3 74.5 - - - +
1835A LEU* 1.3 65.4 + - - +
1837A TYR* 3.2 7.1 + - - +
1838A LEU* 2.9 56.4 + - + +
1853A GLU 5.0 0.6 + - - -
1854A VAL* 3.9 13.0 - - + -
1943A TYR* 4.5 4.2 - - + -
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Residues in contact with LEU1835 (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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1831A ALA 3.0 8.9 + - - +
1832A ALA* 3.5 8.3 - - - +
1834A ARG* 1.3 75.9 - - - +
1836A GLN* 1.3 57.1 + - - +
1838A LEU* 3.3 6.2 + - + -
1839A GLN* 2.9 37.5 + - - +
1840A GLY 4.0 0.2 + - - -
1848A ILE* 4.5 25.4 - - + -
1849A PRO* 3.9 23.1 - - + -
1854A VAL* 3.2 38.1 - - + -
1924A ILE* 3.8 28.0 - - + -
1925A ILE* 5.2 2.7 - - + -
1928A TRP* 3.8 30.3 + - + -
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Residues in contact with GLN1836 (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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1832A ALA 2.9 14.1 + - - +
1833A LEU* 3.4 13.0 - - - +
1834A ARG 3.1 0.2 - - - -
1835A LEU* 1.3 77.4 - - - +
1837A TYR* 1.3 55.8 + - - +
1840A GLY* 3.0 43.7 + - - +
1841A ASP* 3.2 24.9 + - - -
1928A TRP* 2.9 29.3 + - + +
1931A PHE* 3.2 33.9 + - + +
1934A MET* 3.1 40.4 + - + +
1936A GLN* 5.1 2.6 + - - +
1939A ALA* 4.5 3.4 - - + -
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Residues in contact with TYR1837 (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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1805A ALA* 6.0 0.5 - - - +
1808A PHE* 3.5 34.3 - + + -
1809A GLU* 4.1 11.7 + - - -
1833A LEU 2.9 15.9 + - - +
1834A ARG* 3.6 5.4 - - - +
1836A GLN* 1.3 78.8 - - - +
1838A LEU* 1.3 78.2 + - + +
1840A GLY 4.7 1.0 + - - -
1936A GLN* 2.9 79.9 + - + +
1939A ALA* 3.9 12.1 - - + +
1940A MET* 3.4 35.8 - - + +
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Residues in contact with LEU1838 (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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1834A ARG* 2.9 60.3 + - + +
1835A LEU* 4.0 5.4 - - + +
1837A TYR* 1.3 95.1 - - + +
1839A GLN* 1.3 67.8 + - + +
1849A PRO* 4.9 16.4 - - + -
1853A GLU* 6.0 1.6 - - + +
1854A VAL* 4.9 7.4 - - + -
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Residues in contact with GLN1839 (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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1835A LEU* 2.9 19.1 + - - +
1838A LEU* 1.3 83.2 - - + +
1840A GLY* 1.3 63.3 + - - +
1841A ASP 3.8 4.9 + - - +
1846A ALA* 4.9 2.6 - - - +
1847A ALA 3.2 23.1 + - - +
1848A ILE* 4.2 2.8 - - - +
1849A PRO* 3.1 34.0 - - - +
1928A TRP* 3.2 31.6 - - + -
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Residues in contact with GLY1840 (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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1836A GLN* 3.0 29.5 + - - +
1837A TYR 4.6 1.0 + - - -
1838A LEU 3.8 0.4 - - - -
1839A GLN* 1.3 80.4 - - - +
1841A ASP* 1.3 61.2 + - - -
1928A TRP* 3.0 24.9 + - - -
1934A MET 5.4 1.1 - - - -
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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
------------------------------------------------------------
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