Contacts of the strand formed by residues 1810 - 1817 (chain A) in PDB entry 6AJ4
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 THR1810 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1806A ARG* 3.2 8.8 - - - +
1809A GLY* 1.3 72.0 - - - -
1811A TYR* 1.3 63.9 + - - +
1812A PHE* 3.5 27.8 - - + -
1832A LYS* 3.6 3.6 - - - -
1833A GLU* 2.7 47.4 + - - +
1834A PRO 3.5 1.2 + - - -
1835A ALA* 4.2 0.2 - - - +
1836A ILE 3.2 26.2 + - - -
1837A THR* 3.3 26.2 + - - +
1884A TYR* 3.8 17.9 - - + -
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Residues in contact with TYR1811 (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* 3.0 37.9 + - + -
1809A GLY 3.5 15.9 - - - -
1810A THR* 1.3 74.4 - - - +
1812A PHE* 1.3 57.3 + - - +
1830A VAL* 4.2 6.5 - - + -
1831A TYR 3.3 15.3 - - - +
1832A LYS* 3.6 38.8 + - + +
1884A TYR* 3.6 4.6 - - - -
1885A VAL* 2.6 61.7 + - + +
1887A PRO* 4.1 12.1 - - + -
1904A ASN* 4.3 1.2 + - - -
1907A LEU* 3.7 21.1 - - + +
1910A PHE* 3.3 25.8 - + + -
1942A PHE* 3.9 18.4 - + + +
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Residues in contact with PHE1812 (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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1810A THR* 3.5 27.8 - - + -
1811A TYR* 1.3 75.2 - - - +
1813A ARG* 1.3 60.0 + - - +
1814A VAL* 4.5 2.5 - - + -
1830A VAL* 3.3 5.2 - - - +
1831A TYR* 2.8 36.6 + - + +
1833A GLU* 4.2 11.4 - - + -
1837A THR* 3.6 22.9 - - - -
1838A LYS 4.1 0.7 - - - -
1839A LEU* 3.9 32.1 - - + -
1842A ILE* 3.7 41.5 - - + -
1882A ILE* 4.4 9.2 - - + -
1883A THR 3.2 6.7 - - - +
1884A TYR* 3.5 38.6 - + + -
1885A VAL* 4.4 4.3 - - - -
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Residues in contact with ARG1813 (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 PHE* 1.3 71.7 - - - +
1814A VAL* 1.3 70.3 + - - +
1815A GLY 4.3 2.7 - - - +
1828A GLU* 3.2 32.9 + - - +
1829A PHE 3.4 8.7 - - - +
1830A VAL* 4.5 1.3 - - - +
1865A SER* 2.8 29.6 + - - +
1867A PRO* 6.3 0.6 - - - +
1881A GLN* 3.3 23.2 + - - +
1882A ILE* 3.4 2.4 - - - -
1883A THR* 2.6 63.1 + - - +
1885A VAL* 3.8 16.3 - - + +
1912A TYR* 3.2 36.4 + - - -
1936A LEU* 3.6 21.7 - - + +
1951A VAL* 5.2 0.7 - - + -
1954A LYS* 3.9 6.7 - - - +
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Residues in contact with VAL1814 (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 PHE* 4.3 6.3 - - + +
1813A ARG* 1.3 82.6 - - - +
1815A GLY* 1.3 60.7 + - - +
1816A PHE* 3.5 33.7 - - + -
1827A GLN 3.8 0.7 - - - +
1828A GLU* 3.2 2.6 - - - -
1829A PHE* 2.7 39.5 + - - -
1831A TYR* 3.4 39.3 - - + -
1842A ILE* 4.9 1.3 - - + -
1846A LEU* 3.8 26.2 - - + -
1880A ILE* 3.9 8.7 - - + -
1881A GLN 3.3 2.2 - - - +
1882A ILE* 4.6 8.5 - - + -
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Residues in contact with GLY1815 (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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1813A ARG* 4.2 2.6 - - - +
1814A VAL* 1.3 73.7 - - - +
1816A PHE* 1.3 63.6 + - - -
1817A TYR* 3.6 16.3 - - - -
1827A GLN 3.3 8.3 - - - -
1828A GLU* 3.8 14.5 - - - +
1880A ILE* 3.5 10.6 - - - +
1881A GLN* 3.1 32.0 + - - -
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Residues in contact with PHE1816 (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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1814A VAL* 3.5 27.1 - - + -
1815A GLY* 1.3 74.4 - - - -
1817A TYR* 1.3 62.3 + - - +
1821A PHE* 3.9 30.5 - + + -
1824A LEU* 3.7 38.1 - - + +
1825A ASP* 4.3 0.4 - - - -
1826A GLU* 2.6 35.5 + - - -
1827A GLN 3.0 7.9 + - - -
1829A PHE* 3.5 39.5 - + - -
1831A TYR* 3.9 15.3 - - - -
1846A LEU* 4.9 5.4 - - + -
1850A TYR* 4.7 14.8 - + - -
1879A TYR 4.0 0.4 - - - -
1880A ILE* 4.1 19.5 - - + -
1948A ARG* 4.7 1.1 - - - -
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Residues in contact with TYR1817 (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 GLY* 3.6 27.1 - - - -
1816A PHE* 1.3 79.2 - - - +
1818A GLY* 1.3 59.8 + - - +
1821A PHE* 3.4 8.1 - - - -
1825A ASP* 3.3 4.5 - - - -
1826A GLU* 4.6 11.7 - - + -
1827A GLN 5.5 0.7 - - - -
1828A GLU* 4.1 18.1 + - + +
1862A ILE* 4.5 7.9 - - + -
1868A VAL* 3.2 48.7 - - + +
1870A LYS* 3.7 25.6 - - + -
1873A LEU* 4.1 19.1 - - + -
1877A LYS 4.3 0.5 - - - +
1878A ALA* 3.9 0.9 - - - -
1879A TYR* 3.0 40.0 + - + +
1881A GLN* 3.8 12.3 + - + -
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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