Contacts of the strand formed by residues 1878 - 1887 (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 ALA1878 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1817A TYR 3.9 4.7 - - - -
1818A GLY* 5.3 1.1 - - - -
1820A LYS* 4.9 4.0 - - + -
1821A PHE* 3.6 26.7 - - + -
1850A TYR* 5.8 0.4 - - + -
1854A PHE* 3.9 26.5 - - + -
1858A VAL* 3.0 12.8 + - - +
1859A VAL* 3.6 11.3 - - + +
1860A GLU* 2.9 27.2 + - - +
1877A LYS* 1.3 71.8 - - - +
1879A TYR* 1.3 61.9 + - - +
1880A ILE 4.2 0.3 + - - -
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Residues in contact with TYR1879 (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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1816A PHE 4.0 0.2 - - - -
1817A TYR* 3.0 42.2 + - + +
1818A GLY* 6.0 0.4 - - - -
1821A PHE* 3.6 4.9 - - - -
1860A GLU* 3.2 34.7 - - + -
1861A VAL 5.4 0.4 - - - -
1862A ILE* 4.1 20.4 - - + -
1872A LYS 5.3 0.7 + - - -
1873A LEU* 3.4 46.6 - - + +
1874A ASP* 3.1 46.8 + - - +
1877A LYS* 3.3 28.4 + - + +
1878A ALA* 1.3 72.6 - - - +
1880A ILE* 1.3 61.5 + - - +
1881A GLN 4.3 0.2 - - - -
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Residues in contact with ILE1880 (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* 3.9 17.5 - - + -
1815A GLY 3.5 10.1 - - - +
1816A PHE* 4.1 16.8 - - + -
1821A PHE* 4.0 15.5 - - + -
1846A LEU* 4.3 22.9 - - + -
1847A GLU* 4.6 3.4 - - + +
1850A TYR* 4.3 16.8 - - + -
1859A VAL* 4.7 11.7 - - + -
1860A GLU 3.2 8.2 + - - +
1861A VAL* 3.3 10.3 - - + +
1862A ILE* 2.5 35.9 + - - -
1878A ALA 5.0 2.2 - - - +
1879A TYR* 1.3 78.0 - - - +
1881A GLN* 1.3 57.1 + - - +
1882A ILE* 3.6 25.4 - - + -
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Residues in contact with GLN1881 (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* 3.3 33.1 + - - +
1814A VAL* 3.3 2.4 - - - -
1815A GLY* 3.1 29.9 + - - +
1817A TYR* 3.8 19.0 + - + -
1828A GLU* 4.1 3.6 - - - +
1862A ILE* 3.9 21.2 - - + +
1864A ASP 4.0 13.8 + - - +
1865A SER* 3.2 30.1 + - - +
1866A ASN 3.3 16.0 + - - -
1867A PRO* 4.8 1.1 - - - +
1868A VAL* 3.2 25.9 - - - +
1880A ILE* 1.3 73.9 - - - +
1882A ILE* 1.3 60.2 + - - +
1883A THR* 4.3 0.7 - - - +
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Residues in contact with ILE1882 (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* 4.4 12.8 - - + -
1813A ARG 3.4 5.6 - - - +
1814A VAL* 4.6 7.4 - - + -
1839A LEU* 4.2 9.2 - - + +
1842A ILE* 4.2 22.0 - - + -
1843A SER* 3.4 39.3 - - - +
1846A LEU* 3.9 22.4 - - + -
1861A VAL* 4.2 16.5 - - + +
1862A ILE 4.4 3.7 + - - +
1864A ASP 4.0 3.5 - - - +
1880A ILE* 3.6 18.3 + - + -
1881A GLN* 1.3 76.5 - - - +
1883A THR* 1.3 70.5 + - - +
28B PHE* 3.8 21.2 - - + -
31B GLU* 4.5 0.2 - - - +
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Residues in contact with THR1883 (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* 3.2 4.9 - - - -
1813A ARG* 2.6 70.5 + - - +
1839A LEU* 4.5 2.7 - - - -
1864A ASP 3.1 19.1 + - - -
1865A SER* 3.7 10.0 - - - -
1881A GLN* 4.3 1.2 - - - +
1882A ILE* 1.3 79.5 + - - +
1884A TYR* 1.3 74.2 + - - +
1885A VAL* 3.5 1.5 - - + +
1912A TYR* 4.0 19.7 - - + -
27B LYS* 5.3 1.3 - - - +
31B GLU* 4.0 10.1 + - - +
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Residues in contact with TYR1884 (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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1806A ARG* 3.1 29.2 + - - +
1810A THR* 3.8 20.8 - - + -
1811A TYR 4.2 1.8 - - - -
1812A PHE* 3.5 25.5 - + + -
1839A LEU* 4.2 4.0 - - - +
1883A THR* 1.3 82.9 - - - +
1885A VAL* 1.3 74.2 + - - +
1886A GLU* 3.4 36.8 + - + -
1912A TYR* 3.6 9.7 - - - +
25B THR 4.8 5.8 - - - -
26B ASN* 3.2 54.4 + - + +
27B LYS* 5.0 8.5 + - + +
31B GLU* 5.6 0.2 + - - -
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Residues in contact with VAL1885 (chain A).
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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1811A TYR* 2.6 53.9 + - + +
1812A PHE* 4.3 3.6 - - - +
1813A ARG* 3.8 19.3 - - + +
1830A VAL* 4.5 4.7 - - + -
1883A THR 3.5 12.8 - - - +
1884A TYR* 1.3 90.0 - - - +
1886A GLU* 1.3 66.9 + - - +
1887A PRO* 4.4 0.5 - - - +
1910A PHE* 3.5 26.9 - - + -
1911A MET 3.5 10.5 - - - +
1912A TYR* 4.3 17.0 - - + -
1936A LEU* 4.6 5.8 - - + -
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Residues in contact with GLU1886 (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 GLU* 4.7 17.9 - - - +
1884A TYR* 3.4 33.9 + - + +
1885A VAL* 1.3 78.3 - - - +
1887A PRO* 1.3 75.9 - - + +
1910A PHE* 3.0 5.4 - - - -
1911A MET* 2.7 49.5 + - + +
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Residues in contact with PRO1887 (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 GLU* 4.0 18.3 - - + +
1808A PHE* 4.2 11.4 - - + -
1809A GLY 5.6 1.1 - - - +
1811A TYR* 4.1 23.3 - - + -
1885A VAL 4.4 0.7 - - - +
1886A GLU* 1.3 93.7 - - + +
1888A TYR* 1.3 58.8 + - - +
1889A PHE* 4.0 23.1 + - + -
1907A LEU* 3.7 32.8 - - + -
1909A ARG 3.4 8.7 - - - +
1910A PHE* 4.1 7.2 - - + -
1911A MET* 5.6 0.3 - - - +
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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