Contacts of the strand formed by residues 1911 - 1917 (chain A) in PDB entry 2IWO
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 SER1911 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1836A GLU* 3.0 25.4 + - - +
1837A MET 3.6 5.6 - - - -
1838A LYS* 4.5 10.4 - - - +
1889A CYS* 5.5 2.4 - - - -
1909A SER 3.5 3.5 + - - +
1910A GLY* 1.3 72.3 - - - -
1912A ILE* 1.3 61.8 + - - +
1913A GLU 3.9 2.1 + - - -
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Residues in contact with ILE1912 (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 VAL 3.7 0.9 - - - +
1836A GLU* 3.7 2.4 - - - -
1837A MET* 2.8 48.6 + - + +
1839A LYS* 3.7 36.3 - - + -
1845A LEU* 3.9 19.1 - - + -
1889A CYS* 4.2 16.2 - - - -
1905A LEU* 4.0 25.1 - - + +
1908A ALA* 3.7 30.7 - - + +
1909A SER* 4.1 5.2 - - - +
1910A GLY 4.0 8.1 - - - +
1911A SER* 1.3 73.4 - - - +
1913A GLU* 1.3 65.4 + - - +
1914A MET* 3.9 1.0 + - + -
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Residues in contact with GLU1913 (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 THR* 4.4 11.4 - - + -
1835A VAL 3.3 10.3 - - - +
1836A GLU* 3.5 19.0 + - + +
1887A THR* 2.9 24.2 + - - -
1888A ILE* 3.6 3.3 - - - +
1889A CYS* 2.8 31.4 + - - +
1890A GLY* 3.0 30.4 + - - +
1911A SER 3.9 3.2 + - - -
1912A ILE* 1.3 78.0 - - - +
1914A MET* 1.3 66.4 + - - +
1915A GLN* 3.7 5.6 - - - +
1892B SER* 3.4 23.6 + - - -
1894B GLU* 3.7 14.9 - - + +
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Residues in contact with MET1914 (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 THR* 3.6 2.3 - - - +
1835A VAL* 2.8 40.3 + - + +
1837A MET* 4.0 29.2 - - + -
1845A LEU* 5.0 0.2 - - + -
1847A ILE* 4.2 16.4 - - + -
1864A ILE* 5.0 1.1 - - - -
1879A LEU* 4.5 10.3 - - + -
1885A ILE* 3.8 31.4 - - + -
1887A THR 3.3 11.9 - - - +
1888A ILE* 4.5 5.8 - - + -
1905A LEU* 3.9 30.3 - - + -
1912A ILE* 5.1 0.4 - - + -
1913A GLU* 1.3 74.1 - - - +
1915A GLN* 1.3 62.0 + - - +
1916A VAL* 3.8 19.3 - - + -
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Residues in contact with GLN1915 (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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1832A LEU* 4.1 25.3 - - + +
1833A ARG 3.1 7.4 - - - +
1834A THR* 3.2 26.5 + - + +
1885A ILE* 3.7 0.3 - - - +
1886A VAL* 2.8 27.9 + - + -
1887A THR* 2.7 40.7 + - - +
1913A GLU* 3.9 9.6 - - - +
1914A MET* 1.3 75.4 - - - +
1916A VAL* 1.3 67.9 + - - +
1886B VAL* 4.2 10.4 + - - +
1892B SER* 2.7 22.4 + - - -
1893B THR* 5.7 1.0 + - - -
1894B GLU* 3.7 21.2 + - - +
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Residues in contact with VAL1916 (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 LEU* 3.3 8.3 - - - +
1833A ARG* 2.8 60.2 + - + +
1835A VAL* 4.9 0.9 - - + -
1864A ILE* 5.0 0.7 - - + -
1879A LEU* 4.0 18.8 - - + -
1883A ASP* 3.5 31.0 - - + +
1884A ARG 3.1 13.5 - - - +
1885A ILE* 4.1 11.4 - - + -
1886A VAL* 4.3 1.6 - - - +
1914A MET* 3.8 21.5 - - + -
1915A GLN* 1.3 81.2 - - - +
1917A VAL* 1.3 62.6 + - - +
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Residues in contact with VAL1917 (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 LEU* 3.7 31.9 - - + +
1833A ARG* 3.9 4.5 - - - +
1883A ASP* 3.4 3.8 - - - -
1884A ARG* 2.8 53.5 + - + +
1886A VAL* 3.9 14.6 - - + +
1916A VAL* 1.3 78.3 - - - +
1918A ALA* 1.3 63.4 + - - +
1827B PHE* 4.5 7.4 - - + -
1830B MET* 4.2 30.5 - - + +
1831B GLY 5.9 0.2 - - - -
1832B LEU* 4.8 13.0 - - + +
1917B VAL* 5.1 4.5 - - + -
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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