Contacts of the strand formed by residues 1858 - 1867 (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 GLY1858 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1854A GLY* 5.1 1.3 - - - -
1855A SER* 2.7 38.4 + - - -
1856A PRO 3.3 1.6 + - - -
1857A LEU* 1.3 79.5 - - - +
1859A ASP* 1.3 65.1 + - - -
1860A VAL* 3.2 4.4 + - - -
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Residues in contact with ASP1859 (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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1852A GLY 3.7 5.4 - - - -
1853A VAL* 3.6 20.6 - - + +
1854A GLY* 2.9 24.1 + - - -
1857A LEU 4.3 0.2 + - - -
1858A GLY* 1.3 71.4 - - - -
1860A VAL* 1.3 64.3 + - - +
1822B THR* 3.7 13.9 - - - +
1823B GLU* 3.4 36.7 + - + +
1826B TYR* 3.7 5.7 - - - -
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Residues in contact with VAL1860 (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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1851A GLY* 3.6 24.5 - - - -
1852A GLY* 2.8 30.5 + - - -
1855A SER* 3.7 12.6 - - - +
1857A LEU* 4.2 24.5 - - + +
1858A GLY 3.2 8.4 + - - +
1859A ASP* 1.3 78.1 - - - +
1861A PRO* 1.3 72.1 - - + +
1863A PHE* 4.5 9.2 - - + -
1823B GLU* 3.4 6.5 - - - +
1826B TYR* 3.5 26.9 - - + +
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Residues in contact with PRO1861 (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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1851A GLY* 3.9 0.3 - - - -
1852A GLY 4.0 0.2 - - - -
1860A VAL* 1.3 93.8 - - + +
1862A ILE* 1.3 64.9 + - - +
1863A PHE* 3.4 18.2 + - - +
1884A ARG* 3.7 23.7 + - + +
1893A THR* 5.8 0.2 - - - +
1823B GLU* 3.8 14.1 - - + +
1826B TYR* 3.5 32.3 - - + -
1827B PHE* 3.6 45.1 - - + +
1830B MET* 5.0 2.9 - - + -
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Residues in contact with ILE1862 (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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1849A ILE* 4.2 16.6 - - + -
1850A ALA 3.3 8.5 - - - +
1851A GLY 3.7 6.7 - - - +
1852A GLY* 3.5 26.9 - - - +
1860A VAL 3.5 1.4 + - - -
1861A PRO* 1.3 73.6 - - - +
1863A PHE* 1.3 62.0 + - - +
1884A ARG* 3.4 4.7 - - - +
1885A ILE* 2.8 59.5 + - + +
1888A ILE* 5.0 2.0 - - + -
1893A THR* 4.4 18.7 + - + +
1896A MET* 4.5 5.6 - - + +
1897A THR 4.1 9.2 - - - +
1898A HIS* 4.1 5.6 - - + -
1901A ALA* 3.8 26.5 - - + -
1823B GLU* 4.9 1.5 + - - +
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Residues in contact with PHE1863 (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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1849A ILE* 3.3 8.5 - - - +
1850A ALA* 2.9 53.8 + - + -
1851A GLY* 3.6 20.6 - - - -
1857A LEU* 6.5 1.8 - - + -
1860A VAL* 4.5 7.6 - - + -
1861A PRO 3.4 13.5 - - - -
1862A ILE* 1.3 75.3 - - - +
1864A ILE* 1.3 72.6 - - - +
1865A ALA* 3.5 13.6 + - + -
1882A GLY* 5.2 2.2 - - - -
1883A ASP 3.3 13.7 - - - +
1884A ARG* 3.6 36.1 - - + +
1885A ILE* 4.6 1.6 - - - +
1924A GLU* 6.0 0.2 - - - -
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Residues in contact with ILE1864 (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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1847A ILE* 4.3 23.3 - - + -
1848A SER 3.7 4.9 - - - +
1849A ILE* 4.8 0.9 - - + +
1863A PHE* 1.3 72.9 - - - +
1865A ALA* 1.3 60.3 - - - +
1866A MET 3.3 24.2 - - - +
1867A MET* 3.6 17.3 - - + -
1879A LEU* 4.3 27.4 - - + -
1880A ARG 3.8 18.2 - - - +
1881A VAL* 3.7 8.1 - - - +
1882A GLY* 2.8 30.5 + - - -
1883A ASP* 2.9 25.1 + - + +
1885A ILE* 4.2 19.7 - - + -
1914A MET* 5.0 1.1 - - - -
1916A VAL* 5.0 0.2 - - + -
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Residues in contact with ALA1865 (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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1848A SER* 2.9 15.8 + - - +
1849A ILE 5.0 0.2 - - - -
1850A ALA* 4.0 13.7 - - + -
1863A PHE* 3.5 23.1 + - + -
1864A ILE* 1.3 73.8 - - - +
1866A MET* 1.3 71.2 + - + +
1881A VAL* 3.6 13.5 - - - +
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Residues in contact with MET1866 (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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1848A SER* 3.0 49.3 + - - +
1864A ILE* 3.3 5.4 - - - +
1865A ALA* 1.3 90.2 - - + +
1867A MET* 1.3 72.9 + - - +
1881A VAL* 3.8 8.1 - - - -
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Residues in contact with MET1867 (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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1846A GLY 3.4 4.5 - - - +
1847A ILE* 3.6 12.3 - - + +
1864A ILE* 3.6 15.0 - - + -
1866A MET* 1.3 82.9 - - - +
1868A HIS* 1.3 64.5 + - - +
1869A PRO* 3.4 7.1 - - - +
1873A ALA* 3.8 8.5 - - + +
1874A ALA* 3.5 40.8 - - + +
1879A LEU* 3.8 35.0 - - - +
1880A ARG* 4.1 1.6 - - - -
1881A VAL* 3.8 24.1 - - + +
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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
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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