Contacts of the strand formed by residues 1858 - 1867 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1852B GLY 3.0 8.0 - - - +
1854B GLY* 5.9 0.2 - - - -
1855B SER* 2.7 29.4 + - - -
1856B PRO 3.3 1.6 - - - -
1857B LEU* 1.3 78.6 - - - +
1859B ASP* 1.3 65.6 + - - -
1860B VAL* 3.1 5.6 + - - -
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Residues in contact with ASP1859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1852B GLY 3.8 6.1 - - - -
1853B VAL* 3.7 24.5 - - + +
1854B GLY* 3.0 24.6 + - - -
1858B GLY* 1.3 68.9 - - - -
1860B VAL* 1.3 63.3 + - - +
1861B PRO* 4.9 0.7 - - - +
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Residues in contact with VAL1860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1851B GLY* 3.6 23.1 - - - -
1852B GLY* 2.8 27.5 + - - -
1857B LEU* 4.0 37.7 - - + +
1858B GLY 3.1 3.8 + - - +
1859B ASP* 1.3 80.4 - - - +
1861B PRO* 1.4 73.9 - - + +
1863B PHE* 4.6 5.6 - - + -
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Residues in contact with PRO1861 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1850B ALA 3.9 0.7 - - - +
1859B ASP 4.9 0.7 - - - +
1860B VAL* 1.4 95.9 - - + +
1862B ILE* 1.3 64.2 + - - +
1863B PHE* 3.3 18.4 - - - -
1884B ARG* 4.0 41.3 - - + +
1921B ASP* 4.7 1.4 - - - +
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Residues in contact with ILE1862 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1849B ILE* 4.4 17.5 - - + -
1850B ALA 3.2 11.7 - - - +
1851B GLY 3.9 3.4 - - - +
1852B GLY* 3.4 27.8 - - - +
1861B PRO* 1.3 74.0 - - - +
1863B PHE* 1.3 60.4 + - - +
1884B ARG* 3.5 6.6 - - - +
1885B ILE* 2.9 56.7 + - + +
1888B ILE* 5.4 0.7 - - + -
1893B THR* 4.1 26.8 + - + +
1896B MET* 4.4 13.2 - - - +
1897B THR 4.4 1.1 - - - +
1901B ALA* 3.6 26.9 - - + -
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Residues in contact with PHE1863 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1849B ILE* 3.4 5.9 - - - +
1850B ALA* 2.9 62.6 + - + -
1851B GLY 4.4 0.2 - - - -
1857B LEU* 3.8 21.8 - - + -
1860B VAL* 4.6 6.5 - - + -
1861B PRO 3.3 15.5 - - - -
1862B ILE* 1.3 75.5 - - - +
1864B ILE* 1.3 73.1 + - - +
1865B ALA* 4.2 7.0 - - + -
1882B GLY* 4.4 2.9 - - - +
1883B ASP 3.1 17.9 - - - +
1884B ARG* 4.2 1.8 - - - +
1885B ILE* 4.4 5.4 - - - +
1921B ASP* 3.5 45.3 - - + +
1922B VAL* 3.9 15.9 - - + -
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Residues in contact with ILE1864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1847B ILE* 4.5 15.0 - - + -
1848B SER 3.6 5.8 - - - +
1849B ILE* 4.7 1.1 - - + +
1863B PHE* 1.3 74.8 - - - +
1865B ALA* 1.3 62.1 + - - +
1866B MET 3.6 20.4 - - - +
1867B MET* 3.7 16.8 - - + -
1879B LEU* 3.7 42.0 - - + -
1880B ARG 3.8 22.2 - - - +
1881B VAL* 3.7 2.1 - - - +
1882B GLY* 2.8 30.8 + - - -
1883B ASP* 2.9 19.4 + - + +
1885B ILE* 4.3 18.8 - - + -
1914B MET* 4.9 0.7 - - - -
1922B VAL* 4.0 0.2 - - - +
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Residues in contact with ALA1865 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1848B SER* 2.8 15.8 + - - +
1849B ILE 4.8 0.2 - - - -
1850B ALA* 4.0 24.0 - - + -
1863B PHE* 3.5 12.6 + - + -
1864B ILE* 1.3 74.9 - - - +
1866B MET* 1.3 87.3 + - + +
1881B VAL* 3.4 15.6 - - - +
1922B VAL* 4.0 10.0 - - + +
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Residues in contact with MET1866 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1847B ILE* 3.6 0.7 - - - -
1848B SER* 3.0 46.5 + - - +
1864B ILE* 3.5 3.7 - - - +
1865B ALA* 1.3 95.9 - - + +
1867B MET* 1.3 70.9 + - - +
1881B VAL* 4.0 6.7 - - - -
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Residues in contact with MET1867 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1846B GLY 3.4 5.4 - - - +
1847B ILE* 4.0 11.4 - - + -
1864B ILE* 3.7 13.7 - - + -
1866B MET* 1.3 83.8 - - - +
1868B HIS* 1.3 65.1 + - - +
1869B PRO* 3.9 25.6 - - + -
1879B LEU* 3.6 46.7 - - + +
1880B ARG* 4.0 2.2 - - - -
1881B VAL* 3.9 24.5 - - + +
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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