Contacts of the strand formed by residues 1884 - 1888 (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 ARG1884 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1861B PRO* 4.0 31.9 - - + +
1862B ILE 3.5 10.5 - - - +
1863B PHE* 4.3 0.7 - - + -
1882B GLY 3.5 0.6 + - - -
1883B ASP* 1.3 73.7 - - - +
1885B ILE* 1.3 62.3 + - - +
1886B VAL* 3.5 2.4 + - + +
1916B VAL* 3.2 5.6 - - - -
1917B VAL* 2.8 48.8 + - + +
1918B ALA 5.0 0.8 + - - -
1919B GLY* 3.5 29.7 + - - -
1921B ASP* 3.0 41.9 + - - +
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Residues in contact with ILE1885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1849B ILE* 3.8 29.4 - - + -
1862B ILE* 2.9 36.5 + - + +
1863B PHE* 4.6 2.0 - - - -
1864B ILE* 4.3 18.6 - - + -
1883B ASP 4.5 0.9 - - - +
1884B ARG* 1.3 72.0 - - - +
1886B VAL* 1.3 55.8 + - - +
1887B THR 3.6 10.3 - - - +
1888B ILE* 3.6 31.9 - - + -
1893B THR* 2.7 29.3 + - + -
1905B LEU* 5.4 0.2 - - + -
1914B MET* 3.9 33.0 - - + -
1915B GLN 3.8 2.5 - - - -
1916B VAL* 4.2 4.0 - - + -
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Residues in contact with VAL1886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1832A LEU* 4.0 30.3 - - + -
1886A VAL* 4.1 25.4 - - + -
1915A GLN* 4.2 15.3 + - - +
1832B LEU* 4.1 6.5 - - + -
1884B ARG* 4.0 7.6 - - + +
1885B ILE* 1.3 76.5 - - - +
1887B THR* 1.3 63.4 + - + +
1892B SER* 3.5 3.5 + - - -
1893B THR* 3.0 25.7 + - - -
1915B GLN* 2.7 19.5 + - + +
1917B VAL* 3.9 30.7 - - + +
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Residues in contact with THR1887 (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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1886A VAL* 4.9 0.4 - - + -
1887A THR* 3.5 28.5 - - + -
1892A SER* 4.3 6.9 + - - -
1885B ILE* 3.6 6.8 - - - +
1886B VAL* 1.3 88.5 - - + +
1888B ILE* 1.3 64.9 + - - +
1889B CYS 4.3 0.2 - - - -
1890B GLY* 4.5 6.0 + - - -
1891B THR 3.2 19.7 - - - +
1892B SER* 4.1 2.0 - - - -
1893B THR* 4.3 0.9 - - - -
1913B GLU 5.7 0.2 - - - -
1914B MET* 3.3 5.6 - - - -
1915B GLN* 2.6 63.3 + - - +
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Residues in contact with ILE1888 (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* 5.5 0.2 - - + -
1862B ILE* 5.1 0.9 - - + -
1885B ILE* 3.6 22.0 - - + -
1887B THR* 1.3 78.2 - - - +
1889B CYS* 1.3 80.9 + - - +
1890B GLY 3.1 1.1 - - - -
1891B THR* 3.0 24.2 + - - +
1893B THR* 3.9 19.7 - - + -
1896B MET* 4.2 5.2 - - + -
1901B ALA* 4.0 28.7 - - + +
1904B LEU* 3.5 23.1 - - + +
1905B LEU* 3.7 35.9 - - + -
1913B GLU 3.6 6.3 - - - +
1914B MET* 4.0 7.9 - - + +
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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