Contacts of the strand formed by residues 1888 - 1894 (chain B) in PDB entry 4ILG
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 HIS1888 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1881B THR 3.9 1.0 - - - +
1882B LEU* 3.6 2.1 - - - +
1883B ASN* 3.0 31.0 + - + +
1886B THR* 3.2 36.6 + - + +
1887B GLY* 1.3 75.0 - - - +
1889B LEU* 1.3 60.3 + - - +
1890B PHE* 4.1 18.2 + - + -
1989B PHE 3.6 6.1 - - - +
1990B ASN* 3.6 17.9 + - + -
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Residues in contact with LEU1889 (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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1880B PHE* 3.7 44.6 - - + -
1881B THR 3.4 26.2 - - - +
1882B LEU* 4.4 6.5 - - + -
1887B GLY 3.3 5.1 + - - +
1888B HIS* 1.3 73.2 - - - +
1890B PHE* 1.3 67.2 + - - +
1891B LEU* 3.7 10.9 + - + +
1974B LEU* 4.1 20.9 - - + -
1988B LEU* 3.5 8.7 - - - +
1989B PHE* 2.7 61.0 + - + +
1991B ILE* 4.5 10.5 - - + -
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Residues in contact with PHE1890 (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 LEU* 4.4 18.6 - - + -
1879B ILE 3.5 3.5 - - - +
1881B THR* 2.8 48.0 + - + +
1883B ASN* 5.5 1.3 - - + -
1888B HIS* 4.5 22.2 - - + -
1889B LEU* 1.3 72.1 - - - +
1891B LEU* 1.3 60.8 + - - +
1892B LYS* 3.6 1.8 + - - +
1920B LEU* 3.7 45.5 - - + -
1924B LEU* 4.5 22.0 - - + -
1986B MET* 3.8 11.3 - - + +
1987B VAL 4.0 2.2 - - - -
1988B LEU* 3.7 24.5 - - + -
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Residues in contact with LEU1891 (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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1878B CYS* 4.0 22.4 - - + -
1879B ILE 3.5 12.6 - - - +
1880B PHE* 4.3 17.0 - - + -
1889B LEU* 3.7 21.5 - - + -
1890B PHE* 1.3 71.1 - - - +
1892B LYS* 1.3 61.9 + - - +
1893B ILE* 3.5 6.5 + - + +
1969B MET* 4.7 4.3 - - + -
1974B LEU* 4.5 13.0 - - + -
1977B VAL* 4.3 9.6 - - + -
1978B VAL* 4.0 25.4 - - + -
1985B GLN 3.8 0.5 - - - +
1986B MET* 3.5 1.8 - - - -
1987B VAL* 2.9 44.8 + - + +
1989B PHE* 4.1 22.9 - - + -
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Residues in contact with LYS1892 (chain B).
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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1878B CYS* 3.2 3.0 - - - -
1879B ILE* 2.9 58.3 + - + -
1890B PHE 3.6 2.3 + - - +
1891B LEU* 1.3 73.1 - - - +
1893B ILE* 1.3 73.9 + - - +
1894B ILE* 3.5 5.9 + - + +
1916B GLU* 2.9 38.2 + - + +
1984B PRO* 4.2 11.2 - - - +
1985B GLN* 3.6 24.8 - - - +
1986B MET* 3.6 31.5 - - + +
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Residues in contact with ILE1893 (chain B).
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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1876B ASN* 4.9 2.0 - - + -
1877B GLY 3.5 10.3 - - - +
1878B CYS* 4.3 0.7 - - + +
1891B LEU* 4.3 9.4 - - + +
1892B LYS* 1.3 80.5 - - - +
1894B ILE* 1.3 68.4 + - - +
1895B HIS 4.5 1.8 - - - +
1977B VAL* 3.7 24.0 - - + +
1978B VAL* 3.9 24.5 - - + +
1981B ALA* 3.6 23.3 - - + -
1983B GLU 4.9 0.9 - - - +
1984B PRO* 3.6 10.2 - - - +
1985B GLN* 2.7 61.6 + - + +
1987B VAL* 3.6 22.2 - - + -
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Residues in contact with ILE1894 (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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1857B VAL* 4.3 15.2 - - + +
1875B ILE 4.9 0.2 - - - +
1876B ASN* 3.6 2.4 - - - -
1877B GLY 2.7 36.1 + - - +
1878B CYS* 4.1 10.1 - - - +
1879B ILE* 4.0 27.8 - - + -
1892B LYS* 3.8 15.0 - - + +
1893B ILE* 1.3 79.5 - - - +
1895B HIS* 1.3 66.9 + - - +
1898B VAL* 4.2 16.6 - - + -
1899B TRP* 3.9 31.7 + - + +
1912B LYS* 4.4 23.3 - - + -
1916B GLU* 4.7 1.6 - - + -
1984B PRO* 5.4 0.9 - - + -
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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