Contacts of the strand formed by residues 1882 - 1888 (chain B) in PDB entry 2V5P
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 ALA1882 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1876B TYR* 3.7 5.2 - - - -
1877B ARG* 2.7 61.3 + - + +
1880B ASP* 3.3 7.8 - - + +
1881B GLU* 1.3 77.9 - - - +
1883B VAL* 1.3 65.3 + - - +
1884B VAL* 4.7 1.1 - - + -
1954B ILE* 4.9 8.5 - - + -
1955B PHE 3.4 16.2 - - - +
1956B LYS* 4.9 11.0 - - + +
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Residues in contact with VAL1883 (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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1806B LEU* 4.1 18.2 - - + -
1815B PHE* 4.3 20.4 - - + -
1817B LEU* 4.4 18.6 - - + -
1874B LEU* 4.4 7.6 - - + -
1875B ASP 3.8 13.9 - - - +
1876B TYR* 4.3 13.7 - - + -
1881B GLU 5.4 1.1 - - - +
1882B ALA* 1.3 75.8 - - - +
1884B VAL* 1.3 62.6 + - - +
1953B ILE 3.4 1.9 - - - +
1954B ILE* 3.6 0.4 - - - -
1955B PHE* 2.8 47.9 + - + +
1986B VAL* 4.0 24.7 - - + +
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Residues in contact with VAL1884 (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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1873B LYS 3.4 6.9 - - - +
1874B LEU* 3.6 4.5 - - - -
1875B ASP* 3.3 34.9 + - + +
1876B TYR 5.2 1.1 - - - -
1877B ARG* 4.3 29.6 - - + +
1882B ALA 4.4 1.6 - - - +
1883B VAL* 1.3 76.9 - - - +
1885B LEU* 1.3 69.6 + - - +
1886B SER* 4.6 5.6 + - - +
1952B SER* 4.5 10.8 - - - -
1953B ILE 3.4 2.5 - - - +
1954B ILE* 3.9 27.8 - - + -
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Residues in contact with LEU1885 (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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1817B LEU* 6.1 0.2 - - + -
1838B VAL* 3.9 24.7 - - + -
1872B MET* 3.5 44.2 - - + -
1873B LYS 4.3 0.2 - - - +
1874B LEU* 3.7 14.5 - - + +
1883B VAL 3.8 1.4 + - - -
1884B VAL* 1.3 72.2 - - - +
1886B SER* 1.3 68.2 + - - +
1887B TYR* 3.5 27.1 - - + +
1952B SER* 3.1 5.7 - - - -
1953B ILE* 2.7 63.4 + - + +
1955B PHE* 3.8 15.9 - - + -
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Residues in contact with SER1886 (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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1871B SER 4.0 1.7 - - - +
1872B MET* 3.2 2.9 - - - -
1873B LYS* 2.8 52.2 + - - +
1875B ASP* 5.6 1.2 + - - -
1884B VAL* 4.6 7.0 + - - +
1885B LEU* 1.3 81.1 - - - +
1887B TYR* 1.3 67.8 + - - +
1951B SER 3.4 6.7 - - - -
1952B SER* 3.8 14.8 - - - -
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Residues in contact with TYR1887 (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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1836B VAL* 5.5 0.4 - - + -
1837B GLY 3.2 22.7 + - - -
1838B VAL* 3.6 5.5 - - - +
1839B CYS 3.6 2.6 + - - -
1854B GLY* 3.9 18.2 - - - -
1855B VAL* 3.8 20.4 - - + -
1867B GLY* 3.7 14.4 - - - -
1868B ARG 3.4 17.9 - - - +
1869B LEU* 4.2 13.0 - - + -
1871B SER* 3.6 5.6 - - - -
1872B MET* 3.6 40.6 - - + +
1885B LEU* 3.5 29.8 - - + +
1886B SER* 1.3 77.7 - - - +
1888B VAL* 1.3 66.2 + - - +
1950B THR* 4.2 3.1 - - - -
1951B SER* 3.0 40.1 + - - +
1953B ILE* 4.8 6.3 - - + +
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Residues in contact with VAL1888 (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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1769B GLY* 3.6 12.8 - - - +
1770B VAL* 3.5 28.0 - - + +
1867B GLY* 3.5 7.8 - - - -
1868B ARG* 2.8 21.5 + - - +
1871B SER* 2.8 31.3 + - - +
1887B TYR* 1.3 77.0 - - - +
1889B ASN* 1.3 94.7 + - - +
1948B TYR 5.3 0.4 - - - +
1949B ARG 4.1 3.6 - - - +
1950B THR* 3.5 22.0 - - + -
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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