Contacts of the strand formed by residues 1882 - 1888 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1876A TYR* 3.6 7.9 - - - -
1877A ARG* 2.8 54.2 + - + +
1880A ASP* 3.3 16.1 - - + +
1881A GLU* 1.3 77.0 - - - +
1883A VAL* 1.3 64.9 + - - +
1884A VAL 4.1 0.2 - - - -
1954A ILE* 5.0 4.9 - - + -
1955A PHE 3.4 20.4 - - - +
1956A LYS* 5.1 4.9 - - + -
1986A VAL* 6.4 0.2 - - - -
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Residues in contact with VAL1883 (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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1806A LEU* 4.1 12.3 - - + -
1815A PHE* 3.9 27.4 - - + -
1817A LEU* 4.3 13.7 - - + -
1874A LEU* 3.8 25.1 - - + -
1875A ASP 3.6 7.4 - - - +
1876A TYR* 4.3 9.0 - - + -
1881A GLU 5.8 0.2 - - - +
1882A ALA* 1.3 77.4 - - - +
1884A VAL* 1.3 61.8 + - - +
1953A ILE 3.3 2.9 - - - +
1954A ILE* 3.6 0.6 - - - -
1955A PHE* 2.8 40.6 + - + -
1986A VAL* 3.8 28.7 - - + -
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Residues in contact with VAL1884 (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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1873A LYS 3.4 5.9 - - - +
1874A LEU* 3.4 4.6 - - - +
1875A ASP* 2.8 49.3 + - + +
1876A TYR 5.2 0.2 - - - -
1877A ARG* 4.3 26.5 - - + +
1882A ALA 5.0 0.2 - - - -
1883A VAL* 1.3 75.6 - - - +
1885A LEU* 1.3 68.8 + - - +
1886A SER* 4.9 6.0 + - - +
1952A SER* 4.7 10.8 - - - -
1953A ILE 3.6 2.7 - - - +
1954A ILE* 3.8 24.9 - - + -
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Residues in contact with LEU1885 (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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1817A LEU* 5.6 0.4 - - + -
1838A VAL* 3.8 24.7 - - + -
1872A MET* 3.5 36.6 - - + -
1873A LYS 3.4 3.8 - - - -
1874A LEU* 3.7 12.6 - - + -
1883A VAL 3.8 1.0 + - - -
1884A VAL* 1.3 73.0 - - - +
1886A SER* 1.3 70.3 + - - +
1887A TYR* 3.6 25.1 - - + +
1952A SER* 3.1 3.3 - - - -
1953A ILE* 2.6 65.6 + - + +
1955A PHE* 3.7 23.3 - - + -
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Residues in contact with SER1886 (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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1871A SER 3.7 3.3 - - - +
1872A MET* 3.4 3.1 - - - -
1873A LYS* 3.1 43.7 + - - +
1875A ASP* 5.6 1.2 + - - -
1884A VAL* 4.9 6.7 - - - +
1885A LEU* 1.3 77.8 - - - +
1887A TYR* 1.3 66.8 + - - +
1951A SER 3.4 10.5 - - - -
1952A SER* 3.9 12.1 - - - -
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Residues in contact with TYR1887 (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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1836A VAL* 5.6 0.2 - - + -
1837A GLY 2.9 23.4 + - - -
1838A VAL* 3.6 5.4 - - - -
1839A CYS 3.5 12.1 + - - -
1854A GLY* 4.0 18.8 - - - -
1855A VAL* 4.0 12.6 - - + -
1867A GLY* 3.7 24.7 - - - -
1868A ARG 3.9 2.0 - - - +
1869A LEU* 3.7 31.8 - - + +
1871A SER* 3.8 3.8 - - - -
1872A MET* 3.7 23.6 - - + -
1885A LEU* 3.6 26.2 - - + +
1886A SER* 1.3 77.5 - - - +
1888A VAL* 1.3 63.6 + - - +
1950A THR* 4.0 3.6 - - - -
1951A SER* 2.9 45.5 + - - +
1953A ILE* 4.7 10.5 - - + +
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Residues in contact with VAL1888 (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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1769A GLY 3.9 10.3 - - - +
1770A VAL* 3.6 32.5 - - + +
1867A GLY* 3.6 4.3 - - - -
1868A ARG* 2.9 15.2 + - - +
1871A SER* 2.8 37.9 + - - +
1873A LYS* 6.4 1.6 - - + -
1887A TYR* 1.3 75.5 - - - +
1889A ASN* 1.3 91.7 + - - +
1890A GLY 3.6 1.8 - - - -
1949A ARG 4.3 2.5 - - - -
1950A THR* 3.6 23.8 - - + -
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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