Contacts of the strand formed by residues 1855 - 1858 (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 VAL1855 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1834A TYR* 4.2 16.8 - - + -
1835A SER 3.3 9.9 - - - +
1836A VAL* 4.2 17.5 - - + -
1842A ALA* 3.9 0.7 - - - -
1853A GLY 4.3 0.9 - - - -
1854A GLY* 1.3 82.4 - - - +
1856A CYS* 1.3 63.7 + - - +
1857A LEU 4.3 0.4 - - - -
1865A SER* 3.5 5.5 + - - -
1866A PHE* 2.8 39.5 + - + +
1867A GLY 4.2 2.8 + - - -
1887A TYR* 4.0 12.9 - - + -
1951A SER* 3.4 29.4 + - - +
1953A ILE* 5.3 2.9 - - + -
1977A VAL* 5.9 0.4 - - + -
1979A PHE* 3.9 25.1 - - + -
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Residues in contact with CYS1856 (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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1834A TYR* 3.7 3.4 - - - -
1835A SER* 3.1 31.4 + - - -
1842A ALA* 3.7 6.3 - - + +
1843A VAL* 3.7 26.9 - - + -
1849A GLY* 5.4 1.1 - - - -
1850A CYS* 2.0 52.0 - - + -
1855A VAL* 1.3 75.5 - - - +
1857A LEU* 1.3 64.1 + - - +
1858A LEU* 3.2 14.1 + - - +
1863A GLY* 4.2 7.0 - - - -
1864A ALA 3.6 5.6 - - - -
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Residues in contact with LEU1857 (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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1832A ARG* 3.8 39.9 - - + -
1833A THR 4.4 0.7 - - - +
1834A TYR* 3.6 27.9 - - + +
1856A CYS* 1.3 68.9 - - - +
1858A LEU* 1.3 70.2 + - - +
1859A SER* 4.5 4.2 + - - +
1863A GLY* 3.4 4.0 - - - -
1864A ALA* 3.0 32.7 + - + +
1866A PHE* 3.6 24.5 - - + -
1949A ARG* 3.8 20.9 - - - +
1974A GLY* 6.4 0.9 - - - -
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Residues in contact with LEU1858 (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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1826A LYS* 4.2 31.6 - - + +
1831A SER 5.6 0.5 - - - +
1832A ARG* 5.6 0.5 - - - -
1833A THR* 3.2 39.5 + - + +
1835A SER* 4.4 9.0 - - - -
1843A VAL* 4.3 19.7 - - + -
1847A GLN* 4.7 17.3 - - + -
1849A GLY* 6.5 1.3 - - - -
1856A CYS* 3.2 15.6 + - - +
1857A LEU* 1.3 82.5 - - - +
1859A SER* 1.3 64.1 + - - +
1860A GLY* 4.4 12.1 - - - +
1863A GLY* 4.7 4.3 - - - -
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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