Contacts of the strand formed by residues 1868 - 1877 (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 ARG1868 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1792A PRO* 5.1 10.8 + - - +
1793A VAL* 6.1 8.9 - - - +
1795A CYS 5.5 4.2 + - - -
1796A PRO 6.0 0.2 - - - -
1797A ASP* 3.0 27.5 + - - -
1851A LYS 5.4 0.2 - - - +
1852A ASP* 3.3 33.7 + - + +
1865A SER* 5.3 1.8 - - - +
1867A GLY* 1.3 69.9 - - - -
1869A LEU* 1.3 56.9 - - - +
1870A GLN* 3.0 16.3 - - - +
1871A SER* 2.6 49.1 + - - +
1887A TYR* 3.9 3.7 - - - +
1888A VAL 2.9 10.4 + - - +
1889A ASN* 3.4 33.6 + - - +
1890A GLY* 5.2 1.3 - - - -
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Residues in contact with LEU1869 (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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1839A CYS* 3.8 11.2 - - - +
1840A THR* 3.6 31.6 - - - +
1841A PHE* 3.5 48.9 - - + +
1852A ASP 2.6 18.9 + - - +
1854A GLY* 4.3 7.6 - - - +
1867A GLY 3.3 2.4 + - - -
1868A ARG* 1.3 70.3 - - - +
1870A GLN* 1.3 65.5 + - - +
1872A MET* 3.4 22.1 - - - +
1887A TYR* 3.7 29.8 - - + +
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Residues in contact with GLN1870 (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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1797A ASP* 3.4 42.8 + - + +
1798A GLU* 4.3 16.5 + - - +
1841A PHE* 4.5 12.3 - - - -
1852A ASP* 3.3 35.0 + - - +
1868A ARG* 2.9 14.0 + - - +
1869A LEU* 1.3 84.1 + - + +
1871A SER* 1.3 57.2 + - - +
1872A MET* 3.1 11.6 + - - +
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Residues in contact with SER1871 (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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1868A ARG* 2.6 34.0 + - - +
1870A GLN* 1.3 77.2 - - - +
1872A MET* 1.3 62.7 + - - +
1873A LYS* 3.4 13.5 + - - +
1886A SER 3.7 5.7 - - - +
1887A TYR* 4.5 0.3 - - - -
1888A VAL* 2.8 52.1 + - - +
1889A ASN* 4.8 1.8 - - - -
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Residues in contact with MET1872 (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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1800A ARG* 4.4 25.3 + - + +
1804A CYS* 4.4 3.1 - - - -
1817A LEU* 5.2 0.9 - - + -
1838A VAL* 5.1 1.1 - - + -
1839A CYS* 3.6 37.0 - - - -
1868A ARG 4.1 0.8 + - - -
1869A LEU* 3.4 17.1 + - - +
1870A GLN 3.1 5.3 - - - +
1871A SER* 1.3 77.4 + - - +
1873A LYS* 1.3 66.5 + - - +
1874A LEU* 3.8 31.6 - - + -
1885A LEU* 3.5 33.9 - - + -
1886A SER 3.4 7.6 - - - -
1887A TYR* 3.7 18.6 - - + -
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Residues in contact with LYS1873 (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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1800A ARG* 5.4 2.0 - - - +
1871A SER 3.7 10.1 - - - +
1872A MET* 1.3 80.0 - - - +
1874A LEU* 1.3 62.3 + - - +
1875A ASP* 4.4 19.8 + - - +
1884A VAL 3.4 5.5 - - - +
1885A LEU* 3.4 3.6 - - - +
1886A SER* 3.1 42.1 + - - +
1888A VAL* 6.4 1.6 - - + -
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Residues in contact with LEU1874 (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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1800A ARG* 3.3 41.4 + - - +
1804A CYS 4.6 0.2 - - - -
1805A THR 3.4 27.1 - - - +
1806A LEU* 3.9 17.8 - - + +
1817A LEU* 3.8 21.5 - - + -
1872A MET* 3.8 16.6 - - + -
1873A LYS* 1.3 71.1 - - - +
1875A ASP* 1.3 70.2 + - - +
1883A VAL* 3.8 20.2 - - + -
1884A VAL 3.4 13.5 - - - +
1885A LEU* 3.7 21.5 - - + -
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Residues in contact with ASP1875 (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 6.7 - - - -
1873A LYS* 4.4 23.2 + - - +
1874A LEU* 1.3 83.4 - - - +
1876A TYR* 1.3 63.8 + - - +
1883A VAL* 3.6 6.6 - - - +
1884A VAL* 2.8 43.0 + - + +
1886A SER* 5.6 1.4 + - - -
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Residues in contact with TYR1876 (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* 4.0 17.2 - - + +
1808A ASP* 3.9 25.8 + - + +
1811A LEU* 3.7 32.8 - - + +
1813A TYR* 5.5 1.9 + - - -
1815A PHE* 4.0 19.9 - + - -
1875A ASP* 1.3 76.5 - - - +
1877A ARG* 1.3 75.4 + - - +
1878A HIS* 3.2 48.7 + + + -
1881A GLU* 3.8 28.8 + - + +
1882A ALA 3.6 11.0 - - - -
1883A VAL* 4.3 6.5 - - + -
1884A VAL* 5.2 0.7 - - - -
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Residues in contact with ARG1877 (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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1875A ASP 4.1 1.0 + - - -
1876A TYR* 1.3 77.3 - - - +
1878A HIS* 1.3 60.8 + - - +
1879A GLN* 3.4 15.3 - - + +
1880A ASP* 3.4 44.5 + - - +
1881A GLU* 3.2 8.0 - - - -
1882A ALA* 2.8 44.0 + - + +
1884A VAL* 4.3 12.9 - - + +
1954A ILE* 3.5 45.9 - - - +
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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