Contacts of the helix formed by residues 1868 - 1883 (chain A) in PDB entry 5PER
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 LYS1868 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1865A ASP* 5.3 5.0 + - - +
1866A ASP 3.3 0.6 - - - -
1867A SER* 1.3 88.7 + - - +
1869A ASP* 1.3 62.6 + - - +
1870A LEU 3.3 2.5 - - - -
1871A ALA* 3.5 11.3 + - + +
1872A LEU* 3.0 41.7 + - + +
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Residues in contact with ASP1869 (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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1864A ARG* 2.9 41.9 + - - -
1865A ASP 4.3 0.7 - - - +
1866A ASP* 3.2 27.5 + - - +
1867A SER 3.4 0.2 - - - -
1868A LYS* 1.3 80.2 + - - +
1870A LEU* 1.3 54.2 + - - +
1872A LEU* 3.4 2.4 + - - +
1873A CYS* 2.8 40.1 + - - -
1926A LEU* 3.2 32.9 + - + +
1969A PHE* 3.5 11.6 - - - -
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Residues in contact with LEU1870 (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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1866A ASP 4.8 0.4 + - - -
1867A SER 5.0 3.9 + - - +
1868A LYS 3.3 0.8 - - - -
1869A ASP* 1.3 77.9 - - - +
1871A ALA* 1.3 62.4 + - - +
1873A CYS* 3.5 4.7 + - - +
1874A SER* 3.0 24.7 + - - -
1918A LEU* 3.6 46.8 - - + +
1921A GLY* 6.3 0.9 - - - -
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Residues in contact with ALA1871 (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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1867A SER 5.7 0.2 + - - -
1868A LYS* 3.5 14.9 + - + +
1870A LEU* 1.3 79.0 - - - +
1872A LEU* 1.3 60.1 + - + +
1874A SER* 3.5 7.4 + - - -
1875A MET* 3.1 34.2 + - - +
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Residues in contact with LEU1872 (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 LYS* 3.0 39.9 + - + +
1869A ASP* 3.8 1.6 - - - +
1871A ALA* 1.3 76.6 - - + +
1873A CYS* 1.3 60.6 + - - +
1875A MET* 3.2 20.5 + - + +
1876A ILE* 3.0 35.5 + - - +
1968A THR* 3.9 19.7 - - + +
1969A PHE* 3.7 32.5 - - + -
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Residues in contact with CYS1873 (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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1869A ASP 2.8 20.0 + - - +
1870A LEU* 3.9 3.8 - - - +
1872A LEU* 1.3 71.6 - - - +
1874A SER* 1.4 57.4 + - - +
1876A ILE* 3.3 5.7 + - - +
1877A LEU* 2.9 30.1 + - - +
1918A LEU* 4.1 14.1 - - + -
1926A LEU* 3.3 35.0 - - - -
1929A PHE* 3.5 47.0 - - + -
1965A TRP* 4.0 5.6 - - - -
1969A PHE* 4.1 1.3 - - - -
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Residues in contact with SER1874 (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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1870A LEU* 3.0 19.6 + - - -
1871A ALA* 3.6 8.7 - - - -
1873A CYS* 1.4 74.6 - - - +
1875A MET* 1.3 56.3 + - - +
1877A LEU* 3.3 0.8 + - - -
1878A THR* 2.9 34.1 + - - -
1915A ARG* 2.9 24.9 + - - +
1918A LEU* 3.6 15.3 - - - +
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Residues in contact with MET1875 (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 ALA* 3.1 21.6 + - - +
1872A LEU* 3.2 25.3 + - + +
1874A SER* 1.3 73.3 - - - +
1876A ILE* 1.3 67.3 + - + +
1878A THR* 3.3 7.6 + - - -
1879A GLU* 3.1 41.8 + - - +
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Residues in contact with ILE1876 (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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1872A LEU 3.0 21.6 + - - +
1873A CYS* 3.6 5.8 - - - +
1875A MET* 1.3 74.2 - - + +
1877A LEU* 1.3 59.6 + - - +
1879A GLU* 3.1 14.1 + - - +
1880A MET* 2.9 33.2 + - + +
1929A PHE* 5.0 2.2 - - + -
1961A PHE* 3.9 29.8 - - + -
1964A LYS* 4.1 27.1 - - + +
1965A TRP* 4.0 13.9 - - + -
1968A THR* 3.8 24.9 - - + +
1969A PHE* 3.9 24.0 - - + -
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Residues in contact with LEU1877 (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 CYS 2.9 16.6 + - - +
1874A SER 3.6 5.6 - - - +
1876A ILE* 1.3 74.1 - - - +
1878A THR* 1.3 51.8 + - - +
1880A MET* 2.9 24.1 + - + +
1881A GLU* 2.7 46.3 + - + +
1911A PHE* 4.3 26.5 - - + +
1914A ILE* 3.8 22.4 - - + -
1915A ARG* 3.6 51.4 - - + +
1918A LEU* 4.2 9.9 - - + -
1929A PHE* 4.3 5.4 - - + -
1933A VAL* 5.4 0.2 - - + -
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Residues in contact with THR1878 (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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1874A SER* 2.9 17.9 + - - -
1875A MET* 3.6 8.2 - - - +
1876A ILE 3.2 0.2 - - - -
1877A LEU* 1.3 74.9 - - - +
1879A GLU* 1.3 62.6 + - + +
1881A GLU* 3.3 12.3 + - - +
1882A THR* 3.1 42.5 + - + +
1915A ARG* 2.9 20.1 + - - +
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Residues in contact with GLU1879 (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 MET* 3.1 33.8 + - - +
1876A ILE* 3.1 13.0 + - - +
1878A THR* 1.3 81.2 - - + +
1880A MET* 1.3 62.1 + - - +
1882A THR* 3.4 7.9 + - - -
1883A HIS* 3.3 21.3 + - - +
1960A TYR* 3.8 21.0 + - + +
1964A LYS* 2.9 40.4 + - - +
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Residues in contact with MET1880 (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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1876A ILE* 2.9 22.1 + - + +
1877A LEU* 3.4 21.8 - - + +
1879A GLU* 1.3 76.2 - - + +
1881A GLU* 1.3 62.1 + - - +
1883A HIS* 3.2 13.9 + - - +
1886A ALA* 3.2 15.8 - - - +
1911A PHE* 4.0 20.6 - - + -
1929A PHE* 5.2 1.1 - - + -
1933A VAL* 3.7 32.5 - - + -
1937A PHE* 4.5 3.4 - - - -
1957A MET* 3.5 23.0 - - + +
1960A TYR* 4.0 15.3 - - + -
1961A PHE* 3.7 37.2 - - + -
1964A LYS* 5.9 0.7 - - + -
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Residues in contact with GLU1881 (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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1877A LEU* 2.7 22.2 + - + +
1878A THR* 3.5 12.1 + - - +
1880A MET* 1.3 71.8 - - - +
1882A THR* 1.3 61.6 + - + +
1883A HIS 4.3 1.0 - - - +
1886A ALA* 3.9 4.0 - - - +
1890A LEU* 3.7 28.7 - - + +
1911A PHE* 4.3 22.4 - - + +
1912A SER* 5.4 0.9 - - - -
1915A ARG* 2.9 57.3 + - - +
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Residues in contact with THR1882 (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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1878A THR* 3.1 30.6 + - + +
1879A GLU* 3.4 10.7 + - - -
1881A GLU* 1.3 79.7 - - + +
1883A HIS* 1.3 65.9 + - - +
1884A GLU* 3.6 1.7 + - - -
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Residues in contact with HIS1883 (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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1879A GLU 3.3 10.5 + - - +
1880A MET 3.2 14.6 + - - +
1881A GLU 4.3 0.9 - - - +
1882A THR* 1.3 79.1 - - - +
1884A GLU* 1.3 85.7 + - + +
1885A ASP* 3.1 36.2 + - + -
1886A ALA* 3.1 18.7 + - - +
1887A TRP 4.8 0.2 + - - -
1956A ASN* 4.9 8.0 + - + +
1957A MET* 3.4 20.0 - - + -
1960A TYR* 3.6 49.1 - + + +
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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