Contacts of the helix formed by residues 1910 - 1920 (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 ASP1910 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1889A PHE* 3.3 14.6 - - - +
1890A LEU 3.3 4.9 - - - +
1891A LEU 3.5 12.8 - - - +
1892A PRO* 3.3 26.2 - - + +
1908A PRO 5.7 0.2 - - - -
1909A MET* 1.3 79.6 - - - +
1911A PHE* 1.3 62.4 + - - +
1912A SER* 2.6 36.3 + - - -
1913A THR* 2.6 26.5 + - - -
1914A ILE* 3.0 30.7 + - - +
1936A VAL* 3.9 6.7 - - - -
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Residues in contact with PHE1911 (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* 4.3 13.1 - - + +
1880A MET* 3.8 33.4 - - + -
1881A GLU* 4.3 24.7 - - + -
1886A ALA* 3.9 10.3 - - + -
1889A PHE* 2.9 42.1 + + + +
1890A LEU* 4.1 20.6 - - + +
1910A ASP* 1.3 73.3 - - - +
1912A SER* 1.3 53.1 + - - +
1914A ILE* 3.2 16.8 + - + +
1915A ARG* 2.8 35.3 + - - +
1933A VAL* 5.1 1.3 - - + -
1936A VAL* 4.2 10.3 - - + -
1937A PHE* 4.0 29.2 - + - -
1957A MET* 4.2 11.2 - - + -
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Residues in contact with SER1912 (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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1881A GLU* 5.4 0.9 - - - -
1890A LEU 3.2 18.1 + - - -
1891A LEU* 4.1 10.6 - - - +
1892A PRO* 3.7 12.8 - - - +
1910A ASP* 2.6 21.1 + - - -
1911A PHE* 1.3 76.4 - - - +
1913A THR* 1.3 57.7 + - - +
1915A ARG* 3.4 9.3 + - - +
1916A GLU* 3.0 27.2 + - - +
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Residues in contact with THR1913 (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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1892A PRO* 4.3 7.4 - - - +
1908A PRO 5.8 0.2 - - - +
1909A MET* 3.6 26.5 - - + -
1910A ASP* 2.6 30.8 + - - -
1911A PHE 3.3 0.2 - - - -
1912A SER* 1.3 75.8 + - - +
1914A ILE* 1.3 65.3 + - - +
1916A GLU* 3.3 7.1 + - + +
1917A LYS* 2.9 33.4 + - + +
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Residues in contact with ILE1914 (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* 3.8 11.2 - - + -
1909A MET* 3.7 12.1 - - + -
1910A ASP 3.0 22.1 + - - +
1911A PHE* 3.6 14.4 - - + +
1913A THR* 1.3 78.1 - - - +
1915A ARG* 1.3 56.3 + - - +
1917A LYS 3.3 0.5 + - - -
1918A LEU* 2.9 27.5 + - - +
1923A TYR* 3.5 24.5 - - - +
1929A PHE* 3.5 33.2 - - + -
1932A ASP* 3.9 12.3 - - + +
1933A VAL* 3.9 17.9 - - + +
1936A VAL* 3.8 24.0 - - + -
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Residues in contact with ARG1915 (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 37.8 + - - +
1877A LEU* 3.6 18.2 - - + +
1878A THR* 2.9 32.3 + - - +
1881A GLU* 2.9 37.1 + - - +
1911A PHE 2.8 17.4 + - - +
1912A SER* 3.6 8.5 - - - +
1914A ILE* 1.3 77.1 - - - +
1916A GLU* 1.3 58.3 + - - +
1918A LEU* 3.3 7.9 + - - +
1919A SER* 3.0 46.1 + - - +
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Residues in contact with GLU1916 (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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1912A SER 3.0 16.4 + - - +
1913A THR* 3.6 7.2 - - + +
1914A ILE 3.3 0.2 - - - -
1915A ARG* 1.3 79.2 - - - +
1917A LYS* 1.3 55.1 + - + +
1919A SER* 3.5 7.8 + - - -
1920A SER* 2.6 46.0 + - - +
1922A GLN* 5.2 4.7 - - - +
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Residues in contact with LYS1917 (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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1909A MET* 4.4 6.7 - - + +
1913A THR* 2.9 34.1 + - + +
1916A GLU* 1.3 78.1 - - + +
1918A LEU* 1.3 60.8 + - - +
1920A SER* 3.4 5.8 + - - -
1921A GLY 3.4 2.6 + - - -
1922A GLN* 2.9 63.7 + - + +
1923A TYR* 3.6 33.3 + - + +
1932A ASP* 2.8 26.5 + - - +
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Residues in contact with LEU1918 (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* 3.6 38.9 - - + +
1873A CYS* 4.1 13.9 - - + +
1874A SER* 3.6 38.6 - - - +
1877A LEU* 4.2 10.5 - - + -
1914A ILE 2.9 17.8 + - - +
1915A ARG* 3.6 16.2 - - - +
1916A GLU 3.2 0.2 - - - -
1917A LYS* 1.3 77.7 - - - +
1919A SER* 1.3 62.5 + - - +
1920A SER 3.2 1.2 + - - -
1921A GLY* 3.4 8.5 + - - -
1923A TYR* 3.8 25.5 - - + +
1929A PHE* 4.1 13.7 - - + -
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Residues in contact with SER1919 (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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1915A ARG* 3.0 32.7 + - - +
1916A GLU* 3.9 11.0 - - - -
1918A LEU* 1.3 75.6 - - - +
1920A SER* 1.3 56.7 + - - +
1921A GLY 3.6 0.7 - - - -
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Residues in contact with SER1920 (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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1916A GLU* 2.6 32.9 + - - -
1917A LYS 3.4 1.9 + - - -
1918A LEU 3.2 0.4 - - - -
1919A SER* 1.3 75.6 - - - +
1921A GLY* 1.3 63.1 + - - +
1922A GLN* 2.9 30.6 + - - +
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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