Contacts of the helix formed by residues 1902 - 1915 (chain A) in PDB entry 5NP1
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 ASP1902 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1823A ILE* 3.5 28.6 - - + +
1826A LEU* 5.9 3.1 - - + -
1900A CYS 2.7 8.2 + - - +
1901A LEU* 1.3 72.6 - - - +
1903A LYS* 1.3 52.4 + - - +
1905A SER* 2.7 18.3 + - - -
1906A GLN* 2.2 41.5 + - + +
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Residues in contact with LYS1903 (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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1899A CYS* 3.2 44.9 - - + +
1900A CYS* 3.3 8.2 - - - +
1901A LEU 3.0 2.8 - - - +
1902A ASP* 1.3 75.4 - - - +
1904A LYS* 1.3 53.9 + - - +
1906A GLN* 2.9 11.0 + - - +
1907A ARG* 2.6 35.3 + - - +
1947A SER* 6.4 1.6 - - - -
1948A CYS* 5.8 7.9 - - + +
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Residues in contact with LYS1904 (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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1901A LEU* 4.4 8.1 - - - +
1903A LYS* 1.3 77.8 - - - +
1905A SER* 1.3 51.2 + - - +
1907A ARG* 2.7 11.4 + - - +
1908A THR* 2.2 40.2 + - - -
1948A CYS* 5.4 8.9 - - + +
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Residues in contact with SER1905 (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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1857A SER* 5.9 5.4 - - - -
1860A ASN* 5.4 16.0 - - - +
1901A LEU 4.4 4.8 + - - -
1902A ASP* 2.7 33.4 + - - +
1904A LYS* 1.3 74.6 - - - +
1906A GLN* 1.3 62.8 + - - +
1908A THR* 3.0 23.3 + - - -
1909A MET* 3.1 6.1 + - - +
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Residues in contact with GLN1906 (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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1889A LEU* 4.6 21.5 - - + +
1892A GLU* 6.3 1.8 - - + -
1899A CYS* 6.1 1.6 - - + -
1902A ASP* 2.2 26.4 + - + +
1903A LYS* 3.0 13.2 - - - +
1905A SER* 1.3 67.1 - - - +
1907A ARG* 1.3 64.2 + - - +
1909A MET* 2.9 24.6 + - - +
1910A LEU* 3.3 2.8 + - - +
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Residues in contact with ARG1907 (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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1903A LYS 2.6 15.6 + - - +
1904A LYS* 2.7 12.9 + - - +
1906A GLN* 1.3 73.2 - - - +
1908A THR* 1.3 48.5 - - - +
1910A LEU* 2.5 18.2 + - + +
1911A ALA* 2.2 38.4 + - + +
1944A VAL* 6.4 2.9 - - + -
1945A ALA* 6.0 4.3 - - + +
1948A CYS* 5.1 11.9 - - + -
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Residues in contact with THR1908 (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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1860A ASN 6.0 2.5 - - - -
1861A LEU* 6.0 5.2 - - - -
1864A THR* 4.1 5.3 - - - -
1904A LYS 2.2 27.3 + - - -
1905A SER* 3.0 21.3 - - - -
1907A ARG* 1.3 66.6 - - - +
1909A MET* 1.3 49.8 + - - +
1911A ALA* 2.8 11.8 + - - +
1912A VAL* 2.5 37.2 + - - +
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Residues in contact with MET1909 (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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1864A THR* 3.7 24.9 - - - +
1867A GLN* 5.4 6.7 - - + -
1905A SER 3.1 4.0 + - - +
1906A GLN* 2.9 14.1 + - - +
1908A THR* 1.3 76.5 - - - +
1910A LEU* 1.3 51.3 + - - +
1912A VAL* 2.8 3.8 + - - +
1913A VAL* 2.3 38.9 + - - +
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Residues in contact with LEU1910 (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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1906A GLN 3.3 1.2 + - - +
1907A ARG* 2.5 25.9 + - + +
1909A MET* 1.3 75.0 - - - +
1911A ALA* 1.3 49.4 + - - -
1913A VAL* 3.0 10.6 - - + +
1914A ASP* 2.2 38.8 + - - +
1941A VAL* 5.5 11.7 - - + -
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Residues in contact with ALA1911 (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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1907A ARG* 2.2 26.4 + - + +
1908A THR* 2.8 19.9 + - - +
1910A LEU* 1.3 67.1 - - - +
1912A VAL* 1.3 47.8 - - - +
1914A ASP* 2.5 12.0 + - - +
1915A TYR* 2.2 42.4 + - + +
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Residues in contact with VAL1912 (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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1864A THR* 3.6 33.2 - - - -
1865A HIS* 4.9 1.3 - - - +
1908A THR 2.5 12.4 + - - +
1911A ALA* 1.3 72.6 - - - +
1913A VAL* 1.3 57.3 - - - +
1915A TYR* 2.9 5.6 - - + -
1916A MET* 2.1 50.8 + - + +
1917A ARG 3.0 6.1 + - - -
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Residues in contact with VAL1913 (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 2.3 29.1 + - - +
1910A LEU* 3.0 15.5 - - - +
1912A VAL* 1.3 65.1 - - - +
1914A ASP* 1.3 67.5 + - - +
1915A TYR 2.9 0.3 + - - -
1917A ARG* 2.9 30.6 - - + +
1930A ASP* 4.2 8.3 - - - +
1933A TRP 5.4 1.8 - - - +
1934A LEU* 4.8 23.8 - - + +
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Residues in contact with ASP1914 (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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1910A LEU 2.2 28.1 + - - +
1911A ALA* 2.5 13.1 + - - +
1913A VAL* 1.3 68.5 - - - +
1915A TYR* 1.3 57.8 + - + +
1918A ARG* 5.8 0.7 - - - -
1930A ASP* 4.7 14.9 - - - +
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Residues in contact with TYR1915 (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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1911A ALA* 2.2 30.9 + - + +
1912A VAL* 2.9 7.4 - - - -
1913A VAL 2.9 0.6 - - - -
1914A ASP* 1.3 73.6 - - + +
1916A MET* 1.3 57.0 + - + +
1917A ARG* 2.8 13.5 + - - -
1918A ARG* 3.4 16.5 + - - +
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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