Contacts of the helix formed by residues 1904 - 1914 (chain A) in PDB entry 5ZCS
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 LEU1904 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1900A LEU* 4.3 14.6 - - + +
1901A GLN* 3.8 3.3 + - - +
1903A THR* 1.3 80.7 - - - +
1905A ARG* 1.3 76.1 + - - +
1906A VAL 3.3 0.4 - - - -
1907A LEU* 2.9 38.5 + - + +
1908A THR* 3.1 18.3 + - + +
1911A PHE* 5.9 4.5 - - + -
1938A VAL* 4.7 17.3 - - + -
1941A GLN* 5.5 8.7 - - + -
1942A LEU* 5.0 5.2 - - + -
2416A ALA* 3.4 25.8 - - + +
2420A ALA* 5.4 9.6 - - + -
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Residues in contact with ARG1905 (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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1798A PHE* 3.4 44.1 - - + -
1888A PHE* 3.6 30.5 - - + -
1901A GLN* 3.3 44.5 + - - +
1902A ASP 4.7 1.3 - - - +
1903A THR 3.4 0.8 - - - -
1904A LEU* 1.3 88.2 - - - +
1906A VAL* 1.3 60.3 + - - +
1907A LEU 3.2 0.9 - - - -
1908A THR* 3.5 35.5 + - - +
1909A LEU* 4.3 16.8 + - - +
2412A ASP 5.1 0.2 + - - -
2415A MET 3.6 9.3 + - - -
2416A ALA* 3.5 35.2 + - - +
2419A GLU* 4.3 19.8 - - - +
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Residues in contact with VAL1906 (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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1885A VAL* 4.6 5.6 - - + +
1888A PHE* 3.7 31.6 - - + -
1889A PHE* 3.7 39.7 - - + -
1892A ILE* 6.0 2.0 - - + -
1902A ASP 4.7 7.1 + - - +
1903A THR* 3.3 19.9 + - - +
1905A ARG* 1.3 76.3 - - - +
1907A LEU* 1.3 67.9 + - + +
1909A LEU* 4.8 2.6 - - - +
1910A TRP* 3.5 17.7 + - - +
1919A VAL* 6.0 0.3 - - - +
1935A TRP* 5.6 9.0 - - + -
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Residues in contact with LEU1907 (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 THR* 3.7 24.5 - - + +
1904A LEU* 2.9 22.6 + - + +
1906A VAL* 1.3 87.1 - - + +
1908A THR* 1.3 54.4 + - - +
1909A LEU 3.3 2.2 - - - -
1910A TRP* 2.9 30.1 + - + +
1911A PHE* 2.4 55.0 + - + -
1942A LEU* 3.8 36.1 - - + -
1956A LEU* 6.3 1.8 - - + -
1960A LEU* 6.2 2.2 - - + -
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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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1798A PHE* 3.5 28.2 - - - -
1904A LEU* 3.4 16.0 + - + +
1905A ARG* 3.5 26.5 + - - +
1907A LEU* 1.3 74.3 - - - +
1909A LEU* 1.3 66.3 + - - +
1911A PHE* 3.4 21.7 + - + +
1912A ASP* 3.1 30.6 + - - +
2419A GLU* 5.3 11.0 - - + +
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Residues in contact with LEU1909 (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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1798A PHE* 4.4 23.6 - - + -
1801A VAL* 3.8 36.8 - - + -
1884A ALA* 4.9 13.9 - - + -
1885A VAL* 4.9 18.6 - - + -
1888A PHE* 5.2 7.0 - - + -
1905A ARG 4.3 16.4 + - - +
1906A VAL* 5.3 2.5 - - - +
1908A THR* 1.3 82.1 + - - +
1910A TRP* 1.3 55.8 + - - +
1912A ASP* 2.9 9.9 + - + +
1913A TYR* 2.7 42.8 + - + +
1919A VAL* 6.3 0.7 - - - -
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Residues in contact with TRP1910 (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 VAL 3.5 17.8 + - - +
1907A LEU* 2.9 34.1 + - + +
1909A LEU* 1.3 78.1 - - - +
1911A PHE* 1.3 87.9 + + - +
1913A TYR 4.7 0.2 - - - -
1914A GLY* 3.4 40.9 + - - -
1919A VAL* 3.6 24.8 - - + +
1923A LEU* 4.9 9.5 - - + +
1942A LEU* 4.6 8.5 - - + -
1945A ARG* 6.5 0.2 - - + -
1952A LEU* 4.7 3.2 + - - +
1953A VAL* 3.2 51.0 - - + +
1956A LEU* 3.6 33.6 - - + +
1957A ILE* 4.7 13.0 - - + -
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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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1904A LEU* 5.9 4.0 - - + -
1907A LEU* 2.4 43.7 + - + +
1908A THR* 3.5 25.6 - - + +
1909A LEU 3.2 0.4 - - - -
1910A TRP* 1.3 103.0 - + - +
1912A ASP* 1.3 65.3 + - - +
1941A GLN 5.6 3.1 - - - -
1942A LEU* 4.5 16.2 - - + -
1945A ARG* 3.2 57.3 + - + +
1950A ARG* 5.2 7.1 + - - -
1953A VAL* 5.3 8.1 - - + +
2419A GLU 6.1 0.9 - - - -
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Residues in contact with ASP1912 (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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1802A LEU* 6.1 1.2 - - - +
1805A LYS* 4.5 17.9 + - - +
1908A THR* 3.1 16.3 + - - +
1909A LEU* 2.9 14.1 + - + +
1911A PHE* 1.3 86.7 - - - +
1913A TYR* 1.3 87.4 + - + +
1914A GLY 3.7 1.5 + - - -
1915A HIS* 4.8 1.4 + - - -
1950A ARG* 4.6 15.5 + - - -
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Residues in contact with TYR1913 (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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1801A VAL* 5.6 6.7 - - + -
1805A LYS* 6.5 0.9 - - + -
1870A THR* 5.1 9.0 - - + +
1873A LEU* 4.6 14.4 - - + +
1874A SER* 3.9 20.9 + - - -
1877A LEU* 4.6 18.2 - - + -
1909A LEU* 2.7 21.4 + - + +
1910A TRP* 4.7 0.2 - - - -
1912A ASP* 1.3 92.4 - - + +
1914A GLY* 1.3 56.3 + - - +
1915A HIS* 3.2 27.6 + + - -
1916A TRP* 3.6 53.3 - + + -
1919A VAL* 3.7 9.7 - - - +
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Residues in contact with GLY1914 (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 TRP* 3.4 44.9 + - - -
1912A ASP 3.7 1.2 - - - -
1913A TYR* 1.3 74.5 - - - +
1915A HIS* 1.3 56.1 + - - +
1916A TRP 3.3 6.8 + - - +
1919A VAL* 4.4 6.7 - - - +
1950A ARG* 5.8 0.6 - - - +
1952A LEU* 3.4 18.4 - - - +
1953A VAL* 3.6 17.4 - - - +
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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