Contacts of the helix formed by residues 1916 - 1923 (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 TRP1916 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1874A SER* 4.3 21.0 - - - -
1877A LEU* 4.3 23.8 - - + -
1878A LEU* 4.8 11.0 - - + -
1881A THR* 3.8 28.7 - - + -
1913A TYR* 3.6 49.7 - + + -
1914A GLY 3.3 2.8 - - - -
1915A HIS* 1.3 110.4 + + - +
1917A PRO* 1.3 70.9 - - + +
1918A ASP* 4.1 12.3 - - + +
1919A VAL* 3.3 23.9 + - + +
1920A ASN* 3.2 18.5 + - - +
1952A LEU* 4.0 6.6 - - - +
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Residues in contact with PRO1917 (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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1915A HIS 4.2 4.3 - - - +
1916A TRP* 1.3 84.5 - - + +
1918A ASP* 1.3 63.6 + - - +
1920A ASN* 3.2 12.4 + - + +
1921A GLU* 2.9 30.4 + - - +
1952A LEU* 5.8 0.2 - - + -
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Residues in contact with ASP1918 (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 LEU* 4.3 24.8 - - - +
1881A THR* 4.5 23.6 + - + +
1882A VAL* 6.2 3.6 - - + -
1885A VAL* 6.5 0.7 - - - -
1886A GLN* 5.4 0.2 + - - -
1916A TRP* 3.2 10.5 - - + +
1917A PRO* 1.3 81.0 - - - +
1919A VAL* 1.3 59.0 + - + +
1921A GLU* 3.2 22.1 - - - +
1922A ALA* 2.9 29.7 + - - +
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Residues in contact with VAL1919 (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 THR* 5.8 1.3 - - + -
1885A VAL* 5.5 13.2 - - + -
1906A VAL 6.0 0.4 - - - +
1909A LEU 6.3 0.4 - - - -
1910A TRP* 3.6 37.2 - - + +
1913A TYR 3.7 20.9 - - - +
1914A GLY* 4.4 6.1 - - - +
1916A TRP* 3.3 26.2 + - + +
1917A PRO 3.3 0.2 - - - -
1918A ASP* 1.3 75.9 - - + +
1920A ASN* 1.3 63.2 + - - +
1922A ALA* 3.7 6.7 - - + +
1923A LEU* 3.1 31.1 + - + +
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Residues in contact with ASN1920 (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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1916A TRP 3.2 13.0 + - - +
1917A PRO* 3.2 15.6 + - + +
1919A VAL* 1.3 77.6 - - - +
1921A GLU* 1.3 59.6 + - - +
1923A LEU* 3.5 23.7 - - - +
1924A VAL* 3.4 18.5 - - - +
1952A LEU* 4.4 27.2 - - + +
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Residues in contact with GLU1921 (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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1882A VAL* 5.9 1.9 - - - +
1886A GLN* 4.2 15.5 + - - -
1917A PRO 2.9 19.8 + - - +
1918A ASP* 3.2 28.6 - - - +
1920A ASN* 1.3 76.6 - - - +
1922A ALA* 1.3 62.8 + - - +
1923A LEU 3.4 0.2 - - - -
1924A VAL* 3.8 18.2 + - - +
1925A GLU* 4.5 6.6 + - - +
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Residues in contact with ALA1922 (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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1885A VAL* 3.7 29.2 - - + -
1886A GLN* 4.4 13.9 - - - +
1889A PHE* 4.0 9.2 - - + -
1918A ASP 2.9 19.0 + - - +
1919A VAL* 3.3 8.9 + - + +
1921A GLU* 1.3 79.5 - - - +
1923A LEU* 1.3 62.2 + - - +
1924A VAL 3.2 1.6 + - - -
1925A GLU* 3.5 26.6 - - - +
1926A GLY 3.9 2.9 + - - -
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Residues in contact with LEU1923 (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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1889A PHE* 5.1 6.1 - - + -
1910A TRP* 4.9 8.5 - - + +
1919A VAL* 3.1 30.8 + - + +
1920A ASN* 3.5 27.1 - - - +
1922A ALA* 1.3 74.8 - - - +
1924A VAL* 1.3 67.0 + - + +
1925A GLU 3.5 0.4 - - - -
1926A GLY 4.0 2.2 - - - +
1927A VAL* 3.3 38.6 + - + +
1928A LYS* 4.5 14.6 - - - +
1952A LEU* 5.9 5.8 - - + -
1956A LEU* 4.2 35.7 - - + -
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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