Contacts of the helix formed by residues 1892 - 1898 (chain A) in PDB entry 4JKE
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 PRO1892 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1781A ASP* 4.9 0.9 - - - +
1890A GLN* 3.6 9.4 - - + +
1891A LEU* 1.3 84.4 - - + +
1893A PHE* 1.3 66.2 + - - +
1894A GLN* 3.0 13.2 - - + +
1895A ALA* 3.0 17.0 + - - +
1940A LEU* 3.7 31.5 - - + +
1941A ARG* 3.7 23.3 - - + +
1944A HIS* 3.8 30.1 - - + +
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Residues in contact with PHE1893 (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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1779A PHE* 4.7 6.5 - - + -
1781A ASP* 3.3 34.6 + - + +
1784A ASN* 4.0 2.7 - - - -
1808A PHE* 3.6 43.8 - + + -
1810A PHE* 3.6 37.5 - + + -
1817A LEU* 4.8 0.4 - - + -
1864A THR* 5.1 1.3 - - + -
1891A LEU* 3.1 44.5 + - + -
1892A PRO* 1.3 68.6 - - - +
1894A GLN* 1.3 55.3 + - - +
1895A ALA 3.0 0.2 - - - -
1896A CYS* 2.8 42.2 + - - +
1919A LEU* 4.1 21.5 - - + -
1936A LEU* 5.0 0.7 - - + -
1940A LEU* 4.0 18.4 - - + -
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Residues in contact with GLN1894 (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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1781A ASP* 4.2 0.8 + - - -
1783A THR* 4.3 17.6 - - + +
1784A ASN* 3.1 34.5 + - - +
1892A PRO* 3.0 12.1 - - + +
1893A PHE* 1.3 76.8 - - - +
1895A ALA* 1.3 63.2 + - - +
1897A LEU* 3.0 27.9 + - + +
1898A LYS* 4.2 3.3 + - - +
1944A HIS* 3.4 37.0 + - - +
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Residues in contact with ALA1895 (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 3.0 11.8 + - - +
1893A PHE 3.0 0.8 - - - -
1894A GLN* 1.3 82.0 - - - +
1896A CYS* 1.3 56.8 + - - +
1898A LYS* 2.9 36.6 + - - +
1899A VAL* 3.8 7.9 + - - +
1940A LEU* 3.4 34.8 - - + +
1943A LEU* 3.8 17.7 - - + +
1944A HIS* 3.9 10.1 - - + +
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Residues in contact with CYS1896 (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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1808A PHE* 3.6 23.8 - - + -
1817A LEU* 5.7 0.2 - - - -
1893A PHE* 2.8 33.2 + - - +
1895A ALA* 1.3 71.2 - - - +
1897A LEU* 1.3 54.9 + - - -
1898A LYS 3.1 0.2 - - - -
1899A VAL* 2.9 34.3 + - - +
1902A PHE* 3.4 36.6 - - + +
1919A LEU* 5.2 7.0 - - - -
1940A LEU* 3.8 22.7 - - - -
1968A TRP* 5.3 3.8 - - - -
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Residues in contact with LEU1897 (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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1784A ASN* 3.5 31.2 - - + +
1787A ARG* 3.7 43.7 - - - +
1806A ALA* 5.6 0.7 - - + +
1808A PHE* 4.6 9.2 - - + -
1893A PHE 4.9 0.7 - - - +
1894A GLN* 3.0 22.1 + - + +
1896A CYS* 1.3 76.8 - - - +
1898A LYS* 1.3 58.1 + - + +
1899A VAL 3.3 0.8 - - - -
1902A PHE* 5.1 0.2 - - - -
1903A GLY* 3.6 23.8 - - - +
1906A ILE* 3.7 29.8 - - + -
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Residues in contact with LYS1898 (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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1894A GLN 5.0 2.7 - - - +
1895A ALA* 2.9 23.4 + - - +
1897A LEU* 1.3 76.1 - - + +
1899A VAL* 1.3 62.4 + - + +
1900A GLU* 3.8 2.5 + - - -
1943A LEU* 2.9 25.3 + - + +
1944A HIS* 3.4 24.0 + - - +
1947A ASN* 3.5 40.4 - - - +
1951A LYS* 3.2 19.4 + - - +
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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