Contacts of the helix formed by residues 1844 - 1873 (chain A) in PDB entry 5KHU
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 PHE1844 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1843A GLU* 3.8 29.4 - - - +
1845A LEU* 3.8 28.9 - - - +
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Residues in contact with LEU1845 (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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1844A PHE* 3.8 29.4 - - - +
1846A PRO* 3.8 27.6 - - - -
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Residues in contact with PRO1846 (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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1845A LEU* 3.8 24.7 - - - -
1847A VAL* 3.8 29.4 - - - -
1849A LYS* 4.4 18.8 - - - -
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Residues in contact with VAL1847 (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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1846A PRO* 3.8 24.7 - - - -
1848A VAL* 3.8 29.4 - - - +
1850A CYS* 4.4 14.8 - - - +
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Residues in contact with VAL1848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1847A VAL* 3.8 29.8 - - - +
1849A LYS* 3.8 25.4 - - - +
1851A THR* 4.4 17.0 - - - +
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Residues in contact with LYS1849 (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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1846A PRO* 4.4 16.2 - - - -
1848A VAL* 3.8 23.6 - - - +
1850A CYS* 3.8 29.8 - - - +
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Residues in contact with CYS1850 (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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1847A VAL* 4.4 16.8 - - - +
1849A LYS* 3.8 28.9 - - - +
1851A THR* 3.8 27.1 - - - +
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Residues in contact with THR1851 (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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1848A VAL* 4.4 13.9 - - - +
1850A CYS* 3.8 25.1 - - - +
1852A ILE* 3.8 29.8 - - - +
1854A ASN* 4.5 15.9 - - - +
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Residues in contact with ILE1852 (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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1851A THR* 3.8 28.3 - - - +
1853A ASP* 3.8 28.7 - - - +
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Residues in contact with ASP1853 (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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1852A ILE* 3.8 28.9 - - - +
1854A ASN* 3.8 24.7 - - - +
1856A LEU* 4.2 19.5 - - - +
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Residues in contact with ASN1854 (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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1851A THR* 4.5 17.7 - - - +
1853A ASP* 3.8 25.4 - - - +
1855A THR* 3.8 29.8 - - - +
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Residues in contact with THR1855 (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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1854A ASN* 3.8 29.6 - - - +
1856A LEU* 3.8 25.8 - - - +
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Residues in contact with LEU1856 (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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1853A ASP* 4.2 19.1 - - - +
1855A THR* 3.8 28.5 - - - +
1857A ASP* 3.8 29.2 - - - +
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Residues in contact with ASP1857 (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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1856A LEU* 3.8 29.2 - - - +
1858A GLN* 3.8 27.8 - - - +
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Residues in contact with GLN1858 (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 ASP* 3.8 26.7 - - - +
1859A TRP* 3.8 28.9 - - - +
1861A GLN* 4.5 15.3 - - - +
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Residues in contact with TRP1859 (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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1858A GLN* 3.8 26.5 - - - +
1860A LEU* 3.8 30.5 - - - +
1862A VAL* 4.4 16.8 - - - +
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Residues in contact with LEU1860 (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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1859A TRP* 3.8 27.8 - - - +
1861A GLN* 3.8 23.8 - - - +
1864A GLY* 3.7 30.1 - - - +
1865A ASP* 4.2 14.6 - - - +
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Residues in contact with GLN1861 (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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1858A GLN* 4.5 17.7 - - - +
1860A LEU* 3.8 29.2 - - - +
1862A VAL* 3.8 24.7 - - - +
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Residues in contact with VAL1862 (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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1859A TRP* 4.4 17.7 - - - +
1861A GLN* 3.8 29.4 - - - +
1863A GLY* 3.8 23.8 - - - +
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Residues in contact with GLY1863 (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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1862A VAL* 3.8 26.7 - - - +
1864A GLY* 3.7 30.3 - - - +
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Residues in contact with GLY1864 (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 LEU* 3.7 30.5 - - - +
1863A GLY* 3.7 25.4 - - - +
1865A ASP* 3.8 15.9 - - - +
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Residues in contact with ASP1865 (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 LEU* 4.2 14.4 - - - +
1864A GLY* 3.8 29.2 - - - +
1866A MET* 3.8 26.0 - - - +
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Residues in contact with MET1866 (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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1865A ASP* 3.8 26.0 - - - +
1867A CYS* 3.8 28.7 - - - +
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Residues in contact with CYS1867 (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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1866A MET* 3.8 25.8 - - - +
1868A VAL* 3.8 29.4 - - - +
1870A ALA* 4.6 16.2 - - - +
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Residues in contact with VAL1868 (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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1867A CYS* 3.8 25.6 - - - +
1869A HIS* 3.8 29.4 - - - +
1871A TYR* 4.6 15.7 - - - +
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Residues in contact with HIS1869 (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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1868A VAL* 3.8 29.8 - - - +
1870A ALA* 3.8 24.5 - - - +
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Residues in contact with ALA1870 (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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1867A CYS* 4.6 16.4 - - - +
1869A HIS* 3.8 29.2 - - - +
1871A TYR* 3.8 24.7 - - - +
1873A SER* 4.4 17.9 - - - +
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Residues in contact with TYR1871 (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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1868A VAL* 4.6 15.9 - - - +
1870A ALA* 3.8 25.4 - - - +
1872A LEU* 3.8 28.7 - - - +
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Residues in contact with LEU1872 (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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1871A TYR* 3.8 29.2 - - - +
1873A SER* 3.8 24.7 - - - +
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Residues in contact with SER1873 (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 ALA* 4.4 19.7 - - - +
1872A LEU* 3.8 29.6 - - - +
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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