Contacts of the helix formed by residues 1841 - 1864 (chain A) in PDB entry 3KBU
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 PHE1841 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1816A LYS* 4.1 35.2 - - + -
1819A GLU* 4.2 25.1 - - + -
1842A GLU* 1.3 79.8 + - + +
1843A ARG* 3.2 15.4 - - - +
1844A ASP* 3.0 18.5 + - - +
1845A VAL* 2.9 46.8 + - + +
1888A LEU* 4.9 9.4 - - + -
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Residues in contact with GLU1842 (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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1841A PHE* 1.3 94.5 + - + +
1843A ARG* 1.3 57.2 + - - +
1845A VAL* 3.5 6.0 + - - +
1846A HIS* 3.0 29.2 + - - +
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Residues in contact with ARG1843 (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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1841A PHE 4.2 12.3 - - - +
1842A GLU* 1.3 77.1 - - - +
1844A ASP* 1.3 94.5 + - - +
1846A HIS* 3.4 6.7 + - - +
1847A LEU* 3.1 44.5 + - + +
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Residues in contact with ASP1844 (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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1816A LYS* 3.6 35.3 + - + -
1841A PHE* 3.0 19.6 + - - +
1843A ARG* 1.3 104.4 + - - +
1845A VAL* 1.3 62.2 + - - +
1847A LEU* 3.5 11.7 + - - +
1848A LEU* 3.1 23.0 + - - +
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Residues in contact with VAL1845 (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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1816A LYS* 4.5 10.1 - - + -
1841A PHE* 2.9 41.2 + - + +
1842A GLU* 3.9 7.0 - - - +
1844A ASP* 1.3 74.7 - - - +
1846A HIS* 1.3 65.9 + - - +
1848A LEU* 3.3 6.0 + - - +
1849A GLY 3.0 18.2 + - - -
1885A TRP* 3.3 23.0 - - + -
1888A LEU* 4.2 24.2 - - + -
1889A LEU* 4.5 12.6 - - + -
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Residues in contact with HIS1846 (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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1842A GLU 3.0 17.0 + - - +
1843A ARG* 3.7 7.9 - - - +
1844A ASP 3.3 0.2 - - - -
1845A VAL* 1.3 78.9 - - - +
1847A LEU* 1.3 69.6 + - + +
1849A GLY* 3.0 4.8 + - - -
1850A VAL* 3.0 43.1 + - + +
1885A TRP* 5.3 0.9 - - - -
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Residues in contact with LEU1847 (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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1843A ARG* 3.1 41.1 + - + +
1844A ASP* 3.7 11.4 - - - +
1846A HIS* 1.3 82.9 - - + +
1848A LEU* 1.3 61.2 + - - +
1850A VAL* 3.4 13.0 + - + +
1851A GLN* 3.3 26.4 + - - +
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Residues in contact with LEU1848 (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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1809A ILE* 5.4 4.5 - - + +
1812A LEU* 3.7 37.7 - - + +
1813A ILE* 3.8 37.5 - - + -
1816A LYS* 4.1 23.1 - - + -
1844A ASP 3.1 12.9 + - - +
1845A VAL* 3.4 10.5 - - - +
1846A HIS 3.2 0.2 - - - -
1847A LEU* 1.3 77.2 - - - +
1849A GLY* 1.3 57.3 + - - +
1851A GLN* 3.1 17.2 + - + +
1852A VAL* 2.9 33.4 + - + +
1885A TRP* 4.3 4.9 - - + -
1888A LEU* 4.3 11.2 - - + -
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Residues in contact with GLY1849 (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 VAL 3.0 10.1 + - - -
1846A HIS 3.0 5.3 + - - -
1848A LEU* 1.3 72.8 - - - +
1850A VAL* 1.3 61.4 + - - +
1852A VAL* 3.5 3.1 + - - +
1853A GLN* 3.1 26.7 + - - +
1885A TRP* 3.2 36.2 + - - -
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Residues in contact with VAL1850 (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 HIS* 3.0 38.7 + - + +
1847A LEU* 3.7 12.6 - - + +
1848A LEU 3.2 0.2 - - - -
1849A GLY* 1.3 77.0 - - - +
1851A GLN* 1.3 56.3 + - + +
1853A GLN* 3.3 10.5 + - + +
1854A GLN* 2.9 43.7 + - + +
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Residues in contact with GLN1851 (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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1809A ILE* 4.0 22.1 - - + +
1812A LEU* 4.1 12.1 - - - +
1847A LEU* 3.3 16.5 + - - +
1848A LEU* 3.1 26.2 + - + +
1850A VAL* 1.3 73.9 - - + +
1852A VAL* 1.3 61.6 + - - +
1854A GLN* 3.4 14.7 + - - +
1855A PHE* 2.9 29.7 + - - +
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Residues in contact with VAL1852 (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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1809A ILE* 4.4 11.2 - - + -
1813A ILE* 4.3 17.7 - - + -
1848A LEU* 2.9 24.2 + - + +
1849A GLY* 3.7 7.2 - - - +
1851A GLN* 1.3 76.0 - - + +
1853A GLN* 1.3 66.9 + - - +
1855A PHE* 3.1 6.0 + - - +
1856A GLN* 2.9 45.8 + - + +
1881A VAL* 4.1 15.7 - - + -
1882A SER* 5.0 0.7 - - - +
1885A TRP* 4.0 37.0 - - + +
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Residues in contact with GLN1853 (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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1849A GLY 3.1 18.4 + - - +
1850A VAL* 3.6 11.7 - - + +
1852A VAL* 1.3 77.3 - - - +
1854A GLN* 1.3 66.1 + - + +
1856A GLN* 3.3 19.6 + - - +
1857A ASP* 3.2 39.0 + - - +
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Residues in contact with GLN1854 (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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1850A VAL* 2.9 30.0 + - + +
1851A GLN* 3.5 17.9 - - - +
1852A VAL 3.1 0.2 - - - -
1853A GLN* 1.3 79.3 - - + +
1855A PHE* 1.3 62.1 + - - +
1857A ASP* 3.3 13.5 + - - +
1858A VAL* 3.2 26.3 + - + +
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Residues in contact with PHE1855 (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 TYR* 3.3 51.3 - + - -
1805A THR* 3.7 21.3 - - + -
1806A GLY* 3.3 36.1 - - - -
1809A ILE* 3.9 13.2 - - + -
1851A GLN 2.9 17.6 + - - +
1852A VAL* 3.1 5.4 + - - +
1854A GLN* 1.3 73.6 - - - +
1856A GLN* 1.3 64.0 + - + +
1858A VAL* 3.4 7.6 + - + +
1859A ALA* 3.0 23.9 + - - +
1877A LYS* 4.5 6.1 - - + -
1878A GLU* 4.0 15.0 - - + -
1881A VAL* 4.0 28.3 - - + -
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Residues in contact with GLN1856 (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 VAL* 2.9 36.1 + - + +
1853A GLN* 3.4 23.3 - - - +
1855A PHE* 1.3 81.2 - - + +
1857A ASP* 1.3 63.3 + - - +
1859A ALA* 3.2 8.8 + - - +
1860A THR* 3.1 24.7 + - - -
1878A GLU* 4.1 17.1 + - + +
1881A VAL* 5.8 0.9 - - + -
1882A SER* 3.1 29.3 + - - +
1885A TRP* 5.1 4.2 - - - -
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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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1853A GLN* 3.3 36.1 + - - +
1854A GLN* 3.5 12.2 - - - +
1855A PHE 3.3 0.2 - - - -
1856A GLN* 1.3 75.5 - - - +
1858A VAL* 1.3 67.1 + - + +
1860A THR* 3.2 8.6 + - - +
1861A ARG* 3.0 22.9 + - - +
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Residues in contact with VAL1858 (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 ASP 5.9 0.4 - - - +
1802A TYR* 3.6 27.6 - - + -
1854A GLN* 3.2 14.9 + - + +
1855A PHE* 3.6 11.2 - - + +
1856A GLN 3.3 0.2 - - - -
1857A ASP* 1.3 77.1 - - + +
1859A ALA* 1.3 58.1 + - - +
1861A ARG* 3.1 35.3 + - - +
1862A LEU* 2.9 36.3 + - + +
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Residues in contact with ALA1859 (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 TYR* 3.1 33.0 - - - +
1855A PHE* 3.0 13.0 + - + +
1856A GLN 3.2 9.6 + - - +
1858A VAL* 1.3 77.5 - - - +
1860A THR* 1.3 61.4 + - - +
1862A LEU* 4.7 0.7 - - - -
1863A GLN* 3.1 32.8 + - - +
1874A ILE* 3.6 8.2 - - + +
1878A GLU* 3.8 22.0 - - + -
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Residues in contact with THR1860 (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 GLN 3.1 13.4 + - - -
1857A ASP* 3.2 10.8 + - - -
1859A ALA* 1.3 72.2 - - - +
1861A ARG* 1.3 68.8 + - - +
1863A GLN* 3.2 19.1 + - - +
1864A THR* 3.4 13.6 + - - +
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Residues in contact with ARG1861 (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 ASP* 3.2 29.4 + - - +
1857A ASP 3.0 13.0 + - - +
1858A VAL* 3.6 36.2 - - - +
1860A THR* 1.3 76.6 - - - +
1862A LEU* 1.3 76.1 + - + +
1864A THR* 3.0 30.8 - - - +
1865A ALA* 3.9 2.9 + - - +
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Residues in contact with LEU1862 (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 ASP* 4.3 18.6 - - + +
1799A LEU* 4.6 7.0 - - + +
1802A TYR* 3.6 48.2 - - + -
1858A VAL* 2.9 21.9 + - + +
1859A ALA 4.0 4.0 - - - +
1861A ARG* 1.3 97.5 - - - +
1863A GLN* 1.3 66.7 + - - +
1864A THR 3.0 2.2 - - - -
1865A ALA* 2.8 16.4 + - + -
1866A TYR* 3.2 28.8 + - + +
1874A ILE* 4.0 18.4 - - + -
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Residues in contact with GLN1863 (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 ALA* 3.1 32.0 + - - +
1860A THR* 3.2 8.7 + - - +
1862A LEU* 1.3 74.7 - - - +
1864A THR* 1.3 58.0 + - - +
1865A ALA 3.1 0.2 + - - -
1866A TYR 2.8 27.8 - - - +
1871A ALA* 4.0 23.5 + - + +
1874A ILE* 4.1 10.7 - - + +
1875A GLN* 3.0 54.3 + - - +
1878A GLU* 5.4 1.7 - - - +
941D ARG* 3.3 6.9 + - - -
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Residues in contact with THR1864 (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 THR* 3.4 9.2 + - - +
1861A ARG* 3.0 19.2 + - - +
1863A GLN* 1.3 79.6 - - - +
1865A ALA* 1.3 55.9 + - + +
921D ALA* 3.3 17.2 - - - +
922D ARG* 3.6 50.3 - - + +
941D ARG* 3.8 5.9 + - - +
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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
------------------------------------------------------------
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