Contacts of the helix formed by residues 1854 - 1875 (chain A) in PDB entry 4W8F
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 ASP1854 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1823A ASP* 5.0 7.6 - - - +
1826A PHE* 5.6 3.5 - - - -
1853A LEU* 1.3 76.4 - - - +
1855A GLU* 1.3 60.2 + - - +
1856A LYS* 3.3 6.7 - - + +
1857A VAL* 3.7 28.0 - - + +
1858A LEU* 2.6 35.9 + - - +
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Residues in contact with GLU1855 (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 LEU 3.8 0.8 + - - -
1854A ASP* 1.3 71.8 - - - +
1856A LYS* 1.3 58.8 + - + +
1858A LEU* 4.0 7.0 - - - +
1859A SER* 2.9 32.4 + - - -
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Residues in contact with LYS1856 (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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1828A TYR* 6.0 3.6 - - - +
1854A ASP* 4.8 5.4 - - + -
1855A GLU* 1.3 77.7 - - + +
1857A VAL* 1.3 83.6 + - + +
1859A SER* 3.6 5.9 - - - -
1860A ALA* 3.1 24.9 + - - +
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Residues in contact with VAL1857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1826A PHE* 3.7 32.5 - - + -
1828A TYR* 4.4 20.6 - - + -
1853A LEU* 4.3 6.3 - - + -
1854A ASP* 3.1 32.6 + - + +
1856A LYS* 1.3 95.6 - - + +
1858A LEU* 1.3 58.1 + - - +
1860A ALA* 3.3 4.7 + - - +
1861A VAL* 2.9 44.3 + - + +
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Residues in contact with LEU1858 (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 PHE* 3.1 55.9 - - + +
1851A ASN* 5.1 6.7 - - - +
1853A LEU* 3.7 25.7 - - + +
1854A ASP 2.6 21.7 + - - +
1855A GLU* 4.1 6.3 - - - +
1857A VAL* 1.3 71.5 - - - +
1859A SER* 1.3 61.3 + - - +
1861A VAL* 4.6 0.9 - - - -
1862A SER* 2.9 34.0 + - - -
1909A PRO* 3.8 23.3 - - + -
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Residues in contact with SER1859 (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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1855A GLU 2.9 20.9 + - - -
1856A LYS* 3.6 7.4 - - - -
1857A VAL 3.2 0.2 - - - -
1858A LEU* 1.3 79.2 - - - +
1860A ALA* 1.3 58.0 + - - +
1862A SER* 3.5 3.9 - - - -
1863A ALA* 3.0 28.8 + - - +
1911A ASN* 5.1 3.9 + - - +
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Residues in contact with ALA1860 (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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1828A TYR* 3.5 29.2 - - + +
1856A LYS 3.1 14.1 + - - +
1857A VAL 3.8 2.0 - - - +
1859A SER* 1.3 79.1 - - - +
1861A VAL* 1.3 65.0 + - - +
1863A ALA* 3.4 6.7 + - - +
1864A ASN* 3.1 26.9 + - - -
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Residues in contact with VAL1861 (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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1828A TYR* 3.8 17.5 - - + -
1831A LEU* 3.5 27.4 - - + -
1835A LEU* 4.7 2.9 - - + -
1847A PHE* 3.7 30.3 - - + -
1850A PHE* 4.0 8.7 - - + -
1853A LEU* 4.9 5.6 - - + -
1857A VAL* 2.9 29.5 + - + +
1858A LEU* 4.1 4.0 - - - +
1860A ALA* 1.3 74.3 - - - +
1862A SER* 1.3 59.1 + - - +
1864A ASN* 3.2 9.2 + - - +
1865A ILE* 2.9 39.2 + - + +
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Residues in contact with SER1862 (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 PHE* 4.6 4.9 - - - -
1858A LEU* 2.9 24.5 + - - -
1859A SER* 3.5 4.9 - - - -
1861A VAL* 1.3 77.4 - - - +
1863A ALA* 1.3 63.7 + - - +
1865A ILE* 2.9 16.3 + - - +
1866A GLN* 2.9 11.3 + - - +
1909A PRO* 4.3 5.6 - - - +
1911A ASN* 2.2 41.0 + - - -
1912A LEU* 3.4 22.6 - - - +
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Residues in contact with ALA1863 (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 SER 3.0 14.8 + - - +
1860A ALA* 3.8 7.0 - - - +
1861A VAL 3.4 0.2 - - - -
1862A SER* 1.3 79.3 + - - +
1864A ASN* 1.3 63.4 + - - +
1866A GLN* 3.2 9.7 + - - +
1867A GLN* 3.0 29.4 + - + +
1911A ASN* 4.8 5.6 - - - +
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Residues in contact with ASN1864 (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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1828A TYR* 3.3 26.5 + - - -
1832A SER* 5.1 3.4 + - - +
1835A LEU* 4.3 16.7 - - + +
1860A ALA 3.1 11.7 + - - +
1861A VAL* 3.4 9.6 - - - +
1863A ALA* 1.3 75.6 - - - +
1865A ILE* 1.3 66.6 + - - +
1867A GLN* 3.1 9.0 + - - +
1868A ILE* 3.0 28.6 + - - +
1881A LEU* 3.2 17.8 - - + +
1882A LEU* 3.0 44.1 + - - +
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Residues in contact with ILE1865 (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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1835A LEU* 4.2 12.1 - - + -
1847A PHE* 3.6 33.4 - - + -
1850A PHE* 3.9 18.6 - - + -
1861A VAL* 2.9 30.5 + - + +
1862A SER* 2.9 8.0 + - - +
1864A ASN* 1.3 75.9 - - - +
1866A GLN* 1.3 56.1 + - - +
1868A ILE* 3.7 7.9 - - + +
1869A GLN* 2.9 27.2 + - + +
1894A VAL* 4.0 14.6 - - + -
1896A ILE* 4.7 2.7 - - + -
1912A LEU* 3.5 19.7 - - + -
1916A PHE* 3.8 21.3 - - + -
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Residues in contact with GLN1866 (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 SER 2.9 11.1 + - - +
1863A ALA* 3.7 10.6 - - - +
1864A ASN 3.1 0.4 - - - -
1865A ILE* 1.3 73.9 - - - +
1867A GLN* 1.3 63.2 + - - +
1869A GLN* 4.3 3.1 - - - +
1870A ASN* 2.7 58.4 + - + +
1911A ASN* 3.4 38.0 + - + +
1912A LEU* 3.9 10.3 - - + +
1914A LYS* 6.0 2.2 - - - +
1915A SER* 3.8 16.6 + - - +
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Residues in contact with GLN1867 (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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1863A ALA* 3.0 22.0 + - - +
1864A ASN* 3.3 8.1 - - - +
1866A GLN* 1.3 80.4 - - - +
1868A ILE* 1.3 61.4 + - - +
1870A ASN* 4.0 3.7 - - - +
1871A GLY* 3.0 20.1 + - - -
1876A LYS* 4.9 6.6 + - - +
1879A ILE* 3.9 14.7 - - + +
1880A THR* 2.7 39.8 + - - +
1881A LEU* 4.0 17.9 - - + -
1882A LEU 5.5 0.2 - - - +
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Residues in contact with ILE1868 (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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1835A LEU* 3.4 42.0 - - + -
1839A THR* 3.7 29.2 - - + -
1864A ASN 3.0 16.1 + - - +
1865A ILE* 3.7 8.5 - - - +
1867A GLN* 1.3 77.4 - - - +
1869A GLN* 1.3 58.6 + - - +
1871A GLY* 3.1 3.8 + - - -
1872A LEU* 2.9 42.8 + - + +
1879A ILE* 3.7 15.9 - - + -
1881A LEU* 4.3 9.2 - - + -
1888A LEU* 4.1 12.9 - - + +
1892A THR* 4.3 6.5 - - + -
1894A VAL* 4.4 11.4 - - + -
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Residues in contact with GLN1869 (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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1786A LEU* 5.9 0.8 - - - +
1789A LYS 2.9 25.0 + - - +
1790A TYR* 3.7 3.9 - - - -
1791A GLY* 3.1 32.6 + - - +
1865A ILE* 2.9 24.2 + - + +
1866A GLN 4.1 1.1 - - - +
1868A ILE* 1.3 73.4 - - - +
1870A ASN* 1.3 61.9 + - - +
1872A LEU* 3.3 19.9 + - + +
1873A GLN* 3.1 27.4 + - - +
1893A ALA* 4.7 2.6 - - - +
1894A VAL* 4.0 18.9 - - + +
1915A SER* 3.9 18.3 - - - +
1916A PHE* 4.0 22.2 - - + -
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Residues in contact with ASN1870 (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 GLN* 2.7 46.7 + - + +
1867A GLN* 4.0 3.6 - - - +
1869A GLN* 1.3 73.0 - - - +
1871A GLY* 1.3 56.6 + - - +
1873A GLN* 3.1 15.0 + - - +
1874A VAL* 2.9 47.4 + - - +
1876A LYS* 4.3 7.1 + - - +
1915A SER* 5.0 4.6 + - - -
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Residues in contact with GLY1871 (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 GLN 3.0 15.6 + - - -
1868A ILE 3.1 4.5 + - - -
1870A ASN* 1.3 75.9 - - - +
1872A LEU* 1.3 56.2 + - - +
1874A VAL* 4.5 0.4 - - - -
1875A GLY* 3.0 6.9 + - - -
1876A LYS* 3.0 47.9 + - - +
1879A ILE* 4.0 11.9 - - - -
1888A LEU* 3.7 9.3 - - - +
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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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1789A LYS* 3.4 37.1 + - + +
1868A ILE* 2.9 30.5 + - + +
1869A GLN* 3.6 31.6 - - - +
1870A ASN 3.1 0.2 - - - -
1871A GLY* 1.3 75.9 - - - +
1873A GLN* 1.3 64.8 + - - +
1875A GLY* 3.6 7.6 + - - -
1888A LEU* 3.6 19.5 - - + -
1889A SER 3.6 24.0 - - - +
1890A PRO* 4.1 12.3 - - + +
1892A THR* 3.2 29.4 - - - +
1893A ALA* 4.5 1.6 - - - -
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Residues in contact with GLN1873 (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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1788A GLN 4.4 6.1 - - - +
1789A LYS* 3.3 33.0 + - - +
1790A TYR* 3.9 39.3 + - + -
1869A GLN* 3.1 19.3 + - - +
1870A ASN* 3.1 14.3 + - - +
1872A LEU* 1.3 80.1 - - - +
1874A VAL* 1.3 62.8 + - + +
1875A GLY* 4.7 0.2 - - - -
1914A LYS 5.0 0.2 + - - -
1915A SER* 4.0 15.8 + - - +
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Residues in contact with VAL1874 (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 ASN* 2.9 33.8 + - - +
1871A GLY 4.2 2.5 - - - +
1873A GLN* 1.3 80.1 - - + +
1875A GLY* 1.3 56.7 + - - +
1876A LYS* 3.8 31.4 - - + +
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Residues in contact with GLY1875 (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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1789A LYS* 5.8 2.7 - - - -
1871A GLY 3.0 7.0 + - - -
1872A LEU 3.6 6.4 + - - -
1873A GLN 3.4 3.2 - - - -
1874A VAL* 1.3 80.7 - - - +
1876A LYS* 1.3 67.8 + - - +
1877A SER* 3.5 2.1 + - - -
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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