Contacts of the helix formed by residues 1858 - 1873 (chain J) in PDB entry 2BT4
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 HIS1858 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1856J SER* 3.0 15.2 + - - +
1857J ASN* 1.3 85.7 - - + +
1859J GLU* 1.3 66.6 + - - +
1861J GLU* 3.6 19.4 - - + +
1862J LEU* 3.2 23.6 + - - +
1883J TYR* 3.9 3.1 - - - -
2058K HIS* 5.1 2.0 - - + -
2060K GLY* 3.4 21.9 - - - -
2061K GLU* 3.4 12.3 - - + -
2064K ASP* 3.3 20.6 + - - -
2258L HIS* 5.2 1.8 - - + +
2404L PO4 2.7 34.8 + - - +
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Residues in contact with GLU1859 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1858J HIS* 1.3 70.6 - - - +
1860J GLY* 1.3 62.2 + - - +
1862J LEU* 3.3 6.9 + - - +
1863J VAL* 3.1 25.6 + - + +
1883J TYR* 3.5 29.2 + - + +
1887J SER* 2.7 33.4 + - - +
1889J ALA* 3.7 6.2 + - + +
1890J ILE* 4.3 6.9 - - + +
2059K GLU* 3.9 2.6 - - + +
2060K GLY 5.6 0.2 - - - +
2259L GLU* 3.9 3.8 - - - +
2283L TYR* 3.4 31.2 + - - +
2286L THR* 5.2 0.3 + - - -
2404L PO4 3.8 5.2 + - - +
2408L TRS 2.8 45.3 + - - -
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Residues in contact with GLY1860 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1859J GLU* 1.3 76.0 - - - +
1861J GLU* 1.3 61.7 + - - +
1863J VAL* 3.5 4.2 + - - +
1864J ASP* 2.9 32.6 + - - +
2257L ASN* 3.5 25.4 + - - +
2258L HIS* 3.4 20.0 + - - -
2283L TYR* 4.4 0.6 + - - -
2404L PO4 3.1 10.0 + - - -
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Residues in contact with GLU1861 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1856J SER* 2.4 28.4 + - - +
1858J HIS* 3.3 26.5 + - + +
1860J GLY* 1.3 74.6 - - - +
1862J LEU* 1.3 61.5 + - - +
1864J ASP* 3.1 8.7 + - + +
1865J TRP* 2.8 71.0 + - + +
2258L HIS* 3.4 13.4 - - + -
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Residues in contact with LEU1862 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1812J LEU* 4.5 16.3 - - + +
1813J ASN 3.8 22.7 - - - +
1814J GLY* 4.0 9.2 - - - -
1856J SER* 3.9 19.5 - - - +
1858J HIS 3.2 14.3 + - - +
1859J GLU 3.3 6.0 + - - +
1861J GLU* 1.3 77.0 - - - +
1863J VAL* 1.3 61.6 + - - +
1865J TRP* 3.3 23.3 + - + +
1866J ILE* 2.9 32.2 + - + +
1878J ILE* 5.6 5.2 - - + -
1880J PRO* 5.3 2.2 - - + +
1883J TYR* 3.7 27.6 - - + -
1890J ILE* 3.9 17.9 - - + -
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Residues in contact with VAL1863 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1859J GLU 3.1 16.7 + - - +
1860J GLY* 3.6 9.4 - - - +
1862J LEU* 1.3 76.4 - - - +
1864J ASP* 1.3 62.1 + - - +
1866J ILE* 3.2 8.2 + - - +
1867J HIS* 3.1 27.2 + - + +
1889J ALA* 3.9 31.4 - - + +
1890J ILE* 4.0 13.2 - - + -
1893J ALA* 4.1 3.1 - - + -
2215L PRO* 4.7 1.1 - - + -
2216L ASN* 3.6 24.5 - - - +
2257L ASN* 3.5 32.3 - - + +
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Residues in contact with ASP1864 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1860J GLY 2.9 15.3 + - - +
1861J GLU* 3.3 11.5 - - + +
1863J VAL* 1.3 73.5 - - - +
1865J TRP* 1.3 69.6 + - + +
1867J HIS* 3.2 9.7 + - - +
1868J GLU* 3.1 19.2 + - - +
2257L ASN* 2.7 34.7 + - - +
2258L HIS* 3.2 23.0 + - - -
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Residues in contact with TRP1865 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1810J MET* 3.7 8.5 - - + +
1812J LEU* 4.0 22.2 - - + -
1854J ARG* 3.1 59.7 - - + +
1855J GLN* 3.5 22.7 - - - -
1856J SER* 3.5 24.5 - - - -
1861J GLU* 2.8 48.0 + - + +
1862J LEU* 3.7 17.3 - - + +
1863J VAL 3.2 0.2 - - - -
1864J ASP* 1.3 76.3 - - + +
1866J ILE* 1.3 58.4 - - - +
1868J GLU* 3.2 13.2 + - - +
1869J ALA* 2.9 25.1 + - - +
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Residues in contact with ILE1866 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1812J LEU* 3.7 17.5 - - + -
1862J LEU* 2.9 24.2 + - + +
1863J VAL* 3.2 5.8 + - - +
1865J TRP* 1.3 75.8 - - - +
1867J HIS* 1.3 59.2 + - + +
1869J ALA* 3.3 7.4 + - - +
1870J ARG* 2.9 28.2 + - - +
1876J ILE* 4.3 2.7 - - + -
1878J ILE* 4.4 7.9 - - + -
1890J ILE* 3.9 29.2 - - + -
1893J ALA* 3.7 40.4 - - + +
1894J LEU* 3.9 20.0 - - + -
1897J CYS* 3.8 12.9 - - - -
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Residues in contact with HIS1867 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1863J VAL* 3.1 15.2 + - + +
1864J ASP* 3.2 9.0 + - - +
1866J ILE* 1.3 80.0 - - - +
1868J GLU* 1.3 62.0 + - - +
1870J ARG* 3.4 19.5 - - - +
1871J LEU* 3.5 13.9 + - - +
1893J ALA* 4.3 5.6 - - + -
1896J THR* 4.3 7.6 - - - -
2216L ASN* 2.7 30.6 + - - -
2218L ASN* 3.2 39.7 + - - +
2219L LEU* 3.6 25.3 - - + +
2257L ASN* 3.7 20.0 + - - -
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Residues in contact with GLU1868 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1810J MET* 4.5 1.3 - - + -
1852J ASP* 4.7 0.2 - - - +
1854J ARG* 2.9 43.4 + - - -
1864J ASP 3.1 11.2 + - - +
1865J TRP* 3.2 14.8 + - - +
1867J HIS* 1.3 74.9 - - - +
1869J ALA* 1.3 65.3 + - - +
1871J LEU* 3.0 6.2 + - - +
1872J ASN* 3.0 43.5 + - - +
1873J HIS* 4.2 8.6 - - + -
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Residues in contact with ALA1869 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1810J MET* 3.8 30.0 - - + +
1865J TRP 2.9 18.1 + - - +
1866J ILE* 3.7 4.5 - - - +
1868J GLU* 1.3 69.9 - - - +
1870J ARG* 1.3 68.7 + - - +
1871J LEU 3.0 0.9 + - - -
1873J HIS* 3.1 41.3 + - + +
1876J ILE* 3.9 20.2 - - + -
1900J LEU* 4.1 4.8 - - + +
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Residues in contact with ARG1870 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1866J ILE 2.9 15.2 + - - +
1867J HIS* 3.4 12.3 + - - +
1868J GLU 3.2 0.2 - - - -
1869J ALA* 1.3 76.7 - - - +
1871J LEU* 1.3 83.4 + - + +
1873J HIS 5.1 1.6 - - - +
1896J THR* 2.9 46.6 + - - +
1897J CYS* 3.8 17.5 - - - -
1898J ASP* 5.3 3.2 + - - -
1900J LEU* 4.2 10.4 - - - +
2219L LEU* 4.0 23.3 - - - +
2222L GLN* 3.0 49.2 + - - +
2223L ARG* 5.4 2.4 - - - +
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Residues in contact with LEU1871 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1802J ARG* 3.2 23.4 + - - -
1867J HIS 3.9 11.0 - - - +
1868J GLU* 3.0 8.9 + - - +
1869J ALA 3.9 0.2 - - - -
1870J ARG* 1.3 109.8 - - + +
1872J ASN* 1.3 72.4 + - - +
1873J HIS 3.9 0.2 - - - -
2222L GLN* 5.6 0.7 - - - +
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Residues in contact with ASN1872 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1802J ARG* 3.8 19.9 + - - +
1807J ALA* 3.6 15.4 - - - +
1808J PRO* 4.0 6.4 - - - +
1868J GLU* 3.0 30.3 + - - +
1871J LEU* 1.3 95.7 - - - +
1873J HIS* 1.3 80.3 + - + +
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Residues in contact with HIS1873 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1802J ARG* 3.8 13.6 - - - +
1807J ALA* 4.2 1.3 - - - -
1808J PRO* 3.2 34.3 - - + +
1810J MET* 3.4 35.9 - - + +
1852J ASP* 2.8 28.5 + - + +
1868J GLU* 4.3 10.1 - - - -
1869J ALA* 3.1 33.7 + - + +
1870J ARG 5.1 0.7 - - - +
1871J LEU 3.9 0.2 - - - -
1872J ASN* 1.3 96.0 + - + +
1874J CYS* 1.3 62.7 + - - +
1875J GLY 3.4 10.1 - - - +
1900J LEU* 3.5 14.6 - - + +
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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