Contacts of the helix formed by residues 1857 - 1872 (chain C) in PDB entry 5Y3R
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 LYS1857 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C ASN* 5.1 5.4 - - - -
1762C MET 4.2 4.1 + - - +
1763C THR* 2.7 61.2 + - + +
1856C THR* 1.3 94.1 + - - +
1858C LEU* 1.3 60.2 - - + +
1860C GLU* 3.0 12.0 - - - -
1861C SER* 2.2 33.5 + - - -
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Residues in contact with LEU1858 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C VAL* 3.6 28.7 - - + +
353C ASP* 3.1 52.1 + - - +
364C ARG* 4.8 9.6 - - - +
391C ARG* 5.8 4.3 - - + +
394C GLN* 3.3 22.1 + - + +
395C MET* 4.4 22.4 - - - -
1856C THR 3.4 4.2 + - - +
1857C LYS* 1.3 83.6 - - + +
1859C ASN* 1.3 62.6 + - - +
1860C GLU 3.0 0.9 - - - -
1861C SER* 2.7 26.5 + - - -
1862C THR 2.9 9.0 + - - -
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Residues in contact with ASN1859 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C ASP* 5.0 5.8 + - + +
394C GLN* 4.9 0.2 - - - +
1756C PRO* 3.7 20.2 - - + +
1858C LEU* 1.3 75.8 - - - +
1860C GLU* 1.3 61.1 + - - +
1862C THR* 3.0 24.2 + - - +
1863C PHE 3.0 20.1 + - - -
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Residues in contact with GLU1860 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1756C PRO* 4.1 14.8 - - - +
1758C LEU* 3.2 14.6 - - - +
1761C LEU* 2.6 59.7 - - + +
1762C MET* 3.5 2.0 - - - -
1763C THR 3.3 22.6 + - - +
1856C THR 3.2 22.0 - - - +
1857C LYS* 3.0 14.1 - - - +
1859C ASN* 1.3 79.9 - - - +
1861C SER* 1.3 53.7 + - - +
1863C PHE* 3.0 7.9 - - - +
1864C ASP 2.9 24.8 + - - -
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Residues in contact with SER1861 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394C GLN* 3.1 43.3 + - - +
398C THR* 3.3 8.0 - - - +
1763C THR 3.1 16.8 - - - -
1857C LYS 2.2 26.8 + - - -
1858C LEU* 2.7 16.3 + - - -
1860C GLU* 1.3 66.0 - - - +
1862C THR* 1.3 52.7 + - - +
1865C THR* 2.0 45.4 + - - +
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Residues in contact with THR1862 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390C GLN* 3.4 16.3 + - - +
394C GLN* 2.7 25.1 + - - +
1722C PHE* 3.6 21.3 - - + -
1754C GLN 4.7 9.8 - - - +
1756C PRO* 5.5 0.4 - - + -
1858C LEU 2.9 3.0 + - - -
1859C ASN* 3.0 32.7 + - - +
1861C SER* 1.3 77.4 - - - +
1863C PHE* 1.3 64.0 + - - +
1865C THR* 3.2 4.9 - - - -
1866C GLN* 3.0 19.9 + - - +
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Residues in contact with PHE1863 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1751C GLU* 3.2 9.6 - - - -
1755C SER* 3.1 24.5 - - - +
1756C PRO* 3.4 35.8 - - + +
1758C LEU 5.5 0.7 - - - -
1761C LEU 4.7 2.7 - - - -
1762C MET* 3.5 39.3 - - + -
1859C ASN 3.0 6.1 + - - -
1860C GLU* 3.0 12.5 + - - +
1862C THR* 1.3 72.8 - - - +
1864C ASP* 1.3 66.6 + - - +
1866C GLN* 2.6 27.7 + - - +
1867C ILE* 2.8 30.0 + - + +
1888C ASP* 6.0 0.9 - - + -
1892C LYS* 3.1 35.4 - - + -
1894C SER* 4.3 9.4 - - - -
1896C ILE* 3.9 15.0 - - + -
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Residues in contact with ASP1864 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398C THR* 6.1 1.8 - - + -
1762C MET* 3.3 46.5 - - + +
1763C THR* 4.3 12.1 - - - +
1860C GLU 2.9 7.9 + - - +
1863C PHE* 1.3 73.2 - - - +
1865C THR* 1.3 69.3 + - - +
1867C ILE* 3.4 14.1 - - - +
1868C THR* 2.7 38.3 + - - -
1896C ILE* 4.6 1.2 - - - +
1899C VAL* 5.4 8.5 - - - +
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Residues in contact with THR1865 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C GLN* 6.4 0.4 - - + -
393C LYS* 3.1 32.3 + - - +
394C GLN* 4.2 9.5 - - + +
397C LEU* 4.7 8.1 - - - +
398C THR* 5.2 3.9 - - - +
1722C PHE* 3.5 23.3 - - + -
1726C SER* 5.5 0.4 - - - -
1763C THR 5.5 0.4 - - - -
1861C SER* 2.0 39.9 + - - +
1862C THR* 3.2 5.3 - - - -
1864C ASP* 1.3 81.5 - - - +
1866C GLN* 1.3 60.0 + - - +
1868C THR* 3.7 2.3 - - - -
1869C LYS* 2.8 34.6 + - + +
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Residues in contact with GLN1866 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1722C PHE* 3.0 37.3 - - + +
1725C GLN* 3.1 20.6 + - + +
1726C SER* 2.9 46.0 + - - +
1729C PHE* 3.2 20.3 - - + -
1751C GLU* 6.2 1.3 - - + -
1754C GLN* 5.5 2.2 - - + +
1755C SER* 4.2 14.1 - - - +
1862C THR 3.6 1.3 - - - +
1863C PHE 2.6 14.3 + - - +
1865C THR* 1.3 76.8 - - - +
1867C ILE* 1.3 58.6 + - + +
1869C LYS* 3.0 21.1 - - - +
1870C LYS* 2.9 23.6 + - - +
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Residues in contact with ILE1867 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1751C GLU* 3.1 35.2 - - + +
1755C SER* 3.5 14.4 - - - +
1863C PHE* 2.8 39.9 + - + +
1864C ASP* 3.4 10.3 - - - +
1866C GLN* 1.3 76.5 - - + +
1868C THR* 1.3 59.0 + - - +
1869C LYS 3.1 0.9 - - - -
1870C LYS* 2.5 39.9 + - + +
1871C MET* 3.0 10.3 + - + +
1888C ASP* 4.7 5.8 - - + +
1896C ILE* 3.6 28.9 - - + -
1899C VAL* 6.4 0.7 - - + -
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Residues in contact with THR1868 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397C LEU* 5.3 12.1 - - + -
400C THR* 5.5 13.1 - - + +
1817C GLN* 5.8 2.5 - - - +
1864C ASP* 2.7 37.2 + - - -
1865C THR* 3.7 2.2 - - - -
1867C ILE* 1.3 76.0 - - - +
1869C LYS* 1.3 63.6 + - - +
1870C LYS 2.9 1.2 + - - -
1872C GLY* 3.5 15.2 + - - +
1873C TYR* 2.9 21.2 - - + +
1899C VAL* 5.6 9.1 - - + +
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Residues in contact with LYS1869 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393C LYS* 3.1 42.5 - - - +
397C LEU* 3.2 20.0 - - + +
1726C SER* 3.7 36.0 - - - +
1727C ARG* 5.9 2.2 - - - +
1729C PHE* 4.3 9.9 - - - +
1813C SER* 4.7 9.9 + - - -
1865C THR* 2.8 25.3 + - + +
1866C GLN* 3.0 33.0 - - - +
1868C THR* 1.3 75.1 - - - +
1870C LYS* 1.3 58.5 + - - +
1873C TYR* 2.8 43.9 + - + +
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Residues in contact with LYS1870 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1729C PHE* 4.6 17.9 - - + +
1747C LEU* 4.7 18.1 + - + -
1748C ASP* 5.1 0.4 + - - -
1751C GLU* 4.3 13.1 - - + +
1866C GLN 2.9 10.8 + - - +
1867C ILE* 2.5 28.7 + - + +
1869C LYS* 1.3 76.7 - - - +
1871C MET* 1.3 87.1 + - + +
1872C GLY 3.5 0.4 - - - -
1873C TYR* 3.5 13.7 - - - +
1874C TYR* 3.8 6.2 + - - +
1884C LEU* 3.4 41.0 + - - +
1885C PRO* 4.9 0.8 - - - +
1888C ASP* 2.3 43.8 + - - +
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Residues in contact with MET1871 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1747C LEU* 5.8 0.2 - - + -
1867C ILE* 3.0 9.5 + - + +
1870C LYS* 1.3 100.4 - - + +
1872C GLY* 1.3 68.3 + - - +
1873C TYR 3.1 1.1 - - - -
1874C TYR* 3.0 18.2 - - - +
1875C LYS* 2.8 34.9 + - + +
1881C TYR* 3.2 32.8 - - + +
1884C LEU* 3.5 38.1 - - + -
1885C PRO* 3.5 21.5 - - + -
1899C VAL* 5.7 4.0 - - + -
1900C PHE* 6.4 2.7 - - + -
1903C SER* 5.2 7.0 - - - +
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Residues in contact with GLY1872 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1816C ARG* 5.1 6.9 + - - -
1867C ILE 4.4 0.8 + - - -
1868C THR* 3.5 17.3 + - - +
1870C LYS 3.5 0.6 - - - -
1871C MET* 1.3 78.8 - - - +
1873C TYR* 1.3 67.0 + - - +
1875C LYS* 3.7 18.2 + - - +
1899C VAL* 5.3 9.3 - - - +
1903C SER* 5.4 2.9 - - - -
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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