Contacts of the helix formed by residues 1878 - 1892 (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 ASP1878 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1733C THR* 3.1 29.1 - - - +
1734C PRO 4.0 5.0 - - - +
1735C ARG* 3.4 26.8 + - - +
1875C LYS 5.5 0.2 - - - +
1877C LEU* 1.3 84.8 - - - +
1879C VAL* 1.3 56.6 + - - +
1880C MET* 3.3 4.3 - - + +
1881C TYR* 3.0 23.1 - - + +
1882C SER 2.4 31.9 + - - -
1916C ILE* 3.8 14.3 - - - +
1920C TYR* 2.8 7.4 + - - -
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Residues in contact with VAL1879 (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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1740C VAL* 5.6 6.5 - - + -
1878C ASP* 1.3 72.6 - - + +
1880C MET* 1.3 63.3 + - + +
1882C SER* 3.3 2.0 - - - -
1883C ARG* 2.8 35.2 + - - +
1919C CYS* 4.4 5.2 - - + +
1920C TYR* 3.2 24.3 + - + -
1923C PHE* 3.2 43.5 - - + -
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Residues in contact with MET1880 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1734C PRO* 6.3 2.9 - - + -
1739C TYR* 3.1 26.0 - - + +
1740C VAL* 3.1 22.0 - - + +
1743C MET* 3.6 20.9 - - + -
1744C LYS* 3.3 13.5 - - - -
1747C LEU* 5.0 0.2 - - + -
1878C ASP* 3.3 2.3 - - + +
1879C VAL* 1.3 79.8 - - + +
1881C TYR* 1.3 71.8 + - + +
1882C SER 2.9 1.1 - - - -
1883C ARG* 2.7 54.6 + - - +
1884C LEU* 2.9 38.0 + - + +
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Residues in contact with TYR1881 (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* 5.2 1.5 + - + -
1731C PRO 4.8 0.2 + - - -
1732C GLY 2.6 26.9 + - - -
1733C THR* 3.2 27.9 - - + -
1734C PRO* 3.2 12.2 - - + +
1743C MET* 6.5 0.9 - - + -
1871C MET* 3.2 20.4 - - + +
1874C TYR* 3.7 51.8 - + + +
1875C LYS* 4.9 6.2 - - - +
1877C LEU* 3.7 9.2 - - + +
1878C ASP* 3.0 39.8 + - + +
1880C MET* 1.3 87.9 - - + +
1882C SER* 1.3 54.6 + - - +
1884C LEU* 5.3 4.3 - - + -
1885C PRO* 3.0 23.2 - - - +
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Residues in contact with SER1882 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1875C LYS 5.3 3.3 + - - -
1878C ASP 2.4 18.1 + - - -
1879C VAL 3.3 8.7 - - - -
1881C TYR* 1.3 75.6 - - - +
1883C ARG* 1.3 59.0 + - - +
1885C PRO* 3.0 15.4 - - - +
1886C LYS* 3.9 17.0 + - - +
1907C GLU* 6.1 1.6 - - - -
1920C TYR* 3.5 33.8 - - - +
1923C PHE* 3.5 16.5 - - - -
1924C THR* 5.1 1.9 - - - +
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Residues in contact with ARG1883 (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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1740C VAL* 3.0 51.3 + - - +
1744C LYS* 3.2 23.8 - - - +
1879C VAL* 2.8 26.6 + - - +
1880C MET* 2.7 60.4 + - - +
1882C SER* 1.3 71.5 - - - +
1884C LEU* 1.3 53.7 + - - +
1886C LYS* 2.8 10.4 + - + +
1887C ASP* 2.7 48.0 + - - +
1923C PHE* 3.7 28.8 - - + -
1927C MET* 5.7 7.0 - - + -
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Residues in contact with LEU1884 (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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1744C LYS* 4.2 8.1 - - + -
1747C LEU* 3.3 44.2 - - + -
1748C ASP* 3.2 17.0 - - - +
1870C LYS* 3.4 18.8 + - - +
1871C MET* 3.5 22.4 - - + -
1880C MET* 2.9 36.5 + - + +
1881C TYR* 4.4 4.0 - - + +
1883C ARG* 1.3 75.3 - - - +
1885C PRO* 1.3 62.8 - - - +
1887C ASP* 3.0 26.1 + - - +
1888C ASP* 2.9 19.6 + - - -
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Residues in contact with PRO1885 (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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1870C LYS* 4.9 1.8 - - - +
1871C MET* 3.5 29.8 - - + -
1875C LYS* 6.4 0.4 - - - -
1881C TYR 3.0 26.7 - - - +
1882C SER* 3.0 14.8 - - - +
1884C LEU* 1.3 86.5 - - - +
1886C LYS* 1.3 69.6 + - + +
1887C ASP 3.1 0.3 + - - -
1888C ASP* 3.1 3.9 + - + +
1889C VAL* 2.9 30.2 + - - +
1900C PHE* 4.5 19.2 - - + -
1904C CYS* 6.6 0.2 - - - -
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Residues in contact with LYS1886 (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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1882C SER* 4.0 14.8 + - - +
1883C ARG* 2.8 12.9 + - + +
1885C PRO* 1.3 85.8 - - + +
1887C ASP* 1.3 66.3 + - - +
1889C VAL* 3.3 9.9 - - + +
1890C HIS* 3.2 38.1 + - + +
1900C PHE* 5.5 3.6 - - + -
1904C CYS* 3.9 12.3 - - - -
1923C PHE* 5.6 9.4 - - + -
1924C THR* 5.5 5.4 - - + -
1927C MET* 6.0 6.3 - - + -
1937C ARG* 4.5 3.0 + - - -
1940C TYR* 3.7 21.1 - - - -
1941C HIS* 4.3 22.2 - - + +
1944C ALA* 3.3 25.5 - - - +
1945C TYR* 4.0 7.8 - - - +
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Residues in contact with ASP1887 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1744C LYS* 4.6 0.9 - - - +
1748C ASP* 2.6 39.4 - - - +
1883C ARG* 2.7 35.1 + - - +
1884C LEU* 3.0 25.4 + - - +
1886C LYS* 1.3 81.5 - - - +
1888C ASP* 1.3 62.1 + - - +
1890C HIS* 4.1 0.9 - - - +
1891C ALA* 2.9 30.5 + - - +
1937C ARG* 4.6 11.1 + - - +
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Residues in contact with ASP1888 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1748C ASP* 4.3 6.4 - - - +
1751C GLU* 3.3 36.3 - - - +
1752C LEU* 4.7 6.1 - - - +
1863C PHE* 6.0 0.9 - - + -
1867C ILE* 4.7 4.2 - - + +
1870C LYS* 2.3 37.1 + - - +
1884C LEU 2.9 12.6 + - - +
1885C PRO* 4.1 2.7 - - + +
1887C ASP* 1.3 77.5 - - - +
1889C VAL* 1.3 56.3 + - - +
1891C ALA* 2.9 6.2 + - - +
1892C LYS* 2.4 50.0 + - + +
1896C ILE* 4.7 9.9 - - + -
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Residues in contact with VAL1889 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1885C PRO 2.9 21.6 + - - +
1886C LYS* 3.3 18.8 - - + +
1888C ASP* 1.3 75.6 - - - +
1890C HIS* 1.3 77.8 + - + +
1892C LYS 3.5 5.8 - - - -
1893C GLU* 3.1 32.1 + - - +
1896C ILE* 4.3 3.7 - - - +
1897C ASN* 3.0 24.5 - - - +
1900C PHE* 3.5 15.7 - - + -
1936C ARG* 4.8 0.5 - - - -
1940C TYR* 3.3 40.7 - - + -
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Residues in contact with HIS1890 (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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1886C LYS* 3.2 24.4 + - + +
1887C ASP 3.5 0.9 + - - +
1888C ASP 3.1 0.2 - - - -
1889C VAL* 1.3 80.8 - - + +
1891C ALA* 1.3 68.6 + - - +
1934C LEU* 4.4 10.4 - - + +
1936C ARG* 2.8 49.6 + - + +
1937C ARG* 3.0 59.4 + - + +
1940C TYR* 3.0 37.1 - + + +
1941C HIS* 3.6 14.8 - + + -
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Residues in contact with ALA1891 (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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1752C LEU* 4.1 27.8 - - + -
1759C LEU* 3.8 11.8 - - - +
1887C ASP 2.9 21.0 + - - +
1888C ASP* 3.3 9.4 - - - +
1890C HIS* 1.3 80.0 - - - +
1892C LYS* 1.3 59.9 + - - +
1936C ARG* 4.5 0.5 + - - -
1937C ARG* 5.2 2.1 - - - +
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Residues in contact with LYS1892 (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* 2.9 40.9 + - - -
1752C LEU* 3.4 19.7 - - + +
1755C SER 2.7 19.8 + - - -
1756C PRO 2.5 35.2 + - - +
1757C MET 3.2 24.2 - - - +
1758C LEU 4.3 2.2 - - - +
1759C LEU* 3.4 12.1 - - + -
1863C PHE* 3.1 17.9 - - + -
1888C ASP* 2.4 44.8 + - + +
1889C VAL* 3.1 6.0 - - - +
1891C ALA* 1.3 71.1 - - - +
1893C GLU* 1.3 63.8 + - - +
1894C SER* 3.5 2.9 + - - +
1896C ILE* 3.7 5.6 - - + +
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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
------------------------------------------------------------
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