Contacts of the strand formed by residues 1893 - 1899 (chain A) in PDB entry 4M6W
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 ARG1893 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1860A ARG* 3.1 50.7 + - + +
1861A MET* 3.3 47.6 - - + +
1862A VAL 3.3 5.4 + - - -
1891A PHE* 3.9 1.4 - - - +
1892A GLU* 1.3 87.5 - - + +
1894A ILE* 1.3 65.1 + - - +
1931A ARG* 5.7 12.3 - - - +
1952A GLU* 5.4 0.2 + - - -
1955A LYS* 3.3 10.7 - - - +
2102A SO4 2.3 48.5 + - - -
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Residues in contact with ILE1894 (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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1861A MET* 5.1 2.0 - - - +
1862A VAL* 3.6 22.0 - - + +
1864A GLU* 5.8 2.2 - - + -
1884A ILE* 3.9 22.2 - - + +
1887A LEU* 3.7 13.2 - - + -
1888A GLN* 3.5 49.1 - - + +
1891A PHE* 4.2 9.4 - - + +
1893A ARG* 1.3 79.2 - - - +
1895A CYS* 1.3 69.9 + - - +
1896A VAL* 5.5 0.4 - - + -
1929A GLY 4.8 2.9 + - - +
1930A ILE* 3.4 30.0 - - + +
1931A ARG* 3.2 23.4 + - - +
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Residues in contact with CYS1895 (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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1861A MET* 4.4 14.1 - - + -
1862A VAL 3.0 11.6 + - - +
1863A VAL* 3.1 17.0 - - + +
1864A GLU* 2.8 26.2 + - - +
1894A ILE* 1.3 78.8 - - - +
1896A VAL* 1.3 68.6 + - - +
1897A ILE* 4.8 0.2 - - - -
1931A ARG* 3.2 19.3 - - + +
1933A LEU* 3.1 36.1 - - - -
1948A LEU* 3.9 13.0 - - - -
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Residues in contact with VAL1896 (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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1864A GLU* 3.1 15.5 - - + +
1866A ARG* 5.1 3.8 - - + -
1871A MET* 4.9 4.3 - - - -
1880A PHE* 4.1 29.8 - - + -
1884A ILE* 5.2 3.1 - - + -
1894A ILE* 5.5 0.2 - - + -
1895A CYS* 1.3 75.9 - - - +
1897A ILE* 1.3 72.7 + - - +
1898A VAL* 4.3 14.1 - - + -
1925A LEU* 4.6 12.6 - - + -
1930A ILE* 3.8 22.4 - - + -
1931A ARG 3.0 6.9 + - - +
1932A ILE* 3.3 16.9 - - + +
1933A LEU 2.9 23.8 + - - -
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Residues in contact with ILE1897 (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 TYR* 6.1 0.4 - - + -
1863A VAL* 3.6 26.9 - - + -
1864A GLU 2.8 10.8 + - - +
1865A ARG* 3.4 9.3 - - + +
1866A ARG 3.0 27.0 + - - +
1896A VAL* 1.3 74.6 - - - +
1898A VAL* 1.3 61.8 + - - +
1899A GLU* 3.5 2.1 + - + +
1933A LEU* 3.4 22.7 - - + +
1935A SER* 3.8 28.3 - - - -
1941A THR* 3.9 27.8 - - + +
1944A LEU* 4.2 19.1 - - + -
1945A LEU* 3.9 15.7 - - + -
1948A LEU* 5.1 3.8 - - + -
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Residues in contact with VAL1898 (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 ARG 3.4 4.9 - - - +
1868A GLN* 3.9 38.6 - - + +
1871A MET* 4.0 26.0 - - + -
1896A VAL* 4.3 8.1 - - + -
1897A ILE* 1.3 70.4 - - - +
1899A GLU* 1.3 60.3 + - - +
1900A LYS* 5.5 0.3 - - - +
1918A TYR* 5.1 3.8 - - - +
1922A LEU* 5.4 5.8 - - + -
1932A ILE* 3.4 22.7 - - + -
1933A LEU 2.8 9.3 + - - -
1934A PHE* 3.5 28.4 - - + +
1935A SER 3.0 23.7 + - - +
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Residues in contact with GLU1899 (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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1865A ARG* 2.8 41.9 + - + +
1866A ARG 3.0 14.2 + - - +
1867A SER* 3.3 6.3 - - - -
1868A GLN* 2.9 24.9 + - - -
1897A ILE* 3.5 5.1 + - + +
1898A VAL* 1.3 73.4 - - - +
1900A LYS* 1.3 75.0 + - - +
1902A ARG* 4.2 4.2 + - - -
1935A SER* 3.5 11.4 - - - +
1937A CYS* 4.1 6.3 - - - -
1938A GLN* 3.6 21.1 + - - +
1941A THR* 2.8 31.7 + - + +
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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