Contacts of the strand formed by residues 1907 - 1916 (chain C) in PDB entry 6AJL
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 LEU1907 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1808C PHE* 4.0 17.7 - - + -
1811C TYR* 3.1 41.3 - - + +
1887C PRO* 4.0 14.1 - - + -
1889C PHE* 3.5 33.0 - - + -
1897C ARG* 4.0 3.8 - - - +
1904C ASN* 3.7 16.6 - - - +
1905C TYR 4.2 3.1 - - - +
1906C ASN* 1.3 81.2 - - - +
1908C ARG* 1.3 58.1 + - - +
1909C ARG 5.5 1.3 - - - -
1910C PHE* 3.7 19.3 - - + -
1938C THR* 4.5 0.5 + - - -
1941C ALA* 3.4 3.7 - - - +
1942C PHE* 3.0 42.6 + - + +
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Residues in contact with ARG1908 (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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1889C PHE* 6.0 0.4 - - - -
1906C ASN* 2.6 23.8 + - - +
1907C LEU* 1.3 73.7 - - - +
1909C ARG* 1.3 69.2 + - + +
1910C PHE* 3.9 2.9 - - - -
1936C LEU 3.6 1.7 - - - +
1937C THR* 3.6 22.1 - - + +
1938C THR* 3.1 50.1 + - - +
1939C SER 3.3 22.0 + - - -
1940C HIS* 4.4 5.1 - - - +
1941C ALA* 3.8 16.5 - - + +
1952C THR* 5.6 1.4 - - - +
1953C HIS* 6.4 0.2 - - - -
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Residues in contact with ARG1909 (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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1887C PRO* 3.5 4.9 - - - +
1888C TYR* 2.9 58.0 + - + +
1889C PHE* 6.0 0.4 - - - +
1890C ASP* 4.1 18.3 + - - -
1893C GLU* 5.6 4.3 - - - +
1906C ASN 4.7 0.2 + - - -
1907C LEU* 5.5 0.2 - - - -
1908C ARG* 1.3 86.6 + - + +
1910C PHE* 1.3 69.6 + - - +
1935C ILE* 4.3 14.6 - - + +
1936C LEU 3.1 4.7 - - - +
1937C THR* 4.3 18.1 + - + +
1955C GLU* 4.0 24.9 + - - -
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Residues in contact with PHE1910 (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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1811C TYR* 3.5 32.8 - + + -
1830C VAL* 4.0 10.1 - - + -
1885C VAL* 3.6 30.3 - - + -
1886C GLU 3.4 5.4 - - - +
1887C PRO* 3.9 19.5 - - + -
1888C TYR* 4.1 2.0 - - - +
1907C LEU* 3.7 25.6 - - + -
1908C ARG 3.9 5.8 - - - -
1909C ARG* 1.3 78.3 - - - +
1911C MET* 1.3 61.9 + - - +
1934C THR 3.8 0.2 - - - +
1935C ILE* 3.2 3.6 - - - -
1936C LEU* 2.4 53.6 + - + +
1938C THR* 3.8 29.8 - - + -
1942C PHE* 3.6 25.1 - + - -
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Residues in contact with MET1911 (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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1884C TYR 4.4 0.2 - - - +
1885C VAL* 3.4 7.3 - - - +
1886C GLU* 2.9 67.4 + - + +
1888C TYR* 3.5 34.3 - - + -
1910C PHE* 1.3 76.7 - - - +
1912C TYR* 1.3 85.8 + - - +
1913C CYS* 4.0 7.4 - - - -
1933C LYS* 3.5 29.8 - - + +
1934C THR 3.2 11.4 - - - +
1935C ILE* 3.9 9.0 - - + -
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Residues in contact with TYR1912 (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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1813C ARG* 3.5 27.5 + - - -
1865C SER* 3.6 15.9 + - - -
1867C PRO* 5.6 4.3 - - - +
1883C THR* 3.9 17.0 - - + -
1884C TYR 3.8 18.6 - - - +
1885C VAL* 4.0 14.6 - - + -
1911C MET* 1.3 83.8 - - - +
1913C CYS* 1.3 60.5 + - - +
1914C THR* 3.5 25.1 - - + -
1932C ARG 3.7 0.5 - - - +
1933C LYS* 3.7 0.2 - - - -
1934C THR* 3.0 74.7 + - + +
1936C LEU* 3.8 22.9 - - + -
1954C LYS* 3.9 9.5 + - - -
1956C GLU* 5.2 0.9 + - - -
27D LYS* 4.6 4.5 - - - +
31D GLU* 5.6 0.2 - - - -
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Residues in contact with CYS1913 (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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1865C SER* 4.4 2.9 + - - -
1911C MET* 4.0 9.6 - - - -
1912C TYR* 1.3 74.8 - - - +
1914C THR* 1.3 66.9 + - - +
1915C PRO* 4.0 5.8 - - - +
1931C LYS* 3.8 35.7 - - + -
1932C ARG 3.2 3.1 - - - -
1933C LYS* 3.4 36.6 - - - -
1967C GLU* 5.2 0.9 - - - -
27D LYS* 4.5 14.2 - - - +
31D GLU* 4.0 7.6 - - - +
33D VAL* 4.1 10.7 - - + +
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Residues in contact with THR1914 (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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1865C SER* 3.1 32.5 - - - +
1866C ASN* 4.0 9.1 + - - -
1912C TYR* 3.5 26.2 - - + -
1913C CYS* 1.3 76.0 - - - +
1915C PRO* 1.3 68.2 + - - +
1916C PHE* 3.7 1.2 - - - -
1931C LYS* 3.3 3.0 - - - -
1932C ARG* 2.6 73.0 + - - +
1934C THR* 4.3 4.0 - - - +
31D GLU* 5.6 0.2 - - - -
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Residues in contact with PRO1915 (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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1866C ASN* 5.0 5.7 + - - +
1913C CYS 4.0 1.8 - - - +
1914C THR* 1.3 89.0 + - - +
1916C PHE* 1.3 67.6 + - - +
1922C ALA* 3.2 23.3 - - - +
1923C HIS* 4.1 6.1 - - + +
1929C GLN* 3.7 11.9 - - + +
1930C PHE 3.4 6.5 - - - +
1931C LYS* 4.3 5.6 - - + -
30D SER 4.4 2.7 - - - +
31D GLU* 3.1 33.4 - - + +
32D TYR 3.3 24.9 - - - +
33D VAL* 4.6 6.3 - - + -
34D PRO* 4.3 6.7 - - + -
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Residues in contact with PHE1916 (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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1866C ASN* 5.1 2.7 - - - +
1914C THR 3.7 13.5 - - - -
1915C PRO* 1.3 75.6 - - - +
1917C THR* 1.3 73.0 + - - +
1918C LEU* 4.0 19.1 - - + -
1920C GLY 6.2 0.2 - - - -
1921C ARG 3.2 12.1 - - - +
1922C ALA* 3.1 1.8 + - - -
1929C GLN* 3.0 10.2 - - - +
1930C PHE* 2.8 56.3 + + + +
1931C LYS 3.7 6.5 - - - -
1932C ARG* 3.6 54.3 - - + +
1958C ILE* 3.7 27.4 - - + -
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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