Contacts of the strand formed by residues 1948 - 1959 (chain C) in PDB entry 6AJ4
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 ARG1948 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1816C PHE* 4.0 17.6 - - - -
1824C LEU* 4.4 15.3 - - - +
1829C PHE* 3.3 36.0 - - + -
1830C VAL 3.3 7.2 - - - +
1831C TYR* 2.5 57.8 + - + -
1850C TYR* 5.3 2.4 + - - -
1942C PHE* 4.6 0.2 - - - -
1944C TYR* 4.4 1.7 - - - -
1946C LYS* 4.0 19.6 - - + +
1947C THR* 1.3 80.4 + - - +
1949C VAL* 1.3 59.9 + - - +
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Residues in contact with VAL1949 (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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1829C PHE* 3.5 3.6 - - - -
1830C VAL* 3.0 24.7 + - - +
1938C THR* 3.5 19.5 - - + +
1939C SER* 3.9 8.7 - - - +
1940C HIS* 3.3 51.1 - - + +
1941C ALA 5.4 0.7 - - - +
1942C PHE* 3.4 34.9 - - + -
1944C TYR* 4.5 11.7 - - + -
1948C ARG* 1.3 74.3 - - - +
1950C ASN* 1.3 64.6 + - - +
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Residues in contact with ASN1950 (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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1827C GLN* 3.8 21.4 - - - +
1828C GLU 3.0 15.8 + - - +
1829C PHE* 3.3 25.0 - - + +
1938C THR* 3.5 3.4 - - - -
1939C SER* 3.0 38.0 + - - -
1940C HIS* 5.8 1.0 - - - -
1949C VAL* 1.3 77.7 - - - +
1951C VAL* 1.3 68.9 + - - +
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Residues in contact with VAL1951 (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* 5.1 0.2 - - + -
1828C GLU* 2.9 37.5 + - + +
1829C PHE 4.0 11.4 - - - +
1830C VAL* 3.8 29.6 - - + -
1936C LEU* 3.9 26.7 - - + -
1937C THR 3.7 4.9 - - - +
1938C THR* 4.2 2.5 - - + +
1939C SER* 5.7 0.2 - - - -
1950C ASN* 1.3 79.6 + - - +
1952C THR* 1.3 62.8 + - - +
1953C HIS 3.5 21.3 - - - +
1954C LYS* 5.2 2.7 - - + -
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Residues in contact with THR1952 (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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1908C ARG* 5.4 2.0 - - - +
1937C THR* 2.7 29.8 + - + +
1938C THR 3.9 10.1 - - - +
1939C SER* 4.3 14.6 - - - -
1950C ASN 3.7 0.8 + - - -
1951C VAL* 1.3 75.4 - - - +
1953C HIS* 1.3 95.0 + - + +
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Residues in contact with HIS1953 (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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1908C ARG* 6.3 0.4 - - - -
1936C LEU* 3.7 1.9 - - - -
1937C THR* 3.2 41.9 + - + +
1951C VAL* 3.5 13.3 - - - +
1952C THR* 1.3 111.4 + - + +
1954C LYS* 1.3 65.1 + - - +
1955C GLU* 5.4 3.8 - - + +
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Residues in contact with LYS1954 (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 10.4 - - - +
1828C GLU* 3.7 23.2 + - - +
1867C PRO* 4.4 22.0 - - + +
1881C GLN* 5.5 0.4 + - - -
1912C TYR* 3.2 26.3 + - - -
1934C THR* 3.8 18.2 - - + -
1935C ILE 3.4 6.7 + - - -
1936C LEU* 3.9 14.6 - - + -
1937C THR* 4.8 0.2 + - - -
1951C VAL* 5.2 2.5 - - + -
1953C HIS* 1.3 81.1 - - - +
1955C GLU* 1.3 60.3 + - - +
1956C GLU* 3.9 13.9 + - - +
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Residues in contact with GLU1955 (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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1909C ARG* 2.8 35.8 + - - +
1933C LYS 3.8 0.9 - - - +
1934C THR* 3.3 3.3 - - - +
1935C ILE* 2.7 57.7 + - + +
1937C THR* 5.1 5.2 - - - +
1953C HIS* 5.7 2.2 - - + -
1954C LYS* 1.3 76.1 - - - +
1956C GLU* 1.3 62.2 + - - +
1957C ILE* 5.2 2.7 - - + -
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Residues in contact with GLU1956 (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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1867C PRO* 4.7 17.2 - - - +
1912C TYR* 4.7 2.8 + - - -
1932C ARG* 3.4 31.3 + - + -
1933C LYS 3.1 2.5 - - - -
1934C THR* 3.4 36.0 + - + +
1954C LYS* 3.9 15.8 + - - +
1955C GLU* 1.3 73.0 - - - +
1957C ILE* 1.3 66.1 + - - +
1958C ILE* 6.5 0.2 - - + -
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Residues in contact with ILE1957 (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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1888C TYR* 5.1 2.5 - - - +
1931C LYS 3.8 0.5 - - - +
1932C ARG* 3.3 5.1 - - - -
1933C LYS* 2.6 74.9 + - + +
1935C ILE* 3.7 26.0 - - + -
1955C GLU* 5.2 2.9 - - + -
1956C GLU* 1.3 82.3 - - - +
1958C ILE* 1.3 73.8 + - - +
1959C LEU* 4.0 6.8 + - + +
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Residues in contact with ILE1958 (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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1916C PHE* 4.0 27.6 - - + -
1918C LEU* 6.4 0.4 - - + -
1930C PHE* 4.1 18.4 - - + -
1931C LYS 3.7 2.2 - - - +
1932C ARG* 4.9 9.9 - - + +
1956C GLU* 6.5 0.2 - - + -
1957C ILE* 1.3 82.6 - - - +
1959C LEU* 1.3 75.1 + - - +
1960C THR* 4.2 6.6 - - + +
1963C GLU* 3.7 9.9 - - - +
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Residues in contact with LEU1959 (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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1930C PHE* 3.4 8.0 - - - -
1931C LYS* 2.8 68.0 + - - +
1933C LYS* 4.2 19.3 - - + -
1957C ILE* 4.1 13.7 - - + +
1958C ILE* 1.3 78.8 - - - +
1960C THR* 1.3 65.0 + - - +
1963C GLU* 3.4 24.5 - - + +
1964C VAL* 3.6 12.7 - - + +
1967C GLU* 3.8 28.7 - - + +
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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