Contacts of the strand formed by residues 1956 - 1964 (chain A) in PDB entry 3AU5
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 THR1956 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1789A TYR 4.6 6.1 + - - -
1791A PHE* 4.9 8.7 - - - -
1954A GLY 4.1 1.4 + - - -
1955A SER* 1.3 72.5 - - - +
1957A LEU* 1.3 63.6 + - - +
1958A PHE* 3.3 36.3 - - + -
1973A LEU 3.3 0.2 - - - +
1975A VAL 2.7 27.9 + - - -
2032A LEU* 3.2 26.7 - - + +
2036A TYR* 5.2 1.6 + - - -
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Residues in contact with LEU1957 (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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1819A HIS* 3.5 67.2 + - + +
1950A TRP* 4.0 25.4 - - + -
1955A SER* 3.8 9.6 + - - +
1956A THR* 1.3 74.7 - - - +
1958A PHE* 1.3 64.0 + - - +
1959A ASP 4.0 0.6 + - - -
1972A TRP* 3.7 41.7 - - + +
1973A LEU 3.7 1.8 - - - -
1974A GLY* 3.8 20.6 - - - +
1983A TYR* 4.2 13.2 - - + -
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Residues in contact with PHE1958 (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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1956A THR* 3.3 41.1 - - + -
1957A LEU* 1.3 74.2 - - - +
1959A ASP* 1.3 63.5 + - - +
1960A VAL* 3.1 8.9 + - + +
1972A TRP* 4.5 2.0 - - - -
1973A LEU* 2.7 51.8 + - + +
1975A VAL* 3.7 13.2 - - + -
2025A GLU* 4.3 26.0 - - + +
2028A ASP* 3.7 25.6 - - + -
2029A VAL* 3.8 37.0 - - + -
2032A LEU* 3.6 23.6 - - + -
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Residues in contact with ASP1959 (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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1819A HIS* 3.4 24.1 + - - -
1957A LEU 4.0 0.4 + - - -
1958A PHE* 1.3 69.0 - - - +
1960A VAL* 1.3 58.7 + - - +
1971A LEU 3.7 4.9 - - - -
1972A TRP* 3.5 11.7 + - - -
1985A ARG* 2.9 48.2 + - - +
2023A THR* 3.2 16.8 + - - -
2025A GLU* 4.6 11.8 + - - +
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Residues in contact with VAL1960 (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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1958A PHE* 3.5 14.4 - - + +
1959A ASP* 1.3 76.6 - - - +
1961A GLU* 1.3 61.1 + - - +
1971A LEU* 3.1 38.7 + - + +
1973A LEU* 3.8 46.2 - - + +
1985A ARG* 2.8 18.1 + - - +
2021A PHE* 4.3 15.3 - - + -
2022A GLU 4.0 4.3 - - - +
2023A THR* 3.4 29.8 - - + +
2029A VAL* 5.5 0.2 - - + -
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Residues in contact with GLU1961 (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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1960A VAL* 1.3 76.0 - - - +
1962A CYS* 1.3 62.9 + - - +
1963A LYS 3.6 1.6 + - - -
1969A GLN* 3.0 47.5 + - + +
1970A GLU* 4.1 3.5 - - - +
1985A ARG* 3.1 27.3 + - - +
2021A PHE* 3.7 2.8 - - - -
2022A GLU* 2.8 52.6 + - + +
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Residues in contact with CYS1962 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1961A GLU* 1.3 71.4 - - - +
1963A LYS* 1.3 60.2 + - - +
1964A GLU* 3.5 29.8 - - - -
1965A GLY* 3.7 6.1 - - - -
1967A PHE* 3.6 27.7 - - - +
1968A PRO 3.0 23.2 - - - +
1969A GLN* 3.3 21.3 + - - +
1971A LEU* 3.2 20.7 - - + +
2020A LEU 4.5 1.8 - - - -
2021A PHE* 4.3 10.8 - - + -
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Residues in contact with LYS1963 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1961A GLU 3.6 5.2 + - - +
1962A CYS* 1.3 75.4 - - - +
1964A GLU* 1.3 65.4 + - + +
2020A LEU* 4.0 9.8 + - + +
2021A PHE 6.2 0.2 - - - -
2022A GLU* 5.3 9.6 - - + +
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Residues in contact with GLU1964 (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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1962A CYS* 3.4 7.8 - - - -
1963A LYS* 1.3 85.5 - - + +
1965A GLY* 1.3 58.9 + - - +
2018A GLU 5.0 1.0 - - - +
2019A LEU* 4.3 1.7 - - - +
2020A LEU* 3.7 32.2 + - + +
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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