Contacts of the strand formed by residues 1956 - 1962 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1752B ASP* 6.2 0.2 - - - +
1789B TYR* 4.5 8.5 + - - -
1791B PHE* 4.9 7.8 - - - -
1955B SER* 1.3 72.1 - - - +
1957B LEU* 1.3 64.7 + - - +
1958B PHE* 3.2 33.0 - - + -
1973B LEU 3.2 4.9 - - - +
1974B GLY* 3.4 0.3 - - - -
1975B VAL 2.7 31.4 + - - -
2032B LEU* 3.2 26.1 - - + +
2036B TYR* 5.0 2.3 + - - -
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Residues in contact with LEU1957 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1819B HIS* 3.3 58.7 + - + +
1950B TRP* 3.9 21.5 - - + -
1955B SER* 3.6 18.2 - - - +
1956B THR* 1.3 74.3 - - - +
1958B PHE* 1.3 63.5 + - - +
1959B ASP 4.1 0.3 + - - -
1972B TRP* 3.8 35.9 - - + +
1973B LEU 3.7 0.4 - - - -
1974B GLY* 3.9 20.9 - - - -
1983B TYR* 4.1 21.5 - - + -
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Residues in contact with PHE1958 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1752B ASP* 6.1 0.2 - - - -
1956B THR* 3.2 37.0 - - + -
1957B LEU* 1.3 75.2 - - - +
1959B ASP* 1.3 67.4 + - - +
1960B VAL* 3.5 2.4 + - + -
1972B TRP* 3.3 3.7 - - - -
1973B LEU* 2.7 56.1 + - + +
1975B VAL* 4.2 10.8 - - + -
2023B THR* 5.3 2.2 - - - +
2025B GLU* 4.0 22.4 - - + +
2028B ASP* 4.0 30.5 - - + -
2029B VAL* 3.6 31.6 - - + -
2032B LEU* 3.9 16.2 - - + -
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Residues in contact with ASP1959 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1750B HIS* 5.2 9.9 + - - -
1819B HIS* 4.2 17.1 + - - -
1957B LEU 4.1 0.2 + - - -
1958B PHE* 1.3 71.0 - - - +
1960B VAL* 1.3 61.1 + - - +
1971B LEU 3.5 6.3 - - - -
1972B TRP* 3.0 18.8 + - - -
1985B ARG* 2.8 33.6 + - - +
2023B THR* 3.1 20.6 + - - -
2025B GLU* 5.9 0.4 + - - -
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Residues in contact with VAL1960 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1958B PHE* 4.0 6.7 - - + +
1959B ASP* 1.3 80.3 - - - +
1961B GLU* 1.3 58.2 + - - +
1969B GLN 3.6 0.3 - - - +
1970B GLU* 4.2 0.5 - - - -
1971B LEU* 2.8 62.9 + - + +
1972B TRP 3.8 3.8 - - - +
1973B LEU* 3.8 34.5 - - + +
1985B ARG* 3.6 5.3 + - - +
2021B PHE* 4.1 21.5 - - + -
2022B GLU 3.9 5.2 - - - +
2023B THR* 3.5 25.4 - - + +
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Residues in contact with GLU1961 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1960B VAL* 1.3 73.4 - - - +
1962B CYS* 1.3 62.9 + - - +
1963B LYS 3.2 1.6 + - - -
1969B GLN* 3.9 11.0 - - + -
1970B GLU* 5.6 0.2 - - - +
2021B PHE* 3.8 4.5 - - - -
2022B GLU* 3.0 61.2 + - + +
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Residues in contact with CYS1962 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1960B VAL 4.0 0.6 + - - -
1961B GLU* 1.3 69.2 - - - +
1963B LYS* 1.3 69.2 + - - +
1964B GLU 4.9 0.7 - - - -
1965B GLY* 4.4 8.3 - - - -
1966B GLY 4.3 6.3 - - - -
1967B PHE* 3.1 51.8 - - - +
1968B PRO 2.9 23.1 - - - +
1969B GLN* 3.4 13.3 + - - +
1971B LEU* 4.0 8.6 - - + +
2020B LEU 4.4 4.0 - - - -
2021B PHE* 4.6 7.2 - - - -
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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