Contacts of the strand formed by residues 1970 - 1976 (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 GLU1970 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1862A ALA* 5.7 5.4 - - - +
1961A GLU* 4.1 7.6 - - - +
1968A PRO* 4.5 5.1 - - + +
1969A GLN* 1.3 74.4 - - - +
1971A LEU* 1.3 63.8 + - - +
1984A LYS* 3.7 3.5 - - - -
1985A ARG* 2.9 57.5 + - + +
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Residues in contact with LEU1971 (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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1959A ASP* 3.7 1.7 - - - -
1960A VAL* 3.1 36.9 + - + +
1962A CYS* 3.2 28.9 - - + -
1967A PHE* 3.7 13.2 - - + -
1968A PRO* 3.3 36.1 - - + +
1969A GLN 2.9 7.4 + - - +
1970A GLU* 1.3 81.5 - - - +
1972A TRP* 1.3 62.3 + - - +
1982A VAL* 3.8 15.7 - - + -
1983A TYR 3.6 6.3 - - - +
1984A LYS* 4.8 2.5 - - - -
1985A ARG* 3.0 22.7 + - - +
1991A LEU* 4.9 0.2 - - + -
2021A PHE* 3.5 25.6 - - + -
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Residues in contact with TRP1972 (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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1818A GLY 3.1 28.0 - - - -
1819A HIS* 4.0 8.8 - + - -
1821A PRO* 3.7 28.7 - - + -
1950A TRP* 5.3 0.2 - + - -
1957A LEU* 3.7 32.1 - - + -
1958A PHE 3.6 0.9 - - - -
1959A ASP* 3.5 30.9 + - - -
1960A VAL* 4.3 2.2 - - - -
1971A LEU* 1.3 80.2 - - - +
1973A LEU* 1.3 62.1 + - - +
1974A GLY 3.4 0.7 + - - -
1981A SER 3.4 3.8 - - - +
1982A VAL* 3.5 3.1 - - - +
1983A TYR* 2.9 51.8 + + + +
1985A ARG* 3.8 10.5 - - + +
1986A GLY* 3.4 32.1 - - - -
1987A GLU 3.0 28.3 - - - -
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Residues in contact with LEU1973 (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 4.9 - - - +
1957A LEU* 4.5 0.2 - - - -
1958A PHE* 2.7 51.8 + - + +
1960A VAL* 3.8 31.9 - - + +
1972A TRP* 1.3 71.9 - - - +
1974A GLY* 1.3 58.7 + - - +
1975A VAL* 4.7 3.6 - - + -
1980A VAL* 5.8 3.1 - - + -
1981A SER 3.6 3.4 - - - +
1982A VAL* 3.9 15.0 - - + -
2010A TYR* 4.4 6.5 - - + -
2012A ILE* 4.2 19.1 - - + -
2021A PHE* 3.8 36.3 - - + -
2023A THR* 5.9 0.2 - - + -
2029A VAL* 4.2 27.1 - - + -
2033A MET* 4.8 1.6 - - + -
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Residues in contact with GLY1974 (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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1955A SER* 4.7 4.3 - - - -
1956A THR 3.7 5.2 - - - -
1957A LEU* 3.8 20.9 - - - -
1972A TRP 3.4 3.2 + - - -
1973A LEU* 1.3 70.3 - - - +
1975A VAL* 1.3 61.4 + - - -
1976A SER* 5.2 0.7 + - - -
1979A ALA 3.9 0.7 - - - +
1980A VAL* 3.1 4.7 - - - +
1981A SER* 2.7 43.7 + - - -
1983A TYR* 3.9 9.9 - - - -
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Residues in contact with VAL1975 (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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1955A SER* 3.2 1.7 - - - -
1956A THR* 2.7 36.8 + - - +
1958A PHE* 3.7 24.7 - - + -
1973A LEU* 4.3 5.6 - - + +
1974A GLY* 1.3 74.2 - - - +
1976A SER* 1.3 60.6 + - - +
1979A ALA 3.8 2.7 - - - -
1980A VAL* 4.2 11.2 - - + +
1996A TYR* 3.4 23.8 - - - +
2029A VAL* 4.3 16.2 - - + -
2032A LEU* 3.7 31.0 - - + -
2033A MET* 3.9 13.2 - - + +
2036A TYR* 4.0 7.1 - - + -
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Residues in contact with SER1976 (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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1953A TYR 6.0 0.2 - - - -
1954A GLY 4.2 5.6 - - - -
1955A SER* 3.6 24.1 + - - -
1974A GLY 5.2 1.0 + - - -
1975A VAL* 1.3 75.3 - - - +
1977A ALA* 1.3 67.4 + - - +
1978A ASP 3.1 2.6 + - - -
1979A ALA* 2.9 27.7 + - - +
1981A SER* 5.5 1.6 + - - -
1996A TYR* 3.1 19.9 + - - -
2036A TYR* 3.3 15.1 - - - -
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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