Contacts of the helix formed by residues 1925 - 1934 (chain A) in PDB entry 5NP1
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 GLY1925 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1923A SER 2.9 8.7 - - - +
1924A SER* 1.3 76.1 - - - +
1926A THR* 1.3 59.0 + - - -
1927A ILE* 2.8 14.8 - - - -
1928A PHE* 2.9 27.1 + - - +
1929A ASN 3.0 6.8 + - - -
2787A ALA* 5.0 5.9 - - - +
2833A TYR* 6.1 4.9 - - - -
2837A GLU* 5.8 5.2 - - - -
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Residues in contact with THR1926 (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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1918A ARG* 3.9 24.2 - - - -
1923A SER 3.1 11.0 - - - -
1924A SER 2.8 8.8 + - - -
1925A GLY* 1.3 70.5 - - - -
1927A ILE* 1.3 52.8 - - - +
1929A ASN* 2.8 5.3 + - - +
1930A ASP* 2.1 41.8 + - - +
2837A GLU* 5.7 4.7 - - - +
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Residues in contact with ILE1927 (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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1925A GLY* 3.6 7.2 - - - -
1926A THR* 1.3 73.8 - - - +
1928A PHE* 1.3 54.7 + - - +
1930A ASP* 3.2 8.9 - - - +
1931A ALA* 2.3 41.0 + - - +
1960A ILE* 6.1 4.5 - - + -
1963A ASP* 5.8 8.1 - - + -
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Residues in contact with PHE1928 (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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1923A SER* 3.8 9.9 - - - -
1925A GLY* 2.9 18.3 + - - +
1927A ILE* 1.3 78.6 - - - +
1929A ASN* 1.3 50.3 - - - +
1931A ALA* 2.9 8.4 + - - +
1932A PHE* 2.2 41.2 + - - +
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Residues in contact with ASN1929 (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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1917A ARG 5.2 0.9 - - - -
1918A ARG 4.1 10.8 - - - +
1920A LYS 3.2 10.4 - - - +
1921A ARG 3.1 28.0 - - - +
1923A SER* 3.2 18.5 - - - +
1925A GLY 3.0 2.4 + - - -
1926A THR* 2.8 21.2 + - - +
1928A PHE* 1.3 75.4 - - - +
1930A ASP* 1.3 48.7 + - - -
1932A PHE* 3.1 3.9 - - - +
1933A TRP* 2.2 40.1 + - - +
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Residues in contact with ASP1930 (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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1913A VAL* 4.2 17.7 - - - +
1914A ASP* 4.7 12.8 - - - +
1917A ARG* 4.7 3.3 + - + -
1918A ARG 5.5 0.2 + - - -
1926A THR* 2.1 30.0 + - - +
1927A ILE* 3.2 11.2 - - - +
1929A ASN* 1.3 67.2 - - - +
1931A ALA* 1.3 51.6 + - - +
1933A TRP* 2.9 8.5 + - - +
1934A LEU* 2.1 43.3 + - + +
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Residues in contact with ALA1931 (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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1927A ILE 2.3 28.2 + - - +
1928A PHE* 3.1 12.1 - - - +
1930A ASP* 1.3 65.6 - - - +
1932A PHE* 1.3 58.0 + - - +
1934A LEU* 2.8 34.4 + - - +
1936A LEU* 3.5 24.9 + - + +
1964A LYS* 6.5 1.6 - - + -
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Residues in contact with PHE1932 (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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1879A GLN* 6.1 1.2 - - - +
1921A ARG* 3.5 24.5 - - + +
1923A SER* 5.5 0.9 - - - -
1928A PHE 2.2 27.8 + - - +
1929A ASN* 3.1 11.7 - - - +
1931A ALA* 1.3 63.9 - - - +
1933A TRP* 1.3 67.8 + - - +
1934A LEU 2.8 10.6 - - - +
1936A LEU* 5.8 0.4 - - - -
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Residues in contact with TRP1933 (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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1871A THR* 4.7 17.5 - - - -
1913A VAL* 5.4 3.7 - - + +
1917A ARG* 3.4 32.5 - - + -
1920A LYS* 3.4 21.8 + - + -
1921A ARG* 4.4 1.7 - - - +
1929A ASN 2.2 31.7 + - - +
1930A ASP 3.3 3.1 - - - +
1932A PHE* 1.3 67.1 - - - +
1934A LEU* 1.3 61.6 + - - +
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Residues in contact with LEU1934 (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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1879A GLN* 5.6 2.1 - - - +
1882A ARG* 6.5 0.7 - - - -
1913A VAL* 4.8 16.1 - - + +
1930A ASP 2.1 32.2 + - - +
1931A ALA* 2.8 16.3 + - - +
1932A PHE 2.8 14.7 - - - +
1933A TRP* 1.3 71.3 - - - +
1935A ASP* 1.3 60.2 + - - +
1936A LEU* 3.1 10.2 - - - +
1937A ASN 6.5 0.2 - - - -
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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