Contacts of the helix formed by residues 1918 - 1928 (chain A) in PDB entry 4M6W
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 TYR1918 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1868A GLN* 4.8 16.3 + - + +
1871A MET* 3.4 46.7 - - + +
1872A LEU* 3.6 31.9 - - + +
1874A SER* 4.0 13.7 - - - +
1877A LYS* 5.8 0.7 - - - +
1898A VAL* 5.1 3.3 - - + +
1916A LYS 3.0 11.4 + - - +
1917A SER* 1.3 74.9 - - - +
1919A ASP* 1.3 72.6 + - - +
1920A SER* 3.0 2.9 - - - -
1921A LEU* 3.0 38.4 + - + +
1922A LEU* 3.2 38.5 + - + +
1934A PHE* 4.6 12.3 - - - -
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Residues in contact with ASP1919 (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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1916A LYS 3.4 22.7 + - - -
1917A SER* 3.4 4.0 - - - -
1918A TYR* 1.3 88.1 - - - +
1920A SER* 1.3 56.4 + - - +
1922A LEU* 3.6 13.1 + - - +
1923A THR* 3.1 32.7 + - - +
124B GLU 4.7 2.1 - - - +
127B CYS* 4.5 8.6 - - - +
128B LEU* 4.0 38.3 + - + +
131B GLN* 4.2 14.4 - - + -
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Residues in contact with SER1920 (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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1877A LYS* 3.3 18.6 + - - -
1917A SER 3.2 18.0 + - - -
1919A ASP* 1.3 76.6 - - - +
1921A LEU* 1.3 63.4 + - - +
1923A THR* 2.8 20.3 + - - -
1924A THR* 2.8 23.3 - - - +
131B GLN* 3.9 22.4 - - - +
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Residues in contact with LEU1921 (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 MET* 4.1 38.4 - - + +
1874A SER* 5.8 0.7 - - - +
1877A LYS* 3.9 33.6 - - + +
1880A PHE* 3.8 17.3 - - + -
1881A ILE* 4.3 17.0 - - + -
1918A TYR* 3.0 29.4 + - + +
1920A SER* 1.3 82.9 + - - +
1922A LEU* 1.3 62.4 + - + +
1924A THR* 3.4 6.9 + - - +
1925A LEU* 3.2 36.5 + - + +
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Residues in contact with LEU1922 (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 MET* 6.0 1.8 - - - -
1898A VAL* 5.4 4.0 - - + -
1918A TYR* 3.2 46.5 + - + +
1919A ASP* 3.8 15.0 - - - +
1920A SER 3.3 0.2 - - - -
1921A LEU* 1.3 81.5 - - + +
1923A THR* 1.3 57.0 + - + +
1925A LEU* 3.3 19.5 + - + +
1926A ILE* 2.9 41.3 + - + +
1932A ILE* 4.8 23.6 - - + +
1934A PHE* 4.9 12.6 - - + -
117B LEU* 4.9 12.8 - - + -
128B LEU* 5.1 9.4 - - + -
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Residues in contact with THR1923 (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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1919A ASP 3.1 16.8 + - - +
1920A SER* 2.8 24.8 + - - -
1922A LEU* 1.3 72.9 - - + +
1924A THR* 1.3 60.3 + - - +
1926A ILE* 3.8 8.8 - - + +
1927A GLY* 2.8 27.2 + - - -
128B LEU* 4.8 9.9 - - + +
131B GLN* 3.8 24.0 + - + +
132B LEU* 3.9 27.0 - - + +
135B GLU* 3.6 28.0 + - - +
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Residues in contact with THR1924 (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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1877A LYS* 5.7 2.2 - - - -
1881A ILE* 4.8 11.6 - - + +
1920A SER* 2.8 30.2 + - - +
1921A LEU* 3.5 12.5 + - - +
1922A LEU 3.4 0.2 - - - -
1923A THR* 1.3 74.8 + - - +
1925A LEU* 1.3 60.7 + - - +
1927A GLY 3.4 0.7 + - - -
1928A ALA* 2.9 31.2 + - - +
135B GLU* 4.1 15.5 - - - +
143B ASN* 3.8 26.3 - - + +
144B PRO* 5.0 7.6 - - + +
145B LEU* 3.5 16.8 - - - +
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Residues in contact with LEU1925 (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 MET* 5.6 1.8 - - - -
1880A PHE* 4.0 25.6 - - + -
1881A ILE* 6.2 0.7 - - + -
1884A ILE* 4.1 12.3 - - + -
1896A VAL* 4.6 13.5 - - + -
1921A LEU* 3.2 33.0 + - + +
1922A LEU* 3.4 24.5 - - + +
1923A THR 3.2 0.2 - - - -
1924A THR* 1.3 80.8 + - - +
1926A ILE* 1.3 62.2 + - + +
1928A ALA* 3.0 10.7 + - - +
1930A ILE* 3.1 56.1 + - + +
1932A ILE* 5.3 6.7 - - + -
145B LEU* 4.1 9.4 - - + -
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Residues in contact with ILE1926 (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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1922A LEU* 2.9 29.2 + - + +
1923A THR* 3.8 10.3 - - + +
1925A LEU* 1.3 74.0 - - - +
1927A GLY* 1.3 59.4 + - - +
1929A GLY* 2.9 22.2 + - - -
1930A ILE 4.2 6.9 + - - -
1932A ILE* 4.5 11.7 - - + -
86B LYS* 4.6 18.1 + - - +
88B ILE* 4.6 13.2 - - + -
115B VAL* 3.9 34.5 - - + +
117B LEU* 3.8 35.9 - - + -
128B LEU* 6.1 0.4 - - + -
132B LEU* 4.7 11.9 - - + -
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Residues in contact with GLY1927 (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 THR 2.8 21.9 + - - -
1924A THR 3.7 1.6 - - - -
1926A ILE* 1.3 74.7 - - - +
1928A ALA* 1.3 58.7 + - - +
1929A GLY 3.2 1.1 + - - -
86B LYS* 6.3 0.7 - - - -
135B GLU* 4.3 14.6 - - - -
143B ASN* 4.5 5.6 - - - -
146B LEU* 3.9 13.7 - - - +
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Residues in contact with ALA1928 (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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1888A GLN* 4.0 10.0 + - - +
1924A THR 2.9 17.5 + - - +
1925A LEU 3.0 5.8 + - - +
1927A GLY* 1.3 76.1 - - - +
1929A GLY* 1.3 61.3 + - - +
1930A ILE* 3.3 16.4 + - + +
143B ASN* 4.4 1.6 - - - +
145B LEU* 3.5 31.2 - - + +
146B LEU* 4.7 12.8 - - - +
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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