Contacts of the helix formed by residues 1929 - 1941 (chain X) in PDB entry 3SU8
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 LEU1929 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1710X LEU* 4.6 7.2 - - + -
1713X GLY 3.9 7.9 - - - +
1714X ILE* 3.8 37.7 - - + +
1717X GLN* 4.8 5.4 - - + -
1734X LEU* 4.3 13.9 - - + -
1925X MET* 3.3 40.9 + - + +
1926X LYS* 3.7 5.2 - - - +
1927X GLY 3.3 0.4 - - - -
1928X THR* 1.3 78.7 - - + +
1930X GLN* 1.4 57.7 + - - +
1931X LYS 3.5 1.8 - - - -
1932X PHE* 3.3 18.6 + - + +
1933X VAL* 3.0 33.5 + - + +
2008X VAL* 4.0 20.4 - - + -
2012X ILE* 4.7 2.5 - - + -
2038X TYR* 5.2 0.9 - - - +
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Residues in contact with GLN1930 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1926X LYS* 3.1 33.4 + - - +
1927X GLY* 3.5 18.2 - - - +
1928X THR 3.4 2.2 - - - -
1929X LEU* 1.4 76.3 - - - +
1931X LYS* 1.4 56.2 + - - +
1933X VAL* 3.3 2.9 + - - +
1934X ASP* 2.9 59.5 + - - +
2038X TYR* 3.6 12.3 - - - -
2041X ASP* 3.5 20.8 + - - +
2045X TYR* 3.0 27.5 + - - -
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Residues in contact with LYS1931 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1927X GLY 4.9 0.6 + - - -
1928X THR 4.9 3.2 + - - +
1929X LEU 3.5 0.6 - - - -
1930X GLN* 1.4 75.5 - - - +
1932X PHE* 1.4 73.4 + - + +
1934X ASP* 4.0 4.8 - - - +
1935X ASP* 3.0 62.9 + - - +
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Residues in contact with PHE1932 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1706X PRO 4.5 6.1 - - - +
1709X MET* 3.6 48.7 - - + -
1710X LEU* 3.8 25.4 - - + +
1713X GLY* 4.0 20.2 - - - -
1928X THR* 3.7 17.7 - - + -
1929X LEU* 3.3 29.1 + - + +
1930X GLN 3.3 0.6 - - - -
1931X LYS* 1.4 85.9 - - + +
1933X VAL* 1.4 59.7 + - - +
1935X ASP* 3.6 7.6 + - - +
1936X LEU* 3.1 30.0 + - - +
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Residues in contact with VAL1933 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1710X LEU* 3.9 18.8 - - + -
1929X LEU* 3.0 23.3 + - + +
1930X GLN* 3.8 6.1 - - - +
1932X PHE* 1.4 72.9 - - - +
1934X ASP* 1.4 62.6 + - - +
1936X LEU* 3.4 4.6 + - - +
1937X PHE* 3.1 48.9 + - + -
2012X ILE* 4.0 18.4 - - + -
2015X THR* 5.7 0.2 - - + -
2038X TYR* 4.0 31.6 - - + +
2045X TYR* 3.4 21.3 - - - +
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Residues in contact with ASP1934 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1930X GLN* 2.9 40.0 + - - +
1931X LYS* 4.0 5.2 - - - +
1933X VAL* 1.4 73.7 - - - +
1935X ASP* 1.4 56.6 + - - +
1937X PHE* 3.6 3.9 + - - +
1938X GLN* 3.0 44.6 + - - +
2044X ARG* 2.6 31.7 + - - +
2045X TYR* 2.7 20.7 + - - -
2048X MET* 5.0 0.5 - - - +
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Residues in contact with ASP1935 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1706X PRO* 4.2 13.2 - - + -
1931X LYS* 3.0 59.8 + - - +
1932X PHE* 3.9 8.5 + - - +
1934X ASP* 1.4 75.7 - - - +
1936X LEU* 1.3 56.8 + - - +
1938X GLN* 3.4 11.1 + - - +
1939X VAL* 3.1 35.0 + - + +
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Residues in contact with LEU1936 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1703X VAL* 3.9 12.1 - - + -
1706X PRO* 3.9 12.0 - - + +
1707X LEU* 3.8 48.9 - - + +
1710X LEU* 3.8 26.7 - - + -
1932X PHE 3.1 18.8 + - - +
1933X VAL* 3.4 4.7 + - - +
1935X ASP* 1.3 75.2 - - - +
1937X PHE* 1.4 68.4 + - + +
1939X VAL* 3.4 3.3 + - - +
1940X ILE* 3.1 47.5 + - + +
1990X ILE* 4.2 15.7 - - + -
2012X ILE* 5.2 1.1 - - + -
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Residues in contact with PHE1937 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1933X VAL* 3.1 30.3 + - + +
1934X ASP 4.1 2.7 - - - +
1936X LEU* 1.4 87.0 - - + +
1938X GLN* 1.4 59.9 + - - +
1940X ILE* 4.5 5.8 - - + -
1941X LEU* 3.1 40.4 + - + +
1990X ILE* 4.6 3.6 - - + -
2012X ILE* 3.7 36.3 - - + -
2015X THR* 4.0 9.0 - - + -
2016X PHE* 3.7 36.8 - + + -
2019X ALA* 5.7 1.1 - - + -
2045X TYR* 3.7 48.5 - + + -
2048X MET* 3.5 13.1 - - + +
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Residues in contact with GLN1938 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1934X ASP* 3.0 31.5 + - - +
1935X ASP* 3.7 11.5 + - - +
1936X LEU 3.3 0.2 - - - -
1937X PHE* 1.4 74.5 - - - +
1939X VAL* 1.4 57.7 + - + +
1941X LEU 3.4 1.6 - - - -
1942X SER* 2.9 32.0 + - - -
1945X ARG* 6.1 1.3 - - - +
2048X MET* 3.8 19.7 - - + -
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Residues in contact with VAL1939 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1698X PHE* 4.2 10.7 - - + -
1702X SER* 3.4 37.9 - - - +
1703X VAL* 4.0 15.5 - - + -
1706X PRO* 4.1 15.3 - - + -
1935X ASP* 3.1 22.8 + - + +
1936X LEU 3.8 3.4 - - - +
1938X GLN* 1.4 72.5 - - + +
1940X ILE* 1.4 65.9 + - - +
1942X SER* 3.3 19.4 + - - +
1945X ARG* 3.5 32.5 - - - +
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Residues in contact with ILE1940 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1698X PHE* 4.8 7.1 - - - -
1703X VAL* 3.8 21.5 - - + -
1936X LEU* 3.1 44.6 + - + +
1937X PHE* 4.1 6.1 - - + +
1939X VAL* 1.4 75.2 - - - +
1941X LEU* 1.3 62.7 + - + +
1942X SER 3.4 1.8 + - - -
1986X TRP* 3.7 48.4 + - + +
1990X ILE* 4.3 20.9 - - + -
2016X PHE* 3.7 25.1 - - + -
2052X TYR* 3.6 19.7 + - + -
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Residues in contact with LEU1941 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1937X PHE* 3.1 26.5 + - + +
1938X GLN* 3.4 4.3 - - - -
1940X ILE* 1.3 85.0 - - + +
1942X SER* 1.4 60.7 + - - +
1943X THR* 3.6 5.9 + - - +
1982X PRO* 5.7 4.9 - - + -
2016X PHE* 4.2 19.3 - - + -
2019X ALA* 5.8 1.1 - - + -
2020X CYS* 5.6 1.1 - - - -
2045X TYR* 4.8 2.0 - - + +
2048X MET* 4.1 31.4 - - + +
2049X VAL* 3.8 36.8 - - + -
2052X TYR* 3.3 48.8 - - + +
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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