Contacts of the helix formed by residues 1915 - 1929 (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 PRO1915 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1741X ARG* 6.3 1.1 - - - +
1913X ALA 3.3 7.8 - - - +
1914X ILE* 1.4 86.4 - - + +
1916X GLU* 1.3 66.7 + - - +
1917X ILE* 4.0 13.5 - - + -
1918X TYR* 3.0 37.2 + - + -
1919X LEU* 2.9 18.7 + - - +
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Residues in contact with GLU1916 (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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1914X ILE 3.5 2.8 + - - -
1915X PRO* 1.3 70.3 - - + +
1917X ILE* 1.4 66.3 + - + +
1919X LEU* 4.2 11.7 - - + -
1920X THR* 2.7 43.4 + - - +
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Residues in contact with ILE1917 (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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1915X PRO* 4.0 15.5 - - + -
1916X GLU* 1.4 90.0 - - + +
1918X TYR* 1.3 92.9 + - + +
1920X THR* 4.2 4.3 - - - -
1921X ARG* 3.4 24.3 + - - +
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Residues in contact with TYR1918 (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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1736X ASP* 6.2 1.1 - - + -
1739X LEU* 3.7 26.9 - - + +
1741X ARG* 3.6 63.8 + - + +
1914X ILE* 4.2 8.7 - - + -
1915X PRO* 3.0 39.3 + - + +
1917X ILE* 1.3 98.4 - - + +
1919X LEU* 1.3 64.9 + - - +
1920X THR 3.3 0.4 - - - -
1921X ARG* 3.3 14.3 + - - +
1922X LEU* 3.2 28.4 + - + +
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Residues in contact with LEU1919 (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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1914X ILE* 3.9 35.8 - - + +
1915X PRO 2.9 15.3 + - - +
1916X GLU* 3.9 10.8 - - + +
1918X TYR* 1.3 75.0 - - - +
1920X THR* 1.4 52.9 + - - +
1922X LEU* 3.2 14.4 + - + +
1923X LEU* 2.8 56.2 + - + +
2033X ILE* 4.8 5.8 - - + -
2036X LEU* 5.0 18.8 - - + -
2037X LEU* 5.2 4.5 - - + -
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Residues in contact with THR1920 (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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1916X GLU* 2.7 26.5 + - - +
1917X ILE* 4.2 6.1 - - - -
1919X LEU* 1.4 74.5 - - - +
1921X ARG* 1.3 53.3 + - + +
1923X LEU* 3.3 8.7 + - - +
1924X SER* 2.8 37.6 + - - -
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Residues in contact with ARG1921 (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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1731X LYS* 3.3 48.1 + - - +
1732X TYR* 5.5 5.0 - - - -
1733X THR 4.6 1.3 + - - +
1739X LEU* 3.8 29.0 - - + +
1740X LEU* 2.8 34.4 + - - +
1741X ARG* 3.7 14.6 + - - +
1742X GLU 5.4 1.0 - - - -
1743X ASP* 5.6 5.2 - - - +
1917X ILE 3.4 18.6 - - - +
1918X TYR* 3.3 14.6 + - - +
1919X LEU 3.3 0.2 - - - -
1920X THR* 1.3 77.4 - - + +
1922X LEU* 1.3 57.8 - - - +
1924X SER* 3.7 7.5 + - - -
1925X MET* 3.4 20.6 + - - +
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Residues in contact with LEU1922 (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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1733X THR 3.3 26.5 - - - +
1734X LEU* 3.6 24.2 - - - +
1735X ASN 3.8 13.7 - - - +
1736X ASP* 3.9 15.3 - - + +
1739X LEU* 4.0 15.5 - - + -
1914X ILE* 4.3 5.6 - - + -
1918X TYR* 3.2 18.8 + - + +
1919X LEU* 3.2 14.9 + - + +
1921X ARG* 1.3 74.4 - - - +
1923X LEU* 1.4 58.9 + - - +
1924X SER 3.3 0.2 - - - -
1925X MET* 3.3 5.4 + - - +
1926X LYS 3.1 21.3 + - - -
2033X ILE* 3.9 24.2 - - + -
2037X LEU* 3.7 19.9 - - + +
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Residues in contact with LEU1923 (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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1919X LEU* 2.8 48.6 + - + +
1920X THR* 3.8 7.9 - - - +
1922X LEU* 1.4 70.9 - - - +
1924X SER* 1.4 63.0 + - - +
1926X LYS* 3.6 15.3 + - + +
1927X GLY* 3.3 17.7 + - - -
2036X LEU 4.6 5.4 - - - +
2037X LEU* 3.8 40.6 - - + +
2040X ARG* 6.1 7.2 - - - +
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Residues in contact with SER1924 (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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1732X TYR* 6.0 3.7 - - - -
1920X THR* 2.8 19.8 + - - -
1921X ARG* 3.7 9.4 - - - -
1923X LEU* 1.4 75.6 - - - +
1925X MET* 1.4 56.9 + - - +
1927X GLY* 3.4 3.7 + - - -
1928X THR* 2.8 31.2 + - - -
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Residues in contact with MET1925 (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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1714X ILE* 4.4 8.7 - - + -
1717X GLN* 3.7 30.3 - - + -
1718X VAL* 3.8 28.9 - - + -
1732X TYR* 3.8 23.0 - - + +
1733X THR* 3.4 31.4 - - - +
1734X LEU* 3.9 9.0 - - + -
1921X ARG 3.4 9.2 + - - +
1922X LEU 3.3 10.2 + - - +
1924X SER* 1.4 76.4 - - - +
1926X LYS* 1.4 63.4 + - - +
1928X THR* 3.3 14.0 + - - -
1929X LEU* 3.3 35.9 + - + +
2008X VAL* 4.5 3.6 - - + -
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Residues in contact with LYS1926 (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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1734X LEU* 3.7 15.2 - - + +
1922X LEU 3.1 13.2 + - - +
1923X LEU* 3.6 21.5 - - + +
1925X MET* 1.4 74.3 - - - +
1927X GLY* 1.3 61.1 + - - +
1929X LEU* 3.4 5.4 + - - +
1930X GLN* 3.1 41.2 + - - +
2037X LEU* 3.3 30.2 + - + +
2038X TYR* 3.7 31.9 + - + -
2040X ARG* 4.9 15.2 - - - +
2041X ASP* 3.0 28.8 + - - -
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Residues in contact with GLY1927 (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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1923X LEU 3.3 10.3 + - - -
1924X SER 3.4 4.7 + - - -
1925X MET 3.3 0.4 - - - -
1926X LYS* 1.3 81.6 - - - +
1928X THR* 1.3 60.8 + - - +
1930X GLN* 3.4 20.6 + - - +
1931X LYS 4.9 0.9 + - - -
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Residues in contact with THR1928 (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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1717X GLN* 3.3 42.3 + - + +
1924X SER* 2.8 18.4 + - - -
1925X MET* 3.3 9.8 + - - -
1927X GLY* 1.3 74.6 - - - +
1929X LEU* 1.3 61.4 + - + +
1930X GLN 3.7 0.3 + - - -
1931X LYS* 4.9 3.8 + - - +
1932X PHE* 3.7 16.1 - - + -
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Residues in contact with LEU1929 (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* 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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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