Contacts of the helix formed by residues 1935 - 1948 (chain A) in PDB entry 3PZD
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 ASN1935 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1836A GLN 5.9 0.9 - - - -
1933A GLY 3.4 6.0 + - - +
1934A MET* 1.3 75.9 - - - +
1936A GLN* 1.3 58.2 + - - +
1937A GLU* 3.3 10.7 + - - +
1938A GLN* 2.9 46.5 + - - +
1939A ALA* 2.9 27.3 + - - +
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Residues in contact with GLN1936 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1836A GLN 5.4 0.9 - - - +
1837A TYR* 3.0 63.0 + - + +
1838A LEU* 5.1 3.0 + - - +
1935A ASN* 1.3 75.5 - - - +
1937A GLU* 1.3 59.0 + - - +
1939A ALA* 3.1 4.7 + - - +
1940A MET* 2.8 33.7 + - + +
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Residues in contact with GLU1937 (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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1799A LYS* 5.8 5.3 - - + +
1800A ASP* 6.6 0.4 - - + -
1804A PHE* 5.9 0.2 - - - -
1935A ASN* 3.3 8.4 + - - +
1936A GLN* 1.3 78.8 - - - +
1938A GLN* 1.3 57.7 + - + +
1940A MET* 3.7 15.8 + - + +
1941A ALA* 3.0 29.3 + - - +
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Residues in contact with GLN1938 (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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1933A GLY 4.1 3.3 - - - +
1934A MET* 3.5 19.7 - - + +
1935A ASN* 2.9 47.2 + - - +
1937A GLU* 1.3 76.0 - - + +
1939A ALA* 1.3 65.3 + - - +
1941A ALA* 3.3 5.1 + - - +
1942A LYS* 3.0 24.6 + - - +
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Residues in contact with ALA1939 (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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1833A LEU* 4.0 24.6 - - + +
1836A GLN* 4.5 2.5 - - + -
1837A TYR* 4.0 19.1 - - + +
1934A MET* 3.7 23.5 - - + +
1935A ASN 2.9 14.6 + - - +
1936A GLN 3.5 6.7 - - - +
1938A GLN* 1.3 76.6 - - - +
1940A MET* 1.3 58.6 + - - +
1942A LYS* 3.2 1.6 + - - +
1943A TYR* 2.9 31.8 + - - +
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Residues in contact with MET1940 (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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1799A LYS* 3.5 24.5 - - + +
1800A ASP* 5.4 2.0 - - - -
1801A SER 5.6 0.9 - - - +
1804A PHE* 3.8 22.0 - - + -
1805A ALA* 4.2 16.8 - - + +
1808A PHE* 3.8 40.8 - - + -
1837A TYR* 4.2 20.1 - - + +
1936A GLN 2.8 13.8 + - - +
1937A GLU* 4.0 16.8 - - + +
1939A ALA* 1.3 77.9 - - - +
1941A ALA* 1.3 55.1 + - - +
1943A TYR* 3.5 6.4 + - - +
1944A MET* 2.9 30.8 + - - +
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Residues in contact with ALA1941 (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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1799A LYS* 4.6 22.9 - - + +
1804A PHE* 4.5 10.0 - - - -
1937A GLU 3.0 19.6 + - - +
1938A GLN* 3.8 5.8 - - - +
1939A ALA 3.2 0.2 - - - -
1940A MET* 1.3 74.5 - - - +
1942A LYS* 1.3 65.4 + - - +
1944A MET* 3.4 2.2 + - - +
1945A ALA* 2.9 24.4 + - - +
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Residues in contact with LYS1942 (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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1829A VAL* 4.7 5.2 - - - +
1833A LEU* 3.9 25.6 - - + -
1931A PHE* 3.7 25.7 - - - -
1934A MET* 4.6 11.6 - - + +
1938A GLN 3.0 17.7 + - - +
1939A ALA 3.8 2.5 - - - +
1941A ALA* 1.3 75.5 - - - +
1943A TYR* 1.3 63.7 + - - +
1945A ALA* 3.3 6.8 + - + +
1946A LEU* 3.1 43.6 + - + +
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Residues in contact with TYR1943 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1808A PHE* 3.5 34.1 - + + -
1811A ALA* 4.6 1.8 - - + -
1812A HIS* 2.8 51.3 + - + -
1815A VAL* 3.6 14.4 - - + +
1830A LEU* 3.3 44.9 - - + +
1833A LEU* 3.8 20.5 - - + +
1834A ARG* 4.2 7.2 - - + -
1939A ALA 2.9 18.4 + - - +
1940A MET 3.6 4.9 - - - +
1942A LYS* 1.3 78.5 - - - +
1944A MET* 1.3 58.1 + - - +
1946A LEU* 3.3 3.8 + - - +
1947A ILE* 3.1 51.2 + - + +
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Residues in contact with MET1944 (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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1804A PHE* 3.6 29.8 - - + -
1807A MET* 4.1 26.9 - - + +
1808A PHE* 3.6 34.8 - - + -
1811A ALA* 4.1 13.7 - - + -
1940A MET 2.9 22.0 + - - +
1941A ALA 4.0 1.3 - - - +
1943A TYR* 1.3 77.0 - - - +
1945A ALA* 1.3 64.9 + - - +
1947A ILE* 3.4 6.3 + - + +
1948A LYS* 3.0 36.5 + - - +
1953A TYR* 3.6 32.1 - - + +
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Residues in contact with ALA1945 (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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1941A ALA 2.9 17.3 + - - +
1942A LYS* 3.8 7.0 - - + +
1944A MET* 1.3 75.8 - - - +
1946A LEU* 1.3 63.3 + - + +
1948A LYS* 3.3 16.1 + - - +
1949A GLU* 3.4 22.3 + - - +
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Residues in contact with LEU1946 (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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1820A HIS* 4.7 3.7 + - - -
1826A ASN* 5.6 8.7 - - + +
1829A VAL* 3.6 30.7 - - + -
1830A LEU* 3.8 15.3 - - + -
1833A LEU* 3.7 21.1 - - + -
1942A LYS* 3.1 26.2 + - + +
1943A TYR 3.5 7.0 - - - +
1945A ALA* 1.3 74.9 - - + +
1947A ILE* 1.3 64.7 + - - +
1949A GLU* 3.4 35.6 + - - +
1950A TRP 4.3 1.4 + - - -
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Residues in contact with ILE1947 (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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1811A ALA* 4.2 13.0 - - + +
1815A VAL* 3.6 27.8 - - + -
1820A HIS* 3.3 36.5 - - + +
1830A LEU* 3.7 11.9 - - + -
1943A TYR* 3.1 37.4 + - + +
1944A MET* 3.6 12.8 - - + +
1946A LEU* 1.3 76.3 - - - +
1948A LYS* 1.3 56.6 + - - +
1949A GLU 3.1 0.2 - - - -
1950A TRP* 3.1 19.1 + - - +
1953A TYR* 3.4 40.9 - - + +
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Residues in contact with LYS1948 (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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1794A THR* 3.0 40.3 + - - +
1795A ASP* 4.1 24.4 + - - +
1799A LYS* 4.8 9.7 - - - +
1804A PHE* 4.5 11.9 - - - -
1807A MET* 4.6 7.6 - - - -
1944A MET* 3.0 31.8 + - + +
1945A ALA* 3.3 9.1 + - - +
1947A ILE* 1.3 73.7 - - + +
1949A GLU* 1.3 58.8 + - - +
1950A TRP 3.2 10.9 - - - +
1951A PRO* 4.9 1.2 - - - +
1953A TYR* 4.0 24.7 - - + -
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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