Contacts of the helix formed by residues 1927 - 1938 (chain D) in PDB entry 1GZH
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 PRO1927 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1877D VAL* 3.7 17.9 - - + -
1903D HIS* 5.5 5.2 - - - +
1905D SER* 4.0 25.4 - - - +
1925D SER 3.3 7.8 - - - +
1926D CYS* 1.3 86.6 - - - +
1928D ALA* 1.3 66.2 + - - +
1929D SER* 3.1 10.8 - - - +
1930D VAL* 3.1 38.4 + - + +
1931D LEU* 3.4 7.1 + - - +
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Residues in contact with ALA1928 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1926D CYS 3.4 3.0 + - - -
1927D PRO* 1.3 71.4 - - - +
1929D SER* 1.3 62.2 + - - +
1931D LEU* 3.3 16.3 + - + +
1932D LYS* 3.1 29.6 + - + +
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Residues in contact with SER1929 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1927D PRO* 4.1 8.9 - - - +
1928D ALA* 1.3 79.8 - - - +
1930D VAL* 1.3 68.7 + - - +
1932D LYS* 3.7 6.0 + - - +
1933D CYS* 3.1 35.9 + - - -
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Residues in contact with VAL1930 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1875D LEU* 5.1 2.5 - - + -
1877D VAL* 4.5 15.7 - - + -
1903D HIS* 5.5 7.6 - - + +
1914D LEU* 4.4 23.3 - - + +
1920D VAL* 5.1 9.0 - - + -
1926D CYS* 4.0 15.5 - - - -
1927D PRO* 3.1 32.7 + - + +
1929D SER* 1.3 83.2 - - - +
1931D LEU* 1.3 60.8 + - + +
1933D CYS* 3.9 4.5 - - - +
1934D ALA* 3.0 28.9 + - + +
1941D VAL* 6.0 1.3 - - + -
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Residues in contact with LEU1931 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1926D CYS* 3.3 33.0 - - + +
1927D PRO 3.7 10.3 - - - +
1928D ALA* 3.3 15.0 + - + +
1929D SER 3.3 0.4 - - - -
1930D VAL* 1.3 74.5 - - - +
1932D LYS* 1.3 66.5 + - + +
1934D ALA* 3.3 7.5 + - - +
1935D GLU* 3.0 31.4 + - + +
1941D VAL* 4.4 15.5 - - + -
1967D HIS* 3.4 39.5 - - + +
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Residues in contact with LYS1932 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1928D ALA* 3.1 18.9 + - + +
1929D SER* 3.8 7.2 - - - +
1931D LEU* 1.3 79.9 - - + +
1933D CYS* 1.3 62.8 + - - +
1935D GLU* 3.3 22.2 + - - +
1936D ALA* 3.1 21.0 + - - +
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Residues in contact with CYS1933 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1914D LEU* 3.3 27.1 - - + -
1929D SER* 3.1 23.7 + - - +
1930D VAL* 3.9 0.9 - - - +
1932D LYS* 1.3 76.1 - - - +
1934D ALA* 1.3 67.5 + - - +
1936D ALA* 3.0 9.7 + - - +
1937D LEU* 2.9 30.4 + - + +
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Residues in contact with ALA1934 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1914D LEU* 4.3 3.9 - - + +
1920D VAL* 5.2 2.5 - - + -
1930D VAL* 3.0 19.8 + - + +
1931D LEU 3.5 4.7 - - - +
1933D CYS* 1.3 75.6 - - - +
1935D GLU* 1.3 58.2 + - - +
1937D LEU* 3.3 2.1 + - - -
1938D GLN 2.8 24.9 + - - -
1939D LEU* 2.8 46.6 + - + +
1941D VAL* 3.6 19.5 - - + -
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Residues in contact with GLU1935 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1931D LEU* 3.0 17.7 + - + +
1932D LYS* 3.3 30.9 + - - +
1934D ALA* 1.3 75.0 - - - +
1936D ALA* 1.3 56.8 + - - +
1938D GLN* 2.8 28.6 + - - +
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Residues in contact with ALA1936 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1932D LYS 3.1 8.3 + - - +
1933D CYS* 3.0 12.9 + - - +
1935D GLU* 1.3 80.1 - - - +
1937D LEU* 1.3 63.1 + - + +
1938D GLN* 3.4 6.4 + - - +
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Residues in contact with LEU1937 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1914D LEU* 3.4 38.1 - - + +
1915D GLY* 3.8 19.5 - - - +
1933D CYS* 2.9 20.8 + - + +
1934D ALA* 3.9 3.6 - - - +
1936D ALA* 1.3 79.2 - - + +
1938D GLN* 1.3 73.1 + - - +
1939D LEU* 4.3 8.3 - - + +
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Residues in contact with GLN1938 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1934D ALA 2.8 6.6 + - - -
1935D GLU* 2.8 18.0 + - - +
1936D ALA 4.2 5.8 - - - +
1937D LEU* 1.3 82.3 - - - +
1939D LEU* 1.3 58.5 + - - +
1940D PRO* 3.7 7.9 - - - +
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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