Contacts of the helix formed by residues 1943 - 1954 (chain B) 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 SER1943 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1921B VAL* 4.2 4.0 - - - +
1922B THR 3.4 10.5 - - - -
1923B ASP* 5.8 0.2 - - - -
1942B VAL* 1.3 78.1 - - - +
1944B GLN* 1.3 65.5 + - - +
1945B GLU* 3.0 10.4 + - - +
1946B TRP* 3.0 17.8 + - - +
1947B VAL 4.0 1.2 + - - -
1964B LYS 2.6 25.8 + - - -
1965B TYR* 2.5 17.2 + - - -
1966B LYS 3.6 13.9 - - - -
1967B HIS* 4.0 7.9 - - - +
1969B TYR* 5.6 1.8 - - - -
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Residues in contact with GLN1944 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1811B ARG* 5.3 3.2 - - - +
1883B ASN 5.2 1.2 - - - +
1884B PHE* 3.8 20.1 - - + -
1888B TRP* 3.2 46.4 + - + +
1921B VAL* 4.3 10.7 - - - +
1922B THR 4.0 5.3 + - - -
1943B SER* 1.3 74.4 - - - +
1945B GLU* 1.3 65.0 + - + +
1946B TRP 3.1 0.2 - - - -
1947B VAL* 3.1 8.1 + - - +
1948B ILE* 3.0 39.3 + - + +
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Residues in contact with GLU1945 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1811B ARG* 2.9 44.9 + - - -
1854B LEU* 3.7 24.8 - - + +
1943B SER* 3.0 13.0 + - - +
1944B GLN* 1.3 81.9 + - + +
1946B TRP* 1.3 62.0 + - - +
1948B ILE* 3.8 9.5 - - - +
1949B GLN* 2.8 48.2 + - - +
1964B LYS* 3.7 19.3 - - + +
1965B TYR* 4.1 4.5 - - + -
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Residues in contact with TRP1946 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1869B PHE* 4.6 8.3 - + - -
1872B LEU* 4.1 25.1 - - + -
1892B LEU* 5.5 1.1 - - + -
1919B VAL* 4.4 8.1 - - + -
1921B VAL* 4.7 3.4 - - + -
1942B VAL* 3.5 28.5 - - + -
1943B SER 3.0 12.6 + - - +
1945B GLU* 1.3 77.5 - - - +
1947B VAL* 1.3 84.4 + - + +
1949B GLN* 3.9 1.4 - - - +
1950B CYS* 3.0 43.9 + - - -
1956B ARG* 3.8 19.7 - - + -
1957B ILE* 2.8 44.1 + - + +
1958B GLY 3.5 12.1 + - - -
1959B PHE* 3.2 39.9 - + - -
1965B TYR* 3.8 21.0 - + + -
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Residues in contact with VAL1947 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1869B PHE* 3.6 25.6 - - + -
1888B TRP* 3.8 27.4 - - + -
1891B ILE* 4.6 3.8 - - + -
1892B LEU* 4.3 15.9 - - + -
1921B VAL* 3.8 38.1 - - + -
1943B SER 4.5 0.2 - - - +
1944B GLN* 3.1 11.4 + - - +
1946B TRP* 1.3 86.4 - - + +
1948B ILE* 1.3 63.9 + - - +
1950B CYS* 3.0 14.3 + - - +
1951B LEU* 3.1 18.0 + - + +
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Residues in contact with ILE1948 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1811B ARG* 3.7 25.8 - - - +
1816B PHE* 3.7 29.8 - - + -
1888B TRP* 3.4 29.8 - - + -
1944B GLN* 3.0 26.1 + - - +
1945B GLU* 3.8 24.5 - - - +
1947B VAL* 1.3 75.9 - - - +
1949B GLN* 1.3 64.2 + - - +
1951B LEU* 2.9 11.8 + - - +
1952B ILE* 2.9 45.0 + - + +
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Residues in contact with GLN1949 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1811B ARG* 4.5 4.8 - - - +
1852B TYR 3.5 15.6 + - - +
1853B SER* 3.6 10.6 + - - -
1854B LEU* 3.1 38.9 + - + +
1855B GLU 4.8 0.5 + - - -
1945B GLU* 2.8 44.9 + - - +
1946B TRP 3.9 3.1 - - - +
1948B ILE* 1.3 73.2 - - - +
1950B CYS* 1.3 57.7 + - - +
1952B ILE* 4.4 6.2 - - - +
1953B VAL* 2.8 40.6 + - + +
1957B ILE* 4.3 6.7 - - + -
1965B TYR* 3.1 35.2 + - + +
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Residues in contact with CYS1950 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1868B PRO* 4.1 7.6 - - + +
1869B PHE* 3.6 23.1 - - + -
1946B TRP* 3.0 46.7 + - - -
1947B VAL 3.2 8.7 - - - +
1949B GLN* 1.3 76.4 - - - +
1951B LEU* 1.3 58.2 + - - +
1954B GLY* 2.9 22.9 + - - -
1955B GLU 3.2 19.0 + - - +
1956B ARG* 3.8 6.7 - - - -
1957B ILE* 3.7 28.7 - - - +
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Residues in contact with LEU1951 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1816B PHE* 3.9 22.2 - - + +
1819B LEU* 3.9 22.8 - - + +
1820B ALA* 3.5 35.4 - - + +
1865B ARG* 3.0 27.7 + - - +
1868B PRO* 4.0 10.8 - - + -
1869B PHE* 3.9 16.8 - - + -
1888B TRP* 5.3 0.9 - - + -
1891B ILE* 3.8 26.5 - - + -
1947B VAL* 3.1 18.5 + - + +
1948B ILE* 2.9 11.9 + - - +
1950B CYS* 1.3 75.6 - - - +
1952B ILE* 1.3 66.2 + - + +
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Residues in contact with ILE1952 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1811B ARG* 5.6 4.5 - - + +
1816B PHE* 4.4 7.0 - - + -
1819B LEU* 4.1 15.0 - - + -
1850B ALA* 3.4 20.0 - - + +
1851B GLY* 3.8 43.5 - - - +
1852B TYR 4.1 15.5 - - - +
1853B SER* 4.3 11.7 - - - -
1860B LEU* 4.6 7.2 - - + +
1861B ASP 5.1 1.4 - - - +
1865B ARG* 3.3 8.8 + - - -
1948B ILE* 2.9 47.7 + - + +
1949B GLN* 3.8 11.0 - - - +
1951B LEU* 1.3 80.8 - - + +
1953B VAL* 1.3 67.2 + - - +
1954B GLY 3.1 0.2 + - - -
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Residues in contact with VAL1953 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1853B SER* 4.1 19.5 - - - +
1855B GLU* 5.5 6.1 - - + -
1856B GLU* 6.1 0.4 - - + -
1860B LEU* 4.3 16.9 - - + +
1863B GLN* 5.4 8.0 + - - +
1865B ARG* 4.1 0.7 + - - -
1949B GLN* 2.8 34.1 + - + +
1950B CYS 4.4 0.4 - - - +
1952B ILE* 1.3 75.3 - - + +
1954B GLY* 1.3 59.1 + - - +
1955B GLU* 3.8 29.9 - - + +
1957B ILE* 3.9 21.3 - - + -
1965B TYR* 6.0 0.2 - - - +
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Residues in contact with GLY1954 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1863B GLN* 6.5 0.4 - - - -
1865B ARG* 3.2 57.4 - - - +
1866B GLU 4.2 5.4 + - - +
1868B PRO* 4.6 3.1 - - - -
1950B CYS 2.9 9.2 + - - -
1952B ILE 3.1 2.6 - - - -
1953B VAL* 1.3 77.4 - - - +
1955B GLU* 1.3 64.6 + - - +
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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