Contacts of the helix formed by residues 1943 - 1954 (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 SER1943 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1921D VAL* 4.4 3.0 - - - +
1922D THR 3.5 9.4 - - - -
1923D ASP* 6.0 0.2 - - - -
1942D VAL* 1.3 79.4 - - - +
1944D GLN* 1.3 65.0 + - - +
1945D GLU* 3.0 11.0 + - - +
1946D TRP* 3.0 17.3 + - - +
1947D VAL 4.0 0.5 + - - -
1964D LYS 2.5 28.6 + - - -
1965D TYR* 2.5 17.8 + - - -
1966D LYS 3.6 11.7 - - - -
1967D HIS* 3.9 7.4 - - - +
1969D TYR 5.5 2.9 - - - -
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Residues in contact with GLN1944 (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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1883D ASN 4.8 2.6 - - - +
1884D PHE* 3.6 23.2 - - + -
1887D LEU* 5.2 1.1 - - - +
1888D TRP* 2.6 58.1 + - + +
1921D VAL* 4.3 9.4 - - + +
1922D THR 4.0 5.1 + - - -
1943D SER* 1.3 74.8 - - - +
1945D GLU* 1.3 64.4 + - + +
1946D TRP 3.1 0.4 - - - -
1947D VAL* 3.1 8.6 + - - +
1948D ILE* 3.0 34.4 + - + +
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Residues in contact with GLU1945 (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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1811D ARG* 2.5 44.3 + - - -
1854D LEU* 3.6 27.0 - - + +
1943D SER* 3.0 13.2 + - - +
1944D GLN* 1.3 79.1 + - - +
1946D TRP* 1.3 60.4 + - - +
1948D ILE* 3.8 10.9 - - - +
1949D GLN* 2.8 44.7 + - + +
1964D LYS* 3.8 24.7 - - + +
1965D TYR* 4.2 3.8 - - + -
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Residues in contact with TRP1946 (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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1869D PHE* 3.6 26.5 - + - -
1872D LEU* 3.9 26.2 - - + -
1892D LEU* 4.9 1.1 - - + -
1919D VAL* 4.7 2.5 - - + -
1921D VAL* 4.6 8.3 - - + -
1942D VAL* 3.7 25.8 - - + -
1943D SER 3.0 12.3 + - - +
1945D GLU* 1.3 79.3 - - - +
1947D VAL* 1.3 86.6 + - + +
1949D GLN* 3.4 1.9 + - - +
1950D CYS* 3.0 41.6 + - - -
1956D ARG* 3.8 17.5 - - + -
1957D ILE* 2.9 22.6 + - + -
1958D GLY 3.6 17.3 - - - -
1959D PHE* 3.3 38.5 - + - -
1965D TYR* 4.0 25.5 - + + -
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Residues in contact with VAL1947 (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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1869D PHE* 3.5 23.3 - - + -
1888D TRP* 3.8 28.0 - - + -
1891D ILE* 4.6 2.0 - - + -
1892D LEU* 4.0 21.5 - - + -
1921D VAL* 4.1 25.4 - - + -
1943D SER 4.8 0.4 - - - +
1944D GLN* 3.1 11.1 + - - +
1946D TRP* 1.3 97.2 - - + +
1948D ILE* 1.3 63.6 + - - +
1950D CYS* 3.1 13.0 + - - +
1951D LEU* 3.1 18.9 + - + +
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Residues in contact with ILE1948 (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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1811D ARG* 3.9 17.7 - - - +
1816D PHE* 3.7 36.8 - - + -
1888D TRP* 3.4 32.3 - - + -
1944D GLN* 3.0 25.0 + - - +
1945D GLU* 3.7 27.6 - - - +
1947D VAL* 1.3 76.7 - - - +
1949D GLN* 1.3 63.0 + - - +
1951D LEU* 2.9 12.4 + - - +
1952D ILE* 2.9 35.3 + - + +
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Residues in contact with GLN1949 (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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1811D ARG* 4.7 0.8 - - - +
1852D TYR 3.6 17.3 + - - -
1853D SER* 3.6 8.5 + - - -
1854D LEU* 2.8 40.1 + - + +
1855D GLU* 4.3 2.1 + - - +
1945D GLU* 2.8 44.2 + - - +
1946D TRP 3.9 0.9 - - - +
1948D ILE* 1.3 73.6 - - - +
1950D CYS* 1.3 56.9 + - - +
1952D ILE* 4.3 9.9 - - - +
1953D VAL* 2.8 40.2 + - + +
1957D ILE* 3.2 22.2 - - + +
1961D GLN* 5.7 0.2 + - - -
1965D TYR* 3.1 22.4 + - + +
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Residues in contact with CYS1950 (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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1868D PRO* 4.1 10.3 - - + +
1869D PHE* 3.9 16.2 - - + -
1946D TRP* 3.0 60.6 + - - -
1947D VAL 3.1 8.9 + - - +
1949D GLN* 1.3 77.1 - - - +
1951D LEU* 1.3 57.6 + - - +
1954D GLY* 3.0 22.9 + - - -
1955D GLU 3.2 20.0 + - - +
1956D ARG* 4.1 4.0 - - - -
1957D ILE* 3.8 21.3 - - - -
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Residues in contact with LEU1951 (chain D).
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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1816D PHE* 3.8 37.7 - - + +
1819D LEU* 4.1 19.1 - - + +
1820D ALA* 3.5 39.9 - - + +
1865D ARG* 2.6 40.4 + - - +
1868D PRO* 4.4 8.7 - - + -
1869D PHE* 4.1 15.9 - - + -
1888D TRP* 4.9 0.9 - - + -
1891D ILE* 4.0 14.6 - - + -
1947D VAL* 3.1 21.2 + - + +
1948D ILE* 2.9 11.3 + - - +
1950D CYS* 1.3 75.0 - - - +
1952D ILE* 1.3 55.9 + - + +
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Residues in contact with ILE1952 (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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1811D ARG* 4.6 9.2 - - + +
1816D PHE* 5.0 6.3 - - + -
1819D LEU* 4.6 7.6 - - + -
1850D ALA* 3.4 26.8 - - + +
1851D GLY* 3.6 37.5 - - - +
1852D TYR 3.5 26.0 - - - +
1853D SER* 4.4 7.2 - - - +
1860D LEU* 4.7 8.7 - - + +
1861D ASP 5.1 1.2 - - - +
1865D ARG* 2.9 16.6 + - - -
1948D ILE* 2.9 35.7 + - + +
1949D GLN* 3.9 9.9 - - - +
1951D LEU* 1.3 73.7 - - - +
1953D VAL* 1.3 64.8 + - + +
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Residues in contact with VAL1953 (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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1853D SER* 4.2 12.3 - - - +
1855D GLU* 5.3 7.4 - - + -
1856D GLU* 5.7 1.1 - - + -
1860D LEU* 4.1 26.7 - - + +
1863D GLN* 5.7 5.9 + - - +
1865D ARG* 4.0 0.6 + - - -
1949D GLN* 2.8 30.1 + - - +
1952D ILE* 1.3 72.1 - - + +
1954D GLY* 1.3 58.0 + - - +
1955D GLU* 3.9 27.9 - - + +
1957D ILE* 4.0 22.4 - - + -
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Residues in contact with GLY1954 (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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1865D ARG* 3.1 56.1 - - - +
1866D GLU* 4.2 6.9 + - - +
1868D PRO* 4.6 3.8 - - - -
1950D CYS 3.0 11.1 + - - -
1952D ILE 3.1 3.0 - - - -
1953D VAL* 1.3 78.1 - - - +
1955D 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