Contacts of the helix formed by residues 1901 - 1909 (chain E) in PDB entry 2ZLE
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 ASN1901 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1745E GLU 4.1 4.2 + - - -
1746E TYR* 3.8 27.2 - - + +
1750E LYS* 6.5 0.2 - - - -
1862E ASN* 3.4 13.9 - - - +
1866E ASP* 3.7 20.5 + - - +
1869E VAL* 3.2 13.0 - - - -
1899E VAL* 3.0 2.5 - - - +
1900E LYS* 1.3 89.8 - - - +
1902E ILE* 1.3 53.5 + - - +
1903E ALA* 3.2 10.6 + - - +
1904E GLU* 2.8 29.6 + - - +
1905E LEU* 2.8 31.0 + - - +
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Residues in contact with ILE1902 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1746E TYR 3.5 6.5 + - - +
1747E GLY* 3.9 11.0 - - - -
1748E GLN* 4.8 0.4 - - - -
1849E ASN* 2.8 41.3 - - + +
1853E SER* 3.6 25.6 - - - +
1860E MET* 4.5 2.5 - - + -
1861E SER* 3.4 26.0 - - - +
1862E ASN* 3.3 14.7 + - - +
1869E VAL* 3.2 24.7 - - + -
1901E ASN* 1.3 70.7 - - - +
1903E ALA* 1.3 63.7 + - - +
1905E LEU* 3.9 7.2 - - + -
1906E ARG* 3.0 32.1 + - - +
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Residues in contact with ALA1903 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1744E VAL 3.3 15.3 - - - +
1745E GLU* 3.5 6.3 - - - +
1746E TYR* 3.3 33.8 + - - +
1747E GLY 4.3 1.3 - - - +
1901E ASN* 3.2 8.6 + - - +
1902E ILE* 1.3 78.6 - - - +
1904E GLU* 1.3 59.7 + - + +
1906E ARG* 3.8 8.7 + - - +
1907E LYS* 2.9 28.8 + - - +
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Residues in contact with GLU1904 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1898E ALA* 2.9 27.3 - - - +
1899E VAL* 4.5 1.3 - - - -
1900E LYS* 3.0 47.5 + - - +
1901E ASN* 2.8 20.0 + - - +
1903E ALA* 1.3 75.7 - - + +
1905E LEU* 1.3 59.8 + - - +
1907E LYS* 2.7 35.6 + - + +
1908E VAL* 3.1 11.3 + - + +
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Residues in contact with LEU1905 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1853E SER* 4.0 20.0 - - - -
1860E MET* 4.8 10.3 - - + -
1869E VAL* 4.6 4.7 - - + -
1891E ILE* 4.3 18.4 - - + -
1894E ALA* 5.0 4.3 - - - -
1899E VAL* 3.3 42.7 - - + +
1901E ASN 2.8 13.3 + - - +
1902E ILE* 4.0 10.8 - - + +
1904E GLU* 1.3 71.7 - - - +
1906E ARG* 1.3 63.3 + - + +
1908E VAL* 2.9 21.8 + - + +
1909E LEU* 3.1 48.5 + - + +
1918E LEU* 4.8 7.0 - - + -
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Residues in contact with ARG1906 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1624E MET 4.1 0.9 + - - -
1625E VAL* 3.2 40.0 + - - +
1743E MET 3.8 6.1 + - - -
1744E VAL 4.7 2.2 + - - -
1747E GLY* 3.4 25.9 - - - +
1849E ASN* 4.4 6.3 + - - -
1852E ASP* 2.3 56.7 + - - +
1853E SER* 3.4 28.7 - - - +
1902E ILE* 3.0 26.0 + - + +
1903E ALA* 3.9 7.1 + - - +
1905E LEU* 1.3 77.0 - - + +
1907E LYS* 1.3 60.0 + - - +
1908E VAL 3.4 0.3 + - - -
1909E LEU 3.9 1.6 - - - +
1910E ASP* 3.3 24.9 + - + +
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Residues in contact with LYS1907 (chain E).
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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1594E LYS* 5.6 5.1 - - - +
1903E ALA 2.9 16.1 + - - +
1904E GLU* 2.7 24.0 + - + +
1906E ARG* 1.3 73.2 - - - +
1908E VAL* 1.3 60.1 + - + +
1910E ASP* 4.3 6.9 - - - +
1911E SER* 3.5 20.4 + - - -
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Residues in contact with VAL1908 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1894E ALA* 3.7 42.4 - - + +
1895E ASN* 4.5 5.8 - - + -
1896E GLN* 4.5 3.6 - - - +
1897E GLN* 5.7 2.2 - - + +
1898E ALA 5.6 0.9 - - - +
1904E GLU* 3.5 13.9 - - + +
1905E LEU 2.9 6.4 + - - +
1907E LYS* 1.3 82.0 - - + +
1909E LEU* 1.3 60.2 + - + +
1910E ASP 2.8 11.6 + - - -
1911E SER* 3.1 17.4 + - - +
1912E LYS* 3.2 32.2 + - + +
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Residues in contact with LEU1909 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1853E SER 3.7 12.1 - - - +
1854E SER* 3.0 37.2 - - - +
1855E SER* 2.8 27.1 + - - -
1895E ASN* 4.7 4.7 - - + +
1905E LEU* 3.1 44.7 + - + +
1906E ARG 3.6 2.2 + - - +
1908E VAL* 1.3 79.2 - - + +
1910E ASP* 1.3 57.3 + - - +
1912E LYS 5.0 3.4 - - - +
1913E PRO* 4.6 8.8 - - - +
1916E LEU* 3.3 39.7 - - + -
1918E LEU* 4.5 6.1 - - + -
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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