Contacts of the helix formed by residues 1897 - 1908 (chain B) in PDB entry 2IWO
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 THR1897 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1852B GLY* 4.4 1.6 - - - -
1853B VAL* 3.2 30.1 - - + +
1854B GLY* 5.5 0.9 - - - -
1895B GLY 4.6 3.1 - - - +
1896B MET* 1.3 80.4 - - - +
1898B HIS* 1.3 66.8 + - - +
1899B THR* 3.6 8.2 + - - -
1900B GLN* 2.9 48.4 + - - +
1901B ALA* 3.0 21.0 + - - +
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Residues in contact with HIS1898 (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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1849B ILE* 3.4 33.8 - - + +
1850B ALA* 4.1 4.0 - - - -
1851B GLY 2.7 32.3 + - - +
1852B GLY* 3.9 0.4 - - - -
1853B VAL 2.9 13.6 + - - +
1854B GLY 4.7 1.1 - - - +
1855B SER* 3.9 21.2 - - - +
1856B PRO* 5.1 10.4 - - + +
1897B THR* 1.3 72.4 - - - +
1899B THR* 1.3 69.3 + - - +
1901B ALA* 3.2 7.5 + - - +
1902B VAL* 3.1 48.1 + - + +
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Residues in contact with THR1899 (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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1897B THR* 3.3 7.5 + - - -
1898B HIS* 1.3 83.7 - - - +
1900B GLN* 1.3 63.7 + - - +
1902B VAL* 3.8 5.9 - - + +
1903B ASN* 3.0 42.2 + - - +
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Residues in contact with GLN1900 (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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1895B GLY 4.4 1.7 - - - +
1896B MET* 3.6 19.8 - - + +
1897B THR* 2.9 48.1 + - - +
1899B THR* 1.3 77.8 - - - +
1901B ALA* 1.3 56.4 + - - +
1903B ASN* 3.4 5.5 + - - +
1904B LEU* 3.0 30.3 + - - +
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Residues in contact with ALA1901 (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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1849B ILE* 3.8 16.6 - - + -
1862B ILE* 3.6 31.0 - - + -
1888B ILE* 4.0 10.7 - - + +
1896B MET* 3.8 14.5 - - - -
1897B THR 3.0 6.7 + - - +
1898B HIS* 3.2 8.9 + - - +
1900B GLN* 1.3 72.9 - - - +
1902B VAL* 1.3 66.8 + - - +
1904B LEU* 3.3 3.2 + - - +
1905B LEU* 3.1 28.1 + - - +
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Residues in contact with VAL1902 (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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1849B ILE* 3.8 20.4 - - + -
1898B HIS* 3.1 41.3 + - + +
1899B THR* 3.8 6.5 - - + +
1901B ALA* 1.3 73.9 - - - +
1903B ASN* 1.3 66.2 + - - +
1905B LEU* 3.2 5.7 + - - +
1906B LYS* 2.9 49.1 + - + +
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Residues in contact with ASN1903 (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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1899B THR* 3.0 36.9 + - - +
1900B GLN* 3.9 6.1 - - - +
1902B VAL* 1.3 83.3 - - - +
1904B LEU* 1.3 63.7 + - - +
1906B LYS* 4.4 8.3 - - - +
1907B ASN* 3.0 44.4 + - - +
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Residues in contact with LEU1904 (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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1888B ILE* 3.5 43.3 - - + +
1889B CYS* 4.5 12.5 - - + -
1891B THR* 4.6 7.4 - - + +
1896B MET* 4.0 22.9 - - + -
1900B GLN 3.0 16.3 + - - +
1901B ALA 3.6 5.6 - - - +
1903B ASN* 1.3 78.4 - - - +
1905B LEU* 1.3 61.3 + - - +
1907B ASN* 4.1 2.4 - - - +
1908B ALA* 3.2 26.0 + - - +
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Residues in contact with LEU1905 (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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1839B LYS* 2.8 27.7 + - - -
1845B LEU* 3.9 22.7 - - + +
1847B ILE* 4.8 2.9 - - + -
1849B ILE* 4.0 33.9 - - + -
1885B ILE* 5.4 0.2 - - + -
1888B ILE* 3.7 34.1 - - + -
1901B ALA 3.1 17.8 + - - +
1902B VAL* 3.8 3.1 - - - +
1904B LEU* 1.3 75.1 - - - +
1906B LYS* 1.3 61.5 + - + +
1907B ASN 3.6 0.2 + - - -
1908B ALA* 3.7 4.9 + - - -
1912B ILE* 3.8 24.2 - - + +
1914B MET* 4.0 15.9 - - + -
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Residues in contact with LYS1906 (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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1839B LYS* 2.7 19.6 + - - +
1902B VAL* 2.9 38.3 + - + +
1903B ASN* 3.9 10.8 - - - +
1905B LEU* 1.3 78.3 - - + +
1907B ASN* 1.3 61.6 + - - +
1908B ALA 4.1 0.3 - - - +
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Residues in contact with ASN1907 (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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1903B ASN* 3.0 34.8 + - - +
1904B LEU* 4.4 2.9 - - - +
1906B LYS* 1.3 78.8 - - - +
1908B ALA* 1.3 66.4 + - - +
1909B SER* 3.8 3.6 + - - -
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Residues in contact with ALA1908 (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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1839B LYS* 3.0 25.7 + - - +
1889B CYS* 4.2 13.7 - - - -
1904B LEU 3.2 20.8 + - - +
1905B LEU* 4.0 0.4 - - - +
1906B LYS 3.4 1.6 - - - +
1907B ASN* 1.3 79.3 - - - +
1909B SER* 1.3 61.1 + - - +
1912B ILE* 3.5 30.1 - - + -
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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