Contacts of the helix formed by residues 1863 - 1872 (chain B) in PDB entry 4ASI
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 GLY1863 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1758B GLY* 5.1 1.3 - - - -
1862B ILE* 1.3 77.3 - - - +
1864B ILE* 1.3 68.4 + - - -
1866B ALA* 2.7 16.1 + - - +
1867B TYR* 2.9 20.0 + - - -
1884B ILE 2.9 13.1 + - - -
1885B LEU* 4.2 16.8 - - - +
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Residues in contact with ILE1864 (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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1728B PHE* 3.4 32.1 - - + -
1758B GLY* 4.0 9.9 - - - -
1759B ALA* 4.0 6.5 - - + +
1837B SER* 3.7 51.4 - - - +
1840B ILE* 4.3 4.7 - - + -
1841B ALA* 4.1 11.9 - - + -
1862B ILE 3.1 0.8 + - - -
1863B GLY* 1.3 72.1 - - - -
1865B GLY* 1.3 60.1 + - - +
1867B TYR* 3.3 13.8 + - + -
1868B LEU* 2.9 58.3 + - + +
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Residues in contact with GLY1865 (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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1728B PHE* 4.0 8.9 - - - -
1752B TYR* 4.4 1.3 - - - -
1754B SER* 4.0 1.9 + - - -
1756B ASN* 3.6 24.7 - - - -
1861B ALA* 4.0 7.0 - - - -
1862B ILE 2.9 11.7 + - - -
1864B ILE* 1.3 83.3 - - - +
1866B ALA* 1.3 60.9 + - - +
1868B LEU* 3.5 3.3 + - - +
1869B VAL* 3.2 27.9 + - - +
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Residues in contact with ALA1866 (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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1861B ALA* 4.0 2.3 - - - +
1862B ILE 3.8 3.4 - - - -
1863B GLY 2.7 15.2 + - - +
1865B GLY* 1.3 70.8 - - - +
1867B TYR* 1.3 62.0 + - + +
1869B VAL* 3.2 5.2 + - - +
1870B ARG* 3.1 22.2 + - - +
1883B LEU* 3.3 32.5 - - + +
1884B ILE 3.7 23.1 - - - +
1885B LEU* 4.3 11.4 - - + -
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Residues in contact with TYR1867 (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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1841B ALA* 5.5 1.6 - - + -
1863B GLY* 2.9 23.5 + - - -
1864B ILE* 3.8 19.7 - - + +
1866B ALA* 1.3 77.0 - - - +
1868B LEU* 1.3 57.9 + - - +
1870B ARG* 3.2 10.2 + - + +
1871B LEU* 2.8 45.5 + - + +
1885B LEU* 3.7 35.3 - - + +
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Residues in contact with LEU1868 (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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1728B PHE* 3.9 31.9 - - + -
1736B PHE* 4.2 14.4 - - + -
1750B ARG* 4.2 10.0 + - - -
1752B TYR* 4.2 17.3 - - + +
1840B ILE* 3.2 49.4 - - + +
1841B ALA* 3.8 8.3 - - - +
1844B SER* 3.4 11.6 + - - +
1855B SER* 4.2 1.7 + - - -
1864B ILE* 2.9 33.5 + - + +
1865B GLY* 3.8 3.4 - - - +
1867B TYR* 1.3 76.8 - - - +
1869B VAL* 1.3 63.0 + - - +
1871B LEU* 4.1 5.1 - - - +
1872B GLY* 3.2 17.5 + - - -
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Residues in contact with VAL1869 (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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1752B TYR* 4.2 3.8 - - + -
1754B SER* 3.8 26.5 - - - +
1855B SER* 3.7 23.4 + - - -
1857B VAL* 3.9 12.3 - - + -
1861B ALA* 4.4 2.7 - - + -
1865B GLY 3.2 14.7 + - - +
1866B ALA* 3.2 10.3 + - - +
1867B TYR 3.1 0.4 - - - -
1868B LEU* 1.3 78.6 - - - +
1870B ARG* 1.3 63.7 + - + +
1872B GLY 3.5 1.7 + - - -
1873B GLN 3.3 14.0 + - - -
1875B THR* 3.3 36.6 + - + +
1883B LEU* 4.1 17.3 - - + -
1917B VAL* 5.5 1.8 - - + -
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Residues in contact with ARG1870 (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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1866B ALA 3.1 12.6 + - - +
1867B TYR* 3.7 12.3 - - + +
1869B VAL* 1.3 79.9 - - + +
1871B LEU* 1.3 60.4 - - + +
1872B GLY 3.0 1.6 - - - -
1873B GLN* 2.7 63.9 + - - +
1875B THR* 4.9 1.3 - - - -
1916B GLY 4.2 16.2 + - - -
1917B VAL* 4.4 34.5 + - + +
1919B HIS* 5.6 1.0 + - - -
2061B PHE* 5.0 8.1 - - - -
2065B GLN* 3.3 23.2 - - - +
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Residues in contact with LEU1871 (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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1841B ALA* 3.5 38.1 - - + +
1844B SER* 3.9 20.0 - - - -
1845B SER* 4.1 24.3 - - - +
1848B TYR* 3.5 21.0 - - - +
1867B TYR* 2.8 37.8 + - + +
1868B LEU* 4.2 0.9 - - - +
1870B ARG* 1.3 74.3 - - + +
1872B GLY* 1.3 61.5 + - - +
1873B GLN* 3.3 8.4 + - - +
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Residues in contact with GLY1872 (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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1750B ARG* 4.4 7.3 - - - +
1844B SER 5.4 0.4 - - - -
1848B TYR* 4.5 0.2 - - - -
1853B THR* 2.5 40.8 + - - +
1855B SER* 4.4 5.4 - - - -
1868B LEU 3.2 15.0 + - - -
1869B VAL 3.7 6.3 - - - -
1870B ARG 3.0 0.8 - - - -
1871B LEU* 1.3 74.2 - - - +
1873B GLN* 1.3 59.7 + - - +
1874B ARG* 2.8 20.5 + - - -
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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