Contacts of the helix formed by residues 1850 - 1859 (chain A) in PDB entry 5XJY
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 GLY1850 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1820A ILE* 3.3 32.7 - - - +
1823A VAL* 3.6 30.5 - - - +
1844A LEU 5.4 3.4 + - - -
1847A ASP 4.6 0.2 + - - -
1849A VAL* 1.3 84.0 - - - +
1851A ARG* 1.3 64.2 + - - +
1852A ASN 3.4 2.0 + - - -
1853A LEU* 3.5 6.6 + - - +
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Residues in contact with ARG1851 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1737A VAL* 4.2 18.2 - - + +
1741A LEU* 6.6 0.2 - - + -
1820A ILE* 3.7 12.5 - - + +
1845A SER 3.3 25.9 + - - +
1846A TRP* 4.3 4.0 - - - -
1847A ASP 4.0 5.1 + - - +
1850A GLY* 1.3 75.9 - - - +
1852A ASN* 1.3 58.2 + - - +
1854A PHE* 2.9 20.1 + - - +
1855A ALA* 3.0 14.0 + - - +
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Residues in contact with ASN1852 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1846A TRP 5.3 1.6 - - - +
1847A ASP 3.3 18.9 + - - +
1848A LEU* 3.7 18.8 - - + +
1850A GLY 3.4 0.8 - - - -
1851A ARG* 1.3 75.1 - - - +
1853A LEU* 1.3 61.8 + - - +
1855A ALA* 3.9 7.7 - - - +
1856A MET* 2.9 28.8 + - - +
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Residues in contact with LEU1853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1806A VAL* 5.4 16.6 - - + +
1809A ILE 5.2 4.4 - - - +
1810A PHE* 5.9 1.5 - - - -
1820A ILE* 3.8 11.4 - - + -
1848A LEU 5.2 2.8 + - - +
1849A VAL 5.1 5.8 + - - +
1850A GLY 3.5 11.3 + - - +
1851A ARG 3.2 0.6 - - - -
1852A ASN* 1.3 77.6 - - - +
1854A PHE* 1.3 57.4 + - - +
1856A MET* 3.7 4.6 - - - +
1857A ALA* 2.9 32.7 + - - +
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Residues in contact with PHE1854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1741A LEU* 3.8 28.9 - - + -
1744A LEU* 5.0 1.3 - - - -
1816A GLY* 4.5 7.0 - - - +
1820A ILE* 3.4 29.2 - - + +
1851A ARG* 2.9 10.6 + - - +
1853A LEU* 1.3 79.6 - - - +
1855A ALA* 1.3 56.6 + - - +
1857A ALA* 5.1 1.6 - - - -
1858A VAL* 2.9 38.3 + - + +
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Residues in contact with ALA1855 (chain A).
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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1744A LEU* 4.4 10.3 - - + -
1851A ARG 3.0 14.0 + - - +
1852A ASN* 4.2 6.7 - - - +
1854A PHE* 1.3 76.9 - - - +
1856A MET* 1.3 55.3 + - - +
1859A GLU* 2.5 39.4 + - + +
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Residues in contact with MET1856 (chain A).
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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1852A ASN 2.9 20.2 + - - +
1853A LEU* 3.7 6.5 - - - +
1854A PHE 3.2 0.2 - - - -
1855A ALA* 1.3 75.3 - - - +
1857A ALA* 1.3 61.1 + - - +
1859A GLU* 3.7 1.8 - - - +
1860A GLY* 2.9 22.2 + - - -
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Residues in contact with ALA1857 (chain A).
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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1809A ILE 4.0 11.7 - - - +
1810A PHE* 3.4 25.6 - - - +
1812A HIS 4.5 0.9 - - - +
1813A PHE* 3.6 25.8 - - + -
1853A LEU 2.9 16.3 + - - +
1854A PHE* 4.3 1.8 - - - +
1856A MET* 1.3 76.4 - - - +
1858A VAL* 1.3 57.0 + - + +
1860A GLY* 2.5 29.6 + - - -
1861A VAL 3.0 4.5 + - - -
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Residues in contact with VAL1858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1741A LEU* 6.0 3.1 - - + -
1744A LEU* 3.6 18.0 - - + +
1745A TYR* 5.3 2.5 - - + -
1747A TRP* 3.4 14.0 - - - -
1748A SER* 3.6 26.2 - - - -
1813A PHE* 4.9 9.6 - - - +
1854A PHE* 2.9 22.2 + - + +
1857A ALA* 1.3 75.8 - - + +
1859A GLU* 1.3 60.3 + - - +
1861A VAL* 3.3 19.8 - - - +
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Residues in contact with GLU1859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1744A LEU* 3.6 18.8 - - + +
1747A TRP* 4.7 6.2 + - - +
1855A ALA* 2.5 27.5 + - + +
1856A MET* 3.7 2.0 - - - +
1858A VAL* 1.3 75.4 - - - +
1860A GLY* 1.3 56.8 + - - +
1861A VAL 3.2 3.5 + - - -
1862A VAL* 4.4 7.7 + - - +
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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