Contacts of the helix formed by residues 1861 - 1874 (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 VAL1861 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1747A TRP* 3.7 22.0 - - + +
1748A SER* 3.8 18.2 - - - +
1751A PRO* 4.0 6.7 - - + +
1813A PHE* 4.7 10.1 - - + -
1857A ALA 3.0 4.3 + - - +
1858A VAL* 3.3 20.0 - - - +
1859A GLU 3.2 2.8 - - - -
1860A GLY* 1.3 73.6 - - - +
1862A VAL* 1.3 59.2 + - - +
1863A PHE 3.1 2.2 - - - -
1864A PHE* 2.8 28.2 + - + +
1865A LEU 3.0 9.0 + - - -
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Residues in contact with VAL1862 (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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1703A PHE* 6.6 0.2 - - - -
1747A TRP* 4.2 26.6 - - + +
1751A PRO* 5.5 0.9 - - - -
1859A GLU 4.4 6.3 + - - +
1860A GLY* 3.2 1.6 - - - -
1861A VAL* 1.3 78.4 - - - +
1863A PHE* 1.3 55.9 + - - +
1865A LEU* 3.2 11.8 + - + +
1866A ILE* 2.9 26.0 + - - +
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Residues in contact with PHE1863 (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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1860A GLY* 3.3 14.1 + - - +
1861A VAL 3.1 0.2 - - - -
1862A VAL* 1.3 77.7 - - - +
1864A PHE* 1.3 57.7 + - - +
1866A ILE* 3.2 9.2 + - - +
1867A THR* 2.9 24.1 + - - -
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Residues in contact with PHE1864 (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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1748A SER 5.8 0.4 - - - +
1751A PRO* 4.0 12.9 - - + +
1752A LEU* 5.0 15.4 - - + +
1755A PRO* 5.2 1.7 - - - +
1813A PHE* 4.5 18.6 - - + -
1860A GLY 4.2 0.8 + - - -
1861A VAL* 2.8 19.5 + - + +
1863A PHE* 1.3 76.1 - - - +
1865A LEU* 1.3 58.3 + - - +
1867A THR* 3.1 11.4 + - - -
1868A VAL* 3.0 24.3 + - - +
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Residues in contact with LEU1865 (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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1703A PHE* 5.2 13.5 - - + -
1751A PRO* 3.6 26.8 - - + +
1861A VAL 3.0 5.7 + - - -
1862A VAL* 3.2 16.1 + - + +
1864A PHE* 1.3 77.0 - - - +
1866A ILE* 1.3 57.5 + - - +
1868A VAL* 3.0 19.7 + - - +
1869A LEU* 3.0 17.3 + - - +
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Residues in contact with ILE1866 (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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1862A VAL 2.9 12.9 + - - +
1863A PHE* 3.2 12.3 + - - +
1865A LEU* 1.3 76.8 - - - +
1867A THR* 1.3 48.9 - - - +
1869A LEU* 4.6 3.4 - - - +
1870A ILE* 2.7 41.2 + - - +
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Residues in contact with THR1867 (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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1755A PRO* 4.4 5.5 - - - +
1863A PHE 2.9 13.6 + - - -
1864A PHE* 3.1 14.6 + - - -
1866A ILE* 1.3 76.5 - - - +
1868A VAL* 1.3 58.6 + - - +
1870A ILE* 4.3 3.1 - - - +
1871A GLN* 2.9 29.1 + - - +
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Residues in contact with VAL1868 (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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1699A TRP* 5.4 6.1 - - + -
1751A PRO 4.2 4.5 - - - +
1754A TYR* 4.2 20.2 - - + -
1755A PRO* 3.7 28.5 - - + -
1758A PHE* 3.7 8.1 - - + -
1864A PHE 3.0 12.5 + - - +
1865A LEU* 3.0 11.0 + - - +
1867A THR* 1.3 74.5 - - - +
1869A LEU* 1.3 61.5 + - - +
1871A GLN* 2.9 17.8 + - - +
1872A TYR* 3.0 10.9 + - - +
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Residues in contact with LEU1869 (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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1696A VAL* 5.4 15.0 - - + -
1699A TRP* 4.6 24.4 - - + +
1865A LEU 3.0 13.8 + - - +
1866A ILE* 4.8 2.7 - - - +
1868A VAL* 1.3 73.2 - - - +
1870A ILE* 1.3 61.5 + - - +
1872A TYR* 3.2 9.0 + - - +
1873A ARG* 2.9 26.7 + - - +
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Residues in contact with ILE1870 (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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1866A ILE* 2.7 24.4 + - + +
1867A THR* 4.3 4.3 - - - +
1869A LEU* 1.3 77.8 - - - +
1871A GLN* 1.3 60.9 + - - +
1873A ARG* 3.3 17.0 + - - +
1874A PHE* 3.7 10.9 + - - +
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Residues in contact with GLN1871 (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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1755A PRO* 4.7 9.4 - - + -
1758A PHE* 3.2 23.8 - - + -
1867A THR 2.9 23.0 + - - +
1868A VAL* 2.9 8.7 + - - +
1870A ILE* 1.3 77.1 - - - +
1872A TYR* 1.3 56.1 + - - +
1874A PHE* 4.1 11.8 + - - +
1875A PHE 4.5 4.9 + - - +
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Residues in contact with TYR1872 (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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1689A PHE* 6.0 1.9 - - - -
1695A PRO* 5.5 9.7 - - + +
1699A TRP* 3.6 27.6 - - + +
1758A PHE* 3.5 20.8 - - + -
1868A VAL 3.0 8.1 + - - +
1869A LEU 3.2 7.4 + - - +
1870A ILE 3.2 0.2 - - - -
1871A GLN* 1.3 75.5 - - - +
1873A ARG* 1.3 58.8 + - - +
1874A PHE 3.1 2.7 - - - -
1875A PHE* 3.0 21.9 + - - +
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Residues in contact with ARG1873 (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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1695A PRO* 5.8 6.1 - - + -
1869A LEU 2.9 15.7 + - - +
1870A ILE* 3.3 11.3 + - - +
1872A TYR* 1.3 76.2 - - - +
1874A PHE* 1.3 57.5 + - - +
1875A PHE* 3.2 2.9 + - - +
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Residues in contact with PHE1874 (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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1870A ILE 3.7 8.8 + - - +
1871A GLN* 4.4 9.0 - - - +
1872A TYR 3.1 1.4 - - - -
1873A ARG* 1.3 76.2 - - - +
1875A PHE* 1.3 68.2 + - - +
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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