Contacts of the helix formed by residues 1775 - 1786 (chain B) in PDB entry 4J5L
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 THR1775 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1773B ALA 5.9 0.2 - - - +
1774B LEU* 1.3 77.1 - - - +
1776B THR* 1.3 65.4 + - - +
1777B ALA 3.5 2.1 + - - -
1778B GLN* 2.7 31.4 + - - +
1779B ILE* 3.1 21.1 + - - +
1811B ARG* 3.6 0.4 - - - -
1813B ASP* 3.6 10.8 - - - +
1814B SER* 3.3 41.3 - - - +
1816B GLN* 2.7 33.9 + - + +
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Residues in contact with THR1776 (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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1775B THR* 1.3 72.8 - - - +
1777B ALA* 1.3 62.7 + - - +
1779B ILE* 3.3 2.4 + - - +
1780B VAL* 3.0 38.3 + - + +
1805B GLN* 5.3 7.6 - - + -
1808B LEU* 4.0 37.1 + - + +
1811B ARG* 3.6 12.1 + - - +
1813B ASP* 2.9 27.9 + - - +
1814B SER 4.8 0.2 + - - -
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Residues in contact with ALA1777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1526A ASP* 3.8 28.7 - - + +
1530A ARG* 4.0 11.9 - - - +
1775B THR* 3.2 1.9 + - - +
1776B THR* 1.3 80.1 - - - +
1778B GLN* 1.3 56.9 + - - +
1780B VAL* 4.1 4.0 - - - +
1781B LYS* 3.0 29.6 + - - +
1814B SER 5.3 0.6 + - - -
1815B PRO* 4.2 5.8 - - + +
1816B GLN 3.9 16.6 - - - +
1817B LEU* 3.7 9.5 - - + +
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Residues in contact with GLN1778 (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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1701B LEU* 4.2 17.0 - - + +
1705B LEU* 3.8 14.7 - - + +
1773B ALA 4.5 1.0 - - - +
1774B LEU* 3.4 26.8 - - + +
1775B THR* 2.7 44.1 + - - +
1777B ALA* 1.3 74.5 - - - +
1779B ILE* 1.3 65.4 + - - +
1781B LYS* 3.2 2.1 + - - +
1782B VAL* 3.0 30.5 + - + +
1816B GLN* 3.8 18.6 + - - +
1817B LEU* 2.9 36.2 + - - +
1819B MET* 4.3 10.6 - - - +
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Residues in contact with ILE1779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1753B LEU* 3.9 19.4 - - + +
1767B ILE* 4.3 13.0 - - + +
1768B CYS* 5.7 1.1 - - - -
1771B CYS* 3.7 27.4 - - + +
1774B LEU* 3.8 17.7 - - + +
1775B THR 3.1 15.8 + - - +
1776B THR* 3.8 4.3 - - - +
1778B GLN* 1.3 74.3 - - - +
1780B VAL* 1.3 62.2 + - - +
1782B VAL* 3.3 3.9 + - - +
1783B LEU* 3.1 29.8 + - + +
1804B ILE* 4.2 22.2 - - + -
1808B LEU* 3.8 22.2 - - + -
1811B ARG* 3.9 13.7 - - - +
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Residues in contact with VAL1780 (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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1776B THR* 3.0 28.9 + - + +
1777B ALA* 4.1 4.5 - - - +
1779B ILE* 1.3 74.3 - - + +
1781B LYS* 1.3 60.6 + - - +
1783B LEU* 3.4 8.6 + - - +
1784B ASN* 2.9 41.6 + - - +
1801B ILE* 3.8 15.5 - - + -
1804B ILE* 4.9 12.3 - - + -
1805B GLN* 3.9 35.2 - - + +
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Residues in contact with LYS1781 (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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1705B LEU* 2.7 42.1 + - + +
1706B LEU* 4.7 4.4 - - - +
1777B ALA 3.0 19.7 + - - +
1778B GLN 3.2 5.4 + - - +
1780B VAL* 1.3 78.0 - - - +
1782B VAL* 1.3 62.5 + - - +
1784B ASN* 3.2 8.9 + - + +
1785B LEU* 3.0 53.0 + - + +
1817B LEU* 3.9 30.3 - - + -
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Residues in contact with VAL1782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1701B LEU* 5.5 0.4 - - + -
1704B LEU* 5.3 6.3 - - + -
1705B LEU* 3.9 17.3 - - + -
1711B CYS* 4.6 10.8 - - - -
1750B ALA* 4.8 15.0 - - + +
1753B LEU* 3.7 27.1 - - + -
1754B LEU* 3.6 30.1 - - + -
1758B LYS* 6.2 0.9 - - - +
1774B LEU* 5.8 1.8 - - + -
1778B GLN* 3.0 20.3 + - + +
1779B ILE 3.6 7.0 - - - +
1781B LYS* 1.3 76.2 - - - +
1783B LEU* 1.3 64.8 + - + +
1785B LEU* 3.1 15.1 + - - +
1786B TYR* 3.1 14.5 + - + +
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Residues in contact with LEU1783 (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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1753B LEU* 3.8 27.8 - - + -
1758B LYS* 4.1 26.5 - - + +
1767B ILE* 4.8 0.7 - - + -
1779B ILE* 3.1 27.5 + - + +
1780B VAL* 3.7 7.4 - - - +
1782B VAL* 1.3 77.1 - - + +
1784B ASN* 1.3 60.1 + - - +
1786B TYR* 3.8 5.1 + - - -
1795B ARG* 4.9 1.4 + - - -
1796B VAL* 3.5 29.5 - - + +
1800B PHE* 4.4 13.7 - - + -
1801B ILE* 3.8 22.4 - - + +
1804B ILE* 3.8 35.0 - - + -
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Residues in contact with ASN1784 (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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1708B LYS* 4.3 6.9 - - - -
1780B VAL* 2.9 34.1 + - - +
1781B LYS* 3.4 13.0 - - + +
1782B VAL 3.1 0.2 - - - -
1783B LEU* 1.3 79.8 - - - +
1785B LEU* 1.3 63.8 + - + +
1786B TYR 3.3 0.2 - - - -
1795B ARG* 3.2 26.6 + - - +
1801B ILE* 3.4 24.2 - - - +
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Residues in contact with LEU1785 (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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1704B LEU 3.4 17.5 - - - +
1705B LEU* 3.3 30.1 - - - +
1706B LEU 4.1 3.6 - - - +
1707B ARG 4.3 7.2 - - - +
1708B LYS* 3.3 53.9 - - + +
1711B CYS* 3.6 16.4 - - - +
1781B LYS* 3.0 37.6 + - + +
1782B VAL 3.1 1.3 + - - +
1784B ASN* 1.3 80.8 - - + +
1786B TYR* 1.3 58.9 + - - +
1787B THR* 3.0 10.4 + - - +
1795B ARG* 4.9 0.9 - - - -
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Residues in contact with TYR1786 (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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1711B CYS* 3.1 23.1 - - - -
1712B SER* 3.6 6.5 - - - -
1713B TRP* 3.6 40.4 + - - +
1754B LEU* 3.7 12.8 + - + -
1758B LYS* 3.2 33.8 + - + +
1782B VAL* 3.1 14.6 + - + +
1783B LEU* 3.8 2.4 + - - +
1784B ASN 3.3 2.8 - - - -
1785B LEU* 1.3 73.1 - - - +
1787B THR* 1.3 71.4 - - - +
1788B PRO* 4.7 6.4 - - + +
1793B GLU* 6.0 2.5 - - + +
1794B GLU 4.1 17.7 - - - -
1795B ARG* 3.4 25.7 + - - +
1796B VAL* 3.6 28.1 - - + +
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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