Contacts of the helix formed by residues 1773 - 1784 (chain B) in PDB entry 5JCZ
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 THR1773 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1771B ALA 5.7 0.7 - - - +
1772B LEU* 1.3 77.8 - - - +
1774B THR* 1.3 64.0 + - - +
1775B ALA* 3.5 4.0 + - - +
1776B GLN* 2.7 37.0 + - - +
1777B ILE* 3.0 22.7 + - - +
1809B ARG* 4.0 1.6 - - - -
1811B ASP* 4.0 8.5 - - + -
1812B SER* 3.5 33.4 - - - +
1814B GLN* 2.7 38.2 + - + +
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Residues in contact with THR1774 (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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1773B THR* 1.3 73.1 - - - +
1775B ALA* 1.3 62.8 + - - +
1777B ILE* 3.4 1.6 + - - +
1778B VAL* 3.0 41.4 + - + +
1803B GLN* 5.0 9.6 - - + +
1806B LEU* 3.5 52.2 + - + +
1809B ARG* 3.8 0.9 + - - +
1811B ASP* 3.3 23.9 + - - -
1812B SER 5.0 0.2 + - - -
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Residues in contact with ALA1775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1773B THR* 3.2 9.0 + - - +
1774B THR* 1.3 80.5 - - - +
1776B GLN* 1.3 56.4 + - - +
1778B VAL* 3.9 4.5 - - - +
1779B LYS* 3.0 29.6 + - - +
1813B PRO* 4.6 10.3 - - + +
1814B GLN 4.2 8.1 - - - +
1815B LEU* 4.0 15.8 - - + +
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Residues in contact with GLN1776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1699B LEU* 4.6 1.2 - - - +
1703B LEU* 3.7 22.2 - - + +
1771B ALA 4.5 1.4 - - - +
1772B LEU* 3.4 27.6 - - + +
1773B THR* 2.7 48.1 + - - +
1775B ALA* 1.3 77.7 - - - +
1777B ILE* 1.3 62.5 + - - +
1779B LYS* 3.3 3.4 + - - +
1780B VAL* 3.1 30.1 + - + +
1814B GLN* 3.5 25.2 + - - +
1815B LEU* 2.9 32.7 + - - +
1817B MET* 4.1 15.9 - - - +
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Residues in contact with ILE1777 (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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1751B LEU* 3.9 17.2 - - + +
1765B ILE* 4.1 16.2 - - + +
1766B CYS* 5.6 1.1 - - - -
1769B CYS* 3.6 36.3 - - + +
1772B LEU* 3.8 19.1 - - + +
1773B THR 3.0 18.2 + - - +
1774B THR 3.7 3.4 - - - +
1776B GLN* 1.3 77.5 - - - +
1778B VAL* 1.3 62.6 + - - +
1780B VAL* 3.4 3.0 + - - +
1781B LEU* 3.1 26.9 + - + +
1802B ILE* 4.1 21.3 - - + -
1806B LEU* 3.7 21.8 - - + -
1809B ARG* 4.2 4.3 - - - +
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Residues in contact with VAL1778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1774B THR* 3.0 26.2 + - + +
1775B ALA* 4.0 5.2 - - - +
1777B ILE* 1.3 75.7 - - - +
1779B LYS* 1.3 57.3 + - - +
1781B LEU* 3.4 8.5 + - - +
1782B ASN* 2.9 51.0 + - - +
1799B ILE* 3.8 18.8 - - + -
1802B ILE* 4.6 12.6 - - + -
1803B GLN* 3.8 36.3 - - + +
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Residues in contact with LYS1779 (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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1703B LEU* 3.5 40.2 - - + +
1704B LEU* 5.7 1.1 - - - +
1775B ALA 3.0 19.1 + - - +
1776B GLN* 3.4 6.5 - - - +
1778B VAL* 1.3 77.3 - - - +
1780B VAL* 1.3 51.5 + - - +
1782B ASN* 3.0 11.8 + - + +
1783B LEU* 2.7 61.2 + - + +
1815B LEU* 4.3 20.9 - - + +
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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
----------------------------------------------------------
1699B LEU* 5.7 0.4 - - + -
1702B LEU* 5.5 5.6 - - + +
1703B LEU* 3.7 19.5 - - + -
1709B CYS* 4.4 9.9 - - - -
1748B ALA* 4.7 15.3 - - + +
1751B LEU* 3.8 26.9 - - + -
1752B LEU* 3.7 30.3 - - + -
1756B LYS* 6.3 0.7 - - - -
1772B LEU* 5.8 1.8 - - + -
1776B GLN* 3.1 15.5 + - + +
1777B ILE 3.8 6.3 - - - +
1779B LYS* 1.3 74.7 - - - +
1781B LEU* 1.3 58.7 + - + +
1783B LEU* 3.7 6.3 - - - +
1784B TYR* 2.9 30.0 + - + +
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Residues in contact with LEU1781 (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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1751B LEU* 4.0 21.3 - - + -
1756B LYS* 3.9 31.6 - - + -
1765B ILE* 4.5 2.0 - - + -
1777B ILE* 3.1 33.4 + - + +
1778B VAL* 3.6 7.6 - - - +
1780B VAL* 1.3 77.0 - - + +
1782B ASN* 1.3 62.6 + - - +
1784B TYR* 3.6 7.5 - - - +
1793B ARG* 5.1 1.0 + - - -
1794B VAL* 3.5 37.1 - - + +
1798B PHE* 4.2 11.7 - - + -
1799B ILE* 4.4 11.2 - - + +
1802B ILE* 3.8 32.8 - - + -
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Residues in contact with ASN1782 (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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1706B LYS* 4.8 3.3 + - - -
1778B VAL* 2.9 38.9 + - - +
1779B LYS* 3.0 16.5 + - + +
1781B LEU* 1.3 76.8 - - - +
1783B LEU* 1.3 61.7 + - + +
1784B TYR 3.2 1.6 - - - -
1793B ARG* 2.9 28.9 + - - -
1799B ILE* 3.2 23.2 - - - +
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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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1702B LEU 3.4 19.7 - - - +
1703B LEU* 3.3 30.1 - - - +
1704B LEU 4.0 3.8 - - - +
1705B ARG 4.1 8.1 - - - +
1706B LYS* 3.6 39.5 - - + +
1709B CYS* 3.5 21.0 - - - +
1779B LYS* 2.7 44.4 + - + +
1780B VAL 3.7 0.9 - - - +
1782B ASN* 1.3 75.6 - - + +
1784B TYR* 1.3 59.6 + - - +
1785B THR* 2.8 23.2 + - - -
1793B ARG* 4.4 0.4 - - - -
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Residues in contact with TYR1784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1709B CYS* 3.5 13.0 - - - -
1710B SER* 3.7 16.8 - - - -
1711B TRP* 3.6 27.9 + - - +
1752B LEU* 3.5 34.0 + - + -
1756B LYS* 3.7 27.1 + - + -
1780B VAL* 2.9 15.0 + - + +
1781B LEU* 3.6 13.5 - - - +
1782B ASN 3.2 2.2 - - - -
1783B LEU* 1.3 73.9 - - - +
1785B THR* 1.3 58.2 + - - +
1786B PRO* 3.3 35.8 - - + +
1791B GLU* 4.7 5.3 + - + +
1792B GLU 4.7 5.4 - - - -
1793B ARG* 3.5 18.9 + - - +
1794B VAL* 4.0 20.1 + - + -
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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