Contacts of the helix formed by residues 1795 - 1812 (chain B) in PDB entry 2D4Q
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 GLU1795 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1719B PHE* 4.6 14.2 - - + -
1775B GLU 4.2 0.4 - - - -
1793B HIS* 2.8 28.0 + - + +
1794B GLN* 1.3 87.3 - - + +
1796B CYS* 1.3 62.6 + - - +
1797B GLU* 3.3 4.0 - - - -
1798B ALA* 3.0 18.6 + - + +
1799B ILE* 3.0 20.7 + - - +
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Residues in contact with CYS1796 (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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1772B LEU* 4.0 4.9 - - + -
1774B ASP 3.9 5.6 - - - +
1775B GLU 3.3 14.4 + - - +
1776B ASN 3.3 24.7 - - - -
1777B GLN* 3.3 20.4 - - - +
1778B PHE* 3.7 19.3 - - + -
1792B MET 4.0 1.8 - - - -
1793B HIS* 3.3 26.7 - - - -
1795B GLU* 1.3 76.1 - - - +
1797B GLU* 1.3 57.1 + - - +
1799B ILE* 3.6 6.9 - - - +
1800B VAL* 2.8 32.7 + - - +
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Residues in contact with GLU1797 (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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1772B LEU* 3.9 29.7 - - + +
1775B GLU* 4.1 9.6 + - - +
1795B GLU 3.3 1.9 - - - -
1796B CYS* 1.3 77.5 - - - +
1798B ALA* 1.3 67.6 + - + +
1800B VAL* 3.8 2.9 - - - +
1801B GLN* 3.0 58.5 + - - +
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Residues in contact with ALA1798 (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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1719B PHE* 4.0 13.9 - - + -
1795B GLU* 3.0 24.2 + - + +
1797B GLU* 1.3 92.0 - - + +
1799B ILE* 1.3 62.2 + - - +
1801B GLN* 3.5 5.7 + - - +
1802B SER* 3.2 23.9 + - - -
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Residues in contact with ILE1799 (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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1719B PHE* 3.6 42.0 - - + -
1734B ILE* 4.3 17.9 - - + -
1736B VAL* 5.0 0.2 - - + -
1778B PHE* 3.6 35.9 - - + -
1793B HIS* 3.7 37.0 - - + -
1795B GLU 3.0 15.7 + - - +
1796B CYS* 3.1 7.6 + - - +
1798B ALA* 1.3 75.0 - - - +
1800B VAL* 1.3 65.3 + - - +
1802B SER* 3.2 5.7 + - - -
1803B ILE* 3.1 31.6 + - + +
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Residues in contact with VAL1800 (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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1770B ILE* 4.0 18.3 - - + +
1771B CYS 4.4 0.2 - - - +
1772B LEU* 4.1 27.4 - - + +
1778B PHE* 3.5 36.8 - - + -
1796B CYS 2.8 17.6 + - - +
1797B GLU* 3.8 6.7 - - - +
1799B ILE* 1.3 73.4 - - - +
1801B GLN* 1.3 63.2 + - + +
1803B ILE* 3.3 4.4 + - - +
1804B ILE* 2.8 50.1 + - + +
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Residues in contact with GLN1801 (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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1797B GLU* 3.0 51.2 + - - +
1798B ALA* 3.6 7.0 - - - +
1800B VAL* 1.3 78.9 - - - +
1802B SER* 1.3 58.0 + - - +
1804B ILE* 3.2 14.7 + - - +
1805B HIS* 2.9 31.5 + - - +
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Residues in contact with SER1802 (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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1717B LYS* 3.9 25.8 + - - +
1719B PHE* 4.1 8.6 - - - -
1736B VAL* 4.1 22.0 - - - -
1798B ALA 3.2 11.0 + - - -
1799B ILE* 3.2 12.8 - - - -
1801B GLN* 1.3 79.7 - - - +
1803B ILE* 1.3 57.7 + - - +
1805B HIS* 3.4 5.9 + - - +
1806B ILE* 3.0 32.7 + - - +
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Residues in contact with ILE1803 (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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1734B ILE* 4.8 0.7 - - + -
1736B VAL* 4.0 13.2 - - + -
1741B VAL* 3.7 29.8 - - + -
1767B ILE* 3.9 25.6 - - + -
1770B ILE* 3.8 22.0 - - + -
1778B PHE* 4.2 20.0 - - + -
1780B LEU* 4.2 9.9 - - + -
1799B ILE* 3.1 31.9 + - + +
1800B VAL* 3.9 4.5 - - - +
1802B SER* 1.3 72.1 - - - +
1804B ILE* 1.3 62.0 + - - +
1806B ILE* 3.2 7.0 + - + +
1807B ARG* 2.8 29.6 + - - +
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Residues in contact with ILE1804 (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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1770B ILE* 3.9 26.5 - - + +
1800B VAL* 2.8 40.2 + - + +
1801B GLN* 3.6 15.7 - - - +
1803B ILE* 1.3 77.6 - - - +
1805B HIS* 1.3 67.4 + - - +
1807B ARG* 3.2 6.0 + - - +
1808B THR* 2.8 38.2 + - - +
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Residues in contact with HIS1805 (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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1717B LYS* 6.0 4.5 - - - -
1801B GLN 2.9 17.0 + - - +
1802B SER* 3.7 5.8 - - - +
1804B ILE* 1.3 77.5 - - - +
1806B ILE* 1.3 72.0 + - + +
1808B THR* 3.2 7.5 + - - +
1809B ARG* 2.9 40.1 + - + +
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Residues in contact with ILE1806 (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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1736B VAL* 4.2 11.0 - - + -
1737B GLY 2.8 30.3 - - - +
1738B SER* 3.4 28.2 - - - +
1740B ALA* 5.0 4.0 - - - +
1741B VAL* 5.1 5.6 - - + -
1764B ALA* 4.1 17.9 - - + +
1767B ILE* 5.4 0.4 - - + -
1802B SER 3.0 19.9 + - - +
1803B ILE* 3.5 15.5 - - + +
1805B HIS* 1.3 91.2 - - + +
1807B ARG* 1.3 67.6 + - + +
1809B ARG* 3.5 5.7 + - + +
1810B TRP* 3.2 20.1 + - - +
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Residues in contact with ARG1807 (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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1764B ALA* 3.9 20.4 - - + +
1767B ILE* 3.0 38.5 + - + -
1768B GLU* 3.1 23.6 + - - +
1769B GLU* 3.7 4.2 - - - +
1770B ILE* 3.5 29.8 - - + +
1803B ILE* 2.8 20.2 + - + +
1804B ILE* 4.1 6.9 + - - +
1806B ILE* 1.3 78.7 - - + +
1808B THR* 1.3 58.4 + - - +
1810B TRP* 3.2 8.8 + - + +
1811B GLU* 2.9 52.1 + - + +
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Residues in contact with THR1808 (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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1804B ILE* 2.8 29.7 + - - +
1805B HIS* 3.6 8.1 - - - +
1807B ARG* 1.3 76.1 + - - +
1809B ARG* 1.3 66.5 + - - +
1811B GLU* 3.4 11.4 + - - +
1812B LEU* 3.1 43.3 + - + +
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Residues in contact with ARG1809 (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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1738B SER 5.6 3.6 - - - +
1805B HIS* 2.9 27.7 + - + +
1806B ILE* 3.8 8.3 - - + +
1808B THR* 1.3 79.1 - - - +
1810B TRP* 1.3 65.6 + - - +
1812B LEU* 3.5 11.6 + - - +
1813B SER* 3.2 17.3 + - - -
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Residues in contact with TRP1810 (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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1813A SER* 5.9 3.0 + - - -
1739B THR* 6.3 4.5 - - + -
1764B ALA* 3.8 23.8 - - + -
1765B SER* 3.1 47.6 - - - -
1806B ILE 3.2 11.0 + - - +
1807B ARG* 3.3 11.2 - - + +
1809B ARG* 1.3 75.9 - - - +
1811B GLU* 1.3 82.6 + - + +
1813B SER* 2.7 27.1 + - - -
1814B GLN* 3.1 59.7 + - + +
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Residues in contact with GLU1811 (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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1807B ARG* 2.9 51.9 + - + +
1808B THR* 3.4 10.3 + - - +
1810B TRP* 1.3 93.8 - - + +
1812B LEU* 1.3 62.6 + - + +
1813B SER 3.0 4.5 + - - -
1814B GLN* 3.3 19.5 + - - +
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Residues in contact with LEU1812 (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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1590A ARG* 5.8 0.2 + - - -
1707A ALA* 3.7 29.6 - - + +
1708A ALA* 3.6 45.3 - - + +
1711A ALA* 4.3 17.0 - - + +
1808B THR* 3.1 37.8 + - + +
1809B ARG* 3.9 7.6 - - - +
1810B TRP 3.1 0.4 + - - -
1811B GLU* 1.3 78.7 - - + +
1813B SER* 1.3 58.9 + - - +
1814B GLN 3.6 1.6 - - - +
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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