Contacts of the helix formed by residues 1801 - 1817 (chain B) in PDB entry 3AU5
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 SER1801 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1797B VAL* 3.9 2.1 - - - +
1798B PRO* 2.7 35.7 + - - +
1799B LYS 3.1 0.8 + - - -
1800B ASP* 1.3 89.8 + - - +
1802B VAL* 1.3 67.1 + - - +
1803B GLU* 3.7 9.2 + - - +
1804B PHE* 3.2 23.0 + - - +
1805B ALA* 3.2 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1802 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1733B LEU* 4.0 39.0 - - + +
1735B MET* 4.7 4.9 - - + -
1800B ASP 3.9 1.0 + - - +
1801B SER* 1.3 73.5 - - - +
1803B GLU* 1.3 56.2 + - - +
1805B ALA* 3.0 11.5 + - + +
1806B PHE* 2.9 49.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1803 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1735B MET* 3.8 22.5 - - + +
1738B SER* 2.7 41.9 + - - -
1739B ARG* 3.3 6.1 + - - +
1740B ASN* 3.0 23.5 + - - +
1742B PHE* 4.2 8.6 - - + -
1788B LEU* 5.1 0.2 - - + -
1797B VAL* 3.6 23.6 - - + +
1798B PRO* 5.2 2.9 - - - +
1801B SER* 3.1 9.8 + - - +
1802B VAL* 1.3 78.5 - - - +
1804B PHE* 1.3 62.8 + - - +
1806B PHE* 3.0 15.4 + - - +
1807B MET* 3.0 19.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1804 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1797B VAL* 3.7 20.2 - - + +
1798B PRO 3.7 15.7 - - - +
1799B LYS* 3.7 48.5 - - + -
1800B ASP 4.0 4.0 - - - -
1801B SER* 3.2 11.2 + - - +
1803B GLU* 1.3 79.0 - - - +
1805B ALA* 1.3 63.3 + - - +
1807B MET* 3.2 13.5 + - + +
1808B PHE* 3.0 22.7 + - - +
1937B GLU 5.7 0.2 - - - -
1940B MET* 3.6 42.0 - - + -
1941B ALA* 4.3 2.5 - - + -
1944B MET* 3.3 40.6 - - + -
1948B LYS* 5.0 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1805 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1801B SER 3.2 8.7 + - - +
1802B VAL* 3.0 20.3 + - + +
1804B PHE* 1.3 81.0 - - - +
1806B PHE* 1.3 58.8 + - + +
1808B PHE* 3.3 4.0 + - - +
1809B GLU* 3.1 29.1 + - + +
1940B MET* 4.1 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1806 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1706B CYS* 4.0 22.4 - - + -
1707B HIS* 5.7 1.1 - - + -
1733B LEU* 3.9 11.9 - - + -
1735B MET* 3.5 28.5 - - + -
1742B PHE* 4.2 17.9 - + + -
1786B PHE* 3.7 44.6 - + - -
1787B LYS* 5.0 5.2 - - + -
1788B LEU* 5.2 2.0 - - + -
1802B VAL* 2.9 34.2 + - + -
1803B GLU* 3.2 10.3 - - - +
1805B ALA* 1.3 75.4 - - + +
1807B MET* 1.3 65.3 + - + +
1809B GLU* 3.4 6.9 + - + +
1810B GLN* 2.9 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1807 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1740B ASN* 4.6 3.8 - - - +
1788B LEU* 4.6 21.5 - - + -
1791B PHE* 5.1 3.4 - - + -
1794B THR* 3.4 45.3 - - + +
1797B VAL* 3.8 33.9 - - + -
1803B GLU* 3.0 18.1 + - - +
1804B PHE* 3.5 13.5 - - + +
1806B PHE* 1.3 74.8 - - - +
1808B PHE* 1.3 53.6 + - - +
1810B GLN* 3.9 5.7 - - - +
1811B ALA* 2.7 37.0 + - - +
1944B MET* 4.0 12.4 - - + +
1948B LYS* 4.8 2.0 - - - +
1953B TYR* 3.3 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1808 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1804B PHE 3.0 13.5 + - - +
1805B ALA 3.4 8.1 - - - +
1807B MET* 1.3 73.8 - - - +
1809B GLU* 1.3 69.4 + - - +
1811B ALA* 3.1 2.9 + - - +
1812B HIS* 2.8 28.2 + - - +
1833B LEU 5.8 0.4 - - - -
1834B ARG* 3.3 33.0 - - - -
1837B TYR* 3.6 38.1 - + + -
1939B ALA 5.5 0.2 - - - -
1940B MET* 3.5 41.1 - - + -
1943B TYR* 3.2 53.6 - + + -
1944B MET* 3.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1809 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1707B HIS* 3.5 29.6 - - + +
1708B GLY* 3.6 14.0 + - - -
1805B ALA* 3.1 17.0 + - + +
1806B PHE* 4.0 6.3 - - + +
1808B PHE* 1.3 89.7 - - + +
1810B GLN* 1.3 56.9 + - - +
1812B HIS* 3.5 3.1 + - - +
1813B GLU* 3.0 30.7 + - - +
1834B ARG* 2.8 43.9 + - - +
1837B TYR* 4.1 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1810 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1707B HIS* 3.9 22.6 - - + +
1787B LYS* 3.2 21.9 - - + +
1788B LEU* 2.9 55.1 + - - +
1791B PHE* 4.0 16.5 - - + -
1806B PHE* 2.9 21.3 + - + +
1807B MET* 3.9 4.7 - - - +
1809B GLU* 1.3 74.2 - - - +
1811B ALA* 1.3 67.3 + - - +
1813B GLU* 3.2 3.9 + - + +
1814B ALA* 3.0 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1811 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1807B MET 2.7 23.1 + - - +
1808B PHE 3.1 4.2 + - - +
1810B GLN* 1.3 73.1 - - - +
1812B HIS* 1.3 63.9 + - - +
1814B ALA* 3.0 9.7 + - - +
1815B VAL* 2.9 25.6 + - - +
1943B TYR* 4.2 7.4 - - + -
1944B MET* 4.1 17.7 - - - -
1947B ILE* 4.3 11.2 - - + -
1953B TYR* 4.5 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1812 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1808B PHE* 2.8 16.9 + - + +
1809B GLU* 3.8 4.7 - - - +
1811B ALA* 1.3 76.9 - - - +
1813B GLU* 1.3 65.2 + - + +
1815B VAL* 2.9 13.6 + - + +
1816B ILE* 2.9 44.6 + - + +
1830B LEU 5.4 0.7 - - - -
1834B ARG* 3.3 56.3 + - + +
1853B GLU 3.0 20.4 + - - -
1854B VAL* 3.7 14.4 - - - -
1943B TYR* 2.9 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1813 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1707B HIS* 3.1 41.3 - - + +
1708B GLY 5.5 1.1 - - - +
1747B TYR* 2.7 29.7 + - - -
1809B GLU 3.0 12.4 + - - +
1810B GLN* 3.4 10.3 - - + +
1811B ALA 3.2 0.2 - - - -
1812B HIS* 1.3 75.8 - - + +
1814B ALA* 1.3 63.7 + - - +
1816B ILE* 3.3 26.3 - - - +
1817B HIS* 3.3 38.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1814 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1810B GLN* 3.0 13.0 + - + +
1811B ALA* 3.4 11.7 - - - +
1813B GLU* 1.3 76.8 - - - +
1815B VAL* 1.3 58.1 + - + +
1817B HIS* 3.4 3.9 + - - -
1818B GLY 3.4 2.9 + - - -
1819B HIS* 2.8 56.1 + - + +
1820B HIS* 5.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1815 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1811B ALA 2.9 19.3 + - - +
1812B HIS* 2.9 8.4 + - + +
1814B ALA* 1.3 72.2 - - - +
1816B ILE* 1.3 64.6 + - + +
1817B HIS 2.9 9.5 + - - -
1818B GLY* 2.9 14.6 + - - -
1820B HIS* 3.9 18.8 + - + +
1827B LEU* 4.3 28.8 - - + +
1830B LEU* 4.5 9.4 - - + -
1854B VAL 5.4 4.5 - - - +
1855B TYR* 6.1 0.2 - - - -
1856B SER* 3.3 11.2 - - - +
1943B TYR* 3.5 19.5 - - - +
1947B ILE* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1816 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1812B HIS* 2.9 45.9 + - + +
1813B GLU* 3.3 35.7 - - - +
1815B VAL* 1.3 73.4 - - + +
1817B HIS* 1.3 68.0 + - + +
1852B GLU* 3.7 17.8 - - - +
1853B GLU* 3.9 15.7 - - + +
1854B VAL* 3.6 24.2 - - - +
1855B TYR* 3.8 1.6 - - - +
1856B SER* 3.2 27.2 + - - +
1857B LEU 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1817 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1747B TYR* 3.4 16.2 + - - -
1749B GLY 3.4 24.8 + - - -
1750B HIS* 5.0 6.2 + - - -
1813B GLU* 3.3 33.9 + - - +
1814B ALA* 4.0 4.5 - - - +
1815B VAL 2.9 1.4 + - - -
1816B ILE* 1.3 95.6 - - + +
1818B GLY* 1.3 62.1 + - - +
1819B HIS* 3.3 21.1 + - + +
1856B SER* 3.9 2.7 - - - -
1858B GLN* 5.3 4.9 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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