Contacts of the helix formed by residues 1846 - 1865 (chain B) in PDB entry 6TM1
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 PHE1846 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1844B ARG* 3.6 35.0 - - + -
1845B ASP* 1.3 85.8 - - - +
1847B LYS* 1.3 53.5 + - - +
1848B LYS 3.3 0.4 - - - -
1849B LEU* 3.3 22.4 - - + +
1850B SER* 2.5 38.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1847 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1845B ASP* 2.8 15.8 + - - +
1846B PHE* 1.3 71.8 - - - +
1848B LYS* 1.3 69.4 + - + +
1850B SER* 3.1 9.2 + - - -
1851B ASP* 2.9 49.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1848 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1814B TYR* 5.4 3.6 - - - +
1840B PHE* 3.3 32.8 - - + -
1845B ASP* 3.0 36.9 + - - +
1847B LYS* 1.3 88.7 - - + +
1849B LEU* 1.3 55.7 + - - +
1851B ASP* 3.3 9.5 - - - +
1852B LEU* 2.6 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1849 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1837B ILE* 3.6 43.3 - - + -
1840B PHE* 3.5 39.2 - - + +
1841B GLU* 3.7 22.4 - - + +
1844B ARG* 5.3 0.9 - - - -
1845B ASP 4.4 1.6 - - - +
1846B PHE* 3.2 29.9 + - + +
1848B LYS* 1.3 77.6 - - - +
1850B SER* 1.3 56.8 - - - +
1852B LEU* 3.9 3.6 - - + -
1853B TYR* 2.9 43.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1850 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1846B PHE 2.5 18.0 + - - -
1847B LYS* 3.1 14.8 + - - -
1849B LEU* 1.3 72.2 - - - +
1851B ASP* 1.3 61.3 + - - +
1852B LEU 3.1 0.2 - - - -
1853B TYR* 2.9 21.0 + - - +
1854B TYR* 2.9 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1851 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1814B TYR* 5.0 2.1 + - - -
1847B LYS* 2.9 51.7 + - - +
1848B LYS* 3.3 12.0 - - - +
1850B SER* 1.3 74.5 + - - +
1852B LEU* 1.3 68.3 + - - +
1854B TYR* 3.8 17.3 - - + +
1855B ASP* 3.6 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1852 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1814B TYR* 3.1 31.9 - - + +
1833B ASN* 4.2 12.7 + - - +
1836B ILE* 3.4 30.7 - - + -
1837B ILE* 3.9 26.7 - - + +
1840B PHE* 3.9 19.5 - - + -
1848B LYS* 2.6 35.0 + - + +
1849B LEU* 3.6 6.7 - - + +
1851B ASP* 1.3 78.0 + - - +
1853B TYR* 1.3 62.4 + - - +
1854B TYR 3.2 0.2 - - - -
1855B ASP* 2.6 26.1 - - - +
1856B ILE* 3.4 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1853 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1837B ILE* 3.5 52.6 - - + +
1841B GLU* 4.4 5.7 + - - -
1849B LEU* 2.9 33.9 + - + +
1850B SER* 2.9 6.9 + - - +
1852B LEU* 1.3 75.0 - - - +
1854B TYR* 1.3 65.0 + - - +
1856B ILE* 3.7 13.0 + - + +
1857B HIS* 3.4 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1854 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1850B SER* 2.9 14.2 + - - +
1851B ASP* 3.9 17.0 - - + -
1852B LEU 3.2 0.4 - - - -
1853B TYR* 1.3 75.7 - - - +
1855B ASP* 1.3 65.6 + - + +
1857B HIS* 2.9 29.2 + + - +
1858B ARG* 2.4 74.0 + - + +
1865C GLU* 3.1 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1855 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1814B TYR* 6.0 1.9 - - - -
1817B VAL* 4.6 13.5 - - - +
1821B TRP* 4.0 12.4 + - + +
1829B ILE* 3.9 4.6 - - - +
1833B ASN* 3.6 12.5 + - - -
1851B ASP 3.6 12.0 + - - +
1852B LEU* 2.6 28.6 - - - +
1854B TYR* 1.3 83.8 - - + +
1856B ILE* 1.3 73.9 + - - +
1858B ARG* 3.7 12.3 - - + +
1859B SER* 3.3 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1856 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1829B ILE* 3.5 25.6 - - + +
1830B ALA* 3.8 13.9 - - + -
1833B ASN* 3.1 32.5 - - + +
1837B ILE* 5.8 2.9 - - + -
1852B LEU 3.4 17.9 + - - +
1853B TYR* 3.9 15.0 - - + +
1854B TYR 3.1 0.4 - - - -
1855B ASP* 1.3 83.0 + - - +
1857B HIS* 1.3 62.6 + - - +
1859B SER* 2.6 23.2 + - - +
1860B TYR* 3.2 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1857 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1853B TYR 3.4 10.1 + - - +
1854B TYR* 2.9 32.7 + + - +
1856B ILE* 1.3 74.8 - - - +
1858B ARG* 1.3 66.9 + - - +
1859B SER 3.0 10.0 + - - -
1860B TYR* 3.3 5.9 + - - +
1861B LEU* 3.1 51.8 + - + +
1865C GLU* 5.8 1.8 + - - -
1866C VAL* 6.0 3.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1858 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1821B TRP* 3.0 25.6 - - + -
1854B TYR* 2.4 59.9 + - + +
1855B ASP* 3.9 12.6 - - + +
1856B ILE 3.4 0.2 - - - -
1857B HIS* 1.3 79.8 + - - +
1859B SER* 1.3 57.7 + - - +
1861B LEU* 4.4 15.5 - - - +
1862B LYS* 4.0 11.1 + - - +
1865C GLU* 4.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1859 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1821B TRP* 3.4 17.0 - - - -
1826B TYR* 4.0 12.3 + - - -
1829B ILE* 3.0 36.4 - - - +
1855B ASP 3.3 3.5 + - - -
1856B ILE 2.6 21.1 + - - -
1858B ARG* 1.3 76.5 - - - +
1860B TYR* 1.3 79.2 + - - +
1861B LEU 3.1 1.6 - - - -
1862B LYS* 3.1 5.9 + - - +
1863B VAL* 3.0 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1860 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1826B TYR 5.4 2.2 - - - -
1827B GLU* 4.7 18.3 + - - -
1829B ILE* 5.4 0.2 - - + -
1830B ALA* 3.5 25.1 - - + +
1856B ILE* 3.2 41.7 + - + +
1857B HIS* 3.3 6.7 + - - +
1859B SER* 1.3 87.8 + - - +
1861B LEU* 1.3 61.0 + - - +
1863B VAL* 3.2 20.7 + - + +
1864B ALA* 3.3 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1861 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1857B HIS* 3.1 42.2 + - + +
1858B ARG* 4.7 15.7 - - - +
1859B SER 3.1 0.6 - - - -
1860B TYR* 1.3 77.8 - - - +
1862B LYS* 1.3 65.1 + - + +
1863B VAL 3.0 1.1 + - - -
1864B ALA* 3.2 20.1 + - + +
1865B GLU* 3.9 5.0 + - - +
1866C VAL* 5.5 7.6 - - + -
1869C SER* 5.0 10.5 - - - +
1871C LYS* 4.3 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1862 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1821B TRP* 4.6 9.9 - - + -
1826B TYR* 3.7 21.1 - - + +
1858B ARG* 4.0 11.5 + - - +
1859B SER 3.1 8.2 + - - +
1861B LEU* 1.3 82.1 - - + +
1863B VAL* 1.3 60.7 + - - +
1865B GLU* 3.7 6.2 + - - +
1866B VAL* 3.4 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1863 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1826B TYR* 3.4 33.7 - - + +
1827B GLU* 3.2 28.0 - - - +
1859B SER 3.0 11.1 + - - +
1860B TYR* 3.3 18.8 - - + +
1861B LEU 3.0 0.6 - - - -
1862B LYS* 1.3 77.7 - - - +
1864B ALA* 1.3 61.8 + - - +
1865B GLU 3.1 0.2 - - - -
1866B VAL* 2.8 5.7 + - + -
1867B VAL* 2.6 55.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1864 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1860B TYR 3.3 7.6 + - - +
1861B LEU* 3.2 13.4 + - + +
1863B VAL* 1.3 79.9 - - - +
1865B GLU* 1.3 58.2 + - - +
1867B VAL* 4.5 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1865 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1861B LEU 3.9 4.9 + - - +
1862B LYS* 3.7 7.2 + - - +
1863B VAL 3.1 0.8 - - - -
1864B ALA* 1.3 77.0 - - - +
1866B VAL* 1.3 64.0 + - + +
1867B VAL 5.1 0.4 - - - -
1869B SER* 4.0 15.0 + - - -
1871B LYS* 5.3 1.9 - - - +
1870C GLU* 4.0 24.9 + - + +
----------------------------------------------------------
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