Contacts of the helix formed by residues 1829 - 1844 (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 ILE1829 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1817B VAL* 3.9 22.6 - - + +
1820B LEU* 3.9 28.3 - - + -
1821B TRP* 3.7 18.8 - - + +
1826B TYR* 3.2 23.3 - - - +
1827B GLU 2.7 5.6 + - - +
1828B LEU* 1.3 74.6 - - - +
1830B ALA* 1.3 64.6 + - + +
1832B VAL* 3.3 22.5 - - - +
1833B ASN* 3.4 8.7 + - - +
1855B ASP* 3.9 9.4 - - - +
1856B ILE* 3.5 20.5 - - + +
1859B SER* 3.0 39.5 - - - +
1860B TYR* 5.4 0.9 - - + -
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Residues in contact with ALA1830 (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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1827B GLU 3.2 8.1 + - - +
1828B LEU 3.1 0.6 - - - -
1829B ILE* 1.3 77.7 - - - +
1831B ASP* 1.3 64.1 + - - +
1832B VAL 3.1 5.6 + - - -
1833B ASN* 3.4 10.6 + - - +
1834B LYS* 3.8 9.5 + - - +
1856B ILE* 3.8 17.4 - - + +
1860B TYR* 3.5 34.5 - - + +
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Residues in contact with ASP1831 (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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1779B ALA 5.4 2.4 - - - +
1782B SER* 3.7 36.2 - - - +
1783B ILE* 4.5 14.1 - - + +
1828B LEU* 3.3 17.0 + - + +
1830B ALA* 1.3 80.9 - - - +
1832B VAL* 1.3 60.3 + - - +
1834B LYS* 4.3 12.4 - - - +
1835B PRO* 4.4 3.5 - - - +
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Residues in contact with VAL1832 (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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1724B ILE* 5.1 15.7 - - + -
1783B ILE* 4.5 17.7 - - + -
1813B LEU* 3.2 33.6 - - + +
1816B CYS* 5.9 4.9 - - + -
1817B VAL* 4.7 18.6 - - + -
1820B LEU* 5.5 6.5 - - + -
1828B LEU* 3.4 14.8 - - + +
1829B ILE* 3.3 21.3 - - - +
1831B ASP* 1.3 79.4 - - - +
1833B ASN* 1.3 63.2 + - - +
1834B LYS 3.1 5.6 - - - -
1835B PRO* 3.1 17.7 - - - +
1836B ILE* 3.7 0.5 - - - +
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Residues in contact with ASN1833 (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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1814B TYR* 6.2 0.3 - - - -
1817B VAL* 4.9 13.2 - - - +
1829B ILE 3.4 5.8 + - - -
1830B ALA 3.4 3.2 + - - +
1832B VAL* 1.3 82.5 - - - +
1834B LYS* 1.3 63.5 + - - +
1835B PRO 3.6 0.2 - - - -
1836B ILE* 3.2 27.9 + - - +
1837B ILE* 3.0 39.1 + - + +
1852B LEU* 4.2 13.7 + - - +
1855B ASP* 3.6 21.6 + - - -
1856B ILE* 3.1 36.6 - - + +
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Residues in contact with LYS1834 (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 MET 5.3 9.6 - - - +
1830B ALA 3.8 8.9 + - - +
1831B ASP* 4.3 10.8 - - - +
1833B ASN* 1.3 75.6 - - - +
1835B PRO* 1.3 65.6 - - + +
1837B ILE* 3.1 11.3 + - - +
1838B ALA* 2.7 28.7 + - - +
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Residues in contact with PRO1835 (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 MET 4.2 19.7 - - - +
1773B PHE 4.4 7.1 - - - +
1779B ALA* 5.8 4.9 - - + +
1809B LEU* 6.6 0.4 - - + -
1813B LEU* 3.6 16.2 - - + -
1831B ASP 4.4 2.9 - - - +
1832B VAL* 3.1 27.1 - - - +
1834B LYS* 1.3 87.8 - - + +
1836B ILE* 1.3 62.2 + - - +
1838B ALA* 3.6 10.5 - - + +
1839B VAL* 3.3 26.3 + - - +
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Residues in contact with ILE1836 (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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1810B VAL* 3.7 31.2 - - + +
1813B LEU* 3.6 40.8 - - + -
1814B TYR* 4.5 17.7 - - + +
1817B VAL* 5.9 0.4 - - + -
1832B VAL 3.7 6.7 - - - +
1833B ASN* 3.2 25.4 - - - +
1834B LYS 3.2 0.4 - - - -
1835B PRO* 1.3 73.4 - - - +
1837B ILE* 1.3 65.7 + - - +
1839B VAL* 3.0 15.7 + - - +
1840B PHE* 3.0 24.1 + - + -
1852B LEU* 3.4 24.2 - - + -
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Residues in contact with ILE1837 (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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1833B ASN* 3.0 36.2 + - + +
1834B LYS* 3.6 7.4 - - - +
1836B ILE* 1.3 74.5 - - - +
1838B ALA* 1.3 58.1 + - - +
1841B GLU* 2.8 59.5 + - - +
1849B LEU* 3.6 26.2 - - + -
1852B LEU* 3.9 14.4 - - + +
1853B TYR* 3.5 40.4 - - + +
1856B ILE* 5.8 2.7 - - + -
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Residues in contact with ALA1838 (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 MET 5.0 2.2 - - - +
1773B PHE* 3.9 33.1 - - + +
1834B LYS 2.7 20.0 + - - +
1835B PRO* 3.6 13.5 - - + +
1836B ILE 3.1 0.2 - - - -
1837B ILE* 1.3 72.3 - - - +
1839B VAL* 1.3 59.6 + - - +
1841B GLU* 4.5 11.4 - - - +
1842B LYS* 3.9 12.3 + - - +
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Residues in contact with VAL1839 (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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1740B TRP* 5.8 3.8 - - + +
1773B PHE* 5.5 9.2 - - + +
1774B SER* 6.5 1.1 - - - -
1806B GLU* 4.2 25.4 - - + +
1810B VAL* 6.5 1.6 - - + -
1835B PRO 3.3 13.5 - - - +
1836B ILE* 3.0 8.0 + - - +
1838B ALA* 1.3 80.4 - - + +
1840B PHE* 1.3 66.0 + - + +
1841B GLU 3.3 1.1 - - - -
1842B LYS* 2.9 21.0 + - + +
1843B GLN* 2.9 32.1 + - + +
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Residues in contact with PHE1840 (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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1810B VAL* 4.6 13.0 - - + -
1814B TYR* 4.6 12.6 - + - -
1836B ILE* 3.0 29.2 + - + +
1839B VAL* 1.3 80.0 - - + +
1841B GLU* 1.3 52.2 + - - +
1842B LYS 3.0 4.7 - - - -
1843B GLN* 3.4 5.7 - - + +
1844B ARG* 2.4 37.8 + - - -
1845B ASP* 3.7 11.6 + - + +
1848B LYS* 3.3 45.5 - - + -
1849B LEU* 3.5 33.7 - - + -
1852B LEU* 3.9 21.3 - - + -
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Residues in contact with GLU1841 (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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1837B ILE* 2.8 46.9 + - + +
1838B ALA* 4.5 7.6 - - - +
1840B PHE* 1.3 72.5 - - - +
1842B LYS* 1.3 57.7 + - - +
1844B ARG* 3.8 21.0 + - - +
1849B LEU* 4.0 15.2 - - + +
1853B TYR* 4.4 6.6 + - - -
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Residues in contact with LYS1842 (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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1838B ALA 3.9 11.1 + - - +
1839B VAL* 2.9 20.5 + - + +
1841B GLU* 1.3 80.5 - - - +
1843B GLN* 1.3 61.3 + - + +
1844B ARG* 3.9 16.9 + - - +
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Residues in contact with GLN1843 (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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1806B GLU* 3.4 24.2 + - - -
1839B VAL* 2.9 26.0 + - + +
1840B PHE* 3.4 5.8 - - + +
1842B LYS* 1.3 79.8 - - + +
1844B ARG* 1.3 74.7 + - - +
1845B ASP* 3.9 2.6 - - + +
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Residues in contact with ARG1844 (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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1840B PHE 2.4 21.7 + - - -
1841B GLU* 3.8 17.3 + - - +
1842B LYS* 3.9 13.9 + - - +
1843B GLN* 1.3 78.0 - - - +
1845B ASP* 1.3 57.0 + - - +
1846B PHE* 3.6 29.0 - - + -
1849B LEU* 5.3 1.1 - - - -
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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