Contacts of the helix formed by residues 1834 - 1852 (chain B) in PDB entry 6X34
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 SER1834 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1830B PRO* 3.6 13.1 - - - +
1831B VAL 3.1 17.7 - - - +
1832B GLY 3.3 1.8 - - - -
1833B GLY* 1.3 78.1 - - - +
1835B VAL* 1.3 63.1 + - - +
1836B GLU* 3.5 6.6 + - - +
1837B PHE* 3.0 39.5 + - - +
1838B GLN* 3.6 5.7 + - - +
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Residues in contact with VAL1835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1823B GLY* 6.5 0.2 - - - -
1830B PRO* 4.4 18.4 - - + -
1834B SER* 1.3 71.8 - - - +
1836B GLU* 1.3 60.7 + - - +
1838B GLN* 3.3 2.2 + - - -
1839B PHE* 2.9 63.1 + - + +
1930B MET* 5.9 5.2 - - + -
1931B LYS 5.8 2.5 - - - +
1932B LEU* 5.2 4.5 - - + -
1933B PRO* 4.9 16.6 - - + -
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Residues in contact with GLU1836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1834B SER* 3.3 7.0 + - - +
1835B VAL* 1.3 78.8 - - - +
1837B PHE* 1.3 65.2 + - + +
1838B GLN 3.0 0.2 - - - -
1839B PHE* 4.7 2.0 - - - -
1840B VAL* 2.9 48.1 + - + +
1933B PRO* 3.9 29.1 - - + +
1935B SER* 5.7 2.7 - - - +
1936B VAL* 4.8 0.9 - - - -
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Residues in contact with PHE1837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1705B GLY* 3.7 38.3 - - - +
1706B PRO* 4.2 21.3 - - + -
1708B ARG* 4.1 10.4 - - - -
1709B ALA* 5.6 6.7 - - + +
1831B VAL 4.4 5.4 - - - +
1832B GLY 4.1 10.8 - - - +
1833B GLY 5.6 0.2 - - - -
1834B SER* 3.0 26.9 + - - +
1836B GLU* 1.3 81.5 - - + +
1838B GLN* 1.3 57.1 + - - +
1840B VAL* 5.4 0.9 - - + -
1841B PRO* 3.5 21.1 - - - +
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Residues in contact with GLN1838 (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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1708B ARG* 4.9 12.2 + - - +
1819B ALA* 4.8 3.8 - - - +
1830B PRO* 5.5 0.9 - - + -
1831B VAL* 3.3 43.3 - - + +
1834B SER 3.6 6.0 + - - +
1835B VAL* 3.3 5.2 + - - +
1836B GLU 3.0 0.4 - - - -
1837B PHE* 1.3 78.9 - - - +
1839B PHE* 1.3 68.2 + - + +
1840B VAL 3.8 0.4 - - - -
1841B PRO* 4.1 3.8 - - - +
1842B VAL* 3.3 17.5 - - - +
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Residues in contact with PHE1839 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1819B ALA* 3.4 41.5 - - + -
1820B VAL* 5.0 1.3 - - - -
1822B ASP* 5.7 2.5 - - + -
1823B GLY* 4.5 13.9 - - - -
1835B VAL* 2.9 42.2 + - + +
1838B GLN* 1.3 88.8 - - + +
1840B VAL* 1.3 63.1 + - - +
1841B PRO 3.6 0.4 - - - -
1842B VAL* 3.5 4.4 - - + +
1843B LEU* 3.3 40.6 + - + +
1927B LEU* 3.6 31.6 - - + -
1930B MET* 5.5 4.0 - - + -
1932B LEU* 4.3 15.3 - - + -
1933B PRO* 6.1 0.2 - - + -
1936B VAL* 3.6 16.4 - - + -
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Residues in contact with VAL1840 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1836B GLU* 2.9 28.1 + - + +
1837B PHE* 5.4 1.1 - - + -
1839B PHE* 1.3 74.7 - - - +
1841B PRO* 1.3 65.1 - - + +
1843B LEU* 3.4 2.9 + - - +
1844B LYS* 2.9 50.7 + - + +
1935B SER* 3.6 33.4 - - - +
1936B VAL* 3.6 16.6 - - + +
1939B GLN* 6.0 1.3 - - - -
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Residues in contact with PRO1841 (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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1708B ARG* 4.7 5.6 - - + +
1709B ALA* 4.3 22.9 - - + +
1712B TYR* 3.4 48.1 - - + -
1836B GLU 4.0 0.4 - - - +
1837B PHE* 3.5 26.2 - - - +
1838B GLN 4.1 1.8 - - - -
1839B PHE 3.8 3.1 - - - +
1840B VAL* 1.3 97.8 - - + +
1842B VAL* 1.3 57.5 + - - +
1844B LYS* 3.3 8.0 + - + +
1845B LEU 2.9 24.3 + - - -
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Residues in contact with VAL1842 (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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1708B ARG* 4.7 6.5 - - - +
1712B TYR* 4.0 17.2 - - - +
1812B ALA* 4.5 5.2 - - + +
1815B MET* 3.9 14.1 - - + -
1816B LEU* 3.9 34.3 - - + +
1819B ALA* 4.6 11.7 - - + -
1838B GLN 3.3 23.8 - - - +
1839B PHE* 3.5 12.6 - - + +
1841B PRO* 1.3 78.0 - - - +
1843B LEU* 1.3 66.3 + - + +
1845B LEU* 3.3 3.0 + - - +
1846B VAL* 2.9 30.5 + - + +
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Residues in contact with LEU1843 (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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1816B LEU* 6.3 1.8 - - + -
1839B PHE* 3.3 31.4 - - + +
1840B VAL* 3.4 2.8 + - - +
1841B PRO 3.3 0.4 - - - -
1842B VAL* 1.3 85.2 - - + +
1844B LYS* 1.3 62.1 + - - +
1846B VAL* 3.3 11.5 + - + +
1847B SER* 2.9 32.7 + - - -
1866B MET* 5.4 8.1 - - + -
1867B ILE* 6.1 0.9 - - + -
1927B LEU* 4.7 14.4 - - + -
1932B LEU* 6.3 0.2 - - + -
1936B VAL* 4.1 20.6 - - + -
1939B GLN* 4.2 16.2 - - + -
1940B MET* 3.7 33.9 - - + -
1943B LEU* 4.7 10.6 - - + +
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Residues in contact with LYS1844 (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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1713B ASP* 6.0 4.8 - - - +
1716B ILE* 5.3 10.5 - - + -
1840B VAL* 2.9 40.4 + - + +
1841B PRO* 3.7 7.2 - - + +
1843B LEU* 1.3 76.7 - - - +
1845B LEU* 1.3 52.1 + - - +
1847B SER* 3.3 6.7 + - - -
1848B THR* 2.6 39.8 + - - +
1939B GLN* 5.3 9.6 - - + -
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Residues in contact with LEU1845 (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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1698B LEU* 6.2 0.4 - - + -
1712B TYR* 3.8 22.0 - - + -
1715B LEU* 5.5 6.5 - - + -
1716B ILE* 4.5 12.0 - - + +
1812B ALA* 5.4 8.5 - - + -
1841B PRO 2.9 17.4 + - - +
1842B VAL* 3.7 4.5 - - + +
1844B LYS* 1.3 74.3 - - - +
1846B VAL* 1.3 59.8 + - + +
1848B THR* 3.3 6.4 + - - -
1849B LEU* 2.9 38.8 + - + +
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Residues in contact with VAL1846 (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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1812B ALA* 4.4 28.5 - - + +
1813B LEU* 6.1 2.9 - - + -
1816B LEU* 4.6 9.6 - - + -
1842B VAL* 2.9 26.8 + - + +
1843B LEU* 3.7 12.6 - - + +
1845B LEU* 1.3 75.3 - - - +
1847B SER* 1.3 59.3 + - - +
1849B LEU* 3.4 0.7 + - - -
1850B LEU* 2.9 29.6 + - + +
1855B PHE* 3.6 11.8 - - + -
1863B ILE* 4.1 27.4 - - + -
1943B LEU* 4.9 15.0 - - + -
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Residues in contact with SER1847 (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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1728B ARG* 6.0 2.5 - - - -
1843B LEU 2.9 17.9 + - - -
1844B LYS* 3.7 6.1 - - - -
1846B VAL* 1.3 77.5 - - - +
1848B THR* 1.3 57.3 + - - +
1850B LEU* 3.8 1.2 - - - +
1851B VAL* 2.9 34.1 + - - +
1939B GLN* 4.4 6.1 + - - +
1942B ASN* 4.1 21.1 + - - -
1943B LEU* 3.3 36.1 - - - +
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Residues in contact with THR1848 (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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1716B ILE* 3.8 25.7 - - + +
1720B LEU* 3.7 31.9 - - + +
1724B CYS* 4.2 18.8 - - - -
1728B ARG* 6.2 0.2 - - - +
1844B LYS* 2.6 25.6 + - - +
1845B LEU 3.8 3.6 - - - -
1847B SER* 1.3 77.7 - - - +
1849B LEU* 1.3 60.1 + - - +
1851B VAL* 3.3 20.5 - - - +
1852B MET* 3.3 13.3 - - - +
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Residues in contact with LEU1849 (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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1716B ILE* 6.0 1.1 - - + -
1720B LEU* 3.7 33.9 - - + -
1805B LEU* 5.4 7.2 - - + +
1808B LEU* 4.1 37.7 - - + +
1809B ARG* 4.3 2.7 - - + +
1812B ALA* 4.4 7.9 - - + -
1845B LEU* 2.9 23.7 + - + +
1848B THR* 1.3 77.0 - - - +
1850B LEU* 1.3 62.0 + - - +
1852B MET* 3.8 4.4 + - - +
1854B ILE* 3.7 35.2 + - + +
1855B PHE* 3.5 33.8 + - + -
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Residues in contact with LEU1850 (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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1846B VAL* 2.9 18.7 + - + +
1847B SER* 3.9 3.1 - - - +
1849B LEU* 1.3 75.0 - - - +
1851B VAL* 1.3 61.5 + - - +
1852B MET 3.1 2.2 - - - -
1853B GLY* 3.1 11.2 + - - -
1855B PHE* 3.6 25.8 - - + +
1860B VAL* 3.9 24.5 - - + -
1863B ILE* 4.2 13.9 - - + -
1943B LEU* 3.9 20.9 - - + -
1946B TYR* 2.9 31.1 + - + +
1947B PHE* 3.6 33.4 - - + -
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Residues in contact with VAL1851 (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 CYS* 4.4 9.0 - - - -
1727B ARG* 5.4 2.1 - - - +
1728B ARG* 4.1 32.1 - - + +
1731B LEU* 4.7 16.3 - - + +
1847B SER 2.9 21.0 + - - +
1848B THR* 3.3 19.1 - - - +
1850B LEU* 1.3 77.6 - - - +
1852B MET* 1.3 79.0 + - + +
1853B GLY 3.4 0.7 + - - -
1946B TYR* 3.6 40.1 + - + -
1950B GLN* 5.5 0.2 + - - -
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Residues in contact with MET1852 (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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1720B LEU* 3.7 17.5 - - + -
1723B ALA* 3.9 24.0 - - - +
1724B CYS* 3.6 25.8 - - - +
1727B ARG* 3.6 28.3 - - + -
1728B ARG* 5.1 0.7 - - + -
1776B HIS* 4.5 18.4 + - - +
1848B THR 3.3 17.6 + - - +
1849B LEU 4.1 1.3 - - - +
1850B LEU 3.1 1.2 - - - -
1851B VAL* 1.3 103.2 - - + +
1853B GLY* 1.3 59.4 + - - +
1854B ILE* 3.4 28.1 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
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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