Contacts of the helix formed by residues 1834 - 1852 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1830F PRO* 3.6 12.7 - - - +
1831F VAL 3.1 17.5 - - - +
1832F GLY 3.3 2.4 - - - -
1833F GLY* 1.3 79.0 - - - +
1835F VAL* 1.3 63.9 + - - +
1836F GLU* 3.5 6.4 + - - +
1837F PHE* 3.0 40.3 + - - +
1838F GLN* 3.6 5.4 + - - +
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Residues in contact with VAL1835 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1823F GLY* 6.5 0.4 - - - -
1830F PRO* 4.4 19.1 - - + -
1834F SER* 1.3 73.1 - - - +
1836F GLU* 1.3 60.3 + - - +
1838F GLN* 3.3 2.2 + - - -
1839F PHE* 2.9 62.5 + - + +
1930F MET* 5.9 5.4 - - + -
1931F LYS 5.8 2.5 - - - +
1932F LEU* 5.2 4.7 - - + -
1933F PRO* 4.9 16.2 - - + -
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Residues in contact with GLU1836 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1834F SER* 3.3 6.1 + - - +
1835F VAL* 1.3 79.7 - - - +
1837F PHE* 1.3 65.0 + - + +
1838F GLN 3.0 0.4 + - - -
1839F PHE* 4.4 2.9 - - - +
1840F VAL* 2.9 48.1 + - + +
1933F PRO* 3.9 28.6 - - + +
1935F SER* 5.7 2.9 - - - +
1936F VAL* 4.8 0.7 - - - -
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Residues in contact with PHE1837 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1705F GLY* 3.7 37.4 - - - +
1706F PRO* 4.2 20.2 - - + -
1708F ARG* 4.1 10.2 - - - -
1709F ALA* 5.6 7.4 - - + -
1831F VAL 4.4 4.7 - - - +
1832F GLY 4.1 10.1 - - - +
1834F SER* 3.0 27.6 + - - +
1836F GLU* 1.3 81.5 - - + +
1838F GLN* 1.3 57.0 + - - +
1840F VAL* 5.4 0.9 - - + -
1841F PRO* 3.5 21.1 - - - +
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Residues in contact with GLN1838 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1708F ARG* 4.9 12.5 + - - +
1819F ALA* 4.8 4.6 - - + +
1830F PRO* 5.5 0.7 - - + -
1831F VAL* 3.3 42.4 - - + +
1834F SER 3.6 6.8 + - - +
1835F VAL* 3.3 5.7 + - - +
1836F GLU 3.0 0.6 - - - -
1837F PHE* 1.3 79.3 - - - +
1839F PHE* 1.3 67.6 + - + +
1841F PRO* 4.1 3.3 - - - +
1842F VAL* 3.3 17.5 - - - +
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Residues in contact with PHE1839 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1819F ALA* 3.4 41.5 - - + -
1820F VAL* 5.0 2.5 - - - -
1822F ASP* 5.7 3.1 - - + -
1823F GLY* 4.5 13.9 - - - -
1835F VAL* 2.9 41.5 + - + +
1838F GLN* 1.3 90.2 - - + +
1840F VAL* 1.3 63.0 + - - +
1841F PRO 3.6 0.4 - - - -
1842F VAL* 3.5 5.3 - - + +
1843F LEU* 3.3 40.6 + - + +
1927F LEU* 3.6 31.2 - - + -
1930F MET* 5.5 4.7 - - + -
1932F LEU* 4.3 15.0 - - + -
1933F PRO* 6.1 0.2 - - + -
1936F VAL* 3.6 16.4 - - + -
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Residues in contact with VAL1840 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1836F GLU* 2.9 28.3 + - + +
1837F PHE* 5.4 1.3 - - + -
1839F PHE* 1.3 74.1 - - - +
1841F PRO* 1.3 65.5 - - + +
1843F LEU* 3.4 3.4 + - - +
1844F LYS* 2.9 51.0 + - + +
1935F SER* 3.6 33.0 - - - -
1936F VAL* 3.6 16.6 - - + +
1939F GLN* 5.6 1.5 - - - +
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Residues in contact with PRO1841 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1708F ARG* 4.7 4.9 - - + +
1709F ALA* 4.3 22.9 - - + +
1712F TYR* 3.4 47.9 - - + -
1836F GLU 4.0 0.4 - - - +
1837F PHE* 3.5 26.5 - - - +
1838F GLN 4.1 2.0 - - - -
1839F PHE 3.8 2.7 - - - +
1840F VAL* 1.3 96.4 - - + +
1842F VAL* 1.3 58.1 + - - +
1844F LYS* 3.3 8.1 + - + +
1845F LEU 2.9 24.8 + - - -
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Residues in contact with VAL1842 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1708F ARG* 4.7 6.5 - - - +
1712F TYR* 4.0 16.9 - - - +
1812F ALA* 4.5 5.1 - - + +
1815F MET* 3.9 14.6 - - + -
1816F LEU* 3.9 34.5 - - + +
1819F ALA* 4.6 11.7 - - + -
1838F GLN 3.3 24.7 - - - +
1839F PHE* 3.5 12.1 - - + +
1841F PRO* 1.3 78.6 - - - +
1843F LEU* 1.3 66.8 + - + +
1845F LEU* 3.3 2.5 + - - +
1846F VAL* 2.9 30.5 + - + +
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Residues in contact with LEU1843 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1816F LEU* 6.3 2.0 - - + -
1839F PHE* 3.3 30.7 - - + +
1840F VAL 3.4 2.6 + - - +
1841F PRO 3.3 0.4 - - - -
1842F VAL* 1.3 84.3 - - + +
1844F LYS* 1.3 60.3 + - - +
1846F VAL* 3.3 10.9 + - + +
1847F SER* 2.9 32.4 + - - -
1866F MET* 5.4 7.6 - - + -
1867F ILE* 6.1 0.9 - - + -
1927F LEU* 4.7 14.6 - - + -
1936F VAL* 4.1 21.8 - - + -
1939F GLN* 4.2 15.9 - - + -
1940F MET* 3.7 35.0 - - + -
1943F LEU* 4.7 10.8 - - + +
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Residues in contact with LYS1844 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1713F ASP* 6.0 4.6 - - - +
1716F ILE* 5.3 9.2 - - + +
1840F VAL* 2.9 41.8 + - + +
1841F PRO* 3.7 6.7 - - + +
1843F LEU* 1.3 77.1 - - - +
1845F LEU* 1.3 53.2 + - - +
1847F SER* 3.3 6.5 + - - -
1848F THR* 2.6 39.0 + - - +
1939F GLN* 5.3 9.4 - - + -
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Residues in contact with LEU1845 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1698F LEU* 6.2 0.4 - - + -
1712F TYR* 3.8 22.0 - - + -
1715F LEU* 5.5 6.1 - - + -
1716F ILE* 4.5 12.1 - - + +
1812F ALA* 5.4 9.2 - - + -
1841F PRO 2.9 16.9 + - - +
1842F VAL* 3.7 5.2 - - + +
1843F LEU 3.3 0.2 - - - -
1844F LYS* 1.3 74.3 - - - +
1846F VAL* 1.3 59.9 + - + +
1848F THR* 3.3 5.8 + - - -
1849F LEU* 2.9 38.9 + - + +
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Residues in contact with VAL1846 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1812F ALA* 4.4 28.3 - - + +
1813F LEU* 6.0 2.9 - - + -
1816F LEU* 4.6 9.4 - - + -
1842F VAL* 2.9 27.0 + - + +
1843F LEU* 3.3 13.2 + - + +
1845F LEU* 1.3 75.9 - - - +
1847F SER* 1.3 59.3 + - - +
1849F LEU* 3.4 0.7 + - - -
1850F LEU* 2.9 29.8 + - + +
1855F PHE* 3.6 13.0 - - + -
1863F ILE* 4.1 26.9 - - + -
1943F LEU* 4.9 15.5 - - + -
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Residues in contact with SER1847 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1728F ARG* 6.0 2.2 - - - -
1843F LEU 2.9 16.3 + - - -
1844F LYS* 3.7 7.2 - - - -
1846F VAL* 1.3 77.8 - - - +
1848F THR* 1.3 56.4 + - - +
1850F LEU* 3.8 1.4 - - - +
1851F VAL* 2.9 33.8 + - - +
1939F GLN* 4.4 6.4 + - - +
1942F ASN* 4.1 19.6 + - - -
1943F LEU* 3.3 35.7 - - - +
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Residues in contact with THR1848 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1716F ILE* 3.8 25.4 - - + +
1720F LEU* 3.7 31.8 - - + +
1724F CYS* 4.2 19.7 - - - -
1728F ARG* 6.2 0.2 - - - +
1844F LYS* 2.6 25.1 + - - +
1845F LEU 3.3 4.0 + - - -
1847F SER* 1.3 76.2 - - - +
1849F LEU* 1.3 60.8 + - - +
1851F VAL* 3.3 20.3 - - - +
1852F MET* 3.3 13.7 - - - +
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Residues in contact with LEU1849 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1716F ILE* 6.0 0.7 - - + -
1720F LEU* 3.7 34.8 - - + -
1805F LEU* 5.4 7.2 - - + +
1808F LEU* 4.1 38.8 - - + +
1809F ARG* 4.3 2.5 - - + +
1812F ALA* 4.4 7.4 - - + -
1845F LEU* 2.9 22.9 + - + +
1848F THR* 1.3 77.2 - - - +
1850F LEU* 1.3 62.2 + - - +
1852F MET* 3.8 4.1 + - - +
1854F ILE* 3.7 35.2 + - + +
1855F PHE* 3.5 33.6 + - + -
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Residues in contact with LEU1850 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1846F VAL* 2.9 18.2 + - + +
1847F SER* 3.9 3.4 - - - +
1849F LEU* 1.3 75.7 - - - +
1851F VAL* 1.3 63.0 + - - +
1852F MET 3.1 2.0 - - - -
1853F GLY* 3.1 11.7 + - - -
1855F PHE* 3.6 26.2 - - + +
1860F VAL* 3.9 24.2 - - + -
1863F ILE* 4.2 14.4 - - + -
1943F LEU* 3.9 19.5 - - + -
1946F TYR* 2.9 31.2 + - + +
1947F PHE* 3.6 34.1 - - + -
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Residues in contact with VAL1851 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1724F CYS* 4.4 8.7 - - - -
1727F ARG* 5.4 1.6 - - - +
1728F ARG* 4.1 31.9 - - + +
1731F LEU* 4.7 15.9 - - + +
1847F SER 2.9 20.6 + - - +
1848F THR* 3.3 19.3 - - - +
1850F LEU* 1.3 77.1 - - - +
1852F MET* 1.3 80.3 + - + +
1853F GLY 3.4 0.3 + - - -
1946F TYR* 3.6 38.6 + - + -
1950F GLN* 5.5 0.2 + - - -
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Residues in contact with MET1852 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1720F LEU* 3.7 17.0 - - + -
1723F ALA* 3.9 23.8 - - - +
1724F CYS* 3.6 26.9 - - - +
1727F ARG* 3.6 28.3 - - + -
1728F ARG* 5.1 0.9 - - + -
1776F HIS* 4.5 19.2 + - - +
1848F THR 3.3 17.7 + - - +
1849F LEU 4.1 1.8 - - - +
1850F LEU 3.1 1.2 - - - -
1851F VAL* 1.3 103.6 - - + +
1853F GLY* 1.3 59.5 + - - +
1854F ILE* 3.4 27.0 + - + +
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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