Contacts of the helix formed by residues 1834 - 1852 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1830H PRO* 3.6 12.5 - - - +
1831H VAL 3.1 17.3 - - - +
1832H GLY 3.3 2.0 - - - -
1833H GLY* 1.3 79.5 - - - +
1835H VAL* 1.3 62.6 + - - +
1836H GLU* 3.5 6.6 + - - +
1837H PHE* 3.0 40.0 + - - +
1838H GLN* 3.6 5.9 + - - +
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Residues in contact with VAL1835 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1823H GLY* 6.5 0.4 - - - -
1830H PRO* 4.4 18.2 - - + -
1834H SER* 1.3 72.0 - - - +
1836H GLU* 1.3 59.9 + - - +
1838H GLN* 3.3 2.2 + - - +
1839H PHE* 2.9 63.8 + - + +
1930H MET* 5.9 4.9 - - + -
1931H LYS 5.8 2.5 - - - +
1932H LEU* 5.2 4.7 - - + -
1933H PRO* 4.9 15.0 - - + -
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Residues in contact with GLU1836 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1834H SER* 3.3 6.8 + - - +
1835H VAL* 1.3 79.8 - - - +
1837H PHE* 1.3 64.9 + - + +
1839H PHE* 4.4 3.1 - - - +
1840H VAL* 2.9 47.3 + - + +
1933H PRO* 3.9 28.9 - - + +
1935H SER* 5.7 2.7 - - - +
1936H VAL* 4.8 0.7 - - - -
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Residues in contact with PHE1837 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1705H GLY* 3.7 38.0 - - - +
1706H PRO* 4.2 19.7 - - + -
1708H ARG* 4.1 10.4 - - - -
1709H ALA* 5.6 7.0 - - + -
1831H VAL 4.4 5.4 - - - +
1832H GLY 4.1 10.8 - - - +
1834H SER* 3.0 26.9 + - - +
1836H GLU* 1.3 81.4 - - + +
1838H GLN* 1.3 57.0 + - - +
1840H VAL* 5.4 0.9 - - + -
1841H PRO* 3.5 20.8 - - - +
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Residues in contact with GLN1838 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1708H ARG* 4.9 12.2 + - - +
1819H ALA* 4.8 4.2 - - + +
1830H PRO* 5.5 0.9 - - + -
1831H VAL* 3.3 42.2 - - + +
1834H SER 3.6 6.6 + - - +
1835H VAL* 3.3 4.8 + - - +
1836H GLU 3.0 0.6 - - - -
1837H PHE* 1.3 80.4 - - - +
1839H PHE* 1.3 67.7 + - + +
1841H PRO* 4.1 3.9 - - - +
1842H VAL* 3.3 17.5 + - - +
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Residues in contact with PHE1839 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1819H ALA* 3.4 41.7 - - + -
1820H VAL* 5.0 1.3 - - - -
1822H ASP* 5.7 2.9 - - + -
1823H GLY* 4.5 13.7 - - - -
1835H VAL* 2.9 40.9 + - + +
1838H GLN* 1.3 88.3 - - + +
1840H VAL* 1.3 63.5 + - - +
1841H PRO 3.6 0.4 - - - -
1842H VAL* 3.5 4.6 - - + +
1843H LEU* 3.3 39.9 + - + +
1927H LEU* 3.6 30.5 - - + -
1930H MET* 5.5 4.0 - - + -
1932H LEU* 4.3 15.5 - - + -
1933H PRO* 6.1 0.2 - - + -
1936H VAL* 3.6 16.6 - - + -
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Residues in contact with VAL1840 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1836H GLU* 2.9 28.1 + - + +
1837H PHE* 5.4 0.9 - - + -
1839H PHE* 1.3 75.4 - - - +
1841H PRO* 1.3 65.5 - - + +
1843H LEU* 3.4 3.6 + - - +
1844H LYS* 2.9 50.3 + - + +
1935H SER* 3.6 33.7 - - - +
1936H VAL* 3.6 16.8 - - + +
1939H GLN* 5.6 1.1 - - - +
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Residues in contact with PRO1841 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1708H ARG* 4.7 4.0 - - + +
1709H ALA* 4.3 22.7 - - + +
1712H TYR* 3.4 48.2 - - + -
1836H GLU 4.0 0.7 - - - +
1837H PHE* 3.5 26.0 - - - +
1838H GLN 4.1 2.0 - - - +
1839H PHE 3.8 2.2 - - - +
1840H VAL* 1.3 97.2 - - + +
1842H VAL* 1.3 57.9 + - - +
1844H LYS* 3.3 7.5 + - + +
1845H LEU 2.9 24.3 + - - -
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Residues in contact with VAL1842 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1708H ARG* 4.7 6.7 - - - +
1712H TYR* 4.0 17.1 - - - +
1812H ALA* 4.5 4.5 - - - +
1815H MET* 3.9 14.4 - - + -
1816H LEU* 3.9 34.5 - - + +
1819H ALA* 4.6 11.4 - - + -
1838H GLN 3.3 25.5 + - - +
1839H PHE* 3.5 12.3 - - + +
1841H PRO* 1.3 78.4 - - - +
1843H LEU* 1.3 65.8 + - + +
1845H LEU* 3.3 3.0 + - + +
1846H VAL* 2.9 31.3 + - + +
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Residues in contact with LEU1843 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1816H LEU* 6.3 1.6 - - + -
1839H PHE* 3.3 32.1 - - + +
1840H VAL* 3.4 3.0 + - - +
1841H PRO 3.3 0.2 - - - -
1842H VAL* 1.3 83.5 - - + +
1844H LYS* 1.3 60.7 + - - +
1846H VAL* 3.3 10.5 + - + +
1847H SER* 2.9 32.6 + - - -
1866H MET* 5.4 8.3 - - + -
1867H ILE* 6.1 0.9 - - + -
1927H LEU* 4.7 13.9 - - + -
1932H LEU* 6.3 0.2 - - + -
1936H VAL* 4.1 20.6 - - + -
1939H GLN* 4.2 16.4 - - + -
1940H MET* 3.7 34.1 - - + -
1943H LEU* 4.7 10.8 - - + +
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Residues in contact with LYS1844 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1713H ASP* 6.0 4.8 - - - +
1716H ILE* 5.3 9.0 - - + -
1840H VAL* 2.9 41.1 + - + +
1841H PRO* 3.7 6.7 - - + +
1843H LEU* 1.3 76.8 - - - +
1845H LEU* 1.3 53.3 + - - +
1847H SER* 3.3 6.1 + - - -
1848H THR* 2.6 39.0 + - - +
1939H GLN* 5.3 9.4 - - + -
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Residues in contact with LEU1845 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1698H LEU* 6.2 0.2 - - + -
1712H TYR* 3.8 21.5 - - + -
1715H LEU* 5.5 6.7 - - + -
1716H ILE* 4.5 11.8 - - + +
1812H ALA* 5.4 8.7 - - + -
1841H PRO 2.9 17.6 + - - +
1842H VAL* 3.7 4.7 - - - +
1844H LYS* 1.3 74.9 - - - +
1846H VAL* 1.3 60.0 + - + +
1848H THR* 3.3 6.5 + - - -
1849H LEU* 2.9 38.4 + - + +
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Residues in contact with VAL1846 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1812H ALA* 4.4 28.0 - - + +
1813H LEU* 6.0 2.7 - - + -
1816H LEU* 4.6 9.6 - - + -
1842H VAL* 2.9 27.0 + - + +
1843H LEU* 3.7 11.9 - - + +
1845H LEU* 1.3 75.2 - - - +
1847H SER* 1.3 60.0 + - - +
1849H LEU* 3.4 0.9 + - - -
1850H LEU* 2.9 29.5 + - + +
1855H PHE* 3.6 12.6 - - + -
1863H ILE* 4.1 26.5 - - + -
1943H LEU* 4.9 15.3 - - + -
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Residues in contact with SER1847 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1728H ARG* 6.0 2.7 - - - -
1843H LEU 2.9 18.6 + - - -
1844H LYS* 3.7 7.2 - - - -
1846H VAL* 1.3 77.4 - - - +
1848H THR* 1.3 56.9 + - - +
1850H LEU* 3.2 2.0 + - - +
1851H VAL* 2.9 34.2 + - - +
1939H GLN* 4.4 6.2 + - - +
1942H ASN* 4.1 19.7 + - - +
1943H LEU* 3.3 35.9 - - - +
1946H TYR* 6.1 0.2 - - - -
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Residues in contact with THR1848 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1716H ILE* 3.8 26.3 - - + +
1720H LEU* 3.7 33.0 - - + +
1724H CYS* 4.2 18.6 - - - -
1728H ARG* 6.2 0.4 - - - +
1844H LYS* 2.6 24.5 + - - +
1845H LEU 3.3 3.8 + - - -
1847H SER* 1.3 77.1 - - - +
1849H LEU* 1.3 61.6 + - - +
1851H VAL* 3.3 20.3 - - - +
1852H MET* 3.3 13.5 - - - +
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Residues in contact with LEU1849 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1716H ILE* 6.0 1.1 - - + -
1720H LEU* 3.7 33.4 - - + -
1805H LEU* 5.4 7.2 - - + +
1808H LEU* 4.1 38.8 - - + +
1809H ARG* 4.3 2.9 - - + +
1812H ALA* 4.4 7.4 - - + -
1845H LEU* 2.9 24.1 + - + +
1846H VAL 3.9 0.2 - - - +
1848H THR* 1.3 76.7 - - - +
1850H LEU* 1.3 60.9 + - - +
1852H MET* 3.8 4.9 + - - +
1854H ILE* 3.7 34.9 + - + +
1855H PHE* 3.5 33.4 + - + -
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Residues in contact with LEU1850 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1846H VAL* 2.9 17.8 + - + +
1847H SER* 3.2 3.8 + - - +
1849H LEU* 1.3 75.4 - - - +
1851H VAL* 1.3 62.7 + - - +
1852H MET 3.1 1.6 - - - -
1853H GLY* 3.1 11.6 + - - +
1855H PHE* 3.6 26.5 - - + +
1860H VAL* 3.9 24.5 - - + -
1863H ILE* 4.2 14.1 - - + -
1943H LEU* 3.9 20.2 - - + -
1946H TYR* 2.9 31.1 + - + -
1947H PHE* 3.6 32.3 - - + -
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Residues in contact with VAL1851 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1724H CYS* 4.4 8.5 - - - -
1727H ARG* 5.4 2.2 - - + +
1728H ARG* 4.1 33.2 - - + +
1731H LEU* 4.7 16.0 - - + +
1847H SER 2.9 21.3 + - - +
1848H THR* 3.3 20.2 - - - +
1850H LEU* 1.3 77.5 - - - +
1852H MET* 1.3 78.4 + - + +
1853H GLY* 3.4 0.7 + - - -
1946H TYR* 3.6 39.6 + - + -
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Residues in contact with MET1852 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1720H LEU* 3.7 16.8 - - + -
1723H ALA* 3.9 24.9 - - - +
1724H CYS* 3.6 26.7 - - - +
1727H ARG* 3.6 27.6 - - + -
1728H ARG* 5.1 1.3 - - + -
1776H HIS* 4.5 20.1 + - - +
1848H THR 3.3 17.2 + - - +
1849H LEU 4.1 2.0 - - - +
1850H LEU 3.1 0.8 - - - -
1851H VAL* 1.3 103.6 - - + +
1853H GLY* 1.3 59.4 + - - +
1854H 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) + - + + + + + -
------------------------------------------------------------
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