Contacts of the helix formed by residues 1809 - 1820 (chain G) in PDB entry 2VKZ
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 LEU1809 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1667G THR 4.8 1.3 - - - +
1668G GLY* 4.4 1.1 - - - -
1669G GLN* 4.0 31.6 - - + +
1778G GLN* 3.5 43.3 - - + +
1781G LEU* 3.7 31.6 - - + -
1782G THR* 3.8 6.7 - - - +
1807G HIS 2.9 1.0 + - - -
1808G SER* 1.3 77.6 + - - +
1810G GLY* 1.3 60.2 + - - +
1811G GLU 2.9 10.7 + - - -
1812G TYR* 3.0 19.1 + - + +
1813G ALA* 3.9 2.5 + - + +
1831G VAL* 3.6 24.0 - - + -
1834G ARG* 3.8 15.5 - - - +
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Residues in contact with GLY1810 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1666G PHE* 3.3 21.4 - - - +
1667G THR 3.4 21.8 + - - -
1785G GLU* 4.4 0.2 - - - -
1806G GLY* 3.5 6.5 - - - -
1807G HIS 3.3 7.6 + - - -
1809G LEU* 1.3 80.1 - - - +
1811G GLU* 1.3 56.3 + - - +
1812G TYR 3.1 0.7 - - - -
1813G ALA* 3.4 8.3 + - - -
1814G ALA* 2.8 25.3 + - - +
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Residues in contact with GLU1811 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU 5.4 1.3 - - - +
18A LEU* 3.7 15.3 - - + +
21A GLN* 3.2 14.0 - - - +
1806G GLY* 3.5 29.7 - - - +
1808G SER 3.3 14.1 + - - +
1809G LEU 2.9 1.0 + - - -
1810G GLY* 1.3 78.1 - - - +
1812G TYR* 1.3 61.1 + - + +
1814G ALA* 3.8 2.6 - - + +
1815G LEU* 3.1 33.9 + - - +
2010G TYR* 2.5 39.2 + - + -
2011G ILE 4.8 1.1 - - - +
2012G PRO* 3.8 4.4 - - - +
2013G ASN* 3.2 37.5 + - - +
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Residues in contact with TYR1812 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.5 44.7 + - + +
21A GLN* 4.2 9.2 + - - -
1808G SER 4.2 4.7 - - - -
1809G LEU* 3.0 16.8 + - - +
1811G GLU* 1.3 78.1 - - + +
1813G ALA* 1.3 59.9 + - - +
1815G LEU* 3.2 5.2 + - + +
1816G ALA* 2.9 30.7 + - - +
1822G MET* 5.3 8.9 - - + +
1827G LEU* 3.9 20.8 - - + +
1830G VAL* 4.0 23.3 - - + -
1831G VAL* 4.1 15.5 - - + -
1834G ARG* 3.2 39.3 + - - -
1988G PHE* 3.4 23.5 - + - -
1992G LEU* 4.3 9.2 - - + -
1996G ILE* 5.6 0.7 - - + -
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Residues in contact with ALA1813 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1666G PHE* 4.4 2.9 - - + -
1782G THR* 3.7 31.9 - - + +
1785G GLU* 3.1 34.3 - - + +
1786G LYS* 5.1 0.7 - - - +
1809G LEU* 3.9 1.5 + - + +
1810G GLY* 3.4 9.9 + - - +
1812G TYR* 1.3 78.9 - - - +
1814G ALA* 1.3 56.2 + - - +
1816G ALA* 3.7 4.1 - - - +
1817G SER* 2.8 37.5 + - - +
1827G LEU* 4.7 0.2 - - - -
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Residues in contact with ALA1814 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1666G PHE* 3.0 32.9 - - + -
1804G PHE* 4.0 14.6 - - + -
1805G ALA* 4.1 3.8 - - - -
1806G GLY 4.1 15.9 - - - +
1810G GLY 2.8 17.8 + - - +
1811G GLU* 3.9 5.8 - - + +
1812G TYR 3.2 0.2 - - - -
1813G ALA* 1.3 70.8 - - - +
1815G LEU* 1.3 67.1 + - + +
1818G LEU* 3.1 28.8 + - - +
2010G TYR* 6.2 0.4 - - + -
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Residues in contact with LEU1815 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.7 14.1 - - + -
18A LEU* 3.4 29.4 - - + -
1804G PHE* 4.0 3.4 - - + -
1811G GLU 3.1 16.2 + - - +
1812G TYR* 3.8 5.8 - - + +
1814G ALA* 1.3 78.0 - - + +
1816G ALA* 1.3 61.9 + - - +
1819G ALA 3.1 14.7 + - - -
1820G ASP 3.4 0.3 + - - -
1821G VAL* 3.1 31.6 - - + +
1822G MET* 6.5 1.3 - - + -
2006G LEU* 3.3 33.4 - - + -
2010G TYR* 3.4 45.1 - - + +
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Residues in contact with ALA1816 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1786G LYS* 3.1 22.8 + - + -
1812G TYR 2.9 17.3 + - - +
1813G ALA 3.7 3.1 - - - +
1815G LEU* 1.3 77.7 - - - +
1817G SER* 1.3 58.3 + - - +
1820G ASP* 3.0 23.9 + - - +
1821G VAL* 4.4 6.3 - - - +
1822G MET* 4.5 16.3 - - + +
1827G LEU* 3.4 32.8 - - + -
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Residues in contact with SER1817 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1666G PHE* 3.5 26.9 - - - -
1786G LYS* 3.7 37.8 + - - +
1789G PHE* 3.2 33.5 - - - +
1790G GLU* 5.9 0.2 - - - +
1793G LYS* 4.9 5.9 + - - +
1813G ALA 2.8 26.8 + - - -
1814G ALA 4.1 0.4 - - - -
1815G LEU 3.4 0.2 - - - -
1816G ALA* 1.3 76.1 - - - +
1818G LEU* 1.3 59.0 + - - +
1820G ASP* 4.4 5.9 - - - +
2005G ARG* 5.0 0.3 + - - -
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Residues in contact with LEU1818 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1664G PHE* 3.9 22.0 - - + -
1666G PHE* 3.4 33.0 - - + -
1789G PHE* 3.6 25.8 - - + -
1798G ILE* 4.8 4.9 - - + -
1799G PRO 5.7 0.4 - - - +
1802G ALA* 4.2 14.6 - - + +
1804G PHE* 3.4 44.4 - - + -
1814G ALA 3.1 8.1 + - - +
1817G SER* 1.3 76.6 - - - +
1819G ALA* 1.3 60.2 + - - +
2005G ARG* 2.8 26.9 + - - +
2009G LYS* 6.3 0.2 - - + -
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Residues in contact with ALA1819 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1804G PHE* 4.6 3.1 - - + -
1815G LEU 3.1 13.7 + - - +
1818G LEU* 1.3 77.9 - - - +
1820G ASP* 1.3 70.2 + - - +
1821G VAL* 3.1 8.7 + - + -
2000G ASN 4.1 5.9 - - - +
2002G LYS* 5.4 2.6 + - - +
2005G ARG* 2.9 33.8 + - + +
2006G LEU* 3.5 33.0 - - + -
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Residues in contact with ASP1820 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1495G THR* 3.5 44.4 - - - +
1496G LYS* 5.1 3.4 - - - +
1786G LYS* 3.0 26.5 + - - -
1790G GLU* 4.3 3.3 - - - +
1793G LYS* 3.2 19.5 + - - -
1815G LEU 3.4 0.4 + - - -
1816G ALA* 3.0 14.5 + - - +
1817G SER 4.4 3.5 - - - +
1819G ALA* 1.3 77.2 - - - +
1821G VAL* 1.3 61.6 + - - +
1822G MET 3.1 11.5 + - - +
2000G ASN* 3.6 5.9 - - - +
2005G ARG* 3.0 28.7 + - - +
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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