Contacts of the helix formed by residues 1865 - 1876 (chain A) in PDB entry 6AH0
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 ARG1865 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1780A VAL 5.2 0.4 + - - -
1781A ASP* 6.2 0.2 - - - +
1782A ASP 6.1 1.4 - - - +
1863A VAL* 3.2 7.4 - - - +
1864A THR* 1.3 78.4 - - - +
1866A LYS* 1.4 59.1 + - - +
1867A GLY 3.5 2.0 - - - -
1868A MET* 3.4 7.2 + - - +
1869A LEU* 3.0 23.7 + - - -
1886A GLY* 5.8 1.1 - - - -
1887A SER 5.9 0.2 - - - -
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Residues in contact with LYS1866 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1865A ARG* 1.4 68.4 - - - +
1867A GLY* 1.3 65.3 + - - +
1869A LEU* 3.1 3.9 + - - +
1870A ASP* 3.1 18.5 + - - -
1886A GLY* 5.8 6.7 - - - -
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Residues in contact with GLY1867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1865A ARG 3.5 0.6 - - - -
1866A LYS* 1.3 72.7 - - - +
1868A MET* 1.3 68.4 + - - +
1870A ASP* 3.1 10.0 + - - -
1871A PRO* 3.4 9.2 - - - +
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Residues in contact with MET1868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1865A ARG* 3.4 8.3 + - - +
1866A LYS 3.2 0.4 - - - -
1867A GLY* 1.3 77.8 - - - +
1869A LEU* 1.3 62.7 + - - +
1871A PRO* 3.3 1.4 - - - +
1872A LEU* 2.9 21.0 + - - -
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Residues in contact with LEU1869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1863A VAL* 5.7 8.0 - - - +
1865A ARG 3.0 13.9 + - - -
1866A LYS* 3.1 6.6 + - - +
1868A MET* 1.3 74.8 - - - +
1870A ASP* 1.3 64.7 + - - +
1872A LEU* 3.2 2.5 + - - +
1873A GLU* 3.0 20.4 + - - -
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Residues in contact with ASP1870 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1866A LYS 3.1 13.0 + - - -
1867A GLY 3.1 3.6 + - - -
1869A LEU* 1.3 76.9 - - - +
1871A PRO* 1.3 63.9 - - - +
1873A GLU* 3.2 3.7 + - - +
1874A VAL* 3.1 17.2 + - - -
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Residues in contact with PRO1871 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1838A LYS 5.7 6.5 - - - +
1842A ALA* 4.9 7.4 - - - -
1867A GLY 3.4 7.7 - - - +
1868A MET 3.3 5.2 - - - +
1870A ASP* 1.3 74.8 - - - +
1872A LEU* 1.3 62.2 + - - +
1874A VAL* 3.1 11.0 + - - +
1875A HIS* 3.1 11.8 + - - -
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Residues in contact with LEU1872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1842A ALA* 4.9 12.3 - - - +
1868A MET 2.9 18.2 + - - -
1869A LEU* 3.2 3.3 + - - +
1871A PRO* 1.3 71.4 - - - +
1873A GLU* 1.3 64.3 + - - +
1875A HIS 3.3 2.1 + - - -
1876A LEU* 3.0 22.3 + - - -
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Residues in contact with GLU1873 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1869A LEU 3.0 13.6 + - - -
1870A ASP* 3.2 4.2 + - - +
1872A LEU* 1.3 77.3 - - - +
1874A VAL* 1.3 62.6 + - - +
1876A LEU* 3.4 8.2 + - - +
1877A LEU* 3.8 8.3 + - - -
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Residues in contact with VAL1874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1870A ASP 3.1 12.6 + - - -
1871A PRO* 3.1 4.6 + - - -
1873A GLU* 1.3 79.1 - - - +
1875A HIS* 1.3 58.7 + - - +
1876A LEU 3.2 0.7 + - - -
1877A LEU* 3.6 9.5 + - - -
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Residues in contact with HIS1875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1842A ALA* 4.9 15.4 - - - +
1843A GLU* 6.1 0.4 - - - +
1846A ALA* 4.7 7.8 - - - -
1871A PRO 3.1 12.6 + - - -
1872A LEU 3.7 2.9 - - - -
1874A VAL* 1.3 73.2 - - - +
1876A LEU* 1.3 55.0 + - - +
1877A LEU 3.2 6.8 + - - -
1878A ASP 5.1 0.2 + - - -
52F U 4.0 4.3 - - - +
53F A 3.2 24.8 + - - -
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Residues in contact with LEU1876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1846A ALA* 5.7 4.3 - - - +
1872A LEU 3.0 14.7 + - - -
1873A GLU* 3.4 6.3 + - - +
1874A VAL 3.2 0.6 - - - -
1875A HIS* 1.3 76.1 - - - +
1877A LEU* 1.3 60.2 + - - +
1878A ASP 3.2 4.1 + - - -
1879A PHE 3.0 26.9 + - - +
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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