Contacts of the helix formed by residues 1808 - 1822 (chain A) in PDB entry 5KHU
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 THR1808 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1807A GLU* 3.8 29.2 - - - +
1809A SER* 3.8 27.8 - - - +
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Residues in contact with SER1809 (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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1808A THR* 3.8 24.5 - - - +
1810A GLU* 3.7 30.5 - - - +
1812A TRP* 4.7 16.6 - - - +
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Residues in contact with GLU1810 (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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1809A SER* 3.7 29.6 - - - +
1811A LEU* 3.8 25.4 - - - +
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Residues in contact with LEU1811 (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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1810A GLU* 3.8 29.6 - - - +
1812A TRP* 3.8 26.9 - - - +
1814A ILE* 4.3 18.6 - - - +
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Residues in contact with TRP1812 (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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1809A SER* 4.7 16.2 - - - +
1811A LEU* 3.8 26.0 - - - +
1813A GLN* 3.7 30.3 - - - +
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Residues in contact with GLN1813 (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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1812A TRP* 3.7 29.6 - - - +
1814A ILE* 3.8 26.0 - - - +
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Residues in contact with ILE1814 (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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1811A LEU* 4.3 16.8 - - - +
1813A GLN* 3.8 26.0 - - - +
1815A LYS* 3.8 29.2 - - - +
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Residues in contact with LYS1815 (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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1814A ILE* 3.8 28.9 - - - +
1816A LEU* 3.8 26.0 - - - +
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Residues in contact with LEU1816 (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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1815A LYS* 3.8 29.2 - - - +
1817A VAL* 3.8 25.4 - - - +
1819A GLU* 4.5 17.7 - - - +
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Residues in contact with VAL1817 (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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1816A LEU* 3.8 28.7 - - - +
1818A LEU* 3.8 29.4 - - - +
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Residues in contact with LEU1818 (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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1817A VAL* 3.8 25.4 - - - +
1819A GLU* 3.8 29.2 - - - +
1821A PHE* 3.9 23.1 - - - +
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Residues in contact with GLU1819 (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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1816A LEU* 4.5 17.3 - - - +
1818A LEU* 3.8 24.7 - - - +
1820A PHE* 3.7 30.5 - - - +
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Residues in contact with PHE1820 (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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1819A GLU* 3.7 29.6 - - - +
1821A PHE* 3.8 27.1 - - - +
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Residues in contact with PHE1821 (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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1818A LEU* 3.9 20.0 - - - +
1820A PHE* 3.8 26.0 - - - +
1822A SER* 3.8 29.2 - - - +
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Residues in contact with SER1822 (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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1821A PHE* 3.8 29.4 - - - +
1823A SER* 3.8 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