Contacts of the helix formed by residues 855 - 865 (chain A) in PDB entry 6PUO
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 GLY 855 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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854A CYS* 1.3 78.5 - - - +
856A LEU* 1.3 56.2 + - - -
857A MET 3.3 2.0 - - - -
858A LYS* 3.4 18.7 - - - +
859A LYS* 2.6 35.9 + - - +
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Residues in contact with LEU 856 (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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847A LEU 5.0 7.2 - - - +
848A PHE* 4.7 24.7 - - + -
850A ASP* 6.2 6.5 - - + -
854A CYS 3.3 16.7 + - - +
855A GLY* 1.3 71.6 - - - -
857A MET* 1.3 57.6 + - - +
859A LYS* 3.3 8.1 + - + +
860A ALA* 2.9 28.2 + - - +
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Residues in contact with MET 857 (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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855A GLY* 3.3 0.4 - - - -
856A LEU* 1.3 77.1 - - - +
858A LYS* 1.3 61.1 + - - +
860A ALA* 3.4 6.5 + - + +
861A ALA* 2.8 34.0 + - - +
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Residues in contact with LYS 858 (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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854A CYS* 5.9 1.1 - - + -
855A GLY* 3.1 23.0 + - - +
857A MET* 1.3 79.8 - - - +
859A LYS* 1.3 59.1 + - - +
861A ALA* 3.4 5.9 + - - +
862A LEU* 2.9 28.8 + - - +
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Residues in contact with LYS 859 (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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846A GLN 4.3 7.5 + - - -
847A LEU* 3.3 38.6 + - + +
849A TYR* 4.2 4.0 - - - +
850A ASP* 3.4 37.4 - - + +
854A CYS* 5.9 4.5 - - + -
855A GLY 2.6 20.3 + - - +
856A LEU* 3.6 11.4 - - + +
858A LYS* 1.3 74.7 - - - +
860A ALA* 1.3 57.7 + - - +
862A LEU* 3.3 9.1 + - + +
863A TYR* 2.9 27.4 + - - +
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Residues in contact with ALA 860 (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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847A LEU* 4.3 12.9 - - + +
856A LEU 2.9 17.4 + - - +
857A MET* 3.9 8.1 - - + +
859A LYS* 1.3 76.5 - - - +
861A ALA* 1.3 57.8 + - - +
863A TYR* 3.3 1.9 + - - +
864A PHE* 2.9 32.1 + - - +
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Residues in contact with ALA 861 (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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857A MET* 2.8 28.6 + - - +
858A LYS* 3.8 7.6 - - - +
859A LYS 3.3 0.2 - - - -
860A ALA* 1.3 73.2 - - - +
862A LEU* 1.3 65.4 + - - +
864A PHE* 4.0 4.0 - - - +
865A SER* 3.1 26.2 + - - -
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Residues in contact with LEU 862 (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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858A LYS 2.9 17.4 + - - +
859A LYS* 3.6 11.0 - - + +
861A ALA* 1.3 77.6 - - - +
863A TYR* 1.3 62.2 + - - +
865A SER* 3.7 10.0 + - - -
866A ASP* 3.7 10.4 + - - +
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Residues in contact with TYR 863 (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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843A GLU* 5.9 0.4 - - - +
847A LEU* 3.8 31.2 - - + -
859A LYS 2.9 15.2 + - - +
860A ALA* 3.8 4.9 - - - +
861A ALA 3.3 0.2 - - - -
862A LEU* 1.3 77.7 - - - +
864A PHE* 1.3 61.3 + - - +
866A ASP* 3.1 13.4 + - - +
869A ASN* 3.3 24.9 - - + +
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Residues in contact with PHE 864 (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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860A ALA 2.9 17.7 + - - +
861A ALA* 4.5 3.4 - - - +
863A TYR* 1.3 76.9 - - - +
865A SER* 1.3 59.7 + - - +
866A ASP 3.2 6.4 + - - +
869A ASN* 5.3 2.5 - - - -
870A LYS* 4.6 10.2 - - - +
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Residues in contact with SER 865 (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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861A ALA 3.1 20.2 + - - -
862A LEU* 4.0 6.5 - - - -
863A TYR 3.2 0.8 - - - -
864A PHE* 1.3 75.2 - - - +
866A ASP* 1.3 63.1 + - - +
867A PHE 3.7 1.2 + - - -
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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