Contacts of the helix formed by residues 855 - 865 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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854B CYS* 1.3 77.5 - - - +
856B LEU* 1.3 56.7 + - - -
857B MET* 3.3 2.5 - - - -
858B LYS* 3.4 19.0 - - - +
859B LYS* 2.6 35.2 + - - +
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Residues in contact with LEU 856 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847B LEU 5.0 7.2 - - - +
848B PHE* 4.7 24.5 - - + -
850B ASP* 6.2 5.8 - - + -
854B CYS 3.3 17.6 + - - +
855B GLY* 1.3 70.8 - - - -
857B MET* 1.3 57.8 + - - +
859B LYS* 3.3 8.3 + - + +
860B ALA* 2.9 28.6 + - - +
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Residues in contact with MET 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855B GLY* 3.3 0.8 - - - -
856B LEU* 1.3 76.8 - - - +
858B LYS* 1.3 61.0 + - - +
860B ALA* 3.4 7.2 + - + +
861B ALA* 2.8 34.0 + - - +
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Residues in contact with LYS 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854B CYS* 5.9 0.7 - - + -
855B GLY* 3.1 24.3 + - - +
857B MET* 1.3 78.9 - - - +
859B LYS* 1.3 59.8 + - - +
861B ALA* 3.4 6.0 + - - +
862B LEU* 2.9 29.3 + - - +
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Residues in contact with LYS 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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846B GLN 4.3 7.6 + - - -
847B LEU* 3.3 40.0 + - + +
849B TYR* 4.2 3.8 - - - +
850B ASP* 3.4 36.4 - - + +
854B CYS* 5.9 5.2 - - + -
855B GLY 2.6 19.7 + - - +
856B LEU* 3.6 12.6 - - + +
858B LYS* 1.3 73.4 - - - +
860B ALA* 1.3 56.4 + - - +
862B LEU* 3.3 8.9 + - + +
863B TYR* 2.9 27.4 + - - +
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Residues in contact with ALA 860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847B LEU* 4.3 13.8 - - + +
856B LEU 2.9 17.2 + - - +
857B MET* 3.9 8.1 - - + +
859B LYS* 1.3 76.3 - - - +
861B ALA* 1.3 58.2 + - - +
863B TYR* 3.8 1.5 - - - +
864B PHE* 2.9 31.9 + - - +
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Residues in contact with ALA 861 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857B MET* 2.8 28.6 + - - +
858B LYS* 3.8 7.0 - - - +
860B ALA* 1.3 74.3 - - - +
862B LEU* 1.3 65.3 + - - +
864B PHE* 4.0 4.0 - - - +
865B SER* 3.1 26.0 + - - -
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Residues in contact with LEU 862 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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858B LYS 2.9 17.7 + - - +
859B LYS* 3.3 11.0 + - + +
861B ALA* 1.3 78.3 - - - +
863B TYR* 1.3 62.6 + - - +
865B SER* 3.7 8.9 + - - -
866B ASP* 3.7 10.2 + - - +
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Residues in contact with TYR 863 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843B GLU* 5.9 0.9 - - - +
847B LEU* 3.8 30.7 - - + -
859B LYS 2.9 16.5 + - - +
860B ALA* 3.3 4.7 + - - +
862B LEU* 1.3 77.3 - - - +
864B PHE* 1.3 61.7 + - - +
866B ASP* 3.1 14.2 + - - +
869B ASN* 3.3 25.3 - - + +
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Residues in contact with PHE 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860B ALA 2.9 17.4 + - - +
861B ALA* 4.5 4.0 - - - +
863B TYR* 1.3 76.7 - - - +
865B SER* 1.3 60.0 + - - +
866B ASP 3.2 6.4 + - - +
869B ASN* 5.3 2.5 - - - -
870B LYS* 4.6 10.1 - - - +
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Residues in contact with SER 865 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861B ALA 3.1 20.6 + - - -
862B LEU* 4.0 6.7 - - - -
863B TYR 3.2 0.8 - - - -
864B PHE* 1.3 75.8 - - - +
866B ASP* 1.3 63.4 + - - +
867B 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