Contacts of the helix formed by residues 852 - 855 (chain B) in PDB entry 2X36
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 ASP 852 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769B ALA* 3.7 7.4 - - - -
770B TRP* 2.8 44.9 + - + +
848B ALA* 4.0 7.0 - - + +
849B THR* 3.1 27.8 + - - +
850B PRO 3.0 2.2 + - - -
851B LYS* 1.3 76.5 - - - +
853B GLY* 1.3 63.2 + - - +
854B PRO* 3.4 2.2 - - - -
855B SER* 2.7 37.1 + - - -
856B ALA 4.1 0.5 + - - -
892B VAL* 4.9 0.2 - - - +
893B GLY 3.9 7.4 + - - +
898B LYS* 2.8 25.2 + - - -
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Residues in contact with GLY 853 (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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809B VAL* 5.8 0.4 - - - -
810B MET* 3.2 32.9 - - - +
813B SER* 4.6 0.2 + - - -
848B ALA* 4.9 7.6 - - - -
849B THR 3.5 5.2 + - - -
850B PRO* 3.0 9.5 + - - -
852B ASP* 1.3 80.0 - - - +
854B PRO* 1.3 67.1 - - - +
856B ALA* 3.3 18.9 + - - +
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Residues in contact with PRO 854 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809B VAL* 4.4 19.5 - - + -
810B MET* 4.3 0.2 - - - -
813B SER* 3.3 26.4 + - - +
850B PRO 4.2 3.8 - - - +
851B LYS 3.6 12.6 - - - +
852B ASP 3.4 3.4 - - - -
853B GLY* 1.3 86.4 - - - +
855B SER* 1.3 51.1 + - - +
856B ALA 3.1 6.1 - - - -
857B GLY* 2.7 27.4 + - - -
882B GLU* 3.4 37.0 - - + +
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Residues in contact with SER 855 (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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768B LEU 4.7 3.2 + - - -
852B ASP* 2.7 37.5 + - - -
853B GLY 3.2 0.2 - - - -
854B PRO* 1.3 74.8 - - - +
856B ALA* 1.3 58.4 + - - +
857B GLY 3.0 5.4 - - - -
859B THR* 4.3 0.9 + - - -
880B THR* 3.4 20.4 + - - -
881B GLY 2.7 33.7 + - - +
882B GLU* 3.7 2.2 + - - +
892B VAL* 3.4 26.2 - - - +
898B LYS* 3.3 5.6 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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