Contacts of the helix formed by residues 855 - 862 (chain A) in PDB entry 2N8Z
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 855 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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849A ARG* 4.2 4.0 + - - -
854A PRO* 1.3 74.1 - - - +
856A GLN* 1.3 65.4 + - - +
857A ALA 3.1 0.7 - - - -
858A GLU* 2.9 32.3 + - + +
859A TYR* 2.9 35.3 + - + -
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Residues in contact with GLN 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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741A SER* 4.8 4.9 - - - +
821A ALA 5.4 0.7 - - - +
822A ASP* 4.3 21.9 - - - +
823A THR* 4.6 1.3 - - - +
824A ASP* 3.0 39.2 + - - +
852A LEU* 3.7 27.2 - - + +
854A PRO* 2.9 18.1 + - + +
855A ASP* 1.3 77.3 - - - +
857A ALA* 1.3 57.5 + - - +
859A TYR* 3.4 17.5 + - - +
860A CYS* 2.9 34.1 + - - -
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Residues in contact with ALA 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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848A LEU* 3.7 21.9 - - + +
849A ARG* 3.7 27.6 - - - +
852A LEU* 3.2 22.9 + - - +
854A PRO 3.1 8.0 + - - +
856A GLN* 1.3 76.1 - - - +
858A GLU* 1.3 59.2 + - - +
860A CYS* 3.0 5.7 + - - +
861A ILE* 2.9 34.9 + - + +
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Residues in contact with GLU 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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849A ARG* 3.0 39.0 + - - +
855A ASP* 2.9 23.3 + - + +
857A ALA* 1.3 75.2 - - - +
859A TYR* 1.3 63.5 + - + +
861A ILE* 3.3 19.4 + - - +
862A ALA* 3.0 29.1 + - - +
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Residues in contact with TYR 859 (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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855A ASP* 2.9 41.1 + - + +
856A GLN* 3.5 21.8 - - - +
858A GLU* 1.3 82.8 - - + +
860A CYS* 1.3 58.5 + - - +
862A ALA* 3.7 7.7 + - - +
863A ARG* 3.1 52.3 + - - +
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Residues in contact with CYS 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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824A ASP* 6.0 2.9 - - - -
829A VAL* 4.0 19.3 - - - -
833A PHE* 4.5 3.1 - - + -
848A LEU* 4.0 11.7 - - + -
852A LEU* 3.8 24.9 - - - -
856A GLN* 2.9 22.5 + - - +
857A ALA 3.0 9.6 + - - +
859A TYR* 1.3 75.8 - - - +
861A ILE* 1.3 60.8 + - - +
862A ALA 3.1 1.6 - - - -
863A ARG* 3.0 6.0 + - - +
864A MET* 2.9 45.2 + - + +
882A PHE* 6.3 1.3 - - - -
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Residues in contact with ILE 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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845A MET* 3.8 47.6 - - + +
848A LEU* 4.1 17.7 - - + -
849A ARG* 5.2 3.8 - - - +
857A ALA* 2.9 25.3 + - + +
858A GLU* 3.6 25.1 - - - +
860A CYS* 1.3 74.3 - - - +
862A ALA* 1.3 57.9 + - - +
863A ARG 3.1 4.4 + - - -
864A MET* 3.6 8.7 + - - +
877A LEU* 4.2 18.2 - - + +
887A TYR* 2.9 19.4 + - - +
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Residues in contact with ALA 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 GLU 3.0 16.2 + - - +
859A TYR* 3.7 11.4 - - - +
860A CYS 3.1 0.2 - - - -
861A ILE* 1.3 77.0 - - - +
863A ARG* 1.3 63.2 + - - +
887A TYR* 3.2 28.7 - - + -
888A GLY* 3.4 15.6 - - - -
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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
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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