Contacts of the helix formed by residues 859 - 868 (chain A) in PDB entry 6CIM
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 THR 859 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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841A MET* 5.5 1.6 - - - -
855A ARG 4.0 6.1 + - - -
856A LYS* 3.4 18.3 + - - -
857A LEU 2.9 5.3 + - - -
858A MET* 1.3 76.0 + - - +
860A GLN* 1.3 69.3 + - + +
861A GLU* 3.7 22.4 - - + +
862A THR* 2.4 32.9 + - - -
863A VAL* 3.4 7.4 + - - +
883A MET* 4.0 7.1 - - - +
887A LEU* 5.1 4.0 - - + -
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Residues in contact with GLN 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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859A THR* 1.3 74.3 - - + +
861A GLU* 1.3 64.7 + - - +
863A VAL* 3.0 10.9 + - - +
864A ASP* 3.0 34.2 + - - +
880A ARG* 3.4 35.0 + - - +
883A MET* 3.5 19.3 - - - +
884A ASP* 4.0 18.4 + - - +
887A LEU* 3.7 27.6 - - + +
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Residues in contact with GLU 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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840A ARG 5.0 2.9 - - - +
841A MET* 3.5 32.3 - - + +
859A THR* 3.7 14.5 - - + +
860A GLN* 1.3 77.7 - - - +
862A THR* 1.3 61.8 + - - +
864A ASP* 3.2 12.9 + - + +
865A ALA* 3.0 22.0 + - - +
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Residues in contact with THR 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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808A PHE* 4.8 2.6 - - - -
837A LEU* 4.7 3.6 - - + -
841A MET* 3.6 29.6 - - + -
843A LEU* 4.4 3.6 - - + -
856A LYS 3.6 13.9 - - - +
857A LEU* 2.6 44.1 + - + +
859A THR* 2.4 29.4 + - - +
861A GLU* 1.3 76.3 - - - +
863A VAL* 1.3 60.0 + - - +
865A ALA* 3.3 7.5 + - - +
866A VAL* 2.9 33.8 + - - +
883A MET* 4.4 0.9 - - - +
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Residues in contact with VAL 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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804A PHE* 5.4 0.4 - - + -
808A PHE* 4.4 9.0 - - + -
859A THR 3.5 14.4 - - - +
860A GLN* 3.0 12.4 + - - +
862A THR* 1.3 75.2 - - - +
864A ASP* 1.3 60.8 + - - +
866A VAL* 3.3 4.6 + - - +
867A CYS* 2.8 31.5 + - - -
879A LEU* 4.0 38.6 - - + +
880A ARG* 4.1 17.9 - - + +
883A MET* 3.5 38.6 - - + -
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Residues in contact with ASP 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 GLN* 3.0 17.5 + - - +
861A GLU* 3.5 12.9 - - + +
863A VAL* 1.3 75.6 - - - +
865A ALA* 1.3 62.1 + - - +
867A CYS* 3.3 2.6 + - - +
868A GLU* 3.0 27.6 + - - +
880A ARG* 2.7 46.3 + - - +
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Residues in contact with ALA 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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836A HIS* 2.8 37.5 - - + +
837A LEU* 4.8 4.5 - - + -
840A ARG* 4.8 9.4 - - + +
841A MET* 4.0 22.7 - - + -
861A GLU 3.0 12.9 + - - +
862A THR 3.4 10.1 - - - +
863A VAL 3.2 0.2 - - - -
864A ASP* 1.3 75.8 - - - +
866A VAL* 1.3 59.5 + - + +
868A GLU* 3.0 22.4 + - - +
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Residues in contact with VAL 866 (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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808A PHE* 3.7 51.6 - - + +
812A ILE* 4.4 16.2 - - + -
833A LEU* 3.7 23.3 - - + -
836A HIS* 4.7 4.5 - - - +
837A LEU* 4.5 9.0 - - + -
862A THR 2.9 19.6 + - - +
863A VAL 4.1 2.2 - - - +
865A ALA* 1.3 71.9 - - - +
867A CYS* 1.3 57.8 + - - +
869A LEU* 2.9 24.6 + - - +
870A ILE* 3.6 18.8 + - + +
879A LEU* 5.2 0.7 - - + -
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Residues in contact with CYS 867 (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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863A VAL* 2.8 32.2 + - - +
864A ASP 3.5 5.8 - - - +
865A ALA 3.2 0.2 - - - -
866A VAL* 1.3 71.1 - - - +
868A GLU* 1.3 62.1 + - - +
869A LEU 2.9 6.8 + - - -
870A ILE* 3.2 22.2 + - - +
876A HIS* 3.1 63.5 - - + +
879A LEU* 4.8 1.6 - - - -
880A ARG* 3.6 24.9 - - - +
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Residues in contact with GLU 868 (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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836A HIS* 2.9 30.1 + - + +
840A ARG* 3.0 32.7 + - - -
864A ASP* 3.0 18.3 + - - +
865A ALA* 3.0 14.0 + - - +
867A CYS* 1.3 75.9 - - - +
869A LEU* 1.3 60.6 + - - +
870A ILE 3.6 0.7 - - - -
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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