Contacts of the helix formed by residues 859 - 868 (chain j) in PDB entry 5JPQ
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 PRO 859 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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785j ARG* 4.7 17.9 - - + -
788j SER* 3.5 3.6 - - - -
852j HIS 5.4 0.2 - - - +
853j VAL 4.4 7.0 - - - +
854j VAL* 3.0 20.0 - - - +
855j LEU 3.1 11.8 - - - -
856j ASP* 4.5 5.6 - - + +
858j MET* 1.3 81.7 - - - +
860j THR* 1.3 68.8 + - - +
861j ILE 3.1 1.9 + - - -
863j GLN* 3.0 16.5 + - - +
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Residues in contact with THR 860 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837j ASP* 4.1 36.2 - - - +
840j ARG* 4.3 13.7 - - - -
841j LEU* 4.9 7.9 - - - +
854j VAL* 3.1 8.7 + - - -
859j PRO* 1.3 79.0 - - - +
861j ILE* 1.3 58.1 + - - +
863j GLN* 3.1 9.1 - - - +
864j LEU* 2.8 30.0 + - - +
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Residues in contact with ILE 861 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854j VAL* 2.9 24.8 + - + +
855j LEU* 3.5 19.7 - - + -
860j THR* 1.3 74.8 - - - +
862j ALA* 1.3 66.6 + - - +
864j LEU* 3.0 9.4 + - - +
865j TYR* 3.0 19.6 + - - +
877j SER 4.2 4.9 - - - +
878j GLY* 4.3 18.1 - - - -
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Residues in contact with ALA 862 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855j LEU 4.0 3.8 + - - +
857j LEU 2.8 30.1 - - - +
858j MET* 2.9 21.3 - - + -
859j PRO 3.3 3.2 + - - -
861j ILE* 1.3 75.0 - - - +
863j GLN* 1.3 65.0 + - - +
865j TYR* 2.9 18.1 + - + +
866j PHE* 2.9 14.4 + - - +
878j GLY* 5.6 2.9 - - - +
888j GLY 6.4 0.9 - - - -
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Residues in contact with GLN 863 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837j ASP* 5.7 4.3 - - + -
858j MET* 4.4 4.8 - - + +
859j PRO 3.0 14.3 + - - +
860j THR* 3.1 15.7 - - - +
862j ALA* 1.3 79.0 - - - +
864j LEU* 1.3 61.2 + - - +
866j PHE* 3.3 13.7 + - - +
867j THR* 3.4 13.0 + - - -
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Residues in contact with LEU 864 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841j LEU* 5.8 8.1 - - + -
860j THR 2.8 13.9 + - - +
861j ILE* 3.0 12.1 + - - +
863j GLN* 1.3 74.5 - - - +
865j TYR* 1.4 59.4 + - - +
867j THR* 3.3 6.4 + - - +
868j GLY* 2.8 27.7 + - - -
877j SER 5.0 5.4 - - - +
919j VAL* 5.7 8.5 - - + +
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Residues in contact with TYR 865 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861j ILE 3.0 6.5 + - - +
862j ALA* 2.9 11.6 + - - +
864j LEU* 1.4 72.9 - - - +
866j PHE* 1.3 67.6 + - - +
868j GLY* 3.2 19.0 + - - +
872j GLU* 3.7 10.3 - - + +
877j SER* 3.1 47.1 + - - +
878j GLY 3.9 1.8 - - - +
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Residues in contact with PHE 866 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862j ALA 2.9 11.3 + - - +
863j GLN* 3.6 11.0 - - - +
864j LEU 3.2 0.4 - - - -
865j TYR* 1.3 78.2 - - - +
867j THR* 1.3 61.7 + - - +
868j GLY 4.2 2.3 - - - +
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Residues in contact with THR 867 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863j GLN 3.4 7.9 + - - -
864j LEU* 3.3 8.9 + - - -
865j TYR 3.2 0.4 - - - -
866j PHE* 1.3 81.1 - - - +
868j GLY* 1.3 64.2 + - - +
869j ARG* 3.3 3.8 + - - +
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Residues in contact with GLY 868 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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864j LEU 2.8 20.1 + - - -
865j TYR* 3.2 14.4 + - - +
866j PHE 4.2 2.1 - - - +
867j THR* 1.3 73.2 - - - +
869j ARG* 1.4 62.9 + - - -
870j LEU* 3.2 4.4 - - - +
872j GLU* 3.9 11.5 - - - +
919j VAL* 5.2 13.2 - - - -
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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