Contacts of the helix formed by residues 730 - 740 (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 THR 730 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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728j GLY 3.3 4.2 + - - -
729j LEU* 1.3 74.8 - - - +
731j GLN* 1.3 66.4 + - - +
732j GLN* 3.9 5.6 - - - -
733j LEU* 3.5 24.2 - - - +
734j HIS* 2.9 25.8 + - - +
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Residues in contact with GLN 731 (chain j).
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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730j THR* 1.3 74.4 - - - +
732j GLN* 1.3 63.9 + - - +
734j HIS* 4.0 3.7 - - - +
735j LYS* 3.4 19.4 + - - +
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Residues in contact with GLN 732 (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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730j THR* 3.1 5.5 - - - -
731j GLN* 1.3 78.2 - - - +
733j LEU* 1.3 67.4 + - - +
734j HIS 3.3 0.3 + - - -
735j LYS* 3.4 10.5 + - - +
736j PHE* 3.4 10.2 + - - +
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Residues in contact with LEU 733 (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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727j TYR* 5.5 9.0 - - + -
728j GLY 4.6 10.1 - - - +
730j THR* 3.4 19.1 + - - +
732j GLN* 1.3 79.1 - - - +
734j HIS* 1.3 64.6 + - - +
736j PHE* 3.0 23.6 + - - +
737j TRP* 3.2 7.3 + - - +
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Residues in contact with HIS 734 (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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729j LEU* 6.0 3.1 - - + -
730j THR 2.9 20.4 + - - +
731j GLN* 4.0 5.2 - - - +
733j LEU* 1.3 77.6 - - - +
735j LYS* 1.3 50.1 + - - +
737j TRP* 3.0 9.0 + - - +
738j LYS* 2.7 35.5 + - - +
801j LEU* 4.7 5.6 - - - +
802j ALA* 3.8 23.3 - - + +
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Residues in contact with LYS 735 (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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731j GLN 3.4 10.3 + - - +
732j GLN* 3.9 8.5 - - - +
733j LEU 3.3 0.6 - - - -
734j HIS* 1.3 78.7 - - - +
736j PHE* 1.3 52.9 + - - +
738j LYS* 3.6 8.4 - - - +
739j ARG* 2.6 36.7 + - - +
802j ALA* 5.3 1.1 - - - +
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Residues in contact with PHE 736 (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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732j GLN 3.4 6.6 + - - +
733j LEU* 3.0 18.0 + - - +
735j LYS* 1.3 78.7 - - - +
737j TRP* 1.3 58.2 + - - +
739j ARG* 3.3 6.5 + - - +
740j ALA* 2.9 24.1 + - - +
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Residues in contact with TRP 737 (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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725j VAL* 5.9 7.2 - - + -
733j LEU 3.2 5.9 + - - +
734j HIS* 3.0 9.9 + - - +
736j PHE* 1.3 78.2 - - - +
738j LYS* 1.4 59.3 + - - +
740j ALA* 2.7 29.9 + - + +
742j PHE* 3.1 26.0 + - + +
762j MET* 5.3 5.4 - - + -
802j ALA* 5.7 1.1 - - + -
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Residues in contact with LYS 738 (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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734j HIS 2.7 15.5 + - - +
735j LYS* 3.6 10.3 - - - +
737j TRP* 1.4 71.4 - - - +
739j ARG* 1.4 53.8 + - - +
741j GLN* 2.7 24.9 + - - -
742j PHE 4.0 8.8 - - - +
802j ALA* 3.0 39.4 - - + +
803j LEU 4.8 0.4 - - - +
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Residues in contact with ARG 739 (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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651j SER* 5.9 2.9 - - - -
735j LYS 2.6 22.2 + - - +
736j PHE* 3.5 7.6 - - - +
738j LYS* 1.4 72.1 - - - +
740j ALA* 1.3 59.1 + - - +
741j GLN* 3.1 0.9 + - - +
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Residues in contact with ALA 740 (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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651j SER* 5.8 9.2 - - - -
654j LEU* 5.1 17.1 - - + +
736j PHE 2.9 10.0 + - - +
737j TRP* 2.7 23.3 - - + +
739j ARG* 1.3 76.5 - - - +
741j GLN* 1.4 63.6 + - - +
742j PHE* 4.6 2.0 - - + +
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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