Contacts of the strand formed by residues 822 - 829 (chain A) in PDB entry 5J9H
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 GLU 822 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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817A ILE* 6.2 2.2 - - + -
818A GLN* 3.2 11.1 - - - +
819A LEU* 3.1 35.8 + - - +
821A THR* 1.3 79.8 - - + +
823A GLN* 1.3 59.4 + - - +
824A THR* 6.0 0.4 - - - +
836A THR* 3.2 18.3 + - - +
837A THR* 3.4 24.7 + - - +
838A SER* 2.7 45.8 + - - -
839A VAL* 4.4 2.4 + - - +
967A ARG* 3.2 19.1 + - - +
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Residues in contact with GLN 823 (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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716A GLN* 4.9 4.4 - - - +
816A CYS* 4.0 8.7 - - - +
817A ILE 3.3 19.8 + - - +
818A GLN* 3.7 22.7 - - + +
821A THR 3.7 4.0 + - - +
822A GLU* 1.3 75.5 - - - +
824A THR* 1.3 82.8 + - - +
825A CYS* 3.8 25.6 + - - -
836A THR* 5.9 0.2 - - - -
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Residues in contact with THR 824 (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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815A VAL 3.8 1.0 - - - +
816A CYS* 3.5 1.0 - - - -
817A ILE* 3.0 33.4 + - - +
822A GLU* 6.0 0.5 - - - +
823A GLN* 1.3 86.6 + - - +
825A CYS* 1.3 73.7 + - - +
826A LYS* 4.9 1.8 - - + -
834A LEU* 4.6 14.4 - - + +
836A THR* 4.0 28.0 - - + +
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Residues in contact with CYS 825 (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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814A LYS* 4.8 11.0 - - + -
815A VAL 3.2 3.8 - - - -
816A CYS* 2.1 46.2 - - - -
823A GLN* 3.8 15.7 + - - -
824A THR* 1.3 81.6 - - - +
826A LYS* 1.3 63.8 + - - +
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Residues in contact with LYS 826 (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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672A HIS* 6.0 1.6 + - - -
814A LYS* 3.6 5.5 - - - +
815A VAL 2.8 35.8 + - - +
824A THR* 4.9 2.7 - - + -
825A CYS* 1.3 75.8 - - - +
827A THR* 1.3 80.6 + - - +
828A VAL* 3.6 20.6 - - + +
832A ASP* 4.7 8.3 + - - -
833A CYS 4.6 8.9 + - - -
834A LEU* 3.8 35.2 - - + +
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Residues in contact with THR 827 (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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812A THR* 4.9 13.9 - - - +
813A ARG 3.4 9.4 - - - -
814A LYS* 4.0 24.7 - - + +
826A LYS* 1.3 94.4 + - - +
828A VAL* 1.3 60.4 + - - +
829A ASP* 5.3 2.1 + - - +
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Residues in contact with VAL 828 (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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812A THR* 3.4 4.0 - - - -
813A ARG 2.8 33.4 + - - +
815A VAL* 3.4 30.5 - - + -
826A LYS* 3.6 15.5 - - + +
827A THR* 1.3 79.8 - - - +
829A ASP* 1.3 76.1 + - - +
832A ASP* 3.7 30.5 - - + +
833A CYS* 4.0 11.4 - - - +
834A LEU* 4.1 16.8 - - + +
841A VAL 5.3 0.4 - - - +
843A LEU* 3.7 12.2 - - + +
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Residues in contact with ASP 829 (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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810A ARG* 3.0 46.2 + - - +
811A TYR 3.4 7.9 + - - +
812A THR* 4.3 6.6 - - - +
827A THR* 5.3 2.1 + - - +
828A VAL* 1.3 85.0 - - - +
830A SER* 1.3 60.3 + - - +
831A ASN 3.2 3.4 - - - +
832A ASP* 3.1 36.8 + - + +
843A LEU* 3.7 4.7 - - - +
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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