Contacts of the strand formed by residues 813 - 817 (chain A) in PDB entry 5J67
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 TYR 813 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723A PHE* 4.6 3.1 - + + -
753A ILE* 4.1 12.3 - - + -
754A LYS* 3.2 35.9 + - - +
756A PHE* 3.4 23.0 - + - -
765A VAL* 3.6 29.6 - - + -
766A ILE 3.8 3.6 - - - -
767A PRO* 3.7 24.0 - - + -
768A LEU* 3.7 4.5 - - - -
811A ASN* 3.1 40.4 + - - -
812A LEU* 1.3 73.3 - - - +
814A ARG* 1.3 61.3 + - - +
815A VAL* 3.8 6.2 + - + +
858A LEU* 3.6 2.1 - - - +
859A TYR* 2.8 37.8 + - + +
951A PRO* 3.6 28.7 - - + -
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Residues in contact with ARG 814 (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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764A LEU 3.5 3.6 - - - +
765A VAL* 3.7 0.5 - - - -
766A ILE* 3.0 42.9 + - + +
768A LEU* 3.3 25.1 - - + +
813A TYR* 1.3 71.4 - - - +
815A VAL* 1.3 59.3 + - - +
816A LYS* 4.0 21.6 + - - +
856A GLU* 3.6 27.7 + - - +
857A ALA 3.6 7.6 + - - -
858A LEU* 3.9 27.1 - - - +
955A GLU* 4.9 3.4 + - - -
957A ASN* 3.2 29.7 + - - +
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Residues in contact with VAL 815 (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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723A PHE* 3.8 30.5 - - + +
726A MET* 3.3 32.5 - - + +
763A LEU* 4.6 10.5 - - + -
764A LEU 3.6 5.4 - - - +
765A VAL* 4.4 10.3 - - + -
813A TYR 4.0 7.2 - - - +
814A ARG* 1.3 77.5 - - - +
816A LYS* 1.3 68.0 + - - +
856A GLU* 3.5 0.9 - - - -
857A ALA 2.7 40.7 + - - +
859A TYR* 3.5 27.8 - - + -
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Residues in contact with LYS 816 (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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726A MET* 4.1 2.5 - - - -
763A LEU* 3.5 3.5 - - - +
764A LEU* 2.7 50.1 + - + +
766A ILE* 3.5 29.5 - - - +
814A ARG* 4.0 18.4 + - + +
815A VAL* 1.3 78.3 - - - +
817A LEU* 1.3 59.3 + - - +
818A SER* 4.2 2.2 - - - -
855A ALA 3.4 8.1 - - - +
856A GLU* 3.4 40.4 - - + +
958A ARG* 6.0 3.1 - - - +
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Residues in contact with LEU 817 (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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726A MET* 3.5 35.9 - - + +
727A LEU* 4.2 2.2 - - + -
743A PHE* 3.6 26.5 - - + -
762A GLY 3.6 4.0 - - - +
763A LEU* 4.1 7.0 - - + +
816A LYS* 1.3 75.8 - - - +
818A SER* 1.3 64.0 + - - +
819A THR* 4.9 0.2 - - - -
820A ILE* 3.9 27.1 - - + +
853A TYR* 4.3 12.6 - - + -
854A ILE 3.2 21.3 - - - +
855A ALA* 3.4 17.0 + - + +
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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