Contacts of the strand formed by residues 736 - 741 (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 THR 736 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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735A ALA* 1.3 75.2 + - - +
737A PHE* 1.3 72.3 + - - +
738A ASN* 3.1 10.0 + - - +
794A LEU* 3.3 8.4 - - - -
795A ASP* 2.8 46.3 + - - +
796A LYS* 3.5 33.8 + - + +
879A PHE* 5.3 0.2 - - - -
924A LYS* 4.8 5.6 + - - +
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Residues in contact with PHE 737 (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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735A ALA 4.3 0.8 + - - -
736A THR* 1.3 82.7 - - - +
738A ASN* 1.3 80.0 + - - +
739A LEU* 4.2 11.4 - - + -
792A VAL* 3.3 34.1 - - + -
793A TYR 3.9 2.7 - - - -
794A LEU* 4.2 8.0 - - + +
879A PHE* 4.1 14.7 - + + -
897A LEU* 4.6 4.0 - - + -
915A PHE* 3.6 31.9 - + + -
918A ASN 3.8 23.8 - - - -
919A THR* 3.5 42.4 + - + +
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Residues in contact with ASN 738 (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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736A THR* 3.1 16.2 + - - +
737A PHE* 1.3 82.9 + - - +
739A LEU* 1.3 58.9 + - - +
740A LYS* 5.5 1.1 - - + -
792A VAL* 3.3 5.5 - - - +
793A TYR* 2.8 76.6 + - + +
795A ASP* 2.6 37.7 + - - +
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Residues in contact with LEU 739 (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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737A PHE* 4.2 14.4 - - + -
738A ASN* 1.3 73.0 - - - +
740A LYS* 1.3 72.2 + - - +
741A THR* 5.5 0.9 - - - +
791A GLY 3.2 20.6 - - - +
792A VAL* 3.8 15.0 - - + -
901A PHE* 4.1 11.0 - - + -
913A CYS* 3.7 29.8 - - + +
914A GLN* 3.9 2.5 - - - -
915A PHE* 3.6 33.9 - - + +
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Residues in contact with LYS 740 (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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738A ASN* 4.3 1.3 - - + -
739A LEU* 1.3 80.5 - - - +
741A THR* 1.3 63.8 + - - +
755A PRO* 4.6 23.6 - - + -
756A TRP* 3.3 18.0 - - + -
790A CYS* 3.7 2.8 - - - +
791A GLY 3.0 31.5 + - - -
793A TYR* 3.2 35.6 - - + +
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Residues in contact with THR 741 (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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739A LEU* 5.5 0.9 - - - +
740A LYS* 1.3 73.5 - - - +
742A ALA* 1.3 73.6 + - - +
756A TRP* 4.6 1.6 - - - -
788A THR* 4.4 5.6 - - + -
789A ALA 4.1 1.6 - - - -
790A CYS* 3.7 16.6 - - - -
910A THR* 5.4 3.4 - - + +
911A PRO 3.1 29.2 - - - +
912A VAL* 4.0 3.3 - - - +
913A CYS* 3.1 29.1 + - - +
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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