Contacts of the strand formed by residues 718 - 726 (chain A) in PDB entry 2R4B
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 LEU 718 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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713A LEU* 4.5 5.2 - - + -
714A LYS 4.6 5.8 - - - +
715A GLU 3.5 16.4 + - - +
716A THR* 3.1 6.3 - - - +
717A GLU* 1.3 81.3 - - - +
719A LYS* 1.3 60.4 + - - +
720A ARG* 5.3 2.9 - - - +
736A ILE 3.5 2.0 - - - +
737A TRP* 3.8 33.7 - - + -
748A VAL* 4.3 1.3 - - + -
750A ILE* 4.1 21.3 - - + -
787A CYS* 4.1 24.7 - - + -
793A GLN* 4.1 14.8 - - - +
795A VAL* 3.8 37.9 - - + -
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Residues in contact with LYS 719 (chain A).
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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718A LEU* 1.3 73.7 - - - +
720A ARG* 1.3 71.6 + - - +
721A VAL* 5.5 0.7 - - + -
735A GLY* 3.2 4.5 - - - -
736A ILE* 2.9 50.9 + - + +
750A ILE* 4.0 4.6 - - - +
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Residues in contact with ARG 720 (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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718A LEU* 5.3 4.2 - - - +
719A LYS* 1.3 83.9 - - - +
721A VAL* 1.3 65.4 + - - +
722A LYS* 5.7 0.2 - - - -
733A TYR* 3.4 46.5 - - + -
734A LYS 3.6 6.1 - - - +
735A GLY* 4.3 0.7 - - - -
750A ILE* 3.8 22.8 - - + +
752A ILE* 3.4 25.5 - - - +
790A PRO* 5.3 4.4 - - - +
793A GLN* 2.9 34.2 + - - +
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Residues in contact with VAL 721 (chain A).
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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719A LYS* 6.2 0.7 - - + -
720A ARG* 1.3 76.1 - - - +
722A LYS* 1.3 70.6 + - + +
734A LYS* 2.8 36.8 + - + +
735A GLY* 4.0 10.1 - - - +
736A ILE* 4.0 28.5 - - + -
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Residues in contact with LYS 722 (chain A).
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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720A ARG* 3.7 0.6 - - - -
721A VAL* 1.3 90.4 - - + +
723A VAL* 1.3 72.2 + - - +
724A LEU* 4.2 17.5 - - - +
733A TYR* 3.2 12.6 - - - +
734A LYS* 2.8 53.4 + - + +
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Residues in contact with VAL 723 (chain A).
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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722A LYS* 1.3 92.8 + - - +
724A LEU* 1.3 64.2 + - - +
725A GLY* 3.7 26.0 - - - +
726A SER* 5.0 3.8 - - - +
731A THR* 3.9 11.7 - - + -
732A VAL 3.7 5.4 - - - +
733A TYR* 3.6 26.2 - - + -
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Residues in contact with LEU 724 (chain A).
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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1A GW7 4.1 39.2 - - + +
722A LYS* 4.0 17.7 + - - +
723A VAL* 1.3 75.3 - - - +
725A GLY* 1.3 55.1 + - - +
732A VAL* 2.7 35.1 + - + +
733A TYR 3.8 2.0 - - - +
734A LYS* 3.7 38.1 - - + +
749A ALA* 4.4 0.4 - - + -
798A LEU* 3.8 26.5 - - + -
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Residues in contact with GLY 725 (chain A).
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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723A VAL* 3.7 5.0 - - - +
724A LEU* 1.3 80.2 - - - +
726A SER* 1.3 63.9 + - - -
730A GLY 4.6 0.2 - - - -
731A THR* 3.5 3.5 - - - +
732A VAL* 2.8 33.2 + - - +
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Residues in contact with SER 726 (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 VAL* 5.0 4.2 - - - +
725A GLY* 1.3 76.2 - - - -
727A GLY* 1.3 58.1 + - - +
730A GLY 3.3 8.5 - - - -
731A THR* 3.8 24.2 - - - -
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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