Contacts of the strand formed by residues 852 - 860 (chain A) in PDB entry 1R4X
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 VAL 852 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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790A THR* 4.1 1.2 - - - +
791A LEU* 2.8 54.9 + - + +
794A ILE* 3.1 18.8 + - + +
796A THR 3.8 23.6 - - - +
797A LEU* 4.4 7.6 - - + -
800A ALA* 4.1 2.0 - - + -
846A LEU* 3.8 27.8 - - + -
847A LEU 3.3 6.5 - - - +
848A LEU* 3.9 12.8 - - + -
851A THR* 1.3 79.6 + - - +
853A THR* 1.3 74.8 + - - +
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Residues in contact with THR 853 (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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788A THR* 3.9 19.1 - - + -
789A PHE 3.5 14.1 + - - +
790A THR* 4.5 13.7 + - - +
791A LEU* 5.0 0.2 - - - -
845A ARG 4.0 0.2 - - - +
846A LEU* 3.4 1.0 - - - -
847A LEU* 2.9 46.2 + - + +
851A THR 3.9 2.2 + - - -
852A VAL* 1.3 77.0 + - - +
854A MET* 1.3 67.3 + - - +
855A GLN* 6.2 0.7 - - + -
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Residues in contact with MET 854 (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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787A GLU 3.8 1.0 - - - +
788A THR* 3.3 4.6 - - - -
789A PHE* 2.9 48.4 + - + +
791A LEU* 4.1 23.3 - - + -
804A ILE* 3.4 32.1 - - + -
844A SER* 3.2 24.5 - - - +
845A ARG 3.2 7.4 - - - +
846A LEU* 3.8 14.1 - - + -
852A VAL* 4.9 0.2 - - + -
853A THR* 1.3 79.8 - - - +
855A GLN* 1.3 63.8 + - - +
856A VAL* 3.8 10.3 - - + -
873A VAL* 3.5 31.6 - - + +
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Residues in contact with GLN 855 (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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786A GLU* 3.4 25.5 + - + +
788A THR* 3.7 14.1 + - + +
843A ARG* 3.5 2.9 + - - +
844A SER* 3.3 1.7 - - - -
845A ARG* 2.8 61.4 + - + +
853A THR* 6.2 0.7 - - + -
854A MET* 1.3 74.3 - - - +
856A VAL* 1.3 61.1 + - - +
857A THR* 3.9 2.2 + - - +
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Residues in contact with VAL 856 (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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786A GLU* 3.1 3.7 + - - -
787A GLU 2.9 37.0 + - - +
789A PHE* 3.7 27.8 - - + -
842A VAL* 3.7 26.0 - - + -
843A ARG 3.4 3.6 - - - +
844A SER* 3.8 17.7 - - - +
854A MET* 3.8 17.0 - - + -
855A GLN* 1.3 76.1 - - - +
857A THR* 1.3 64.5 + - - +
869A ILE* 4.5 7.0 - - + -
870A LEU* 3.8 17.6 - - + +
873A VAL* 4.3 7.6 - - + -
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Residues in contact with THR 857 (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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776A TRP* 3.6 13.8 - - + -
784A GLU* 3.5 31.9 - - + +
785A LYS 3.3 8.5 - - - +
786A GLU* 3.4 20.5 - - + +
842A VAL* 3.4 4.0 - - - +
843A ARG* 2.8 71.0 + - - +
855A GLN* 3.9 2.5 + - - +
856A VAL* 1.3 75.7 - - - +
858A ALA* 1.3 64.2 + - - +
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Residues in contact with ALA 858 (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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776A TRP* 4.4 0.9 - - - -
783A PHE 3.8 2.4 - - - +
784A GLU* 3.3 7.6 - - - +
785A LYS 3.0 29.1 + - - +
840A ILE* 4.2 7.2 - - + -
841A LEU 3.3 9.9 - - - +
842A VAL* 4.3 8.3 - - + -
857A THR* 1.3 75.8 - - - +
859A ARG* 1.3 61.4 + - - +
866A VAL* 3.9 30.0 - - + +
869A ILE* 4.3 12.6 - - + -
870A LEU* 4.9 4.2 - - + +
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Residues in contact with ARG 859 (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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776A TRP* 3.0 73.1 + - + +
777A ASP* 4.2 6.1 + - - +
779A VAL* 3.9 11.4 - - + +
780A GLY* 3.3 28.3 + - - +
781A ASP* 3.7 20.0 + - - +
784A GLU* 2.9 39.7 + - + +
839A ASP 4.1 0.2 - - - +
840A ILE* 3.6 2.3 - - - +
841A LEU* 3.0 34.3 + - + +
858A ALA* 1.3 78.7 - - - +
860A SER* 1.3 63.5 + - - +
866A VAL* 3.8 4.0 - - - -
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Residues in contact with SER 860 (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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779A VAL* 3.5 15.6 - - - +
780A GLY 4.9 2.5 + - - +
782A GLU* 5.7 0.7 - - - +
783A PHE* 3.7 23.1 + - - +
838A HIS* 4.2 3.8 - - - +
839A ASP 2.8 21.5 + - - -
840A ILE* 4.1 3.4 - - - -
859A ARG* 1.3 77.1 - - - +
861A LEU* 1.3 62.7 + - - +
862A GLU* 3.1 27.4 + - - +
865A PRO* 3.6 16.1 - - - +
866A VAL* 3.7 10.9 - - - +
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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