Contacts of the strand formed by residues 783 - 790 (chain A) in PDB entry 2X5Y
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 LYS 783 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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780A GLU* 5.1 4.8 + - - -
781A GLU 4.7 5.4 + - - +
782A GLY* 1.3 75.5 - - - +
784A LEU* 1.3 65.9 + - - +
785A LEU* 3.5 26.6 + - + +
843A ALA 3.3 2.1 - - - +
844A GLN* 4.3 1.1 - - - -
845A VAL* 2.8 36.4 + - - +
847A VAL* 3.6 35.6 - - + +
850A PHE* 6.1 0.9 - - - -
877A PHE* 4.5 13.5 - - + -
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Residues in contact with LEU 784 (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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743A VAL* 5.8 2.7 - - + -
746A HIS* 3.3 33.3 + - + +
782A GLY 6.1 0.4 - - - -
783A LYS* 1.3 74.2 - - - +
785A LEU* 1.3 68.3 + - - +
786A PHE* 5.0 0.3 - - - -
822A LYS 5.1 0.2 - - - +
842A VAL* 3.8 24.5 - - + -
843A ALA 3.3 6.7 - - - +
844A GLN* 3.8 27.8 - - + -
888A GLN* 4.4 4.3 - - + -
889A TYR* 4.3 24.5 - - + +
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Residues in contact with LEU 785 (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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783A LYS* 4.0 24.0 - - + +
784A LEU* 1.3 82.0 - - - +
786A PHE* 1.3 65.6 + - - +
820A PHE* 3.8 23.6 - - + -
821A ALA 3.6 15.7 - - - +
822A LYS* 3.8 17.0 - - + +
842A VAL* 3.3 4.8 - - - -
843A ALA* 2.9 32.0 + - - +
845A VAL* 3.8 30.1 - - + -
847A VAL* 4.2 5.8 - - + -
877A PHE* 3.7 30.7 - - + -
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Residues in contact with PHE 786 (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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743A VAL* 5.5 0.9 - - + -
746A HIS* 3.5 58.3 - + + -
747A PHE* 3.9 19.7 - + + -
785A LEU* 1.3 76.7 - - - +
787A TYR* 1.3 62.4 + - - +
819A TYR 4.4 0.2 - - - +
820A PHE* 3.6 7.0 - - - -
821A ALA* 2.9 38.9 + - + +
822A LYS 3.6 16.6 - - - -
823A ASP* 4.5 0.2 - - - -
824A ALA* 3.3 44.9 - - + -
827A SER* 4.0 3.2 + - - -
840A MET* 3.9 18.8 - - + -
841A PHE 3.4 1.3 - - - -
842A VAL* 3.8 25.8 - - + -
891A ILE* 4.6 0.2 - - + -
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Residues in contact with TYR 787 (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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785A LEU 5.4 0.2 - - - +
786A PHE* 1.3 76.0 - - - +
788A ALA* 1.3 75.9 + - - +
789A THR* 3.8 14.6 + - + -
797A ILE* 5.1 0.4 - - + -
802A PHE* 3.5 34.8 - + + -
807A HIS* 3.7 16.1 + - + +
808A GLU* 2.8 46.0 + - - +
809A THR* 4.5 2.0 + - - -
818A ILE* 3.4 16.8 - - + +
819A TYR 3.3 28.0 - - - -
820A PHE* 3.9 20.6 - + + -
827A SER* 3.5 3.4 - - - -
840A MET* 3.9 2.5 - - - -
841A PHE* 2.8 40.2 + - + +
843A ALA* 5.9 0.2 - - + -
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Residues in contact with ALA 788 (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 TYR* 1.3 82.5 - - - +
789A THR* 1.3 63.3 + - - +
809A THR* 5.1 6.1 + - - -
827A SER* 2.8 39.5 + - - +
828A HIS* 4.2 0.9 - - - +
831A CYS* 3.9 19.7 - - + +
838A VAL* 4.4 6.1 - - + -
839A VAL 3.4 10.1 - - - +
840A MET* 3.7 16.0 - - + -
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Residues in contact with THR 789 (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 TYR* 4.2 12.9 - - + +
788A ALA* 1.3 76.7 - - - +
790A SER* 1.3 73.7 + - - +
793A TYR* 3.6 19.3 - - + +
797A ILE* 3.9 12.8 - - + +
807A HIS* 5.0 7.4 + - - +
831A CYS* 4.4 5.6 - - - -
833A TYR* 4.1 12.1 - - - -
838A VAL* 3.3 6.8 - - - +
839A VAL* 2.9 33.4 + - + -
841A PHE* 3.7 35.2 - - + -
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Residues in contact with SER 790 (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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789A THR* 1.3 92.0 + - - +
791A ARG* 1.3 66.5 + - - +
792A ALA* 3.2 16.0 + - - +
793A TYR* 3.0 32.8 + - - +
794A VAL* 4.0 1.9 + - - +
833A TYR* 3.7 31.8 - - - -
837A ASN* 3.4 20.0 + - - +
839A VAL* 4.4 1.1 - - - -
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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