Contacts of the strand formed by residues 774 - 784 (chain F) in PDB entry 2X36
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 GLY 774 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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770F TRP* 3.2 12.1 - - - +
771F THR* 2.8 28.1 + - - +
773F MET* 1.3 83.7 - - - +
775F GLY* 1.3 58.7 + - - -
897F GLU* 3.9 20.6 - - - -
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Residues in contact with GLY 775 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769F ALA 3.4 11.9 - - - -
770F TRP* 4.3 0.2 - - - -
771F THR* 3.1 7.5 + - - -
774F GLY* 1.3 74.1 - - - -
776F SER* 1.3 65.2 + - - -
897F GLU* 4.1 17.2 + - - +
901F ALA* 3.7 13.5 - - - +
904F ARG* 6.2 0.5 - - - -
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Residues in contact with SER 776 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768F LEU* 3.5 4.7 - - - -
769F ALA* 2.8 36.5 + - - +
771F THR* 3.5 22.2 + - - +
773F MET* 6.0 0.7 - - - +
775F GLY* 1.3 76.2 + - - -
777F THR* 1.3 65.0 + - - +
778F LEU* 3.9 5.4 - - - -
847F GLY* 6.0 1.1 - - - -
901F ALA* 3.6 8.9 - - - +
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Residues in contact with THR 777 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766F MET* 2.9 53.0 - - + +
767F GLY 3.5 5.4 - - - +
768F LEU* 4.1 8.5 - - + +
776F SER* 1.3 74.4 - - - +
778F LEU* 1.3 58.8 + - - +
779F PHE* 4.3 7.1 + - - -
901F ALA* 3.0 34.7 + - - +
902F ALA* 5.3 0.9 - - - -
904F ARG* 5.3 0.3 - - - +
905F ALA* 4.1 10.5 - - + +
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Residues in contact with LEU 778 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766F MET* 3.7 3.4 - - - -
767F GLY* 2.9 44.1 + - - +
769F ALA* 3.7 30.7 - - + -
776F SER* 5.5 3.4 - - - -
777F THR* 1.3 76.4 - - - +
779F PHE* 1.3 64.0 + - - +
780F VAL* 3.6 26.9 - - + -
810F MET* 6.1 0.7 - - + -
844F VAL* 5.0 4.9 - - + -
845F PRO* 3.2 42.8 - - + +
846F GLU 4.6 6.7 - - - +
847F GLY* 5.4 0.4 - - - -
848F ALA* 5.2 3.8 - - + +
856F ALA* 5.9 4.3 - - + -
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Residues in contact with PHE 779 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759F VAL 5.3 5.6 - - - -
760F THR* 4.8 15.3 - - + -
764F VAL* 3.9 20.2 - - + -
765F VAL 3.6 9.6 - - - -
766F MET* 4.0 38.4 - - + -
777F THR 4.8 6.5 - - - -
778F LEU* 1.3 76.8 - - - +
780F VAL* 1.3 62.7 + - - +
781F GLU* 3.8 24.3 + - + +
843F HIS* 3.9 0.5 - - - +
845F PRO* 2.9 30.2 - - + +
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Residues in contact with VAL 780 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763F GLY 3.5 1.6 - - - +
764F VAL* 3.3 5.4 - - - +
765F VAL 2.8 39.4 + - - +
778F LEU* 3.6 24.7 - - + -
779F PHE* 1.3 73.4 - - - +
781F GLU* 1.3 60.6 + - - +
842F LEU* 4.2 18.4 - - + -
843F HIS 3.6 5.8 - - - +
844F VAL* 4.5 13.2 - - + -
845F PRO* 4.5 0.9 - - + -
856F ALA* 5.3 3.8 - - + -
859F THR* 3.8 23.3 - - + -
860F ILE* 4.2 16.6 - - + -
863F ALA* 4.0 19.6 - - + +
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Residues in contact with GLU 781 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763F GLY 3.5 2.9 - - - -
764F VAL* 3.8 28.5 - - + +
779F PHE* 4.1 17.8 - - - +
780F VAL* 1.3 80.9 - - - +
782F THR* 1.3 66.8 + - - +
841F HIS* 3.5 1.4 + - - +
842F LEU* 3.9 0.5 - - - +
843F HIS* 2.8 54.1 + - + +
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Residues in contact with THR 782 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762F PRO 4.3 2.9 - - - +
763F GLY* 2.9 17.5 + - - +
764F VAL* 5.0 2.1 - - - +
781F GLU* 1.3 81.7 - - - +
783F SER* 1.3 61.2 + - - +
840F ILE* 4.0 2.7 - - - -
841F HIS* 3.1 13.0 - - - +
842F LEU* 4.0 17.5 - - + -
860F ILE* 5.8 0.2 - - + -
863F ALA* 3.2 36.7 + - + -
864F LEU* 4.1 19.7 + - + -
867F LEU* 3.4 29.6 - - - +
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Residues in contact with SER 783 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782F THR* 1.3 76.2 - - - +
784F LEU* 1.3 67.5 + - - +
840F ILE* 3.6 5.2 - - - +
841F HIS* 3.1 45.3 + - - +
867F LEU* 3.9 10.1 - - - -
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Residues in contact with LEU 784 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783F SER* 1.3 81.2 + - - +
785F ARG* 1.3 75.0 + - - +
834F TYR* 3.3 29.2 + - + +
838F SER* 3.4 28.5 - - - +
839F HIS 3.4 16.2 - - - +
840F ILE* 5.0 0.7 - - + +
867F LEU* 4.1 3.7 - - + +
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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