Contacts of the helix formed by residues 776 - 787 (chain A) in PDB entry 4BL8
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 776 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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751A THR* 5.0 8.3 - - - -
760A GLU* 4.3 25.6 - - + +
774A LEU* 4.3 7.8 + - + +
775A LEU* 1.3 76.0 - - - +
777A GLU* 1.3 65.9 + - - +
778A GLU* 3.8 14.4 + - - +
779A PHE* 3.2 25.5 + - - +
780A VAL* 3.0 20.7 + - - +
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Residues in contact with GLU 777 (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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729A LEU 6.1 0.7 - - - -
730A LEU* 4.1 20.3 - - + +
751A THR* 4.7 14.3 - - + +
775A LEU 3.9 0.6 + - - -
776A THR* 1.3 73.2 - - - +
778A GLU* 1.3 79.6 + - - +
780A VAL* 3.1 8.4 + - - +
781A GLU* 3.0 34.1 + - + +
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Residues in contact with GLU 778 (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 THR* 3.2 11.8 - - - +
777A GLU* 1.3 98.7 + - - +
779A PHE* 1.3 61.7 + - - +
781A GLU* 3.4 6.6 + - - +
782A LYS* 3.3 34.0 + - - +
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Residues in contact with PHE 779 (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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764A TYR* 4.7 3.1 - - - -
775A LEU* 4.1 21.5 - - + -
776A THR* 3.2 21.4 + - - +
778A GLU* 1.3 77.2 - - - +
780A VAL* 1.3 59.4 + - - +
782A LYS* 4.6 10.8 - - + +
783A MET* 2.9 56.3 + - + +
804A TRP* 3.8 38.6 - + + -
806A GLU* 3.7 44.4 - - + +
807A LYS* 4.8 4.5 - - + -
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Residues in contact with VAL 780 (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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725A LEU* 3.8 33.8 - - + +
729A LEU* 4.3 14.1 - - + +
730A LEU* 3.8 23.8 - - + -
775A LEU* 3.6 33.4 - - + +
776A THR 3.0 19.9 + - - +
777A GLU* 3.1 8.5 + - - +
779A PHE* 1.3 76.0 - - - +
781A GLU* 1.3 60.2 + - - +
783A MET* 3.3 7.1 + - - +
784A LEU* 3.0 30.8 + - + +
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Residues in contact with GLU 781 (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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726A ARG* 5.8 1.2 + - - -
730A LEU* 3.4 28.7 - - + +
777A GLU* 3.0 34.0 + - + +
778A GLU* 3.7 6.5 - - - +
780A VAL* 1.3 79.3 - - - +
782A LYS* 1.3 61.0 + - + +
784A LEU* 3.6 11.4 + - - +
785A GLU* 3.5 23.1 + - - +
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Residues in contact with LYS 782 (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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778A GLU* 3.3 21.2 + - - +
779A PHE* 4.1 12.6 - - + +
781A GLU* 1.3 75.7 - - + +
783A MET* 1.3 66.4 + - - +
784A LEU 3.1 1.8 - - - -
785A GLU* 3.1 29.5 + - - +
786A ASP* 3.0 23.1 + - - +
804A TRP* 5.7 0.7 - - - +
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Residues in contact with MET 783 (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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721A ILE* 5.7 1.8 - - - -
725A LEU* 4.0 22.7 - - + -
748A PHE* 5.6 1.6 - - - -
775A LEU* 3.9 18.2 - - + -
779A PHE* 2.9 69.0 + - + +
780A VAL* 3.3 5.8 + - - +
782A LYS* 1.3 77.1 - - - +
784A LEU* 1.3 60.6 + - - +
786A ASP* 3.3 1.8 + - - +
787A LEU* 3.2 30.8 + - + +
804A TRP* 3.7 29.4 - - + +
807A LYS* 3.5 27.4 - - - +
809A LEU* 5.8 1.3 - - - -
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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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722A PRO* 3.8 30.7 - - + +
725A LEU* 4.0 12.6 - - + -
726A ARG* 3.5 66.9 + - + +
730A LEU* 4.4 8.1 - - + -
780A VAL* 3.0 25.1 + - + +
781A GLU* 3.7 12.8 - - - +
782A LYS 3.1 0.2 - - - -
783A MET* 1.3 75.8 - - - +
785A GLU* 1.3 63.6 + - - +
787A LEU* 3.3 21.2 - - + +
788A GLU* 3.5 4.9 - - - +
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Residues in contact with GLU 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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781A GLU 3.5 13.6 + - - +
782A LYS* 3.1 24.5 + - - +
784A LEU* 1.3 79.9 - - - +
786A ASP* 1.3 61.4 + - - +
788A GLU* 2.9 25.9 - - - +
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Residues in contact with ASP 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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782A LYS* 3.0 22.9 + - - +
783A MET 3.3 7.8 + - - +
784A LEU 3.3 0.4 - - - -
785A GLU* 1.3 82.0 - - - +
787A LEU* 1.3 59.1 + - + +
788A GLU* 3.8 3.4 + - - +
802A TYR* 3.3 23.2 - - + -
804A TRP* 4.0 30.6 + - + -
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Residues in contact with LEU 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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721A ILE* 3.7 35.2 - - + -
722A PRO* 5.0 13.4 - - + +
725A LEU* 4.5 9.0 - - + -
783A MET* 3.2 22.0 + - + +
784A LEU* 3.3 12.4 + - + +
785A GLU 3.2 0.8 - - - -
786A ASP* 1.3 83.4 - - - +
788A GLU* 1.3 70.9 + - - +
789A ASP* 4.1 14.4 + - - +
802A TYR* 3.9 24.0 - - + -
804A TRP* 3.8 25.4 - - + -
809A LEU* 4.2 14.6 - - + -
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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