Contacts of the helix formed by residues 776 - 786 (chain A) in PDB entry 3BWT
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 ASP 776 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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739A ASP* 4.7 7.4 - - - +
769A GLU* 3.1 14.2 + - - +
774A LYS 4.0 0.9 + - - +
775A TYR* 1.3 73.7 - - - +
777A TYR* 1.3 90.1 + - + +
778A THR 3.2 0.7 - - - -
779A HIS* 3.3 15.6 + - - +
780A LYS* 3.4 36.8 + - - +
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Residues in contact with TYR 777 (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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739A ASP* 2.9 45.2 + - - +
742A CYS* 3.5 38.4 - - + -
743A ASP* 2.7 33.7 + - - -
746A LEU* 4.4 20.4 - - + -
765A ILE* 3.6 19.1 - - + -
769A GLU* 2.8 19.9 + - - +
776A ASP* 1.3 88.9 + - + +
778A THR* 1.3 66.2 - - - +
780A LYS* 3.6 13.0 + - + +
781A ILE* 2.8 34.3 + - + +
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Residues in contact with THR 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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765A ILE* 4.7 0.6 - - - +
766A ILE* 3.6 41.7 - - + +
769A GLU* 2.6 35.3 + - - +
775A TYR* 3.9 22.4 - - + -
777A TYR* 1.3 77.6 - - - +
779A HIS* 1.3 63.1 + - - +
781A ILE* 3.6 2.0 - - - +
782A VAL* 3.0 30.6 + - + +
808A THR* 4.8 0.2 - - + -
810A ILE* 4.9 0.9 - - + -
811A VAL* 4.1 29.2 - - + -
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Residues in contact with HIS 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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775A TYR* 3.3 43.7 + - + +
776A ASP* 3.3 7.6 + - - +
777A TYR 3.2 0.4 - - - -
778A THR* 1.3 79.4 - - - +
780A LYS* 1.3 58.6 + - + +
782A VAL* 3.5 4.8 + - + +
783A HIS* 3.0 30.0 + - - +
810A ILE* 3.2 20.9 + - + +
811A VAL* 4.1 17.0 - - + +
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Residues in contact with LYS 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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743A ASP* 5.1 4.0 + - - -
746A LEU* 3.8 33.7 - - + +
776A ASP* 3.4 31.1 + - - +
777A TYR* 3.1 20.1 + - + +
779A HIS* 1.3 76.2 - - + +
781A ILE* 1.3 63.6 + - - +
783A HIS* 3.5 8.3 + - - +
784A LEU* 3.3 27.1 + - + +
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Residues in contact with ILE 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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746A LEU* 3.9 18.8 - - + -
749A VAL* 4.2 8.7 - - + -
762A VAL* 3.9 35.2 - - + +
765A ILE* 4.1 22.7 - - + -
766A ILE* 4.0 24.7 - - + -
777A TYR* 2.8 24.1 + - + +
778A THR 3.6 3.1 - - - +
780A LYS* 1.3 70.3 - - - +
782A VAL* 1.3 68.1 + - - +
784A LEU* 2.9 15.2 + - - +
785A LEU* 3.0 38.6 + - + +
805A ILE* 4.7 3.1 - - + -
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Residues in contact with VAL 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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766A ILE* 5.3 0.7 - - + -
778A THR* 3.0 24.1 + - + +
779A HIS* 3.8 5.8 - - - +
781A ILE* 1.3 75.6 - - + +
783A HIS* 1.3 60.0 + - - +
785A LEU* 4.6 0.7 - - - +
786A LYS* 2.9 59.5 + - + +
805A ILE* 4.1 27.1 - - + -
811A VAL* 3.8 35.9 - - + +
814A PRO* 5.1 7.0 - - + -
815A MET* 4.7 8.7 - - + +
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Residues in contact with HIS 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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779A HIS 3.0 18.5 + - - +
780A LYS* 3.6 8.3 - - - +
781A ILE 3.2 0.2 - - - -
782A VAL* 1.3 78.8 - - - +
784A LEU* 1.3 72.7 + - + +
786A LYS* 4.9 5.8 - - - +
787A PRO* 3.5 16.5 - - - +
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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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746A LEU* 4.0 27.6 - - + +
749A VAL* 3.7 31.4 - - + -
750A ASP* 4.9 6.2 - - - +
780A LYS 3.3 15.0 + - - +
781A ILE* 2.9 8.0 + - - +
783A HIS* 1.3 89.3 - - + +
785A LEU* 1.3 63.6 + - + +
786A LYS 3.6 0.2 - - - -
787A PRO* 3.7 8.5 - - - +
788A ARG* 4.7 10.0 + - - +
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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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749A VAL* 3.9 24.2 - - + +
750A ASP* 4.4 6.7 - - - +
753A THR* 3.8 28.7 - - + +
781A ILE* 3.0 32.4 + - + +
782A VAL* 4.5 1.8 - - - +
784A LEU* 1.3 77.9 - - - +
786A LYS* 1.3 67.3 + - - +
787A PRO* 3.2 3.4 - - - -
788A ARG* 2.9 24.4 + - - +
789A ALA* 3.5 7.3 + - - -
792A LEU* 3.7 20.9 - - + +
801A VAL* 3.5 31.6 - - + -
802A ILE* 4.8 3.7 - - + +
805A ILE* 4.6 7.4 - - + -
815A MET* 4.9 1.8 - - - -
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Residues in contact with LYS 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 VAL* 2.9 28.4 + - + +
783A HIS* 4.9 3.8 - - - +
785A LEU* 1.3 76.2 - - - +
787A PRO* 1.3 59.7 - - + +
788A ARG 2.7 11.3 + - - -
789A ALA* 2.9 12.6 + - - +
814A PRO* 3.5 42.2 + - + +
815A MET* 4.0 20.3 - - + +
818A GLU* 3.2 46.0 + - + +
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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