Contacts of the helix formed by residues 774 - 791 (chain A) in PDB entry 3IAY
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 774 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A PRO* 3.7 1.9 - - - +
772A THR* 2.9 17.9 + - - +
773A THR* 1.3 81.4 + - - +
775A LEU* 1.3 65.9 + - - +
776A LYS* 3.4 11.2 + - - +
777A GLU* 3.0 33.7 + - + +
778A ALA* 3.1 19.1 + - - +
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Residues in contact with LEU 775 (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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603A PRO* 3.8 17.4 - - + +
773A THR 3.8 3.4 + - - -
774A ASP* 1.3 72.3 + - - +
776A LYS* 1.3 67.4 + - - +
778A ALA* 3.1 4.5 + - - +
779A MET* 3.0 36.0 + - - +
804A ALA* 3.7 28.9 - - + -
806A PHE* 4.2 25.2 - - + -
821A TRP* 3.3 48.5 - - + -
824A PRO* 3.7 19.3 - - + +
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Residues in contact with LYS 776 (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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774A ASP* 3.4 10.5 + - - +
775A LEU* 1.3 79.7 - - - +
777A GLU* 1.3 56.7 + - - +
779A MET* 3.2 7.8 + - + +
780A ASP* 2.5 59.6 + - - +
824A PRO* 4.0 30.6 - - + +
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Residues in contact with GLU 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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753A LYS* 4.2 24.3 + - - +
772A THR* 3.0 24.8 + - + -
774A ASP* 3.0 26.0 + - - +
775A LEU 3.2 0.2 - - - -
776A LYS* 1.3 77.1 - - - +
778A ALA* 1.3 59.4 + - - +
780A ASP* 3.3 8.3 + - + +
781A LEU* 2.9 48.3 + - + +
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Residues in contact with ALA 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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603A PRO* 3.6 29.2 - - + +
605A ALA* 3.9 14.9 - - + +
770A PHE* 4.0 9.2 - - + -
772A THR* 3.8 13.9 - - + +
774A ASP 3.1 11.6 + - - +
775A LEU* 3.1 10.0 + - + +
777A GLU* 1.3 80.5 - - - +
779A MET* 1.3 57.7 + - + +
781A LEU* 3.5 5.8 + - - +
782A GLY* 2.9 25.8 + - - -
804A ALA* 5.5 1.6 - - + -
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Residues in contact with MET 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 LEU* 3.0 29.0 + - + +
776A LYS* 3.2 8.3 + - + +
778A ALA* 1.3 76.8 - - - +
780A ASP* 1.3 59.7 + - - +
782A GLY* 3.3 0.9 + - - -
783A THR* 3.0 33.6 + - - -
801A PHE* 3.7 35.2 - - + -
804A ALA* 4.0 10.5 - - + -
821A TRP* 3.9 7.6 - - - +
822A THR* 3.3 42.8 - - - +
823A ASN* 3.5 4.9 - - - +
824A PRO* 3.9 24.9 - - + -
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Residues in contact with ASP 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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776A LYS* 2.5 54.0 + - - +
777A GLU* 3.7 8.5 - - + +
779A MET* 1.3 76.9 - - - +
781A LEU* 1.3 66.6 + - + +
783A THR* 3.4 6.8 + - - -
784A GLU* 3.0 23.9 + - - +
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Residues in contact with LEU 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 TYR* 4.0 28.4 + - + -
752A TYR* 4.3 15.3 - - + -
770A PHE* 3.7 41.8 - - + -
772A THR* 4.6 4.0 - - + -
777A GLU* 2.9 43.8 + - + +
780A ASP* 1.3 76.7 - - + +
782A GLY* 1.3 54.4 + - - +
784A GLU* 3.7 10.2 - - - +
785A ALA* 2.7 37.4 + - - +
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Residues in contact with GLY 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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605A ALA* 4.2 1.1 - - - -
607A LEU* 3.5 22.7 - - - +
770A PHE* 3.6 15.7 - - - -
778A ALA 2.9 18.2 + - - -
779A MET 3.3 2.4 + - - -
780A ASP 3.2 0.4 - - - -
781A LEU* 1.3 77.6 - - - +
783A THR* 1.3 55.9 + - - +
785A ALA* 3.4 0.9 + - - +
786A ALA* 3.0 25.6 + - - +
801A PHE* 3.7 12.3 - - - -
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Residues in contact with THR 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 MET 3.0 17.6 + - - -
780A ASP* 3.7 7.5 + - - -
781A LEU 3.3 0.2 - - - -
782A GLY* 1.3 73.2 - - - +
784A GLU* 1.3 66.0 + - - +
786A ALA* 3.4 3.9 + - - +
787A LYS* 3.2 24.7 + - + +
801A PHE* 3.6 24.7 - - + +
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Residues in contact with GLU 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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745A LYS* 4.3 5.5 - - - -
746A TYR* 2.7 32.4 + - - +
752A TYR* 3.8 9.6 + - - -
780A ASP 3.0 18.4 + - - +
781A LEU* 3.7 10.9 - - - +
783A THR* 1.3 76.6 - - - +
785A ALA* 1.3 63.7 + - - +
787A LYS* 3.2 9.6 + - + +
788A TYR* 3.0 23.0 + - + +
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Residues in contact with ALA 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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607A LEU* 4.2 11.7 - - + -
742A VAL* 4.6 7.6 - - + -
746A TYR* 3.3 32.0 + - + -
770A PHE* 4.0 13.0 - - + -
781A LEU 2.7 21.6 + - - +
782A GLY 3.7 3.6 - - - +
784A GLU* 1.3 74.4 - - - +
786A ALA* 1.3 57.5 + - - +
788A TYR* 3.3 3.5 + - - +
789A VAL* 2.8 35.3 + - - +
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Residues in contact with ALA 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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607A LEU* 4.2 4.2 - - + +
782A GLY 3.0 14.8 + - - +
783A THR* 3.9 4.3 - - - +
785A ALA* 1.3 75.9 - - - +
787A LYS* 1.3 54.7 + - - +
790A SER* 2.7 37.8 + - - -
799A LEU* 3.2 38.9 - - + +
800A GLU* 3.6 3.4 - - - -
801A PHE 3.6 24.5 - - - +
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Residues in contact with LYS 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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783A THR* 3.2 16.4 + - + +
784A GLU* 3.6 11.7 - - + +
786A ALA* 1.3 73.9 - - - +
788A TYR* 1.3 69.5 + - - +
790A SER* 3.5 11.6 + - - -
791A THR* 3.4 20.4 + - + +
799A LEU 5.0 0.7 - - - -
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Residues in contact with TYR 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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741A ALA* 4.2 23.8 + - + +
742A VAL* 6.0 0.2 - - - -
745A LYS* 3.5 42.4 - - + +
746A TYR* 4.7 3.6 - + - +
784A GLU* 3.0 17.4 + - + +
785A ALA* 3.7 4.3 - - - +
787A LYS* 1.3 75.3 - - - +
789A VAL* 1.3 75.2 + - + +
791A THR* 2.5 35.4 + - + -
792A LEU* 3.8 34.8 + - + +
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Residues in contact with VAL 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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738A THR* 3.8 16.2 - - + +
741A ALA* 4.4 10.8 - - + -
742A VAL* 4.0 25.1 - - + -
785A ALA 2.8 24.9 + - - +
788A TYR* 1.3 83.1 - - + +
790A SER* 1.3 57.0 + - - +
792A LEU* 2.9 33.5 + - + +
793A PHE* 3.4 25.4 - - + -
799A LEU* 3.5 28.9 - - + -
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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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786A ALA 2.7 22.5 + - - -
787A LYS* 3.7 8.0 - - - -
788A TYR 3.1 0.4 - - - -
789A VAL* 1.3 76.8 - - - +
791A THR* 1.3 60.6 + - - +
792A LEU 3.1 1.5 + - - -
793A PHE* 3.3 24.6 + - - +
797A ILE 4.5 7.3 - - - +
798A ASN* 3.5 20.2 + - - +
799A LEU* 2.7 32.6 + - - +
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Residues in contact with THR 791 (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 LYS* 3.4 18.2 - - + +
788A TYR* 2.5 25.7 + - + +
790A SER* 1.3 76.0 - - - +
792A LEU* 1.3 70.8 + - - +
793A PHE 3.3 4.5 + - - +
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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