Contacts of the helix formed by residues 767 - 779 (chain A) in PDB entry 3APO
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 767 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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661A ARG* 4.6 7.3 + - - -
709A GLU* 3.7 11.2 - - - +
765A SER* 3.2 6.0 + - - +
766A ARG* 1.3 77.7 - - - +
768A ALA* 1.3 67.5 + - - +
769A LYS* 3.9 12.0 - - - +
770A THR* 3.0 30.6 + - - +
771A ILE* 3.0 24.9 + - - +
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Residues in contact with ALA 768 (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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709A GLU* 2.8 29.7 + - - +
712A LEU* 3.7 30.3 - - + -
713A LEU* 3.9 24.7 - - - +
716A MET* 3.9 7.6 - - - -
767A ASP* 1.3 70.9 - - - +
769A LYS* 1.3 56.8 + - - +
771A ILE* 3.4 6.8 + - - +
772A ALA* 2.9 31.2 + - - +
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Residues in contact with LYS 769 (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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604A THR 5.3 9.8 + - - -
606A THR* 5.1 13.1 + - - -
608A LEU* 5.7 10.1 - - - -
661A ARG* 6.0 1.1 - - - +
712A LEU* 6.1 1.8 - - + -
716A MET* 3.9 24.2 - - + +
767A ASP* 3.3 12.3 + - - +
768A ALA* 1.3 79.0 - - + +
770A THR* 1.3 62.0 + - - +
772A ALA* 3.6 1.9 + - - +
773A ALA* 3.2 23.6 + - - +
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Residues in contact with THR 770 (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 SER* 3.4 28.0 - - - +
767A ASP* 3.0 21.2 + - - +
769A LYS* 1.3 75.2 - - - +
771A ILE* 1.3 65.3 + - - +
773A ALA* 3.3 6.8 + - - +
774A LEU* 3.0 26.3 + - + +
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Residues in contact with ILE 771 (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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692A VAL* 4.7 3.6 - - + -
706A PHE* 4.4 14.1 - - + -
713A LEU* 3.7 27.8 - - + -
746A VAL* 5.1 3.8 - - + -
763A ILE* 3.8 24.2 - - + -
765A SER* 3.4 31.4 - - - +
766A ARG* 4.2 3.4 - - - -
767A ASP 3.0 23.5 + - - +
768A ALA* 3.8 6.5 - - - +
770A THR* 1.3 75.3 - - - +
772A ALA* 1.3 56.2 + - - +
774A LEU* 3.3 9.3 + - - +
775A ILE* 2.8 50.9 + - + +
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Residues in contact with ALA 772 (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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713A LEU* 3.9 8.7 - - + +
716A MET* 3.8 20.6 - - + -
717A ILE* 4.1 22.2 - - + -
768A ALA 2.9 18.1 + - - +
769A LYS 3.7 5.2 - - - +
770A THR 3.3 0.2 - - - -
771A ILE* 1.3 76.2 - - - +
773A ALA* 1.3 63.0 + - - +
775A ILE* 3.0 6.2 + - - +
776A TYR* 2.9 38.3 + - + -
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Residues in contact with ALA 773 (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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769A LYS 3.2 13.7 + - - +
770A THR* 3.7 5.8 - - - +
772A ALA* 1.3 76.1 - - - +
774A LEU* 1.3 65.8 + - - +
775A ILE 3.1 0.5 + - - -
776A TYR* 3.1 10.8 + - - +
777A GLY* 2.8 24.4 + - - -
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Residues in contact with LEU 774 (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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762A GLN 5.8 0.4 - - - +
763A ILE* 3.7 40.2 - - + -
764A ASN 6.0 0.2 - - - +
765A SER* 5.8 3.6 - - - -
770A THR* 3.0 15.3 + - + +
771A ILE* 3.4 9.4 - - - +
773A ALA* 1.3 75.4 - - - +
775A ILE* 1.3 61.7 + - + +
777A GLY* 3.7 2.2 + - - -
778A LYS* 3.1 45.0 + - + +
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Residues in contact with ILE 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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692A VAL* 4.0 23.8 - - + -
713A LEU* 4.5 8.5 - - + -
717A ILE* 4.9 7.4 - - + -
721A VAL* 3.8 28.3 - - + -
748A LEU* 3.8 32.5 - - + -
763A ILE* 4.6 4.7 - - + -
771A ILE* 2.8 42.3 + - + +
772A ALA* 3.0 7.8 + - - +
774A LEU* 1.3 70.8 - - - +
776A TYR* 1.3 69.1 + - + +
778A LYS* 3.0 15.2 + - - +
779A LEU* 3.1 21.2 + - + +
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Residues in contact with TYR 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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716A MET* 3.4 25.2 + - + +
717A ILE* 3.6 26.0 - - + +
720A LYS* 3.5 46.0 - - + +
721A VAL* 5.4 0.7 - - + -
772A ALA* 2.9 32.8 + - + +
773A ALA* 3.8 8.1 - - - +
775A ILE* 1.3 76.5 - - + +
777A GLY* 1.3 64.1 + - - +
779A LEU* 3.0 21.5 + - + +
780A GLU* 2.9 23.2 - - - +
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Residues in contact with GLY 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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773A ALA 2.8 19.7 + - - -
774A LEU* 4.0 2.5 - - - -
776A TYR* 1.3 73.4 - - - +
778A LYS* 1.3 61.0 + - - +
780A GLU* 3.6 19.6 - - - +
781A THR* 3.7 11.3 + - - +
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Residues in contact with LYS 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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748A LEU* 4.0 16.8 - - + -
750A GLN* 3.1 33.5 + - - +
761A GLU* 2.7 42.4 + - - -
774A LEU* 3.1 36.9 + - + +
775A ILE* 3.0 6.9 + - - +
777A GLY* 1.3 76.2 - - - +
779A LEU* 1.3 60.5 + - + +
780A GLU 3.2 4.5 + - - -
781A THR* 3.3 24.3 + - - +
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Residues in contact with LEU 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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690A HIS* 3.9 41.7 - - + +
720A LYS* 4.4 13.2 - - + +
721A VAL* 3.8 24.9 - - + -
748A LEU* 5.6 0.7 - - + -
750A GLN* 3.9 24.9 - - + +
775A ILE* 3.1 25.4 + - + +
776A TYR* 3.0 17.2 + - + +
778A LYS* 1.3 76.5 - - - +
780A GLU* 1.3 59.0 + - - +
781A THR 3.5 2.6 - - - +
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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