Contacts of the helix formed by residues 823 - 836 (chain B) in PDB entry 5J67
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 ALA 823 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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741B GLN* 3.5 24.9 - - + +
742B VAL 2.9 25.4 + - - +
743B PHE 3.7 10.1 - - - +
744B GLN* 3.7 12.7 - - - +
822B LEU* 1.3 74.2 - - - +
824B ALA* 1.3 62.2 + - - +
825B GLY* 4.4 1.6 - - - +
826B PHE* 3.8 6.9 - - + +
827B THR* 2.7 32.2 + - - -
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Residues in contact with ALA 824 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744B GLN* 5.0 6.5 + - - +
822B LEU 4.0 0.6 + - - -
823B ALA* 1.3 75.7 - - - +
825B GLY* 1.3 63.1 + - - +
827B THR* 3.3 3.1 + - - -
828B ASN* 3.0 32.5 + - - +
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Residues in contact with GLY 825 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823B ALA* 4.4 1.6 - - - +
824B ALA* 1.3 79.8 - - - +
826B PHE* 1.3 61.2 + - - +
828B ASN* 3.6 10.6 + - - +
829B VAL* 3.4 20.6 + - - +
849B TYR* 3.4 15.3 + - - -
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Residues in contact with PHE 826 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741B GLN 3.6 15.7 + - - +
742B VAL* 3.6 32.1 - - + +
822B LEU* 3.8 30.7 - - + -
823B ALA* 3.7 7.7 + - + +
824B ALA 3.3 0.8 - - - -
825B GLY* 1.3 76.2 - - - +
827B THR* 1.3 59.1 + - - +
829B VAL* 3.3 6.1 - - - +
830B LEU* 3.0 49.7 + - + +
845B PHE* 3.7 27.6 - + - -
849B TYR* 3.6 34.4 + + - -
962B LEU* 4.5 12.8 - - + -
965B LEU* 3.9 24.0 - - + -
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Residues in contact with THR 827 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822B LEU* 3.7 21.0 - - + +
823B ALA 2.7 23.5 + - - -
824B ALA* 3.9 3.4 - - - -
826B PHE* 1.3 75.4 - - - +
828B ASN* 1.3 56.3 + - - +
830B LEU* 3.9 15.3 - - + -
831B LYS* 2.8 58.5 + - + +
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Residues in contact with ASN 828 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824B ALA* 3.0 28.4 + - - +
825B GLY* 3.7 11.8 - - - +
826B PHE 3.3 0.4 - - - -
827B THR* 1.3 79.3 - - - +
829B VAL* 1.3 63.9 + - + +
831B LYS* 3.4 20.5 + - - +
832B ILE* 3.4 20.6 + - - +
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Residues in contact with VAL 829 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825B GLY 3.4 14.1 + - - +
826B PHE 3.3 15.5 - - - +
828B ASN* 1.3 76.7 - - + +
830B LEU* 1.3 58.2 + - - +
832B ILE* 3.5 17.3 - - + +
833B LEU* 3.2 37.1 + - + +
845B PHE* 3.9 13.5 - - + -
849B TYR* 3.6 32.1 - - + +
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Residues in contact with LEU 830 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822B LEU* 4.5 5.8 - - + -
826B PHE* 3.0 44.5 + - + +
827B THR* 3.7 13.2 - - + +
829B VAL* 1.3 79.1 - - + +
831B LYS* 1.3 60.4 + - - +
832B ILE 3.5 0.2 - - - -
833B LEU* 4.7 3.5 - - + +
834B THR* 3.4 23.6 + - - -
845B PHE* 4.4 18.8 - - + -
962B LEU 5.8 0.7 - - - +
965B LEU 3.8 22.4 - - - +
966B ILE* 4.2 34.8 - - + +
971B THR* 6.1 2.0 - - + -
975B PHE* 6.2 1.8 - - + -
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Residues in contact with LYS 831 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827B THR* 2.8 41.8 + - + +
828B ASN* 3.6 16.4 - - - +
829B VAL 3.3 0.4 - - - -
830B LEU* 1.3 76.1 - - - +
832B ILE* 1.3 61.3 + - + +
834B THR* 3.1 24.6 - - - +
835B LYS* 3.5 13.7 + - - +
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Residues in contact with ILE 832 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828B ASN 3.4 11.4 + - - +
829B VAL* 3.5 26.5 - - + +
831B LYS* 1.3 78.3 - - + +
833B LEU* 1.3 80.8 + - + +
834B THR 3.5 0.5 + - - -
835B LYS* 4.0 12.9 + - - +
836B GLU* 3.7 18.4 + - - +
841B GLU* 5.2 0.9 - - - +
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Residues in contact with LEU 833 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829B VAL* 3.2 19.7 + - + +
830B LEU* 4.7 4.0 - - + +
832B ILE* 1.3 95.5 - - + +
834B THR* 1.3 65.4 + - - +
835B LYS 3.3 0.2 - - - -
836B GLU* 3.1 22.3 + - - +
837B SER* 4.9 0.3 - - - -
841B GLU* 3.2 43.3 - - + +
842B LEU* 4.5 19.1 - - + +
845B PHE* 3.8 41.7 - - + -
971B THR* 4.7 5.0 - - + +
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Residues in contact with THR 834 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830B LEU 3.4 16.3 + - - +
831B LYS* 3.1 24.9 - - - +
833B LEU* 1.3 77.8 - - - +
835B LYS* 1.3 76.3 + - + +
837B SER* 4.5 6.4 + - - -
966B ILE* 4.7 2.0 - - - +
968B ASP* 3.2 20.2 + - - +
971B THR* 2.6 47.8 + - - +
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Residues in contact with LYS 835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831B LYS* 3.5 26.5 + - - +
832B ILE* 4.0 12.6 + - - +
833B LEU 3.3 0.2 - - - -
834B THR* 1.3 83.7 - - + +
836B GLU* 1.3 54.8 + - - +
837B SER* 2.8 22.3 + - - -
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Residues in contact with GLU 836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832B ILE 3.7 14.7 + - - +
833B LEU* 3.1 17.1 + - - +
835B LYS* 1.3 73.7 - - - +
837B SER* 1.3 62.3 + - - +
838B SER* 3.0 19.5 + - - +
841B GLU* 3.2 38.8 - - - +
842B LEU* 5.4 3.3 - - - +
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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