Contacts of the helix formed by residues 922 - 932 (chain A) in PDB entry 5J9H
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 GLY 922 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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732A TRP* 3.5 7.6 - - - -
880A GLY* 3.4 14.0 - - - +
881A ASP 3.3 25.9 - - - -
882A PRO* 5.4 1.0 - - - +
884A ASP* 2.9 16.9 + - - -
921A SER* 1.3 71.7 - - - +
923A TYR* 1.3 56.3 + - - +
925A ARG* 3.2 4.3 + - - +
926A MET* 2.9 29.1 + - - +
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Residues in contact with TYR 923 (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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732A TRP* 3.3 31.3 - + + +
733A MET 4.8 1.0 + - - +
734A ASP* 3.7 39.7 - - + +
800A VAL* 3.5 40.7 - - + +
859A LEU* 4.3 17.0 - - + +
884A ASP* 4.8 0.2 + - - -
921A SER* 3.4 1.0 + - - -
922A GLY* 1.3 75.7 - - - +
924A LYS* 1.3 63.6 + - + +
926A MET* 3.1 5.9 + - + +
927A ILE* 2.9 60.9 + - + +
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Residues in contact with LYS 924 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A ASP* 3.4 22.2 + - - +
735A ALA 3.0 27.9 + - - -
736A THR* 4.8 6.1 + - - +
920A ILE* 3.7 20.8 - - + +
921A SER* 3.4 14.2 + - - +
922A GLY 3.4 0.4 - - - -
923A TYR* 1.3 84.3 - - + +
925A ARG* 1.3 61.9 + - - +
927A ILE* 4.0 5.1 - - - +
928A ALA* 3.2 24.9 + - - +
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Residues in contact with ARG 925 (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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880A GLY* 3.6 22.7 + - - +
918A ASN* 2.7 31.3 + - - -
920A ILE* 3.6 41.3 - - + +
921A SER 3.2 10.6 + - - +
922A GLY 3.5 7.0 - - - +
923A TYR 3.2 0.2 - - - -
924A LYS* 1.3 73.3 - - - +
926A MET* 1.3 66.3 + - - +
928A ALA* 3.9 6.0 + - - +
929A THR* 3.6 20.1 + - - +
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Residues in contact with MET 926 (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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732A TRP* 3.8 28.9 - - + -
857A LEU* 4.0 15.0 - - + -
859A LEU* 4.8 3.4 - - + -
867A LEU* 4.1 20.0 - - + -
869A PHE* 3.7 22.4 - - + -
882A PRO* 6.2 2.9 - - + -
922A GLY 2.9 12.9 + - - +
923A TYR* 3.4 13.9 - - + +
925A ARG* 1.3 75.9 - - - +
927A ILE* 1.3 83.8 + - + +
929A THR* 3.0 9.9 + - - +
930A LYS* 2.9 37.0 + - - -
933A PHE* 3.8 17.7 - - + -
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Residues in contact with ILE 927 (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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859A LEU* 4.8 9.4 - - + -
923A TYR* 2.9 55.6 + - + +
924A LYS* 3.6 6.9 + - - +
926A MET* 1.3 86.8 - - + +
928A ALA* 1.3 64.6 + - - +
930A LYS* 3.2 45.7 + - + +
3B BMA 5.5 8.1 - - - +
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Residues in contact with ALA 928 (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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924A LYS 3.2 17.9 + - - +
925A ARG* 4.0 8.3 - - - +
926A MET 3.2 0.2 + - - -
927A ILE* 1.3 78.6 - - - +
929A THR* 1.3 57.9 + - - +
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Residues in contact with THR 929 (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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925A ARG 3.6 15.9 - - - +
926A MET* 3.0 7.2 + - - +
928A ALA* 1.3 76.7 - - + +
930A LYS* 1.3 62.6 + - - +
931A ASP 3.2 2.9 - - - -
932A SER* 2.6 41.5 + - - +
933A PHE* 3.8 15.3 - - + -
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Residues in contact with LYS 930 (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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859A LEU* 5.9 1.1 - - + -
867A LEU* 5.1 9.3 - - + +
926A MET* 2.9 16.2 + - - +
927A ILE* 3.2 42.3 + - + +
928A ALA 3.5 0.8 + - - -
929A THR* 1.3 75.8 - - - +
931A ASP* 1.3 72.0 + - - +
932A SER 3.1 4.8 + - - -
933A PHE* 3.3 25.7 + - - +
2B NAG 4.2 22.1 + - - +
3B BMA 3.3 32.7 + - - +
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Residues in contact with ASP 931 (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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929A THR 3.1 2.0 + - - -
930A LYS* 1.3 90.6 - - - +
932A SER* 1.3 60.7 + - - +
933A PHE 3.3 7.0 + - - +
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Residues in contact with SER 932 (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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929A THR* 2.6 36.4 + - - +
931A ASP* 1.3 76.3 - - - +
933A PHE* 1.3 74.9 + - - +
934A GLN* 5.7 1.0 + - - -
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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