Contacts of the helix formed by residues 884 - 897 (chain A) in PDB entry 3RJO
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 THR 884 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690A ARG* 3.3 44.0 - - - +
883A SER* 1.3 77.3 - - - +
885A ARG* 1.3 58.2 + - - +
886A THR* 3.6 10.3 + - - -
887A ARG* 3.2 29.2 + - + +
888A LEU* 3.0 24.9 + - - +
915A ILE* 4.4 1.2 - - - +
919A ILE* 3.8 9.6 - - - +
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Residues in contact with ARG 885 (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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884A THR* 1.3 71.7 - - - +
886A THR* 1.3 51.9 + - - +
888A LEU* 3.1 7.3 + - + +
889A GLU* 2.8 41.0 + - + +
919A ILE* 3.8 20.3 - - + +
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Residues in contact with THR 886 (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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884A THR* 3.3 9.7 - - - -
885A ARG* 1.3 78.4 - - - +
887A ARG* 1.3 59.1 + - + +
889A GLU* 3.2 8.4 + - - +
890A GLU* 2.9 37.2 + - - +
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Residues in contact with ARG 887 (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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689A LYS 5.4 5.4 + - - +
846A TYR* 4.0 24.2 + - - -
847A PRO* 5.4 7.5 - - - +
850A TRP* 4.0 11.3 - - - -
854A ARG* 5.5 1.2 - - - +
882A PHE* 3.6 53.0 - - + -
883A SER 5.1 0.7 - - - +
884A THR* 3.2 23.6 + - + +
886A THR* 1.3 78.5 - - + +
888A LEU* 1.3 58.6 + - - +
890A GLU* 2.6 49.3 + - - +
891A VAL* 2.9 33.4 + - - +
915A ILE* 5.2 0.4 - - - -
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Residues in contact with LEU 888 (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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884A THR 3.0 12.5 + - - +
885A ARG* 3.1 11.9 + - + +
887A ARG* 1.3 76.5 - - - +
889A GLU* 1.3 58.8 + - - +
891A VAL* 3.4 5.2 + - + +
892A LYS* 2.9 58.9 + - + +
912A ILE* 4.5 15.3 - - + -
915A ILE* 3.9 23.5 - - + +
916A GLU* 3.8 26.9 - - + +
919A ILE* 3.5 20.2 - - + -
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Residues in contact with GLU 889 (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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885A ARG* 2.8 20.7 + - + +
886A THR* 3.6 10.3 - - - +
888A LEU* 1.3 72.6 - - - +
890A GLU* 1.3 56.7 + - - +
892A LYS* 3.7 24.8 + - - +
893A GLY* 2.7 32.7 + - - -
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Residues in contact with GLU 890 (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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850A TRP* 2.8 27.5 + - + +
854A ARG* 4.4 17.2 + - - +
886A THR* 2.9 21.4 + - + +
887A ARG* 2.6 52.5 + - - +
889A GLU* 1.3 75.9 - - - +
891A VAL* 1.3 56.6 + - - +
893A GLY* 3.3 1.2 + - - -
894A PHE* 2.9 30.5 + - - +
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Residues in contact with VAL 891 (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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850A TRP* 3.7 24.2 - - + +
879A THR* 4.1 16.4 - - + -
882A PHE* 4.3 8.3 - - + -
887A ARG 2.9 18.8 + - - +
888A LEU 3.8 3.8 - - - +
890A GLU* 1.3 76.7 - - - +
892A LYS* 1.3 64.0 + - - +
894A PHE* 3.3 0.7 + - - -
895A PHE* 3.1 50.1 + - + -
908A VAL* 5.4 1.3 - - - +
911A THR* 5.3 5.4 - - - -
912A ILE* 4.3 17.5 - - + -
915A ILE* 3.8 28.7 - - + -
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Residues in contact with LYS 892 (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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888A LEU* 2.9 36.8 + - + +
889A GLU* 3.7 21.9 + - - +
891A VAL* 1.3 77.5 - - - +
893A GLY* 1.3 53.8 + - - +
895A PHE* 5.2 1.1 - - - -
896A SER* 2.8 41.6 + - - -
912A ILE* 3.7 33.6 - - + +
916A GLU* 3.6 21.0 + - - -
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Residues in contact with GLY 893 (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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889A GLU 2.7 18.7 + - - -
890A GLU* 3.6 1.8 - - - -
892A LYS* 1.3 75.8 - - - +
894A PHE* 1.3 63.0 + - - +
896A SER* 3.6 5.1 + - - -
897A SER* 3.1 25.7 + - - -
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Residues in contact with PHE 894 (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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850A TRP* 4.0 13.9 - + + -
853A LEU* 5.4 1.1 - - + -
854A ARG* 3.5 51.4 - - + +
857A TRP* 3.9 26.2 - + + -
890A GLU 2.9 20.0 + - - +
891A VAL 3.3 2.4 + - - +
893A GLY* 1.3 71.3 - - - +
895A PHE* 1.3 98.9 + + - +
897A SER* 2.8 25.8 + - - -
898A LEU* 3.5 28.6 - - + +
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Residues in contact with PHE 895 (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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850A TRP* 3.6 30.5 - + - -
853A LEU* 4.5 4.7 - - + -
857A TRP* 3.9 21.1 - + - -
875A VAL* 3.9 33.4 - - + -
879A THR* 4.8 1.8 - - + -
891A VAL* 3.1 41.0 + - + +
892A LYS* 4.4 1.1 - - - +
894A PHE* 1.3 91.2 - + - +
896A SER* 1.3 66.2 + - - +
897A SER 3.1 1.3 - - - -
898A LEU* 3.3 25.6 + - + +
903A SER* 3.1 24.8 - - - -
905A LEU* 5.4 0.7 - - + -
908A VAL* 3.5 39.9 - - + -
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Residues in contact with SER 896 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A LYS* 2.8 25.8 + - - -
893A GLY* 3.6 6.4 + - - -
895A PHE* 1.3 73.6 - - - +
897A SER* 1.3 59.0 + - - +
898A LEU 3.2 1.4 + - - -
899A LYS* 4.0 7.9 + - - -
903A SER* 4.2 9.4 - - - -
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Residues in contact with SER 897 (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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893A GLY 3.1 16.8 + - - -
894A PHE* 2.8 20.3 + - - -
895A PHE 3.1 0.6 - - - -
896A SER* 1.3 76.5 + - - +
898A LEU* 1.3 64.4 + - - +
899A LYS* 3.6 2.2 - - - +
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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