Contacts of the helix formed by residues 887 - 904 (chain A) in PDB entry 2B49
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 887 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650A PHE* 3.6 10.7 - - - -
886A GLN* 1.3 95.6 - - + +
888A SER* 1.3 66.0 + - - +
889A SER* 2.8 26.2 + - - +
890A GLN* 3.0 27.2 + - - +
891A TYR 3.0 17.7 + - - -
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Residues in contact with SER 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A LEU* 5.4 6.8 - - - +
650A PHE* 3.7 17.4 - - - -
651A GLU* 3.6 28.5 + - - -
887A THR* 1.3 72.9 - - - +
889A SER* 1.3 55.2 + - - +
891A TYR* 3.1 1.5 + - - +
892A LYS* 2.6 38.8 + - - +
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Residues in contact with SER 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813A GLY* 4.9 9.8 - - - -
814A VAL* 3.8 22.8 - - - +
887A THR* 2.8 23.5 + - - +
888A SER* 1.3 82.8 + - - +
890A GLN* 1.3 54.8 + - - +
892A LYS* 3.8 9.0 - - - +
893A PHE* 2.9 30.0 + - - +
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Residues in contact with GLN 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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809A TRP* 4.6 6.0 - - + +
814A VAL* 4.2 17.3 - - + -
847A GLY* 3.5 26.2 - - - -
848A ARG* 4.0 11.7 - - - +
851A VAL* 3.8 19.5 - - + +
885A VAL* 3.7 5.3 - - + -
886A GLN* 2.8 32.6 + - - +
887A THR* 3.0 27.3 + - - +
889A SER* 1.3 82.3 + - - +
891A TYR* 1.3 56.8 + - - +
893A PHE* 3.3 4.3 + - - +
894A VAL* 3.0 33.4 + - - +
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Residues in contact with TYR 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A VAL* 3.6 24.2 + - + +
647A LEU* 4.7 7.2 - - + -
650A PHE* 3.5 56.3 - + + -
870A PRO* 3.6 15.8 - - + +
871A LEU* 3.1 33.2 + - - +
874A VAL* 3.7 27.8 - - + -
885A VAL* 3.8 8.0 - - + +
887A THR 3.0 13.8 + - - +
888A SER* 3.1 6.7 + - - +
890A GLN* 1.3 72.1 - - - +
892A LYS* 1.3 68.2 + - - +
894A VAL* 3.2 8.9 + - + +
895A CYS* 3.0 46.7 + - - -
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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
----------------------------------------------------------
647A LEU* 5.8 8.7 - - + -
888A SER 2.6 21.7 + - - +
889A SER* 3.8 7.9 - - - +
891A TYR* 1.3 74.7 - - - +
893A PHE* 1.3 62.9 + - - +
895A CYS* 3.3 7.8 + - - +
896A GLU* 3.2 49.8 + - + +
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Residues in contact with PHE 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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809A TRP* 4.1 10.5 - + - -
814A VAL* 3.9 21.8 - - + -
815A PRO* 3.7 43.5 - - + -
818A SER* 3.9 30.7 - - - -
821A PHE* 4.0 23.1 - + + -
851A VAL* 3.9 28.0 - - + -
855A MET* 5.5 0.9 - - + -
889A SER 2.9 18.5 + - - +
890A GLN 3.4 5.6 - - - +
892A LYS* 1.3 76.2 - - - +
894A VAL* 1.3 65.4 + - - +
896A GLU* 3.6 10.3 + - - +
897A ALA* 3.0 31.1 + - + +
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Residues in contact with VAL 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A VAL* 3.7 38.1 - - + +
854A THR* 3.3 33.7 - - + -
855A MET* 3.4 18.0 - - - +
870A PRO* 5.0 2.9 - - + -
874A VAL* 6.1 0.2 - - + -
885A VAL* 5.0 5.2 - - + -
890A GLN 3.0 21.0 + - - +
891A TYR* 3.4 14.8 - - + +
893A PHE* 1.3 77.1 - - - +
895A CYS* 1.3 62.2 + - - +
897A ALA 3.3 1.2 + - - -
898A ILE* 2.9 40.3 + - + +
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Residues in contact with CYS 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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646A VAL* 4.0 17.3 - - + -
870A PRO* 4.3 16.6 - - + -
891A TYR* 3.0 53.6 + - - +
892A LYS* 3.7 6.7 - - - +
894A VAL* 1.3 76.8 - - - +
896A GLU* 1.3 64.4 + - + +
898A ILE* 3.1 11.6 + - - +
899A LEU* 3.0 21.5 + - - +
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Residues in contact with GLU 896 (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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892A LYS* 3.2 44.0 + - + +
893A PHE* 4.0 9.2 - - - +
895A CYS* 1.3 77.0 - - + +
897A ALA* 1.3 57.8 + - - +
899A LEU* 3.2 8.8 + - - +
900A ARG* 2.9 30.0 + - - +
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Residues in contact with ALA 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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818A SER* 4.4 18.8 - - - -
822A LEU* 4.2 13.4 - - + +
855A MET* 3.9 17.9 - - + -
893A PHE* 3.0 27.1 + - + +
894A VAL 3.5 4.3 - - - +
896A GLU* 1.3 77.6 - - - +
898A ILE* 1.3 62.1 + - - +
900A ARG* 3.1 9.9 + - - +
901A VAL* 3.0 27.5 + - - +
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Residues in contact with ILE 898 (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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854A THR* 4.3 6.5 - - + -
855A MET* 3.4 20.0 - - + -
858A ALA* 3.5 21.5 - - + -
862A THR* 5.3 0.2 + - - -
868A ILE* 4.1 32.1 - - + -
870A PRO* 4.0 24.9 - - + -
894A VAL* 2.9 34.9 + - + +
895A CYS* 3.1 8.9 + - - +
897A ALA* 1.3 75.0 - - - +
899A LEU* 1.3 64.2 + - - +
901A VAL* 3.1 21.7 - - + +
902A TYR* 3.2 10.3 + - + +
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Residues in contact with LEU 899 (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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895A CYS 3.0 11.8 + - - +
896A GLU* 3.7 9.6 - - - +
898A ILE* 1.3 79.3 - - - +
900A ARG* 1.3 56.8 + - - +
902A TYR* 3.5 6.2 - - - +
903A GLU* 2.9 49.8 + - - +
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Residues in contact with ARG 900 (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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817A ASP* 3.4 14.1 + - - -
818A SER* 3.5 21.1 + - - +
819A SER* 3.1 30.2 + - - +
822A LEU* 4.6 9.9 - - + +
896A GLU 2.9 15.3 + - - +
897A ALA* 3.1 11.2 + - - +
899A LEU* 1.3 74.1 - - - +
901A VAL* 1.3 55.5 + - - +
903A GLU* 3.2 7.8 + - - +
904A GLU* 2.7 51.6 + - + +
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Residues in contact with VAL 901 (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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822A LEU* 3.7 33.4 - - + -
826A ASN* 5.8 1.1 - - - +
855A MET* 4.9 3.6 - - + -
858A ALA 5.4 2.0 - - - +
859A MET* 4.3 24.2 - - + -
862A THR* 4.2 25.5 - - + +
897A ALA 3.0 14.0 + - - +
898A ILE* 3.1 26.0 - - + +
900A ARG* 1.3 76.0 - - - +
902A TYR* 1.3 63.7 + - - +
904A GLU* 3.4 17.8 - - - -
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Residues in contact with TYR 902 (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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862A THR* 4.5 17.9 - - + +
868A ILE* 6.0 5.2 - - + -
898A ILE* 3.2 10.5 + - + +
899A LEU* 3.5 10.8 - - - +
901A VAL* 1.3 85.8 - - + +
903A GLU* 1.3 80.1 + - + +
904A GLU 4.1 3.5 - - - +
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Residues in contact with GLU 903 (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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899A LEU* 2.9 33.2 + - - +
900A ARG* 3.9 6.7 - - - +
902A TYR* 1.3 91.7 - - + +
904A GLU* 1.3 59.7 + - + +
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Residues in contact with GLU 904 (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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900A ARG* 2.7 35.2 + - + +
901A VAL* 3.4 17.0 - - - +
902A TYR 4.1 3.5 - - - +
903A GLU* 1.3 75.8 - - - +
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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