Contacts of the helix formed by residues 820 - 844 (chain A) in PDB entry 5XJY
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 ASN 820 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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789A PHE 6.1 0.3 - - - -
790A GLY* 5.5 0.9 - - - -
793A TYR* 3.9 24.2 - - + +
819A PHE* 1.3 86.0 - - + +
821A LEU* 1.3 65.7 + - - +
822A THR* 3.2 11.7 - - - +
823A THR* 3.3 15.2 + - - +
824A SER* 3.6 4.9 + - - -
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Residues in contact with LEU 821 (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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721A PHE* 5.6 2.8 - - + -
790A GLY* 5.4 3.6 - - - +
793A TYR* 3.7 35.2 - - + -
794A PHE* 5.6 5.8 - - + -
820A ASN* 1.3 74.9 - - - +
822A THR* 1.3 59.5 + - - +
824A SER* 2.9 24.8 + - - -
825A VAL* 2.9 16.7 + - - +
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Residues in contact with THR 822 (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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820A ASN* 3.2 7.7 - - - +
821A LEU* 1.3 78.4 - - - +
823A THR* 1.3 55.9 + - - +
825A VAL* 4.4 4.7 - - - +
826A SER* 2.9 31.0 + - - -
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Residues in contact with THR 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775A LEU* 5.0 6.7 - - - +
776A LYS* 2.8 38.1 + - - +
819A PHE 3.6 22.9 - - - -
820A ASN* 3.3 14.0 + - - +
821A LEU 3.2 0.6 - - - -
822A THR* 1.3 78.7 - - - +
824A SER* 1.3 58.0 + - - +
826A SER* 4.3 2.2 - - - -
827A MET* 2.9 19.1 + - - +
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Residues in contact with SER 824 (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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721A PHE* 4.3 12.3 - - - -
786A ALA* 3.5 29.5 - - - +
789A PHE* 5.6 2.2 - - - -
790A GLY* 3.7 25.4 - - - -
820A ASN 3.6 2.3 + - - -
821A LEU* 2.9 13.6 + - - -
823A THR* 1.3 79.4 - - - +
825A VAL* 1.3 58.1 + - - +
827A MET* 3.9 1.0 - - - +
828A MET* 2.9 29.7 + - - +
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Residues in contact with VAL 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A PHE* 4.8 11.6 - - + -
724A VAL* 5.1 12.9 - - + +
821A LEU 2.9 14.0 + - - +
822A THR* 4.4 5.2 - - - +
824A SER* 1.3 77.1 - - - +
826A SER* 1.3 58.0 + - - +
828A MET* 3.6 7.3 - - - +
829A LEU* 2.9 30.7 + - - +
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Residues in contact with SER 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A LYS* 4.6 4.0 - - - -
822A THR 2.9 21.6 + - - -
823A THR* 3.8 5.6 - - - -
824A SER 3.2 0.2 - - - -
825A VAL* 1.3 75.4 - - - +
827A MET* 1.3 60.2 + - - +
829A LEU* 3.3 3.1 + - - +
830A PHE* 2.9 32.7 + - - +
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Residues in contact with MET 827 (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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775A LEU* 5.9 0.7 - - + -
776A LYS* 3.7 14.5 - - + +
779A ALA* 3.8 32.0 - - + +
780A SER* 5.0 2.3 - - - +
786A ALA* 4.0 12.3 - - + -
823A THR 2.9 17.9 + - - +
826A SER* 1.3 73.9 - - - +
828A MET* 1.3 53.3 + - - +
830A PHE* 4.7 3.6 - - - +
831A ASP* 2.8 39.1 + - - +
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Residues in contact with MET 828 (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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721A PHE* 5.7 3.4 - - + -
724A VAL* 3.8 24.5 - - + -
725A PHE* 6.1 0.7 - - - -
728A VAL* 3.4 23.9 - - + +
783A SER* 5.9 1.3 - - - +
786A ALA* 4.4 8.9 - - + +
824A SER 2.9 20.2 + - - +
825A VAL* 3.6 5.8 - - - +
826A SER 3.2 0.2 - - - -
827A MET* 1.3 78.3 - - - +
829A LEU* 1.3 57.4 + - - +
831A ASP* 3.3 4.0 + - - +
832A THR 2.9 22.9 + - - -
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Residues in contact with LEU 829 (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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724A VAL* 5.2 3.8 - - + +
728A VAL* 5.2 1.1 - - - -
825A VAL 2.9 19.1 + - - +
826A SER* 4.0 3.6 - - - +
828A MET* 1.3 73.2 - - - +
830A PHE* 1.3 60.5 + - - +
832A THR* 3.1 8.5 + - - -
833A PHE* 3.0 26.5 + - - +
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Residues in contact with PHE 830 (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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780A SER* 5.6 7.8 + - - +
826A SER 2.9 18.1 + - - +
827A MET* 4.6 3.6 - - - +
829A LEU* 1.3 77.8 - - - +
831A ASP* 1.3 58.0 + - - +
833A PHE* 3.9 6.4 - - - +
834A LEU* 3.0 29.1 + - - +
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Residues in contact with ASP 831 (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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728A VAL* 4.5 10.3 - - + -
732A GLN* 4.2 7.1 + - - +
779A ALA 4.2 14.1 - - - +
780A SER* 4.3 16.7 - - - +
781A LEU 5.9 0.2 - - - -
782A LEU 4.9 6.3 - - - +
783A SER* 4.9 7.4 - - - +
827A MET 2.8 23.9 + - - +
828A MET* 3.6 5.8 - - - +
830A PHE* 1.3 76.0 - - - +
832A THR* 1.3 58.7 + - - +
834A LEU* 3.6 2.5 + - - +
835A TYR* 2.9 27.7 + - - +
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Residues in contact with THR 832 (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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727A VAL* 5.0 5.2 - - - -
728A VAL* 3.9 21.1 - - - +
731A LEU* 3.4 29.0 - - - +
828A MET 2.9 14.7 + - - -
829A LEU* 3.1 11.0 + - - -
831A ASP* 1.3 75.2 - - - +
833A PHE* 1.3 60.8 + - - +
835A TYR* 3.1 7.8 + - - +
836A GLY* 2.9 23.4 + - - -
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Residues in contact with PHE 833 (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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731A LEU* 5.6 0.2 - - - -
829A LEU 3.0 15.9 + - - +
830A PHE* 3.9 7.2 - - - +
831A ASP 3.4 0.2 - - - -
832A THR* 1.3 75.3 - - - +
834A LEU* 1.3 58.5 + - - +
836A GLY* 3.2 2.4 + - - -
837A VAL* 3.0 27.7 + - - +
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Residues in contact with LEU 834 (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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780A SER* 4.9 13.0 - - - +
830A PHE 3.0 18.3 + - - +
831A ASP* 3.9 6.1 - - - +
833A PHE* 1.3 75.7 - - - +
835A TYR* 1.3 56.9 + - - +
837A VAL* 3.5 7.9 + - - +
838A MET* 2.9 26.9 + - - +
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Residues in contact with TYR 835 (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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728A VAL* 6.1 0.4 - - + -
731A LEU* 4.0 25.0 - - + +
732A GLN* 3.6 20.6 - - - +
735A LEU* 3.8 21.4 - - + +
831A ASP 2.9 20.1 + - - +
832A THR* 3.1 6.9 + - - +
834A LEU* 1.3 76.8 - - - +
836A GLY* 1.3 56.6 + - - +
838A MET* 3.3 4.7 + - - +
839A THR* 2.9 24.3 + - - -
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Residues in contact with GLY 836 (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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731A LEU* 4.9 11.2 - - - +
832A THR 2.9 13.2 + - - -
833A PHE* 3.2 4.6 + - - -
835A TYR* 1.3 73.0 - - - +
837A VAL* 1.3 61.8 + - - +
838A MET 3.2 0.2 - - - -
839A THR* 3.0 22.5 + - - -
840A TRP* 3.0 16.5 + - - +
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Residues in contact with VAL 837 (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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833A PHE 3.0 15.8 + - - +
834A LEU* 3.8 8.7 - - - +
835A TYR 3.4 0.2 - - - -
836A GLY* 1.3 75.8 - - - +
838A MET* 1.3 58.1 + - - +
840A TRP* 4.5 2.9 - - - +
841A TYR* 2.9 34.9 + - + +
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Residues in contact with MET 838 (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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735A LEU* 3.9 24.9 - - + +
738A THR* 5.1 0.2 - - - +
834A LEU 2.9 15.3 + - - +
835A TYR 3.4 9.6 - - - +
836A GLY 3.2 0.2 - - - -
837A VAL* 1.3 76.0 - - - +
839A THR* 1.3 57.5 + - - +
841A TYR* 4.6 2.7 - - - -
842A ILE* 2.8 34.8 + - + +
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Residues in contact with THR 839 (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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682A TRP* 5.6 14.9 - - - -
731A LEU* 5.8 3.4 - - - -
734A PHE* 5.0 20.0 - - - -
735A LEU* 5.6 3.4 - - - +
738A THR* 5.1 9.1 + - - +
835A TYR 2.9 13.5 + - - -
836A GLY* 3.0 14.3 + - - -
838A MET* 1.3 76.5 - - - +
840A TRP* 1.3 59.4 + - - +
842A ILE* 3.7 2.1 - - - +
843A GLU* 2.9 28.5 + - - +
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Residues in contact with TRP 840 (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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836A GLY 3.0 13.5 + - - +
837A VAL* 4.5 2.7 - - - +
839A THR* 1.3 75.7 - - - +
841A TYR* 1.3 59.1 + - - +
843A GLU* 2.9 23.1 + - - +
844A ALA* 3.0 16.3 + - - +
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Residues in contact with TYR 841 (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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837A VAL 2.9 21.5 + - - +
838A MET* 3.9 2.9 - - - -
840A TRP* 1.3 76.1 - - - +
842A ILE* 1.3 57.0 + - - +
844A ALA* 4.4 5.5 - - - +
845A VAL* 3.8 15.4 + - - +
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Residues in contact with ILE 842 (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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738A THR* 3.9 28.9 + - + +
739A LEU* 4.7 11.8 - - + +
838A MET* 2.8 24.0 + - + +
841A TYR* 1.3 76.4 - - - +
843A GLU* 1.3 63.1 + - - +
844A ALA 3.5 0.4 - - - -
845A VAL* 3.7 11.9 + - - +
846A PHE* 3.8 13.7 + - - +
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Residues in contact with GLU 843 (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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668A LYS* 6.2 1.1 - - - +
678A ASN* 6.1 3.1 - - - +
682A TRP* 5.4 14.8 - - + +
738A THR* 4.6 9.0 - - - +
839A THR 2.9 17.5 + - - +
840A TRP* 2.9 10.4 + - - +
842A ILE* 1.3 78.9 - - - +
844A ALA* 1.3 58.3 + - - +
845A VAL 3.2 5.4 + - - -
846A PHE 3.9 12.7 + - - -
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Residues in contact with ALA 844 (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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840A TRP 3.0 12.9 + - - +
841A TYR* 4.4 4.2 - - - +
842A ILE 3.5 0.2 - - - -
843A GLU* 1.3 75.3 - - - +
845A VAL* 1.3 57.3 + - - +
846A PHE 3.7 0.4 - - - -
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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