Contacts of the helix formed by residues 842 - 866 (chain A) in PDB entry 1NST
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 LEU 842 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839A GLU* 6.4 0.4 - - + -
840A MET 4.1 10.3 - - - +
841A ASP* 1.3 73.8 - - - +
843A ASP* 1.3 63.3 + - - +
845A ARG* 3.4 18.1 + - + +
846A ALA* 3.0 28.4 + - - +
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Residues in contact with ASP 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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731A HIS* 4.4 10.5 - - + +
841A ASP* 3.3 15.3 + - - +
842A LEU* 1.3 75.4 - - - +
844A SER* 1.3 61.4 + - - +
846A ALA* 3.4 5.5 + - - +
847A PHE* 2.8 30.9 + - - +
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Residues in contact with SER 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730A PHE* 4.3 15.8 - - - +
731A HIS* 2.9 39.6 + - - +
734A ILE* 4.0 10.3 - - - +
840A MET* 4.5 2.0 - - - -
841A ASP* 3.2 28.9 + - - +
842A LEU 3.3 0.2 - - - -
843A ASP* 1.3 76.3 - - - +
845A ARG* 1.3 65.5 + - - +
847A PHE* 3.3 1.8 + - - +
848A LEU* 3.0 31.3 + - - +
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Residues in contact with ARG 845 (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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707A ALA* 4.9 7.0 - - + +
708A ASP* 2.7 33.1 + - - -
839A GLU* 5.3 3.8 - - - +
840A MET* 3.4 58.7 + - - +
841A ASP 2.9 17.2 + - - +
842A LEU* 3.5 20.8 - - - +
844A SER* 1.3 76.7 - - - +
846A ALA* 1.3 53.3 + - - +
848A LEU* 3.0 8.6 + - - +
849A LYS* 2.8 37.8 + - + +
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Residues in contact with ALA 846 (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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842A LEU 3.0 14.1 + - - +
843A ASP* 3.7 6.3 - - - +
845A ARG* 1.3 81.1 - - - +
847A PHE* 1.3 62.8 + - - +
849A LYS* 3.0 21.4 + - - +
850A ASP* 3.1 18.4 + - - +
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Residues in contact with PHE 847 (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 HIS* 4.2 9.6 - + + -
734A ILE* 3.5 42.2 - - + -
735A THR* 3.7 26.2 - - + -
752A LEU* 5.9 0.9 - - + -
843A ASP 2.8 23.0 + - - +
844A SER* 3.4 6.5 - - - +
845A ARG 3.2 0.2 - - - -
846A ALA* 1.3 73.7 - - - +
848A LEU* 1.3 71.0 + - + +
850A ASP* 3.4 7.3 + - - +
851A TYR* 3.2 28.0 + + + +
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Residues in contact with LEU 848 (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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707A ALA* 3.7 34.3 - - + +
710A ALA* 5.0 1.8 - - + -
730A PHE* 3.9 31.9 - - + -
734A ILE* 3.9 11.9 - - + -
752A LEU* 3.8 26.9 - - + -
840A MET* 4.4 2.5 - - - -
844A SER 3.0 17.2 + - - +
845A ARG 3.0 7.9 + - - +
847A PHE* 1.3 88.9 - - + +
849A LYS* 1.3 67.4 + - - +
851A TYR* 3.2 8.8 + - + +
852A TYR* 3.1 38.3 + - + -
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Residues in contact with LYS 849 (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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705A ASN* 6.4 0.2 - - - +
707A ALA* 5.3 1.9 - - - +
845A ARG* 2.8 18.1 + - + +
846A ALA* 3.0 16.1 + - - +
848A LEU* 1.3 77.5 - - - +
850A ASP* 1.3 64.1 + - - +
852A TYR* 4.1 1.6 - - - +
853A ARG* 3.2 22.9 + - - +
876A GLU 4.3 3.6 + - - -
877A ASP* 3.3 56.2 + - - +
879A GLN 4.7 4.8 + - - -
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Residues in contact with ASP 850 (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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846A ALA* 3.1 12.9 + - - +
847A PHE* 3.6 11.2 - - - +
849A LYS* 1.3 79.3 - - - +
851A TYR* 1.3 64.0 + - - +
852A TYR 3.4 0.3 + - - -
853A ARG* 3.4 23.4 - - - +
854A ASP 4.8 0.3 + - - -
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Residues in contact with TYR 851 (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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752A LEU* 4.4 23.1 - - + +
756A TRP* 3.1 35.5 + - - -
847A PHE* 3.2 19.8 + + + +
848A LEU* 3.2 18.7 + - + +
850A ASP* 1.3 81.5 - - - +
852A TYR* 1.3 96.8 + + - +
854A ASP* 4.8 3.6 + - - +
855A HIS* 3.9 16.4 + + - -
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Residues in contact with TYR 852 (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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705A ASN* 5.5 0.2 - - - -
706A PRO* 3.4 40.8 + - + +
707A ALA* 3.9 9.0 - - + -
751A CYS 4.2 0.9 + - - -
752A LEU* 2.8 37.4 + - + +
755A GLY* 3.6 29.8 - - - -
756A TRP* 4.0 4.0 - + - -
848A LEU* 3.1 34.9 + - + +
849A LYS* 4.5 1.3 - - - +
851A TYR* 1.3 99.1 - + - +
853A ARG* 1.3 67.2 + - - +
854A ASP 3.1 2.9 - - - -
855A HIS* 2.7 22.9 + + + -
856A ASN* 2.7 43.1 + - - +
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Residues in contact with ARG 853 (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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849A LYS 3.2 14.7 + - - +
850A ASP* 3.4 20.5 + - - +
852A TYR* 1.3 75.1 - - - +
854A ASP* 1.3 65.5 + - - +
856A ASN* 3.3 9.4 + - - +
857A ILE* 2.9 53.7 + - + +
877A ASP* 5.0 4.3 - - - -
878A LEU* 4.6 3.6 - - + +
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Residues in contact with ASP 854 (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 ASP 4.8 0.2 + - - -
851A TYR 4.8 4.3 + - - +
852A TYR 2.9 1.4 + - - -
853A ARG* 1.3 80.8 + - - +
855A HIS* 1.3 69.5 + - + +
856A ASN 3.1 1.6 - - - -
857A ILE* 3.0 20.3 + - + +
858A GLU* 2.9 36.1 + - - +
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Residues in contact with HIS 855 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A GLY 4.9 1.1 - - - +
756A TRP* 3.3 68.1 + + + +
757A TYR 5.7 0.4 - - - +
758A ALA* 4.4 7.4 + - - +
759A THR* 4.9 6.0 + - - -
851A TYR* 3.9 27.3 + + - -
852A TYR* 2.7 27.4 + + + +
854A ASP* 1.3 76.7 + - + +
856A ASN* 1.3 61.4 + - - +
858A GLU* 3.3 6.9 + - - +
859A LEU* 2.9 28.2 + - - +
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Residues in contact with ASN 856 (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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705A ASN* 5.7 0.8 - - - +
706A PRO* 3.9 18.5 - - - +
755A GLY 5.4 1.2 - - - +
757A TYR* 5.4 2.3 - - - -
852A TYR* 2.7 34.5 + - - +
853A ARG 3.4 5.8 - - - +
855A HIS* 1.3 73.5 - - - +
857A ILE* 1.3 63.3 + - - +
859A LEU* 3.7 7.5 - - - +
860A SER* 3.1 24.4 + - - -
873A TRP* 4.0 24.1 - - - -
874A LEU* 3.7 11.1 - - + +
877A ASP* 2.9 39.1 + - - +
878A LEU* 4.0 4.6 - - + +
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Residues in contact with ILE 857 (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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853A ARG* 2.9 52.4 + - + +
854A ASP* 3.0 25.1 + - - +
856A ASN* 1.3 76.6 - - - +
858A GLU* 1.3 69.2 + - - +
860A SER* 3.3 10.1 + - - +
861A LYS* 3.2 41.8 + - + +
878A LEU* 4.5 14.8 - - + -
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Residues in contact with GLU 858 (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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758A ALA* 4.2 14.1 - - + -
854A ASP* 2.9 24.0 + - - +
855A HIS* 3.6 10.5 - - - +
857A ILE* 1.3 81.9 - - - +
859A LEU* 1.3 62.6 + - - +
861A LYS* 3.0 40.3 + - - +
862A LEU* 2.9 23.2 + - - +
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Residues in contact with LEU 859 (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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703A LEU* 4.0 12.3 - - + -
757A TYR* 4.0 16.6 - - + -
758A ALA* 3.8 27.3 - - + +
761A ILE* 3.9 19.3 - - + -
855A HIS 2.9 17.4 + - - +
856A ASN* 3.7 10.3 - - - +
858A GLU* 1.3 75.8 - - - +
860A SER* 1.3 57.3 + - - +
862A LEU* 3.1 5.0 + - + -
863A LEU* 2.9 70.6 + - + +
871A PRO* 4.9 0.2 - - + -
873A TRP* 4.8 9.2 - - + -
874A LEU* 3.6 21.5 - - + -
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Residues in contact with SER 860 (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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856A ASN 3.1 15.2 + - - -
857A ILE* 3.3 7.3 + - - +
859A LEU* 1.3 79.1 - - - +
861A LYS* 1.3 66.1 + - - +
864A TYR* 3.2 23.9 + - - +
870A LEU* 3.6 19.5 - - - +
874A LEU* 4.1 15.7 - - - +
878A LEU* 3.5 25.4 - - - +
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Residues in contact with LYS 861 (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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857A ILE* 3.2 28.9 + - - +
858A GLU* 3.0 42.4 + - - +
860A SER* 1.3 82.4 + - - +
862A LEU* 1.3 60.0 + - - +
864A TYR* 3.4 8.1 + - - +
865A LYS* 2.9 29.7 + - - +
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Residues in contact with LEU 862 (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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758A ALA* 3.5 40.2 - - + +
761A ILE* 3.8 14.6 - - + -
762A GLU* 3.6 32.3 - - + +
765A LEU* 3.8 23.3 - - + -
858A GLU 2.9 12.6 + - - +
859A LEU* 3.5 9.4 - - + +
861A LYS* 1.3 74.0 - - - +
863A LEU* 1.3 56.4 + - + +
865A LYS* 3.0 23.2 + - + +
866A MET* 2.7 45.8 + - - +
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Residues in contact with LEU 863 (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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761A ILE* 4.4 4.5 - - + -
775A VAL* 3.8 39.7 - - + -
859A LEU* 2.9 56.1 + - + +
862A LEU* 1.3 74.9 - - + +
864A TYR* 1.3 57.4 + - - +
866A MET* 2.7 28.9 + - - -
867A GLY 2.8 10.6 + - - -
868A GLN* 3.0 19.9 + - + +
869A THR 4.4 6.5 - - - +
870A LEU* 3.9 11.7 - - + -
871A PRO* 3.7 25.4 - - + -
874A LEU* 4.3 3.4 - - + -
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Residues in contact with TYR 864 (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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860A SER 3.2 17.7 + - - +
861A LYS* 3.5 8.1 - - - +
863A LEU* 1.3 76.8 - - - +
865A LYS* 1.3 61.3 + - - +
867A GLY* 3.0 18.9 + - - -
868A GLN 4.4 7.2 - - - -
870A LEU* 4.1 10.9 - - + +
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Residues in contact with LYS 865 (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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762A GLU* 5.1 8.0 + - - +
765A LEU* 5.0 12.0 - - + +
770A ALA* 5.5 1.4 - - - +
861A LYS 2.9 12.7 + - - +
862A LEU* 3.0 33.4 + - + +
864A TYR* 1.3 79.8 - - + +
866A MET* 1.3 62.5 + - + +
867A GLY 3.2 0.8 + - - -
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Residues in contact with MET 866 (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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761A ILE* 3.5 31.4 - - + -
765A LEU* 4.1 29.2 - - + -
770A ALA* 4.1 21.7 - - + +
773A ILE* 3.6 37.5 - - + -
775A VAL* 4.3 2.9 - - + -
862A LEU* 2.7 31.2 + - + +
863A LEU* 2.7 14.8 + - - +
865A LYS* 1.3 78.1 - - + +
867A GLY* 1.3 61.1 + - - +
868A GLN* 3.7 27.4 + - + +
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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
------------------------------------------------------------
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