Contacts of the helix formed by residues 2868 - 2897 (chain B) in PDB entry 6X34
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 SER2868 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2866B THR 4.1 1.2 + - - -
2867B LEU* 1.3 77.0 - - - +
2869B ARG* 1.3 62.1 + - - +
2870B GLU* 3.3 8.1 - - - -
2871B LEU* 3.9 10.6 - - - +
2872B GLN* 3.0 27.0 + - - +
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Residues in contact with ARG2869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2868B SER* 1.3 76.2 - - - +
2870B GLU* 1.3 63.7 + - - +
2872B GLN* 3.9 5.1 - - - +
2873B ALA* 3.0 25.3 + - - +
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Residues in contact with GLU2870 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2868B SER* 3.3 6.0 - - - -
2869B ARG* 1.3 79.0 - - - +
2871B LEU* 1.3 56.9 + - - +
2873B ALA* 3.4 5.3 + - - +
2874B MET* 3.1 28.8 + - - +
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Residues in contact with LEU2871 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2867B LEU* 4.2 11.7 - - + -
2868B SER* 3.5 21.2 + - - +
2869B ARG 3.4 0.6 - - - -
2870B GLU* 1.3 77.9 - - - +
2872B GLN* 1.3 57.9 + - - +
2874B MET* 3.5 6.4 + - - +
2875B ALA* 3.0 27.7 + - - +
2927B LEU* 5.3 15.1 - - + +
2937B VAL 6.0 1.8 - - - +
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Residues in contact with GLN2872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2867B LEU* 4.7 9.3 - - + +
2868B SER 3.0 19.9 + - - +
2869B ARG* 3.9 6.3 - - - +
2871B LEU* 1.3 76.7 - - - +
2873B ALA* 1.3 61.9 + - - +
2875B ALA* 3.4 14.4 + - - +
2876B GLU* 3.5 10.4 + - - +
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Residues in contact with ALA2873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2869B ARG 3.0 17.5 + - - +
2870B GLU* 3.9 5.6 - - - +
2871B LEU 3.3 0.2 - - - -
2872B GLN* 1.3 78.5 - - - +
2874B MET* 1.3 60.6 + - - +
2876B GLU* 3.3 19.5 + - - +
2877B GLN* 3.9 4.3 + - - +
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Residues in contact with MET2874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2870B GLU 3.1 17.2 + - - +
2871B LEU* 3.9 7.2 - - - +
2873B ALA* 1.3 74.5 - - - +
2875B ALA* 1.3 64.4 + - - +
2877B GLN* 3.3 16.9 + - - +
2878B LEU* 3.5 10.7 + - - +
2937B VAL* 6.5 1.3 - - + -
2939B ARG* 6.2 3.8 - - + -
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Residues in contact with ALA2875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2871B LEU 3.0 17.9 + - - +
2872B GLN* 3.6 9.6 - - - +
2873B ALA 3.2 0.4 - - - -
2874B MET* 1.3 77.4 - - - +
2876B GLU* 1.3 60.1 + - - +
2878B LEU* 3.4 2.8 + - - +
2879B ALA* 2.9 26.7 + - - +
2920B ARG* 5.6 1.7 - - + +
2923B ALA* 3.4 30.5 - - + +
2924B GLN* 4.9 5.8 - - + +
2927B LEU* 5.6 4.3 - - + -
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Residues in contact with GLU2876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2872B GLN 3.5 7.9 + - - +
2873B ALA* 3.3 12.9 + - - +
2874B MET 3.2 1.0 - - - -
2875B ALA* 1.3 79.0 - - - +
2877B GLN* 1.3 56.2 + - - +
2879B ALA* 3.9 5.5 - - - +
2880B GLU* 2.9 30.1 + - - +
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Residues in contact with GLN2877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2873B ALA 3.9 4.2 + - - +
2874B MET* 3.3 12.0 + - - +
2875B ALA 3.3 0.8 - - - -
2876B GLU* 1.3 79.4 - - - +
2878B LEU* 1.3 58.0 + - - +
2880B GLU* 3.4 5.1 + - - +
2881B ASN* 3.0 28.4 + - - +
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Residues in contact with LEU2878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2812B SER* 6.3 2.9 - - - -
2874B MET 3.5 8.8 + - - +
2875B ALA* 3.4 8.4 + - - +
2877B GLN* 1.3 74.9 - - - +
2879B ALA* 1.3 66.0 + - - +
2881B ASN* 3.4 7.6 + - - +
2882B TYR* 3.2 20.8 + - - +
2923B ALA* 3.9 17.5 - - + +
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Residues in contact with ALA2879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2875B ALA 2.9 17.7 + - - +
2876B GLU* 3.9 7.2 - - - +
2878B LEU* 1.3 77.7 - - - +
2880B GLU* 1.3 60.7 + - - +
2882B TYR* 3.4 2.9 + - - +
2883B HIS* 3.3 17.3 + - - +
2916B LYS 5.5 0.2 - - - +
2919B ASP* 3.4 49.1 - - + +
2920B ARG* 3.9 9.4 - - + +
2923B ALA* 3.9 2.4 - - + +
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Residues in contact with GLU2880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2876B GLU 2.9 18.7 + - - +
2877B GLN* 3.9 5.6 - - - +
2878B LEU 3.3 0.2 - - - -
2879B ALA* 1.3 74.5 - - - +
2881B ASN* 1.3 60.4 + - - +
2883B HIS* 3.4 3.8 + - - +
2884B ASN* 3.0 28.4 + - - +
2908B TYR* 4.1 26.7 - - + +
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Residues in contact with ASN2881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2739B PRO* 5.1 3.8 - - - +
2740B VAL* 5.7 10.1 - - + +
2815B ALA* 5.2 14.8 - - + -
2877B GLN 3.0 17.9 + - - +
2878B LEU* 3.7 7.4 - - - +
2879B ALA 3.3 0.4 - - - -
2880B GLU* 1.3 75.0 - - - +
2882B TYR* 1.3 59.9 + - - +
2884B ASN* 3.4 6.8 + - - +
2885B THR* 2.9 29.3 + - - -
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Residues in contact with TYR2882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2878B LEU 3.2 11.2 + - - +
2879B ALA* 3.7 9.6 - - - +
2880B GLU 3.3 0.4 - - - -
2881B ASN* 1.3 78.3 - - - +
2883B HIS* 1.3 58.0 + - - +
2885B THR* 3.4 5.7 + - - -
2886B TRP* 3.0 31.0 + - - +
2919B ASP* 4.8 11.4 - - + +
2922B LYS* 5.8 6.3 - - + -
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Residues in contact with HIS2883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2879B ALA 3.3 11.2 + - - +
2880B GLU* 3.8 10.1 - - - +
2881B ASN 3.3 0.4 - - - -
2882B TYR* 1.3 78.6 - - - +
2884B ASN* 1.3 53.6 + - - +
2886B TRP* 3.8 3.9 - - - +
2887B GLY* 2.7 32.2 + - - -
2908B TYR* 5.0 12.3 - - + -
2919B ASP* 5.1 7.3 - - + +
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Residues in contact with ASN2884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2737B PRO* 3.4 16.4 - - + +
2738B ARG 4.1 24.2 - - - +
2739B PRO* 4.2 13.7 - - + +
2880B GLU 3.0 16.7 + - - +
2881B ASN* 3.8 6.5 - - - +
2883B HIS* 1.3 73.4 - - - +
2885B THR* 1.3 61.3 + - - +
2888B ARG* 3.0 26.3 + - - +
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Residues in contact with THR2885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2739B PRO* 4.1 16.3 - - - +
2881B ASN 2.9 17.2 + - - -
2882B TYR* 3.8 6.5 - - - -
2884B ASN* 1.3 78.3 - - - +
2886B TRP* 1.3 60.8 + - - +
2888B ARG* 3.5 3.3 + - - +
2889B LYS* 3.2 22.5 + - - +
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Residues in contact with TRP2886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2882B TYR 3.0 18.5 + - - +
2883B HIS* 4.2 3.6 - - - +
2885B THR* 1.3 75.7 - - - +
2887B GLY* 1.3 58.6 + - - +
2889B LYS* 3.5 5.6 + - - +
2890B LYS* 3.0 30.1 + - - +
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Residues in contact with GLY2887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2737B PRO* 4.3 9.0 - - - -
2883B HIS 2.7 23.4 + - - -
2884B ASN 4.0 0.9 - - - -
2885B THR 3.3 0.2 - - - -
2886B TRP* 1.3 75.0 - - - +
2888B ARG* 1.3 59.5 + - - +
2890B LYS* 3.5 5.1 + - - +
2891B LYS* 3.2 23.2 + - - +
2904B LEU 5.9 2.5 - - - -
2905B LEU* 6.1 5.1 - - - +
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Residues in contact with ARG2888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2737B PRO* 3.9 17.4 - - + +
2739B PRO* 5.3 6.7 - - + -
2884B ASN 3.0 18.3 + - - +
2885B THR* 3.9 4.9 - - - +
2886B TRP 3.3 0.2 - - - -
2887B GLY* 1.3 75.4 - - - +
2889B LYS* 1.3 63.7 + - - +
2891B LYS* 3.5 6.8 + - - +
2892B GLN* 3.3 20.8 + - - +
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Residues in contact with LYS2889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2885B THR 3.2 16.9 + - - +
2886B TRP* 3.5 6.0 + - - +
2888B ARG* 1.3 74.6 - - - +
2890B LYS* 1.3 59.5 + - - +
2892B GLN* 3.5 4.6 + - - +
2893B GLU* 3.0 29.5 + - - +
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Residues in contact with LYS2890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2886B TRP 3.0 18.3 + - - +
2887B GLY* 3.9 6.3 - - - +
2888B ARG 3.3 0.2 - - - -
2889B LYS* 1.3 75.0 - - - +
2891B LYS* 1.3 60.3 + - - +
2893B GLU* 3.9 5.2 - - - +
2894B LEU* 3.0 31.2 + - - +
2902B HIS* 5.8 7.6 - - + -
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Residues in contact with LYS2891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2887B GLY 3.2 16.8 + - - +
2888B ARG* 3.8 7.2 - - - +
2889B LYS 3.3 0.4 - - - -
2890B LYS* 1.3 77.5 - - - +
2892B GLN* 1.3 60.7 + - - +
2894B LEU* 4.1 3.9 - - - +
2895B GLU* 3.2 23.9 + - - +
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Residues in contact with GLN2892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2888B ARG 3.3 13.8 + - - +
2889B LYS* 4.1 5.2 - - - +
2890B LYS 3.3 0.2 - - - -
2891B LYS* 1.3 77.6 - - - +
2893B GLU* 1.3 64.6 + - - +
2895B GLU* 4.1 4.4 - - - +
2896B ALA* 3.2 24.4 + - - +
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Residues in contact with GLU2893 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2889B LYS 3.0 18.8 + - - +
2890B LYS* 4.0 6.3 - - - +
2892B GLN* 1.3 76.1 - - - +
2894B LEU* 1.3 64.5 + - - +
2896B ALA* 3.5 5.7 + - - +
2897B LYS* 3.4 21.5 + - - +
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Residues in contact with LEU2894 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2890B LYS 3.0 18.6 + - - +
2891B LYS* 4.1 5.2 - - - +
2893B GLU* 1.3 75.7 - - - +
2895B GLU* 1.3 62.3 + - - +
2897B LYS* 3.2 11.2 + - - +
2898B GLY 3.5 0.5 + - - -
2899B GLY* 2.8 38.6 + - - +
2900B GLY* 4.9 10.3 - - - +
2901B THR* 5.4 3.4 - - - +
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Residues in contact with GLU2895 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2891B LYS 3.2 16.8 + - - +
2892B GLN* 4.1 5.2 - - - +
2894B LEU* 1.3 77.2 - - - +
2896B ALA* 1.3 61.1 + - - +
2897B LYS 3.4 0.7 + - - -
2898B GLY* 3.4 9.7 + - - -
2899B GLY* 3.9 12.2 + - - +
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Residues in contact with ALA2896 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2892B GLN 3.2 18.4 + - - +
2893B GLU* 3.9 7.2 - - - +
2894B LEU 3.3 0.6 - - - -
2895B GLU* 1.3 76.3 - - - +
2897B LYS* 1.3 58.3 + - - +
2898B GLY 3.4 0.8 + - - -
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Residues in contact with LYS2897 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2893B GLU 3.4 13.9 + - - +
2894B LEU* 3.2 8.6 + - - +
2895B GLU 3.2 0.8 - - - -
2896B ALA* 1.3 77.1 - - - +
2898B GLY* 1.3 56.2 + - - +
2899B GLY 3.7 3.7 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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