Contacts of the helix formed by residues 2868 - 2897 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2866H THR 4.1 1.8 + - - -
2867H LEU* 1.3 77.4 - - - +
2869H ARG* 1.3 63.0 + - - +
2870H GLU* 3.3 8.3 - - - -
2871H LEU* 3.9 10.3 - - - +
2872H GLN* 3.0 26.5 + - - +
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Residues in contact with ARG2869 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2868H SER* 1.3 76.2 - - - +
2870H GLU* 1.3 61.6 + - - +
2872H GLN* 3.5 5.3 + - - +
2873H ALA* 3.0 25.6 + - - +
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Residues in contact with GLU2870 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2868H SER* 3.3 5.1 - - - -
2869H ARG* 1.3 79.3 - - - +
2871H LEU* 1.3 56.6 + - - +
2873H ALA* 3.4 5.3 + - - +
2874H MET* 3.1 28.2 + - - +
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Residues in contact with LEU2871 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2867H LEU* 4.2 12.3 - - + -
2868H SER* 3.5 20.9 + - - +
2870H GLU* 1.3 78.3 - - - +
2872H GLN* 1.3 58.1 + - - +
2874H MET* 3.5 5.8 + - - +
2875H ALA* 3.0 28.1 + - - +
2927H LEU* 5.3 14.4 - - + +
2937H VAL 6.0 1.8 - - - +
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Residues in contact with GLN2872 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2867H LEU* 4.7 9.8 - - + +
2868H SER 3.0 18.6 + - - +
2869H ARG* 3.9 6.7 - - - +
2871H LEU* 1.3 76.1 - - - +
2873H ALA* 1.3 62.7 + - - +
2875H ALA* 3.4 15.1 + - - +
2876H GLU* 3.5 10.6 + - - +
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Residues in contact with ALA2873 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2869H ARG 3.0 17.2 + - - +
2870H GLU* 3.9 6.1 - - - +
2872H GLN* 1.3 77.7 - - - +
2874H MET* 1.3 60.7 + - - +
2876H GLU* 3.3 20.0 + - - +
2877H GLN* 3.9 4.2 + - - +
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Residues in contact with MET2874 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2870H GLU 3.1 16.8 + - - +
2871H LEU* 3.9 7.0 - - - +
2872H GLN 3.3 0.2 - - - -
2873H ALA* 1.3 74.9 - - - +
2875H ALA* 1.3 63.5 + - - +
2877H GLN* 3.3 16.8 + - - +
2878H LEU* 3.5 10.9 + - - +
2937H VAL* 6.5 1.3 - - + -
2939H ARG* 6.2 3.6 - - + -
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Residues in contact with ALA2875 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2871H LEU 3.0 17.9 + - - +
2872H GLN* 3.6 10.3 - - - +
2873H ALA 3.2 0.6 - - - -
2874H MET* 1.3 75.4 - - - +
2876H GLU* 1.3 59.9 + - - +
2878H LEU* 3.4 2.5 + - - +
2879H ALA* 2.9 27.1 + - - +
2920H ARG* 5.6 1.5 - - - +
2923H ALA* 3.4 31.1 - - + +
2924H GLN* 4.9 5.6 - - + +
2927H LEU* 5.6 4.5 - - + -
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Residues in contact with GLU2876 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2872H GLN 3.5 8.0 + - - +
2873H ALA* 3.3 13.1 + - - +
2874H MET 3.2 0.6 - - - -
2875H ALA* 1.3 78.8 - - - +
2877H GLN* 1.3 56.8 + - - +
2879H ALA* 3.5 6.2 + - - +
2880H GLU* 2.9 29.6 + - - +
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Residues in contact with GLN2877 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2873H ALA 3.9 4.2 + - - +
2874H MET* 3.3 12.2 + - - +
2875H ALA 3.3 0.6 - - - -
2876H GLU* 1.3 79.0 - - - +
2878H LEU* 1.3 57.7 + - - +
2880H GLU* 3.4 5.9 + - - +
2881H ASN* 3.0 27.5 + - - +
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Residues in contact with LEU2878 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2812H SER* 6.3 2.9 - - - -
2874H MET 3.5 8.2 + - - +
2875H ALA* 3.4 9.3 + - - +
2876H GLU 3.3 0.2 - - - -
2877H GLN* 1.3 76.4 - - - +
2879H ALA* 1.3 65.3 + - - +
2881H ASN* 3.4 7.7 + - - +
2882H TYR* 3.2 20.8 + - - +
2923H ALA* 3.9 16.8 - - + -
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Residues in contact with ALA2879 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2875H ALA 2.9 18.5 + - - +
2876H GLU* 3.9 7.0 - - - +
2878H LEU* 1.3 78.4 - - - +
2880H GLU* 1.3 61.0 + - - +
2882H TYR* 3.4 2.9 + - - +
2883H HIS* 3.3 17.2 + - - +
2916H LYS 5.5 0.2 - - - +
2919H ASP* 3.4 48.4 - - + +
2920H ARG* 3.9 9.9 - - + +
2923H ALA* 3.9 1.3 - - + +
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Residues in contact with GLU2880 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2876H GLU 2.9 18.5 + - - +
2877H GLN* 3.9 6.5 - - - +
2879H ALA* 1.3 74.7 - - - +
2881H ASN* 1.3 60.7 + - - +
2883H HIS* 3.4 4.0 + - - +
2884H ASN* 3.0 27.8 + - - +
2908H TYR* 4.1 27.9 - - + +
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Residues in contact with ASN2881 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2739H PRO* 5.1 3.4 - - - +
2740H VAL* 5.7 10.1 - - + +
2815H ALA* 5.2 14.8 - - + -
2877H GLN 3.0 17.4 + - - +
2878H LEU* 3.7 8.5 - - - +
2879H ALA 3.3 0.4 - - - -
2880H GLU* 1.3 75.7 - - - +
2882H TYR* 1.3 58.9 + - - +
2884H ASN* 3.4 6.2 + - - +
2885H THR* 2.9 29.1 + - - -
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Residues in contact with TYR2882 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2878H LEU 3.2 10.3 + - - +
2879H ALA* 3.7 10.5 - - - +
2880H GLU 3.3 0.4 - - - -
2881H ASN* 1.3 79.5 - - - +
2883H HIS* 1.3 57.4 + - - +
2885H THR* 3.8 4.5 - - - -
2886H TRP* 3.0 30.8 + - - +
2919H ASP* 4.8 11.0 - - + +
2922H LYS* 5.8 6.1 - - + -
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Residues in contact with HIS2883 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2879H ALA 3.3 10.4 + - - +
2880H GLU* 3.8 9.2 - - - +
2881H ASN 3.3 0.4 - - - -
2882H TYR* 1.3 79.0 - - - +
2884H ASN* 1.3 53.9 + - - +
2886H TRP* 4.2 3.5 - - - +
2887H GLY* 2.7 32.4 + - - -
2908H TYR* 5.0 12.8 - - + +
2919H ASP* 5.1 7.7 - - + +
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Residues in contact with ASN2884 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2737H PRO* 3.4 17.1 - - + +
2738H ARG 4.1 24.7 - - - +
2739H PRO* 4.2 13.7 - - + +
2880H GLU 3.0 17.4 + - - +
2881H ASN* 3.8 6.7 - - - +
2882H TYR 3.3 0.2 - - - -
2883H HIS* 1.3 73.5 - - - +
2885H THR* 1.3 60.1 + - - +
2888H ARG* 3.0 26.7 + - - +
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Residues in contact with THR2885 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2739H PRO* 4.1 16.5 - - - +
2881H ASN 2.9 17.2 + - - -
2882H TYR* 3.8 6.3 - - - -
2883H HIS 3.3 0.2 - - - -
2884H ASN* 1.3 77.9 - - - +
2886H TRP* 1.3 61.6 + - - +
2888H ARG* 3.9 2.8 - - - +
2889H LYS* 3.2 22.9 + - - +
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Residues in contact with TRP2886 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2882H TYR 3.0 17.7 + - - +
2883H HIS* 4.2 3.8 - - - +
2885H THR* 1.3 75.8 - - - +
2887H GLY* 1.3 59.5 + - - +
2889H LYS* 3.5 5.0 + - - +
2890H LYS* 3.0 30.4 + - - +
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Residues in contact with GLY2887 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2737H PRO* 4.3 8.7 - - - -
2883H HIS 2.7 23.8 + - - -
2884H ASN 4.0 0.4 - - - -
2886H TRP* 1.3 74.7 - - - +
2888H ARG* 1.3 60.4 + - - +
2890H LYS* 3.5 5.9 + - - +
2891H LYS* 3.2 22.5 + - - +
2904H LEU 5.9 2.0 - - - -
2905H LEU* 6.1 6.1 - - - +
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Residues in contact with ARG2888 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2737H PRO* 3.9 16.9 - - + +
2739H PRO* 5.3 6.7 - - + -
2884H ASN 3.0 18.8 + - - +
2885H THR* 3.9 4.9 - - - +
2886H TRP 3.3 0.2 - - - -
2887H GLY* 1.3 75.1 - - - +
2889H LYS* 1.3 62.4 + - - +
2891H LYS* 3.5 6.4 + - - +
2892H GLN* 3.3 21.1 + - - +
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Residues in contact with LYS2889 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2885H THR 3.2 17.0 + - - +
2886H TRP* 4.0 6.3 - - - +
2887H GLY 3.3 0.2 - - - -
2888H ARG* 1.3 74.5 - - - +
2890H LYS* 1.3 60.5 + - - +
2892H GLN* 3.5 5.0 + - - +
2893H GLU* 3.0 29.7 + - - +
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Residues in contact with LYS2890 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2886H TRP 3.0 18.4 + - - +
2887H GLY* 3.9 7.4 - - - +
2888H ARG 3.3 0.2 - - - -
2889H LYS* 1.3 74.7 - - - +
2891H LYS* 1.3 60.7 + - - +
2893H GLU* 4.0 5.6 - - - +
2894H LEU* 3.0 30.8 + - - +
2902H HIS* 5.8 7.2 - - + -
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Residues in contact with LYS2891 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2887H GLY 3.2 16.5 + - - +
2888H ARG* 3.8 7.4 - - - +
2889H LYS 3.3 0.6 - - - -
2890H LYS* 1.3 78.1 - - - +
2892H GLN* 1.3 59.5 + - - +
2894H LEU* 4.1 4.3 - - - +
2895H GLU* 3.2 23.7 + - - +
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Residues in contact with GLN2892 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2888H ARG 3.3 13.5 + - - +
2889H LYS* 4.1 5.2 - - - +
2890H LYS 3.3 0.2 - - - -
2891H LYS* 1.3 77.0 - - - +
2893H GLU* 1.3 62.6 + - - +
2895H GLU* 4.1 4.4 - - - +
2896H ALA* 3.2 23.7 + - - +
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Residues in contact with GLU2893 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2889H LYS 3.0 18.6 + - - +
2890H LYS* 4.0 6.3 - - - +
2892H GLN* 1.3 76.3 - - - +
2894H LEU* 1.3 63.9 + - - +
2896H ALA* 3.5 6.5 + - - +
2897H LYS* 3.4 22.0 + - - +
----------------------------------------------------------
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Residues in contact with LEU2894 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2890H LYS 3.0 18.5 + - - +
2891H LYS* 4.1 4.7 - - - +
2892H GLN 3.4 0.2 - - - -
2893H GLU* 1.3 75.9 - - - +
2895H GLU* 1.3 63.2 + - - +
2897H LYS* 3.2 11.4 + - - +
2898H GLY 3.5 0.5 + - - -
2899H GLY* 2.8 39.5 + - - +
2900H GLY* 4.9 10.8 - - - +
2901H THR* 5.4 3.6 - - - +
----------------------------------------------------------
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Residues in contact with GLU2895 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2891H LYS 3.2 16.2 + - - +
2892H GLN* 4.1 5.2 - - - +
2893H GLU 3.4 0.2 - - - -
2894H LEU* 1.3 78.9 - - - +
2896H ALA* 1.3 60.8 + - - +
2897H LYS 3.4 0.5 + - - -
2898H GLY* 3.4 10.2 + - - -
2899H GLY* 3.9 11.6 + - - +
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Residues in contact with ALA2896 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2892H GLN 3.2 19.5 + - - +
2893H GLU* 3.9 6.3 - - - +
2894H LEU 3.3 0.6 - - - -
2895H GLU* 1.3 77.3 - - - +
2897H LYS* 1.3 57.9 + - - +
2898H GLY 3.4 0.8 + - - -
----------------------------------------------------------
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Residues in contact with LYS2897 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2893H GLU 3.4 14.2 + - - +
2894H LEU* 3.2 7.5 + - - +
2895H GLU 3.2 1.2 - - - -
2896H ALA* 1.3 74.9 - - - +
2898H GLY* 1.3 58.1 + - - +
2899H GLY 3.7 3.3 - - - +
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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