Contacts of the helix formed by residues 2868 - 2897 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2866D THR 4.1 1.8 + - - -
2867D LEU* 1.3 76.2 - - - +
2869D ARG* 1.3 62.0 + - - +
2870D GLU* 3.3 8.7 - - - -
2871D LEU* 3.9 10.5 - - - +
2872D GLN* 3.0 27.2 + - - +
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Residues in contact with ARG2869 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2868D SER* 1.3 75.7 - - - +
2870D GLU* 1.3 63.4 + - - +
2872D GLN* 3.5 5.4 + - - +
2873D ALA* 3.0 25.1 + - - +
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Residues in contact with GLU2870 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2868D SER* 3.3 5.2 - - - -
2869D ARG* 1.3 79.5 - - - +
2871D LEU* 1.3 57.8 + - - +
2873D ALA* 3.4 4.9 + - - +
2874D MET* 3.1 28.9 + - - +
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Residues in contact with LEU2871 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2867D LEU* 4.2 11.9 - - + -
2868D SER* 3.5 20.9 + - - +
2869D ARG 3.4 0.4 - - - -
2870D GLU* 1.3 79.2 - - - +
2872D GLN* 1.3 57.1 + - - +
2874D MET* 3.5 6.1 + - - +
2875D ALA* 3.0 27.5 + - - +
2927D LEU* 5.3 13.5 - - + +
2937D VAL 6.0 2.0 - - - +
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Residues in contact with GLN2872 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2867D LEU* 4.7 9.1 - - + +
2868D SER 3.0 18.8 + - - +
2869D ARG* 3.9 6.1 - - - +
2870D GLU 3.3 0.2 - - - -
2871D LEU* 1.3 76.7 - - - +
2873D ALA* 1.3 61.6 + - - +
2875D ALA* 3.4 15.1 + - - +
2876D GLU* 3.5 11.3 + - - +
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Residues in contact with ALA2873 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2869D ARG 3.0 17.9 + - - +
2870D GLU* 3.9 5.6 - - - +
2871D LEU 3.3 0.2 - - - -
2872D GLN* 1.3 78.2 - - - +
2874D MET* 1.3 60.6 + - - +
2876D GLU* 3.3 19.8 + - - +
2877D GLN* 3.9 4.5 + - - +
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Residues in contact with MET2874 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2870D GLU 3.1 17.7 + - - +
2871D LEU* 3.9 6.3 - - - +
2872D GLN 3.3 0.2 - - - -
2873D ALA* 1.3 75.3 - - - +
2875D ALA* 1.3 63.7 + - - +
2877D GLN* 3.3 16.3 + - - +
2878D LEU* 3.5 11.1 + - - +
2937D VAL* 6.5 1.3 - - + -
2939D ARG* 6.2 3.6 - - + -
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Residues in contact with ALA2875 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2871D LEU 3.0 17.3 + - - +
2872D GLN* 3.6 9.9 - - - +
2873D ALA 3.2 0.4 - - - -
2874D MET* 1.3 76.5 - - - +
2876D GLU* 1.3 59.8 + - - +
2878D LEU* 3.4 2.8 + - - +
2879D ALA* 2.9 27.5 + - - +
2920D ARG* 5.7 1.3 - - - +
2923D ALA* 3.4 30.2 - - + +
2924D GLN* 4.9 6.1 - - + +
2927D LEU* 5.6 4.9 - - + -
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Residues in contact with GLU2876 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2872D GLN 3.5 6.5 + - - +
2873D ALA* 3.3 13.8 + - - +
2874D MET 3.2 0.8 - - - -
2875D ALA* 1.3 78.9 - - - +
2877D GLN* 1.3 57.5 + - - +
2879D ALA* 3.5 5.9 + - - +
2880D GLU* 2.9 29.5 + - - +
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Residues in contact with GLN2877 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2873D ALA 3.9 3.8 + - - +
2874D MET* 3.3 12.9 + - - +
2875D ALA 3.3 0.2 - - - -
2876D GLU* 1.3 78.7 - - - +
2878D LEU* 1.3 58.0 + - - +
2880D GLU* 3.4 5.5 + - - +
2881D ASN* 3.0 28.4 + - - +
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Residues in contact with LEU2878 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2812D SER* 6.3 2.5 - - - -
2874D MET 3.5 8.7 + - - +
2875D ALA* 3.4 8.0 + - - +
2876D GLU 3.3 0.4 - - - -
2877D GLN* 1.3 76.4 - - - +
2879D ALA* 1.3 65.2 + - - +
2881D ASN* 3.4 6.6 + - - +
2882D TYR* 3.2 21.0 + - - +
2923D ALA* 3.9 17.3 - - + -
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Residues in contact with ALA2879 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2875D ALA 2.9 18.3 + - - +
2876D GLU* 3.9 6.7 - - - +
2877D GLN 3.3 0.2 - - - -
2878D LEU* 1.3 78.3 - - - +
2880D GLU* 1.3 61.5 + - - +
2882D TYR* 3.4 2.9 + - - +
2883D HIS* 3.3 17.7 + - - +
2916D LYS 5.5 0.2 - - - +
2919D ASP* 3.4 48.6 - - + +
2920D ARG* 3.9 9.9 - - + +
2923D ALA* 3.9 1.5 - - + +
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Residues in contact with GLU2880 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2876D GLU 2.9 18.8 + - - +
2877D GLN* 3.9 6.5 - - - +
2879D ALA* 1.3 73.6 - - - +
2881D ASN* 1.3 60.8 + - - +
2883D HIS* 3.4 4.6 + - - +
2884D ASN* 3.0 27.2 + - - +
2908D TYR* 4.1 26.7 - - + +
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Residues in contact with ASN2881 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2739D PRO* 5.1 3.1 - - - +
2740D VAL* 5.7 10.1 - - + +
2815D ALA* 5.2 14.8 - - + -
2877D GLN 3.0 17.4 + - - +
2878D LEU* 3.7 8.5 - - - +
2879D ALA 3.3 0.2 - - - -
2880D GLU* 1.3 76.1 - - - +
2882D TYR* 1.3 59.0 + - - +
2884D ASN* 3.4 6.6 + - - +
2885D THR* 2.9 29.3 + - - -
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Residues in contact with TYR2882 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2878D LEU 3.2 10.1 + - - +
2879D ALA* 3.7 10.5 - - - +
2880D GLU 3.3 0.2 - - - -
2881D ASN* 1.3 78.8 - - - +
2883D HIS* 1.3 58.2 + - - +
2885D THR* 3.4 5.7 + - - -
2886D TRP* 3.0 31.2 + - - +
2919D ASP* 4.8 11.0 - - + +
2922D LYS* 5.8 5.8 - - + -
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Residues in contact with HIS2883 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2879D ALA 3.3 10.8 + - - +
2880D GLU* 3.8 9.4 - - - +
2881D ASN 3.3 0.4 - - - -
2882D TYR* 1.3 79.0 - - - +
2884D ASN* 1.3 53.5 + - - +
2886D TRP* 4.2 3.8 - - - +
2887D GLY* 2.7 32.4 + - - -
2908D TYR* 5.0 13.0 - - + +
2919D ASP* 5.1 6.9 - - + +
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Residues in contact with ASN2884 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2737D PRO* 3.4 16.6 - - + +
2738D ARG 4.1 24.5 - - - +
2739D PRO* 4.2 12.8 - - + +
2880D GLU 3.0 17.6 + - - +
2881D ASN* 3.8 6.3 - - - +
2883D HIS* 1.3 74.3 - - - +
2885D THR* 1.3 59.8 + - - +
2888D ARG* 3.0 26.5 + - - +
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Residues in contact with THR2885 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2739D PRO* 4.1 16.1 - - - +
2881D ASN 2.9 18.5 + - - -
2882D TYR* 3.8 6.3 - - - -
2883D HIS 3.3 0.2 - - - -
2884D ASN* 1.3 78.1 - - - +
2886D TRP* 1.3 62.6 + - - +
2888D ARG* 3.5 3.0 + - - +
2889D LYS* 3.2 22.9 + - - +
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Residues in contact with TRP2886 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2882D TYR 3.0 17.6 + - - +
2883D HIS* 4.2 3.4 - - - +
2885D THR* 1.3 75.4 - - - +
2887D GLY* 1.3 59.8 + - - +
2889D LYS* 3.5 5.7 + - - +
2890D LYS* 3.0 30.0 + - - +
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Residues in contact with GLY2887 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2737D PRO* 4.3 9.2 - - - -
2883D HIS 2.7 23.6 + - - -
2884D ASN 4.0 0.7 - - - -
2886D TRP* 1.3 75.2 - - - +
2888D ARG* 1.3 60.4 + - - +
2890D LYS* 3.5 5.9 + - - +
2891D LYS* 3.2 22.3 + - - +
2904D LEU 5.9 2.5 - - - -
2905D LEU* 6.1 5.8 - - - +
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Residues in contact with ARG2888 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2737D PRO* 3.9 16.9 - - + +
2739D PRO* 5.3 6.7 - - + -
2884D ASN 3.0 20.0 + - - +
2885D THR* 3.9 4.7 - - - +
2887D GLY* 1.3 75.5 - - - +
2889D LYS* 1.3 62.8 + - - +
2891D LYS* 3.5 6.5 + - - +
2892D GLN* 3.3 20.8 + - - +
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Residues in contact with LYS2889 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2885D THR 3.2 17.2 + - - +
2886D TRP* 4.0 6.3 - - - +
2887D GLY 3.3 0.2 - - - -
2888D ARG* 1.3 74.5 - - - +
2890D LYS* 1.3 61.2 + - - +
2892D GLN* 3.5 5.3 + - - +
2893D GLU* 3.0 29.2 + - - +
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Residues in contact with LYS2890 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2886D TRP 3.0 18.4 + - - +
2887D GLY* 3.9 6.7 - - - +
2888D ARG 3.3 0.2 - - - -
2889D LYS* 1.3 73.6 - - - +
2891D LYS* 1.3 60.7 + - - +
2893D GLU* 3.9 4.8 - - - +
2894D LEU* 3.0 30.7 + - - +
2902D HIS* 5.8 8.1 - - + -
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Residues in contact with LYS2891 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2887D GLY 3.2 16.8 + - - +
2888D ARG* 3.8 7.0 - - - +
2889D LYS 3.3 0.4 - - - -
2890D LYS* 1.3 77.8 - - - +
2892D GLN* 1.3 60.9 + - - +
2894D LEU* 3.6 4.3 + - - +
2895D GLU* 3.2 24.3 + - - +
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Residues in contact with GLN2892 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2888D ARG 3.3 13.7 + - - +
2889D LYS* 3.5 5.4 + - - +
2890D LYS 3.3 0.2 - - - -
2891D LYS* 1.3 76.7 - - - +
2893D GLU* 1.3 64.8 + - - +
2895D GLU* 4.1 5.2 - - - +
2896D ALA* 3.2 24.3 + - - +
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Residues in contact with GLU2893 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2889D LYS 3.0 18.6 + - - +
2890D LYS* 4.0 6.5 - - - +
2891D LYS 3.3 0.2 - - - -
2892D GLN* 1.3 76.3 - - - +
2894D LEU* 1.3 62.9 + - - +
2896D ALA* 3.5 6.5 + - - +
2897D LYS* 3.4 21.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU2894 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2890D LYS 3.0 18.9 + - - +
2891D LYS* 4.1 4.9 - - - +
2893D GLU* 1.3 75.1 - - - +
2895D GLU* 1.3 62.2 + - - +
2897D LYS* 3.2 11.8 + - - +
2898D GLY 3.5 0.2 + - - -
2899D GLY* 2.8 39.4 + - - +
2900D GLY* 4.9 10.5 - - - +
2901D THR* 5.4 3.4 - - - +
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Residues in contact with GLU2895 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2891D LYS 3.2 16.4 + - - +
2892D GLN* 4.1 5.4 - - - +
2894D LEU* 1.3 79.5 - - - +
2896D ALA* 1.3 61.9 + - - +
2897D LYS 3.4 0.5 + - - -
2898D GLY* 3.4 9.7 + - - -
2899D GLY* 3.9 11.5 + - - +
----------------------------------------------------------
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Residues in contact with ALA2896 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2892D GLN 3.2 18.6 + - - +
2893D GLU* 3.9 7.0 - - - +
2894D LEU 3.3 0.2 - - - -
2895D GLU* 1.3 77.1 - - - +
2897D LYS* 1.3 57.4 + - - +
2898D GLY 3.4 0.6 + - - -
----------------------------------------------------------
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Residues in contact with LYS2897 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2893D GLU 3.4 14.6 + - - +
2894D LEU* 3.2 7.7 + - - +
2895D GLU 3.2 0.6 - - - -
2896D ALA* 1.3 75.8 - - - +
2898D GLY* 1.3 56.8 + - - +
2899D 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