Contacts of the helix formed by residues 3160 - 3186 (chain G) in PDB entry 1PDW
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 THR3160 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3105G ILE* 3.8 0.2 - - - +
3145G ARG* 3.4 43.1 - - + +
3146G VAL* 4.9 0.2 - - - -
3155G SER* 2.3 27.6 + - - -
3156G ARG* 3.3 9.8 + - + -
3157G GLY 2.9 31.5 + - - +
3159G GLY* 1.3 77.8 - - - +
3161G SER* 1.3 59.6 + - - +
3162G PHE 3.3 3.1 - - - -
3163G GLU* 3.3 13.4 + - - +
3164G PHE* 2.8 29.5 + - - +
3386H VAL 3.6 7.4 - - - +
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Residues in contact with SER3161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3018G GLU* 3.7 14.5 + - - +
3021G ILE* 3.7 32.4 - - - +
3022G PRO* 4.5 2.8 - - - +
3105G ILE* 3.6 13.0 - - - +
3157G GLY 3.4 0.8 + - - -
3158G PRO* 2.8 31.0 + - - +
3159G GLY 3.5 0.2 - - - -
3160G THR* 1.3 79.0 - - - +
3162G PHE* 1.3 53.0 + - - +
3164G PHE* 3.2 9.7 - - - +
3165G ALA* 2.7 36.2 + - - +
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Residues in contact with PHE3162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3021G ILE* 4.0 26.2 - - + -
3025G VAL* 4.4 4.5 - - + -
3159G GLY 5.2 3.8 + - - +
3160G THR 3.3 0.8 - - - -
3161G SER* 1.3 74.1 - - - +
3163G GLU* 1.3 61.1 + - + +
3165G ALA* 3.1 3.6 + - - +
3166G LEU* 2.7 41.3 + - + +
3185G LEU* 4.0 27.4 - - + -
3187G LEU* 4.0 29.8 - - + -
3217H MSE 3.8 30.3 - - - -
3221H ILE* 4.3 5.8 - - + -
3358H PRO* 3.3 34.3 - - + -
3359H GLY* 4.3 3.4 - - - -
3362H PHE* 4.3 20.4 - + - -
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Residues in contact with GLU3163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3145G ARG* 2.7 56.5 + - - +
3146G VAL* 3.7 17.0 - - + +
3159G GLY 3.5 8.7 - - - +
3160G THR* 3.3 7.6 + - - +
3162G PHE* 1.3 78.3 - - + +
3164G PHE* 1.3 57.7 + - - +
3166G LEU* 3.8 8.5 - - + +
3167G ALA* 2.9 31.2 + - - +
3388H LYS* 5.1 4.9 - - - +
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Residues in contact with PHE3164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3022G PRO* 4.0 19.7 - - + -
3071G VAL* 4.1 13.2 - - + -
3103G ALA* 3.5 37.0 - - + -
3104G ALA* 3.9 15.7 - - - -
3105G ILE* 4.0 27.4 - - + -
3146G VAL* 3.9 6.9 - - - +
3153G LEU* 3.5 31.0 - - + -
3155G SER* 3.6 21.8 - - - -
3160G THR 2.8 18.7 + - - +
3161G SER* 3.2 5.6 - - - +
3163G GLU* 1.3 76.9 - - - +
3165G ALA* 1.3 63.2 + - - +
3167G ALA* 3.2 6.4 + - - +
3168G ILE* 3.1 37.2 + - + +
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Residues in contact with ALA3165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3021G ILE* 4.4 0.4 - - + +
3022G PRO* 3.8 19.5 - - + +
3025G VAL* 3.6 34.5 - - + -
3026G MSE 4.9 1.6 - - + +
3161G SER 2.7 20.4 + - - +
3162G PHE 3.6 3.4 - - - +
3164G PHE* 1.3 76.3 - - - +
3166G LEU* 1.3 56.5 + - - +
3168G ILE* 3.1 15.1 + - - +
3169G VAL* 3.0 29.8 + - - +
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Residues in contact with LEU3166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3025G VAL* 4.0 19.1 - - + -
3162G PHE* 2.7 25.3 + - + +
3163G GLU* 4.0 7.6 - - + +
3165G ALA* 1.3 69.0 - - - +
3167G ALA* 1.3 64.9 + - - +
3169G VAL* 3.3 8.5 + - + +
3170G GLU* 2.9 25.2 + - - +
3178G ALA* 4.3 24.1 - - + +
3181G VAL* 4.6 7.2 - - + -
3182G LYS* 3.9 40.8 - - + +
3185G LEU* 4.6 4.9 - - + -
3187G LEU* 3.9 18.2 - - + -
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Residues in contact with ALA3167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3146G VAL* 4.1 17.3 - - + -
3148G LYS* 5.6 3.1 - - + +
3153G LEU* 3.9 18.1 - - + +
3163G GLU 2.9 19.1 + - - +
3164G PHE 3.4 5.8 - - - +
3166G LEU* 1.3 75.8 - - - +
3168G ILE* 1.3 63.0 + - - +
3170G GLU* 3.3 8.1 + - - +
3171G ALA* 3.0 24.1 + - - +
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Residues in contact with ILE3168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3022G PRO* 5.1 2.9 - - + -
3026G MSE 3.6 28.0 - - + -
3031G ILE* 5.1 0.2 - - + -
3069G VAL* 4.2 20.0 - - + -
3071G VAL* 4.2 12.3 - - + -
3101G LEU* 4.7 2.2 - - + -
3103G ALA* 3.7 31.2 - - + -
3153G LEU* 4.2 12.6 - - + -
3164G PHE* 3.1 35.2 + - + +
3165G ALA* 3.3 11.9 - - - +
3167G ALA* 1.3 74.8 - - - +
3169G VAL* 1.3 63.9 + - - +
3171G ALA* 3.2 5.8 + - - +
3172G LEU* 3.0 27.7 + - + +
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Residues in contact with VAL3169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3025G VAL* 4.0 21.1 - - + +
3026G MSE 4.2 10.1 - - + -
3029G ALA* 3.6 35.0 - - + -
3031G ILE* 4.3 9.4 - - + -
3165G ALA 3.0 17.6 + - - +
3166G LEU* 3.3 11.0 + - + +
3168G ILE* 1.3 75.3 - - - +
3170G GLU* 1.3 58.2 + - - +
3173G ASN* 2.8 31.8 + - + +
3174G GLY 3.6 0.3 + - - -
3177G VAL* 4.2 6.1 - - + +
3178G ALA* 3.8 28.0 - - + +
3181G VAL* 4.8 2.7 - - + -
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Residues in contact with GLU3170 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3166G LEU 2.9 16.9 + - - +
3167G ALA* 3.6 7.5 - - - +
3169G VAL* 1.3 77.4 - - - +
3171G ALA* 1.3 61.9 + - - +
3174G GLY* 2.8 35.6 + - - -
3175G LYS* 3.0 52.0 - - + +
3178G ALA* 4.1 10.7 - - + +
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Residues in contact with ALA3171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3101G LEU* 4.0 22.4 - - + -
3148G LYS* 4.1 22.4 - - - +
3153G LEU* 5.1 0.2 - - + -
3167G ALA 3.0 14.0 + - - +
3168G ILE 3.6 7.4 - - - +
3170G GLU* 1.3 79.2 - - - +
3172G LEU* 1.3 63.6 + - + +
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Residues in contact with LEU3172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3004G LYS* 2.6 47.7 + - + +
3005G ARG 4.5 1.8 - - - +
3031G ILE* 3.9 20.9 - - + -
3068G ASP* 3.8 39.7 - - + +
3069G VAL* 3.7 26.5 - - + -
3101G LEU* 4.1 19.7 - - + -
3168G ILE* 3.0 19.8 + - + +
3169G VAL 4.1 1.3 - - - +
3171G ALA* 1.3 83.6 - - + +
3173G ASN* 1.3 62.0 + - - +
3174G GLY 3.7 0.7 - - - -
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Residues in contact with ASN3173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1173C ASN 5.7 0.5 - - - +
1176C GLU* 4.7 6.7 - - - +
3004G LYS* 3.1 33.3 + - - +
3029G ALA* 2.9 28.5 + - - +
3030G GLY 4.7 2.4 + - - -
3031G ILE* 3.6 22.4 - - - +
3169G VAL* 2.8 15.9 + - + +
3172G LEU* 1.3 74.0 - - - +
3174G GLY* 1.3 57.8 + - - +
3176G GLU 5.3 0.2 + - - -
3177G VAL* 3.2 37.0 - - + +
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Residues in contact with GLY3174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3169G VAL 4.1 0.3 - - - +
3170G GLU* 2.8 29.7 + - - -
3172G LEU 3.7 1.2 - - - -
3173G ASN* 1.3 75.9 - - - +
3175G LYS* 1.3 65.0 + - - -
3176G GLU 3.4 2.5 - - - -
3177G VAL* 3.6 0.5 + - - +
3178G ALA* 3.2 22.0 + - - +
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Residues in contact with LYS3175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3170G GLU* 3.0 33.1 - - + +
3174G GLY* 1.3 69.8 - - - -
3176G GLU* 1.3 63.9 + - + +
3178G ALA* 3.3 8.0 + - - +
3179G ALA* 2.9 30.2 + - - +
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Residues in contact with GLU3176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002C ALA 6.1 0.2 - - - -
1003C SER* 4.8 12.1 + - - -
1004C LYS* 5.1 3.3 + - - +
1029C ALA 4.3 11.2 - - - +
1030C GLY* 4.5 10.6 - - - +
1173C ASN* 3.5 37.8 - - - +
1177C VAL* 4.1 7.6 - - + +
3174G GLY 3.4 0.6 - - - -
3175G LYS* 1.3 74.7 - - + +
3177G VAL* 1.3 68.2 + - + +
3179G ALA* 3.0 4.3 + - - -
3180G GLN* 2.7 46.0 + - - +
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Residues in contact with VAL3177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1173C ASN 5.3 2.2 - - - +
1176C GLU* 3.8 25.6 - - + -
1177C VAL* 3.9 22.0 - - + -
1180C GLN* 3.7 20.6 - - - +
3029G ALA* 4.0 20.0 - - + +
3169G VAL* 4.2 1.8 - - + -
3173G ASN* 3.2 43.3 - - + +
3174G GLY 3.6 1.5 + - - +
3175G LYS 3.4 0.2 - - - -
3176G GLU* 1.3 76.3 - - + +
3178G ALA* 1.3 62.7 + - - +
3180G GLN 3.4 0.3 + - - -
3181G VAL* 3.1 22.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA3178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3166G LEU* 4.3 14.2 - - + +
3169G VAL* 3.8 19.2 - - + +
3170G GLU* 4.1 19.7 - - + +
3174G GLY 3.2 12.9 + - - +
3175G LYS* 3.4 9.9 - - - +
3176G GLU 3.1 0.4 - - - -
3177G VAL* 1.3 80.2 - - - +
3179G ALA* 1.3 57.1 + - - +
3181G VAL* 3.3 3.3 + - - +
3182G LYS* 3.0 30.9 + - - +
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Residues in contact with ALA3179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3175G LYS 2.9 17.0 + - - +
3176G GLU* 3.0 7.4 + - - +
3178G ALA* 1.3 75.8 - - - +
3180G GLN* 1.3 70.5 + - - +
3182G LYS* 3.3 8.2 + - - +
3183G ALA* 3.3 24.1 + - - +
3191G GLU* 4.5 17.0 - - - +
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Residues in contact with GLN3180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029C ALA 5.2 4.4 + - - -
1177C VAL* 4.3 9.9 - - - +
1180C GLN* 3.0 46.4 - - + +
3176G GLU* 2.7 42.6 + - - +
3177G VAL 3.8 0.4 - - - +
3179G ALA* 1.3 86.2 - - - +
3181G VAL* 1.3 58.5 + - - +
3183G ALA* 4.2 3.1 - - - +
3184G PRO* 3.0 26.9 - - - +
3191G GLU* 5.4 1.2 - - - +
----------------------------------------------------------
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Residues in contact with VAL3181 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1180C GLN* 4.4 4.7 - - - +
3025G VAL* 3.9 24.5 - - + +
3028G ARG* 3.8 34.4 + - + +
3029G ALA* 3.7 33.2 - - + -
3166G LEU* 4.6 5.6 - - + -
3169G VAL* 4.8 2.0 - - + -
3177G VAL* 3.1 20.7 + - + +
3178G ALA* 3.8 5.8 - - - +
3180G GLN* 1.3 76.2 - - - +
3182G LYS* 1.3 63.3 + - - +
3184G PRO* 3.3 11.5 - - - +
3185G LEU* 3.4 14.9 + - + +
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Residues in contact with LYS3182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3166G LEU* 3.9 30.0 - - + +
3178G ALA 3.0 18.3 + - - +
3179G ALA* 3.3 8.9 + - - +
3181G VAL* 1.3 76.1 - - - +
3183G ALA* 1.3 64.9 + - - +
3185G LEU* 3.1 27.3 + - - +
3186G VAL 4.0 1.9 + - - -
3187G LEU* 4.1 17.1 + - + -
3189G ASP* 3.0 48.7 + - - +
3190G LEU 5.7 0.6 + - - -
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Residues in contact with ALA3183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3179G ALA 3.3 12.6 + - - +
3180G GLN* 4.2 3.4 - - - +
3182G LYS* 1.3 79.2 - - - +
3184G PRO* 1.3 69.4 - - + +
3185G LEU 3.2 0.9 + - - -
3186G VAL* 3.5 11.4 + - - +
3191G GLU* 4.7 17.3 - - + +
----------------------------------------------------------
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Residues in contact with PRO3184 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3028G ARG* 4.5 14.4 + - - +
3180G GLN 3.0 25.6 - - - +
3181G VAL* 3.3 11.0 - - - +
3183G ALA* 1.3 88.6 - - + +
3185G LEU* 1.3 59.7 + - - +
3186G VAL 3.2 0.4 - - - -
3326H HIS* 2.8 38.4 + - + +
3328H LEU* 5.8 5.4 - - + -
3358H PRO* 4.4 3.1 - - - +
----------------------------------------------------------
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Residues in contact with LEU3185 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3025G VAL* 4.7 6.7 - - + -
3028G ARG* 3.6 39.0 - - - +
3162G PHE* 4.0 14.8 - - + -
3166G LEU* 4.6 11.4 - - + -
3181G VAL* 3.4 18.8 - - + +
3182G LYS* 3.1 15.4 + - - +
3184G PRO* 1.3 74.8 - - - +
3186G VAL* 1.3 64.8 + - - +
3187G LEU* 4.0 28.0 - - + -
3217H MSE 3.9 17.5 - - + -
3358H PRO* 3.4 13.0 - - + +
3359H GLY 2.7 31.2 + - - +
----------------------------------------------------------
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Residues in contact with VAL3186 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3182G LYS 4.0 0.4 + - - -
3183G ALA 3.5 10.2 + - - +
3184G PRO 3.2 12.9 - - - +
3185G LEU* 1.3 84.3 - - - +
3187G LEU* 1.3 65.4 + - - +
3326H HIS* 3.5 22.7 - - + +
3327H PRO* 4.3 11.2 - - + -
3345H ARG* 3.1 25.5 + - + +
3356H ARG* 3.7 32.8 - - + +
3357H GLY* 4.3 10.5 - - - +
3359H GLY* 3.7 4.4 - - - -
3360H THR* 4.0 6.7 - - + -
----------------------------------------------------------
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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