Contacts of the helix formed by residues 3175 - 3197 (chain C) in PDB entry 5Y3R
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 PRO3175 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3126C LEU* 4.5 27.4 - - + -
3130C GLN* 5.5 0.9 - - - +
3173C MET* 3.6 16.6 + - + +
3174C ASP* 1.3 94.6 - - + +
3176C MET* 1.3 63.3 + - - +
3177C ASN* 3.5 10.2 + - - +
3178C ILE* 3.6 31.2 - - + +
3179C TRP* 3.7 12.9 + - - +
3783C GLN* 3.5 13.2 - - + +
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Residues in contact with MET3176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2959C ALA* 5.8 5.8 - - - +
3174C ASP 3.4 1.9 + - - +
3175C PRO* 1.3 69.8 - - - +
3177C ASN* 1.3 77.2 + - - +
3178C ILE 3.3 1.1 - - - -
3179C TRP* 2.9 34.1 + - + +
3180C ASP* 3.0 24.0 + - - +
3249C GLN* 3.0 38.4 - - + +
3251C ASN* 3.1 34.5 - - + +
3254C LEU* 4.9 15.7 - - + -
3783C GLN* 4.9 0.6 - - - +
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Residues in contact with ASN3177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2926C LEU* 5.6 2.8 - - - +
3005C LEU* 3.4 40.6 + - + +
3130C GLN* 3.1 23.5 - - - +
3175C PRO* 4.9 8.5 - - - +
3176C MET* 1.3 82.8 + - - +
3178C ILE* 1.3 65.5 - - + +
3180C ASP* 2.9 12.7 + - - +
3181C ASP* 2.7 21.8 + - - +
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Residues in contact with ILE3178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3126C LEU* 4.5 9.0 - - + +
3130C GLN* 3.1 40.8 - - + +
3133C GLN* 3.1 37.0 - - + +
3134C ALA* 5.8 0.7 - - + +
3137C GLU* 5.6 0.7 - - - +
3170C ASP* 5.3 1.1 - - - +
3173C MET* 5.6 5.6 - - + -
3175C PRO* 3.6 35.0 - - + +
3177C ASN* 1.3 72.4 - - + +
3179C TRP* 1.3 54.5 + - - +
3180C ASP 2.7 2.9 + - - -
3181C ASP* 2.5 36.3 + - + +
3182C ILE* 2.9 25.9 + - + +
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Residues in contact with TRP3179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3172C LYS* 3.1 30.7 - - + +
3173C MET 5.2 1.8 - - - +
3175C PRO 3.9 3.8 - - - +
3176C MET* 2.9 42.2 + - + +
3178C ILE* 1.3 77.0 - - - +
3180C ASP* 1.3 85.2 + - - +
3182C ILE* 3.1 22.0 - - - +
3183C ILE* 4.3 1.6 - - - +
3242C MET* 2.9 33.1 + - + +
3245C SER* 2.6 37.3 + - - -
3246C ALA* 3.2 18.2 - - + -
3249C GLN* 2.8 33.7 - - - +
3254C LEU* 5.3 7.9 - - + -
3255C ALA* 5.6 2.5 - - - -
3258C LEU* 3.9 20.3 - - + +
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Residues in contact with ASP3180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3005C LEU 4.7 11.3 - - - +
3006C ALA* 4.9 0.7 - - - -
3007C GLU* 6.3 2.5 - - + -
3046C ARG* 5.8 2.7 - - - +
3176C MET* 3.0 14.9 + - - +
3177C ASN* 2.9 10.6 + - - +
3178C ILE 2.7 3.2 + - - -
3179C TRP* 1.3 102.5 - - - +
3181C ASP* 1.3 56.8 + - - +
3182C ILE 2.6 17.4 + - - -
3183C ILE* 2.7 29.0 + - + +
3184C THR* 3.0 10.8 + - + -
3254C LEU* 3.7 23.8 - - - +
3257C LYS* 5.9 3.4 - - - -
3258C LEU* 4.9 6.4 - - - +
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Residues in contact with ASP3181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3046C ARG* 4.6 14.0 + - - -
3130C GLN* 2.0 43.3 + - + +
3134C ALA* 5.1 8.5 - - + -
3177C ASN* 2.7 14.7 - - - +
3178C ILE* 2.5 17.0 + - + +
3180C ASP* 1.3 72.2 - - - +
3182C ILE* 1.3 58.2 + - + +
3184C THR* 1.9 35.5 + - - +
3185C ASN* 2.8 16.5 - - - +
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Residues in contact with ILE3182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3137C GLU* 4.6 17.3 - - - +
3170C ASP* 5.0 15.0 - - + +
3171C ALA 5.5 2.0 - - - +
3172C LYS* 3.3 33.4 - - + +
3178C ILE* 2.9 22.0 + - + +
3179C TRP* 3.1 32.3 - - - +
3180C ASP 2.6 3.2 + - - -
3181C ASP* 1.3 68.9 - - + +
3183C ILE* 1.3 61.2 + - - +
3184C THR 2.7 3.8 + - - -
3185C ASN* 2.4 37.9 + - - +
3186C ARG* 2.8 24.2 + - + +
3242C MET* 3.4 16.8 - - + -
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Residues in contact with ILE3183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3053C LEU* 5.6 0.2 - - - -
3179C TRP 4.3 5.2 - - - +
3180C ASP* 2.7 31.2 + - + +
3182C ILE* 1.3 75.4 - - - +
3184C THR* 1.3 67.6 + - + +
3186C ARG* 3.7 11.2 - - - -
3187C CYS* 2.9 25.3 + - - -
3238C MET* 3.3 33.7 - - + +
3239C LYS* 4.1 11.4 - - + +
3242C MET* 3.5 35.2 - - + +
3258C LEU* 5.0 9.0 - - + -
3261C GLU* 3.7 19.3 - - - +
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Residues in contact with THR3184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3007C GLU* 5.8 6.3 - - + -
3046C ARG* 6.1 2.2 - - - +
3049C LEU* 5.5 11.9 - - + -
3053C LEU* 4.5 10.8 - - + -
3180C ASP* 3.0 21.4 + - + +
3181C ASP* 1.9 39.9 + - - +
3182C ILE 2.7 0.2 + - - -
3183C ILE* 1.3 83.1 - - + +
3185C ASN* 1.3 77.0 + - - -
3187C CYS* 3.0 1.6 + - - +
3188C PHE* 3.0 46.9 + - + -
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Residues in contact with ASN3185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3091C LEU* 4.7 2.1 - - - +
3134C ALA* 3.9 17.3 - - - +
3137C GLU* 2.8 28.3 + - + +
3138C ILE* 4.2 13.1 - - - +
3181C ASP* 2.8 17.8 + - - +
3182C ILE* 2.4 9.1 + - - +
3184C THR* 1.3 98.4 + - - +
3186C ARG* 1.3 65.4 + - + +
3188C PHE* 2.8 25.4 + - - +
3189C PHE* 2.9 40.8 + - + -
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Residues in contact with ARG3186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3137C GLU* 5.6 9.4 - - - +
3140C GLU* 5.9 0.2 + - - -
3163C THR* 4.3 1.2 + - - -
3166C ASN* 2.3 56.1 + - - +
3167C ARG* 3.0 53.8 + - - +
3170C ASP* 4.1 12.5 + - - +
3182C ILE* 2.8 28.3 + - - +
3183C ILE* 3.5 10.5 - - - +
3185C ASN* 1.3 76.7 - - - +
3187C CYS* 1.3 55.5 + - - +
3189C PHE* 2.6 34.9 + - - -
3190C LEU* 2.8 22.1 + - - +
3238C MET* 3.4 21.1 - - + -
3242C MET* 4.4 4.3 - - + +
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Residues in contact with CYS3187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3053C LEU* 4.4 28.2 - - + +
3183C ILE* 2.9 27.7 + - - -
3184C THR 3.4 6.5 - - - +
3186C ARG* 1.3 73.3 - - - +
3188C PHE* 1.3 62.1 + - + +
3189C PHE 2.7 10.9 + - - -
3190C LEU* 4.7 4.3 - - - +
3191C SER* 2.9 27.2 + - - -
3238C MET* 3.5 26.4 - - - -
3261C GLU* 5.2 4.7 - - - -
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Residues in contact with PHE3188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3049C LEU* 3.9 27.8 - - + -
3052C LEU* 3.2 45.8 - - + -
3053C LEU* 3.5 14.4 - - + -
3088C LEU* 6.5 0.9 - - + -
3091C LEU* 3.4 44.4 - - + +
3092C LEU* 4.8 5.2 - - + -
3141C PHE* 3.9 1.9 - - - -
3184C THR* 3.0 45.5 - - - -
3185C ASN* 2.8 11.6 + - - +
3187C CYS* 1.3 73.3 - - + +
3189C PHE* 1.3 67.3 + - + +
3191C SER* 2.6 21.2 + - - -
3192C LYS* 3.8 8.7 + - - +
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Residues in contact with PHE3189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3091C LEU* 3.4 32.8 - - + -
3137C GLU* 4.5 7.9 - - + -
3138C ILE* 3.3 31.0 - - + -
3140C GLU* 6.0 0.4 - - - -
3141C PHE* 3.3 41.9 - + + -
3144C PHE* 5.6 1.8 - + + -
3166C ASN* 6.1 3.8 - - + +
3185C ASN* 2.9 37.0 - - + -
3186C ARG* 2.6 24.2 + - - +
3187C CYS 2.7 0.2 + - - -
3188C PHE* 1.3 77.4 - - + +
3190C LEU* 1.3 55.3 + - + +
3191C SER 2.9 0.9 - - - -
3192C LYS* 2.6 25.8 + - - +
3193C ILE* 2.7 23.6 + - + +
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Residues in contact with LEU3190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3163C THR* 5.1 0.2 - - - +
3167C ARG* 3.2 25.8 - - - +
3186C ARG* 2.8 35.1 + - - +
3187C CYS* 4.2 3.8 - - - +
3189C PHE* 1.3 74.3 - - + +
3191C SER* 1.3 61.3 + - - +
3193C ILE* 3.1 15.9 - - + +
3194C GLU* 2.9 22.3 + - - +
3231C ILE* 3.3 23.7 - - + +
3234C CYS* 3.2 42.0 - - - +
3235C LYS* 3.5 26.2 + - + -
3238C MET* 4.5 8.7 - - + -
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Residues in contact with SER3191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3053C LEU 5.5 4.9 - - - -
3054C GLN 5.8 3.6 - - - -
3091C LEU 5.3 0.7 + - - -
3187C CYS 2.9 14.0 + - - -
3188C PHE* 2.6 29.0 + - - -
3190C LEU* 1.3 75.3 - - - +
3192C LYS* 1.3 73.2 + - - +
3193C ILE 2.9 1.0 + - - -
3194C GLU* 3.0 7.7 + - - +
3195C GLU* 2.9 27.2 + - - +
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Residues in contact with LYS3192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3091C LEU 5.0 5.6 - - - +
3092C LEU 5.8 0.2 - - - +
3094C ASP* 3.2 48.4 + - + +
3141C PHE* 3.2 37.2 - - + -
3145C ILE* 3.9 14.8 - - + -
3188C PHE 3.9 4.9 - - - +
3189C PHE 2.6 4.9 + - - +
3191C SER* 1.3 80.2 + - - +
3193C ILE* 1.3 50.1 + - - +
3195C GLU* 2.9 31.0 + - - +
3196C LYS* 2.8 73.3 + - + +
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Residues in contact with ILE3193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3141C PHE* 5.4 4.0 - - + -
3144C PHE* 5.9 6.3 - - + -
3160C LEU* 3.5 35.9 - - + -
3163C THR* 4.7 7.9 - - - +
3189C PHE* 2.7 22.9 + - + +
3190C LEU* 3.1 21.3 - - + +
3192C LYS* 1.3 68.7 - - - +
3194C GLU* 1.3 55.6 + - - +
3196C LYS* 2.7 8.5 + - - -
3197C LEU* 2.6 44.3 + - + +
3231C ILE* 3.3 39.3 - - + -
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Residues in contact with GLU3194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3190C LEU 2.9 11.8 + - - +
3191C SER* 3.8 3.9 - - - +
3193C ILE* 1.3 79.8 - - - +
3195C GLU* 1.3 61.0 + - - +
3197C LEU* 3.2 38.4 + - + +
3198C THR* 4.4 3.5 + - - -
3228C SER* 3.9 12.3 + - - +
3231C ILE* 4.2 13.2 - - + -
3235C LYS* 3.9 19.3 + - - -
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Residues in contact with GLU3195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3091C LEU 5.2 1.7 - - - +
3092C LEU 4.6 10.5 - - - +
3191C SER* 2.9 12.1 + - - +
3192C LYS* 2.9 57.0 + - + +
3194C GLU* 1.3 77.6 - - - +
3196C LYS* 1.3 61.5 + - + +
3197C LEU 3.3 0.2 - - - -
3198C THR* 4.0 9.0 + - - -
3199C PRO* 3.7 9.9 - - - +
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Residues in contact with LYS3196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3094C ASP* 5.3 2.8 + - - -
3145C ILE* 4.9 2.4 - - - +
3148C GLN* 3.1 33.0 - - - +
3154C GLN* 4.1 18.7 - - - +
3192C LYS* 2.8 60.8 + - + +
3193C ILE* 2.7 6.3 + - - +
3195C GLU* 1.3 79.4 - - + +
3197C LEU* 1.3 64.2 + - - +
3198C THR 3.0 1.6 - - - -
3199C PRO* 3.1 38.4 - - + +
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Residues in contact with LEU3197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3154C GLN* 5.9 0.3 - - - +
3157C LEU* 4.3 28.6 - - + +
3160C LEU* 5.9 1.6 - - + -
3193C ILE* 2.6 32.6 + - + +
3194C GLU* 3.2 36.3 + - + +
3196C LYS* 1.3 74.5 - - - +
3198C THR* 1.3 62.0 + - - +
3199C PRO 4.6 2.3 - - - -
3227C ILE* 3.6 46.9 - - + +
3228C SER* 3.7 13.5 - - - +
3230C LEU* 5.3 4.3 - - + -
3231C ILE* 4.3 4.5 - - + -
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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