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Table 2 Analysis of the rmsd from ideal geometry, 3D Profile, and G-factor.

From: Molecular models of NS3 protease variants of the Hepatitis C virus

Genbank access code Residue Range rmsd 3D Profile* G-factor**
   Bond Lengths (Å) Bond Angles (°) Total Score Sideal Score Torsion Angles Covalent Geometry
AJ238800 1027 – 1657 0.020 2.171 299.14 1.03S 0.01 -0.17
AJ238799 1027 – 1657 0.021 2.425 166.68 0.58S 0.07 -0.21
AF139594 1028 – 1658 0.021 2.193 152.89 0.53S 0.09 -0.20
D17763 1033 – 1663 0.019 2.143 290.96 1.00S 0.03 -0.14
AF054247 1027 – 1657 0.020 2.162 288.28 1.00S 0.07 -0.16
AF054248 1027 – 1657 0.020 2.194 292.48 1.01S 0.01 -0.19
AF054249 1027 – 1657 0.020 2.207 290.64 1.00S 0.05 -0.18
D50409 1031 – 1661 0.020 2.188 287.09 0.99S 0.02 -0.17
D84262 1032 – 1662 0.020 2.181 276.59 0.95S 0.06 -0.17
D84263 1025 – 1665 0.020 2.173 283.17 0.98S 0.01 -0.16
D84264 1029 – 1659 0.020 2.174 296.59 1.02S 0.03 -0.15
D84265 1027 – 1657 0.020 2.155 277.67 0.96S 0.02 -0.15
D10749 1027 – 1657 0.020 2.589 287.57 0.99S 0.02 -0.16
D13558 1027 – 1657 0.020 2.157 280.60 0.97S 0.04 -0.15
D14853 1027 – 1657 0.020 2.168 274.13 0.95S 0.02 -0.16
D00944 1031 – 1661 0.020 2.149 287.90 0.99S 0.40 -0.15
D10988 1031 – 1661 0.020 2.171 287.55 0.99S 0.02 -0.16
AF046866 1033 – 1663 0.020 2.957 281.07 0.97S 0.03 -0.16
D49374 1035 – 1665 0.020 2.163 292.23 1.01S 0.02 -0.15
Y11604 1027 – 1657 0.020 2.382 281.93 0.97S 0.02 -0.16
Y13184 1028 – 1658 0.020 2.166 296.66 1.02S 0.02 -0.15
Y12083 1031 – 1661 0.020 2.271 290.58 1.00S -0.01 -0.21
U16362 1027 – 1657 0.020 2.186 280.49 0.97S 0.01 -0.16
U45476 1027 – 1657 0.020 2.398 281.26 0.97S 0.03 -0.17
AJ000009 1027 – 1657 0.020 2.168 290.86 1.00S 0.03 -0.16
M67463 1027 – 1657 0.020 2.139 281.59 0.97S 0.03 -0.14
D63822 1031 – 1661 0.020 2.385 284.43 0.98S 0.03 -0.16
D63821 1032 – 1662 0.020 2.420 269.09 0.93S 0.03 -0.18
D14484 1027 – 1657 0.020 2.234 285.83 0.99S 0.00 -0.19
D11168 1027 – 1657 0.020 2.160 289.57 1.00S 0.04 -0.15
D11355 1027 – 1657 0.020 2.148 306.49 1.06 0.04 -0.14
D50480 1027 – 1657 0.020 2.123 291.79 1.01S 0.05 -0.13
D50481 1027 – 1657 0.020 2.151 277.60 0.96S 0.06 -0.14
D50482 1027 – 1657 0.020 2.172 284.69 0.98S 0.03 -0.16
D50483 1027 – 1657 0.020 2.149 291.04 1.00S 0.06 -0.15
D50485 1027 – 1657 0.020 2.138 293.16 1.01S 0.03 -0.14
D50484 1027 – 1657 0.020 2.204 289.47 1.00S 0.00 -0.17
D28917 1033 – 1663 0.020 2.221 295.32 1.02S 0.03 -0.19
D30613 1027 – 1657 0.020 2.248 282.94 0.98S 0.02 -0.20
D10934 1027 – 1657 0.020 2.434 289.87 1.00S 0.00 -0.18
AF207762 1027 – 1657 0.020 2.367 308.61 1.07S 0.04 -0.15
  1. *Total Score: is the sum of the 3D-1D scores (statistical preferences) of each residue present in protein. Ideal Score: Sideal = exp(-0.83+1.008xln(L)); where L is number of amino acids.
  2. Sideal Score: is compatibility of the sequence with their 3D structure. It is obtained Total Score / Ideal Score. Sideal Score above 0.45Sideal.
  3. **Ideally, scores should be above -0.5. Values below -1.0 may need investigation.