
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   16 (  127),  selected   16 , name T0316TS609_1-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS609_1-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M     284           -
LGA    M     284      S     285          3.730
LGA    S     285      T     286          2.672
LGA    T     286      S     287          2.758
LGA    S     287      L     288          1.142
LGA    L     288      E     289          0.915
LGA    E     289      A     290          1.658
LGA    A     290      S     291          1.238
LGA    S     291      Q     292          2.119
LGA    Q     292      V     293          3.317
LGA    -       -      H     294           -
LGA    -       -      F     295           -
LGA    -       -      T     296           -
LGA    -       -      R     297           -
LGA    -       -      E     298           -
LGA    -       -      M     299           -
LGA    -       -      P     300           -
LGA    -       -      E     301           -
LGA    -       -      E     302           -
LGA    -       -      F     303           -
LGA    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      T     308           -
LGA    -       -      A     309           -
LGA    -       -      K     310           -
LGA    -       -      F     311           -
LGA    -       -      R     312           -
LGA    -       -      Y     313           -
LGA    -       -      R     314           -
LGA    -       -      Q     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    -       -      S     318           -
LGA    -       -      K     319           -
LGA    -       -      V     320           -
LGA    -       -      T     321           -
LGA    -       -      V     322           -
LGA    -       -      H     323           -
LGA    -       -      V     324           -
LGA    -       -      K     325           -
LGA    -       -      G     326           -
LGA    -       -      E     327           -
LGA    -       -      K     328           -
LGA    -       -      T     329           -
LGA    -       -      E     330           -
LGA    -       -      V     331           -
LGA    -       -      I     332           -
LGA    -       -      F     333           -
LGA    -       -      A     334           -
LGA    -       -      E     335           -
LGA    -       -      P     336           -
LGA    -       -      Q     337           -
LGA    -       -      R     338           -
LGA    -       -      A     339           -
LGA    -       -      I     340           -
LGA    -       -      T     341           -
LGA    -       -      P     342           -
LGA    -       -      G     343           -
LGA    -       -      Q     344           -
LGA    -       -      A     345           -
LGA    -       -      V     346           -
LGA    -       -      V     347           -
LGA    -       -      F     348           -
LGA    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    -       -      C     354           -
LGA    -       -      L     355           -
LGA    -       -      G     356           -
LGA    -       -      G     357           -
LGA    -       -      G     358           -
LGA    V     293      L     359          0.974
LGA    H     294      I     360          1.111
LGA    F     295      D     361          1.412
LGA    T     296      N     362          1.700
LGA    -       -      A     363           -
LGA    -       -      Y     364           -
LGA    -       -      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    R     297      V     369           #
LGA    E     298      C     370          3.130
LGA    M     299      Q     371          2.551
LGA    -       -      Y     372           -
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   16   90    5.0     15    2.22     0.00     13.607     0.647

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.687947 * X  +   0.348753 * Y  +  -0.636475 * Z  +  30.783957
  Y_new =  -0.136950 * X  +  -0.923601 * Y  +  -0.358058 * Z  +  29.901917
  Z_new =  -0.712723 * X  +  -0.159160 * Y  +   0.683150 * Z  + -88.533363 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.228896    2.912696  [ DEG:   -13.1148    166.8852 ]
  Theta =   0.793373    2.348220  [ DEG:    45.4569    134.5431 ]
  Phi   =  -2.945091    0.196501  [ DEG:  -168.7413     11.2587 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0316TS609_1-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS609_1-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   16   90   5.0   15   2.22    0.00  13.607
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS609_1-D3
PFRMAT TS
TARGET T0316
MODEL 1
PARENT 1wy5_A                                           
ATOM   2220  N   MET   284      22.655   4.780 -11.534  1.00303.87       1SG    
ATOM   2221  CA  MET   284      23.662   5.639 -11.011  1.00303.87       1SG    
ATOM   2222  CB  MET   284      24.421   6.416 -12.097  1.00303.87       1SG    
ATOM   2223  CG  MET   284      25.243   5.506 -13.011  1.00303.87       1SG    
ATOM   2224  SD  MET   284      26.690   4.745 -12.220  1.00303.87       1SG    
ATOM   2225  CE  MET   284      27.701   6.248 -12.324  1.00303.87       1SG    
ATOM   2226  C   MET   284      22.885   6.603 -10.184  1.00303.87       1SG    
ATOM   2227  O   MET   284      21.713   6.837 -10.445  1.00303.87       1SG    
ATOM   2228  N   SER   285      23.494   7.148  -9.126  1.00235.45       1SG    
ATOM   2229  CA  SER   285      22.818   8.037  -8.226  1.00235.45       1SG    
ATOM   2230  CB  SER   285      21.350   7.669  -7.888  1.00235.45       1SG    
ATOM   2231  OG  SER   285      21.212   6.283  -7.602  1.00235.45       1SG    
ATOM   2232  C   SER   285      23.617   7.947  -6.983  1.00235.45       1SG    
ATOM   2233  O   SER   285      24.674   8.561  -6.865  1.00235.45       1SG    
ATOM   2234  N   THR   286      23.115   7.182  -6.000  1.00224.05       1SG    
ATOM   2235  CA  THR   286      23.909   6.991  -4.832  1.00224.05       1SG    
ATOM   2236  CB  THR   286      23.285   6.077  -3.818  1.00224.05       1SG    
ATOM   2237  OG1 THR   286      22.029   6.593  -3.401  1.00224.05       1SG    
ATOM   2238  CG2 THR   286      24.235   5.956  -2.614  1.00224.05       1SG    
ATOM   2239  C   THR   286      25.167   6.348  -5.321  1.00224.05       1SG    
ATOM   2240  O   THR   286      25.129   5.495  -6.206  1.00224.05       1SG    
ATOM   2241  N   SER   287      26.322   6.762  -4.771  1.00168.82       1SG    
ATOM   2242  CA  SER   287      27.576   6.260  -5.253  1.00168.82       1SG    
ATOM   2243  CB  SER   287      28.287   7.217  -6.225  1.00168.82       1SG    
ATOM   2244  OG  SER   287      27.512   7.377  -7.404  1.00168.82       1SG    
ATOM   2245  C   SER   287      28.497   6.051  -4.093  1.00168.82       1SG    
ATOM   2246  O   SER   287      28.058   5.854  -2.962  1.00168.82       1SG    
ATOM   2247  N   LEU   288      29.820   6.074  -4.374  1.00169.84       1SG    
ATOM   2248  CA  LEU   288      30.826   5.784  -3.392  1.00169.84       1SG    
ATOM   2249  CB  LEU   288      32.248   5.748  -3.998  1.00169.84       1SG    
ATOM   2250  CG  LEU   288      33.393   5.224  -3.094  1.00169.84       1SG    
ATOM   2251  CD1 LEU   288      34.727   5.257  -3.857  1.00169.84       1SG    
ATOM   2252  CD2 LEU   288      33.502   5.956  -1.746  1.00169.84       1SG    
ATOM   2253  C   LEU   288      30.764   6.832  -2.337  1.00169.84       1SG    
ATOM   2254  O   LEU   288      30.706   8.029  -2.616  1.00169.84       1SG    
ATOM   2255  N   GLU   289      30.791   6.382  -1.070  1.00 87.25       1SG    
ATOM   2256  CA  GLU   289      30.698   7.298   0.022  1.00 87.25       1SG    
ATOM   2257  CB  GLU   289      29.486   7.045   0.935  1.00 87.25       1SG    
ATOM   2258  CG  GLU   289      29.499   5.669   1.606  1.00 87.25       1SG    
ATOM   2259  CD  GLU   289      28.253   5.558   2.471  1.00 87.25       1SG    
ATOM   2260  OE1 GLU   289      27.457   6.534   2.492  1.00 87.25       1SG    
ATOM   2261  OE2 GLU   289      28.081   4.494   3.125  1.00 87.25       1SG    
ATOM   2262  C   GLU   289      31.920   7.155   0.861  1.00 87.25       1SG    
ATOM   2263  O   GLU   289      32.603   6.132   0.854  1.00 87.25       1SG    
ATOM   2264  N   ALA   290      32.219   8.234   1.600  1.00 52.78       1SG    
ATOM   2265  CA  ALA   290      33.319   8.318   2.507  1.00 52.78       1SG    
ATOM   2266  CB  ALA   290      34.357   9.386   2.134  1.00 52.78       1SG    
ATOM   2267  C   ALA   290      32.675   8.734   3.780  1.00 52.78       1SG    
ATOM   2268  O   ALA   290      31.449   8.704   3.870  1.00 52.78       1SG    
ATOM   2269  N   SER   291      33.473   9.093   4.804  1.00 85.85       1SG    
ATOM   2270  CA  SER   291      32.901   9.446   6.071  1.00 85.85       1SG    
ATOM   2271  CB  SER   291      33.943   9.989   7.067  1.00 85.85       1SG    
ATOM   2272  OG  SER   291      33.315  10.320   8.297  1.00 85.85       1SG    
ATOM   2273  C   SER   291      31.878  10.517   5.860  1.00 85.85       1SG    
ATOM   2274  O   SER   291      30.685  10.269   6.026  1.00 85.85       1SG    
ATOM   2275  N   GLN   292      32.295  11.733   5.458  1.00178.06       1SG    
ATOM   2276  CA  GLN   292      31.292  12.733   5.235  1.00178.06       1SG    
ATOM   2277  CB  GLN   292      31.352  13.878   6.258  1.00178.06       1SG    
ATOM   2278  CG  GLN   292      32.641  14.697   6.185  1.00178.06       1SG    
ATOM   2279  CD  GLN   292      32.565  15.789   7.242  1.00178.06       1SG    
ATOM   2280  OE1 GLN   292      31.822  14.891   6.851  1.00178.06       1SG    
ATOM   2281  NE2 GLN   292      33.802  16.274   6.951  1.00178.06       1SG    
ATOM   2282  C   GLN   292      31.558  13.332   3.895  1.00178.06       1SG    
ATOM   2283  O   GLN   292      31.096  14.433   3.599  1.00178.06       1SG    
ATOM   2284  N   VAL   293      32.280  12.594   3.031  1.00100.97       1SG    
ATOM   2285  CA  VAL   293      32.592  13.136   1.743  1.00100.97       1SG    
ATOM   2286  CB  VAL   293      34.038  13.513   1.577  1.00100.97       1SG    
ATOM   2287  CG1 VAL   293      34.896  12.238   1.624  1.00100.97       1SG    
ATOM   2288  CG2 VAL   293      34.195  14.323   0.280  1.00100.97       1SG    
ATOM   2289  C   VAL   293      32.254  12.098   0.725  1.00100.97       1SG    
ATOM   2290  O   VAL   293      31.998  10.944   1.061  1.00100.97       1SG    
ATOM   2291  N   HIS   294      32.191  12.512  -0.554  1.00128.28       1SG    
ATOM   2292  CA  HIS   294      31.868  11.625  -1.632  1.00128.28       1SG    
ATOM   2293  ND1 HIS   294      28.928   9.981  -2.931  1.00128.28       1SG    
ATOM   2294  CG  HIS   294      29.906  10.924  -3.160  1.00128.28       1SG    
ATOM   2295  CB  HIS   294      30.421  11.860  -2.109  1.00128.28       1SG    
ATOM   2296  NE2 HIS   294      29.470   9.823  -5.081  1.00128.28       1SG    
ATOM   2297  CD2 HIS   294      30.227  10.813  -4.478  1.00128.28       1SG    
ATOM   2298  CE1 HIS   294      28.706   9.353  -4.113  1.00128.28       1SG    
ATOM   2299  C   HIS   294      32.762  12.022  -2.761  1.00128.28       1SG    
ATOM   2300  O   HIS   294      32.703  13.158  -3.224  1.00128.28       1SG    
ATOM   2301  N   PHE   295      33.621  11.111  -3.248  1.00 93.06       1SG    
ATOM   2302  CA  PHE   295      34.485  11.518  -4.317  1.00 93.06       1SG    
ATOM   2303  CB  PHE   295      35.976  11.267  -4.033  1.00 93.06       1SG    
ATOM   2304  CG  PHE   295      36.744  11.746  -5.217  1.00 93.06       1SG    
ATOM   2305  CD1 PHE   295      37.079  13.073  -5.347  1.00 93.06       1SG    
ATOM   2306  CD2 PHE   295      37.128  10.862  -6.201  1.00 93.06       1SG    
ATOM   2307  CE1 PHE   295      37.788  13.513  -6.439  1.00 93.06       1SG    
ATOM   2308  CE2 PHE   295      37.836  11.297  -7.296  1.00 93.06       1SG    
ATOM   2309  CZ  PHE   295      38.167  12.627  -7.417  1.00 93.06       1SG    
ATOM   2310  C   PHE   295      34.130  10.739  -5.532  1.00 93.06       1SG    
ATOM   2311  O   PHE   295      34.082   9.512  -5.496  1.00 93.06       1SG    
ATOM   2312  N   THR   296      33.831  11.437  -6.645  1.00151.73       1SG    
ATOM   2313  CA  THR   296      33.555  10.708  -7.845  1.00151.73       1SG    
ATOM   2314  CB  THR   296      32.109  10.344  -8.014  1.00151.73       1SG    
ATOM   2315  OG1 THR   296      31.314  11.518  -8.091  1.00151.73       1SG    
ATOM   2316  CG2 THR   296      31.674   9.482  -6.818  1.00151.73       1SG    
ATOM   2317  C   THR   296      33.927  11.557  -9.010  1.00151.73       1SG    
ATOM   2318  O   THR   296      33.581  12.736  -9.072  1.00151.73       1SG    
ATOM   2319  N   ARG   297      34.642  10.956  -9.980  1.00295.88       1SG    
ATOM   2320  CA  ARG   297      35.014  11.670 -11.164  1.00295.88       1SG    
ATOM   2321  CB  ARG   297      36.515  11.993 -11.244  1.00295.88       1SG    
ATOM   2322  CG  ARG   297      37.406  10.748 -11.235  1.00295.88       1SG    
ATOM   2323  CD  ARG   297      38.900  11.065 -11.315  1.00295.88       1SG    
ATOM   2324  NE  ARG   297      39.146  11.717 -12.632  1.00295.88       1SG    
ATOM   2325  CZ  ARG   297      39.410  10.954 -13.733  1.00295.88       1SG    
ATOM   2326  NH1 ARG   297      39.439   9.594 -13.629  1.00295.88       1SG    
ATOM   2327  NH2 ARG   297      39.640  11.552 -14.939  1.00295.88       1SG    
ATOM   2328  C   ARG   297      34.696  10.773 -12.311  1.00295.88       1SG    
ATOM   2329  O   ARG   297      34.804   9.553 -12.204  1.00295.88       1SG    
ATOM   2330  N   GLU   298      34.268  11.359 -13.444  1.00229.44       1SG    
ATOM   2331  CA  GLU   298      33.962  10.539 -14.577  1.00229.44       1SG    
ATOM   2332  CB  GLU   298      32.503  10.659 -15.048  1.00229.44       1SG    
ATOM   2333  CG  GLU   298      31.491  10.088 -14.051  1.00229.44       1SG    
ATOM   2334  CD  GLU   298      30.099  10.273 -14.637  1.00229.44       1SG    
ATOM   2335  OE1 GLU   298      29.994  10.878 -15.737  1.00229.44       1SG    
ATOM   2336  OE2 GLU   298      29.120   9.809 -13.993  1.00229.44       1SG    
ATOM   2337  C   GLU   298      34.826  10.997 -15.702  1.00229.44       1SG    
ATOM   2338  O   GLU   298      35.027  12.195 -15.897  1.00229.44       1SG    
ATOM   2339  N   MET   299      35.383  10.038 -16.463  1.00285.52       1SG    
ATOM   2340  CA  MET   299      36.194  10.400 -17.585  1.00285.52       1SG    
ATOM   2341  CB  MET   299      37.117   9.270 -18.071  1.00285.52       1SG    
ATOM   2342  CG  MET   299      38.019   9.676 -19.239  1.00285.52       1SG    
ATOM   2343  SD  MET   299      39.335  10.849 -18.797  1.00285.52       1SG    
ATOM   2344  CE  MET   299      40.266   9.668 -17.779  1.00285.52       1SG    
ATOM   2345  C   MET   299      35.252  10.728 -18.690  1.00285.52       1SG    
ATOM   2346  O   MET   299      34.163  10.164 -18.783  1.00285.52       1SG    
TER
END
