
#######################################################
#                                                     #
#                        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   40 (  160),  selected   40 , name T0301AL333_3-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected  191 , name T0301_D2.pdb
# PARAMETERS: T0301AL333_3-D2.T0301_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    P     219      D     187           #
LGA    T     220      G     188          1.247
LGA    G     256      G     189          1.790
LGA    A     257      A     190          1.528
LGA    L     258      I     191          1.606
LGA    R     259      F     192          1.845
LGA    M     260      P     193          3.628
LGA    -       -      T     194           -
LGA    -       -      G     195           -
LGA    -       -      N     196           -
LGA    -       -      L     197           -
LGA    -       -      V     198           -
LGA    -       -      D     199           -
LGA    -       -      D     200           -
LGA    -       -      L     201           -
LGA    -       -      E     202           -
LGA    -       -      V     203           -
LGA    -       -      P     204           -
LGA    -       -      G     205           -
LGA    -       -      V     206           -
LGA    -       -      G     207           -
LGA    -       -      T     208           -
LGA    -       -      F     209           -
LGA    -       -      K     210           -
LGA    -       -      A     211           -
LGA    -       -      T     212           -
LGA    -       -      M     213           -
LGA    -       -      I     214           -
LGA    G     261      N     215          1.872
LGA    L     262      A     216          4.186
LGA    I     263      G     217           -
LGA    K     264      I     218          5.631
LGA    T     265      P     219          2.694
LGA    P     266      T     220          2.505
LGA    E     267      V     221          3.595
LGA    E     268      F     222          2.609
LGA    A     269      -       -           -
LGA    A     270      -       -           -
LGA    T     271      -       -           -
LGA    R     272      -       -           -
LGA    Q     273      V     223          4.865
LGA    H     274      N     224           #
LGA    T     275      A     225          4.331
LGA    -       -      E     226           -
LGA    P     276      E     227          2.625
LGA    G     292      I     228          5.247
LGA    K     293      G     229          2.282
LGA    L     294      Y     230          0.764
LGA    V     295      R     231           -
LGA    -       -      G     232           -
LGA    -       -      T     233           -
LGA    -       -      E     234           -
LGA    -       -      L     235           -
LGA    -       -      R     236           -
LGA    -       -      E     237           -
LGA    -       -      E     238           -
LGA    -       -      I     239           -
LGA    -       -      N     240           -
LGA    -       -      G     241           -
LGA    -       -      D     242           -
LGA    -       -      P     243           -
LGA    -       -      Q     244           -
LGA    -       -      Q     245           -
LGA    -       -      L     246           -
LGA    A     296      A     247           #
LGA    A     297      R     248          2.332
LGA    G     298      F     249          2.053
LGA    D     299      E     250          3.418
LGA    I     300      R     251          2.279
LGA    -       -      I     252           -
LGA    -       -      R     253           -
LGA    -       -      V     254           -
LGA    D     301      A     255          2.023
LGA    A     362      G     256          2.347
LGA    S     363      A     257          3.263
LGA    -       -      L     258           -
LGA    -       -      R     259           -
LGA    -       -      M     260           -
LGA    -       -      G     261           -
LGA    Q     364      L     262          2.114
LGA    A     365      I     263          2.641
LGA    -       -      K     264           -
LGA    N     366      T     265           #
LGA    G     367      P     266          0.416
LGA    E     368      E     267          1.345
LGA    -       -      E     268           -
LGA    -       -      A     269           -
LGA    -       -      A     270           -
LGA    -       -      T     271           -
LGA    -       -      R     272           -
LGA    -       -      Q     273           -
LGA    -       -      H     274           -
LGA    -       -      T     275           -
LGA    -       -      P     276           -
LGA    -       -      K     277           -
LGA    -       -      I     278           -
LGA    -       -      A     279           -
LGA    -       -      F     280           -
LGA    -       -      V     281           -
LGA    -       -      A     282           -
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      R     285           -
LGA    -       -      D     286           -
LGA    -       -      Y     287           -
LGA    -       -      R     288           -
LGA    -       -      T     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      G     292           -
LGA    -       -      K     293           -
LGA    -       -      L     294           -
LGA    -       -      V     295           -
LGA    -       -      A     296           -
LGA    -       -      A     297           -
LGA    -       -      G     298           -
LGA    -       -      D     299           -
LGA    -       -      I     300           -
LGA    -       -      D     301           -
LGA    -       -      L     302           -
LGA    -       -      L     303           -
LGA    -       -      V     304           -
LGA    -       -      R     305           -
LGA    -       -      A     306           -
LGA    -       -      L     307           -
LGA    -       -      S     308           -
LGA    -       -      M     309           -
LGA    -       -      G     310           -
LGA    -       -      K     311           -
LGA    -       -      L     312           -
LGA    -       -      H     313           -
LGA    -       -      H     314           -
LGA    -       -      A     315           -
LGA    -       -      M     316           -
LGA    -       -      M     317           -
LGA    -       -      G     318           -
LGA    -       -      T     319           -
LGA    -       -      A     320           -
LGA    -       -      A     321           -
LGA    -       -      V     322           -
LGA    -       -      A     323           -
LGA    -       -      I     324           -
LGA    -       -      G     325           -
LGA    -       -      T     326           -
LGA    -       -      A     327           -
LGA    -       -      A     328           -
LGA    -       -      A     329           -
LGA    -       -      I     330           -
LGA    -       -      P     331           -
LGA    -       -      G     332           -
LGA    -       -      T     333           -
LGA    -       -      L     334           -
LGA    -       -      V     335           -
LGA    -       -      N     336           -
LGA    -       -      L     337           -
LGA    -       -      A     338           -
LGA    -       -      A     339           -
LGA    -       -      G     340           -
LGA    -       -      G     341           -
LGA    -       -      G     342           -
LGA    -       -      E     343           -
LGA    -       -      R     344           -
LGA    -       -      S     345           -
LGA    -       -      A     346           -
LGA    -       -      V     347           -
LGA    -       -      R     348           -
LGA    -       -      F     349           -
LGA    -       -      G     350           -
LGA    -       -      H     351           -
LGA    -       -      P     352           -
LGA    -       -      S     353           -
LGA    -       -      G     354           -
LGA    -       -      T     355           -
LGA    -       -      L     356           -
LGA    -       -      R     357           -
LGA    -       -      V     358           -
LGA    -       -      G     359           -
LGA    -       -      A     360           -
LGA    -       -      E     361           -
LGA    -       -      A     362           -
LGA    -       -      S     363           -
LGA    -       -      Q     364           -
LGA    -       -      A     365           -
LGA    -       -      N     366           -
LGA    -       -      G     367           -
LGA    -       -      E     368           -
LGA    -       -      W     369           -
LGA    -       -      T     370           -
LGA    -       -      V     371           -
LGA    -       -      T     372           -
LGA    -       -      K     373           -
LGA    -       -      A     374           -
LGA    -       -      I     375           -
LGA    -       -      M     376           -
LGA    -       -      S     377           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   40  191    5.0     30    2.92    10.00      9.643     0.995

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.917984 * X  +  -0.078223 * Y  +  -0.388826 * Z  +  91.706070
  Y_new =  -0.263938 * X  +  -0.611274 * Y  +   0.746110 * Z  +  17.910906
  Z_new =  -0.296043 * X  +   0.787543 * Y  +   0.540494 * Z  +   3.329387 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.969321   -2.172271  [ DEG:    55.5380   -124.4620 ]
  Theta =   0.300547    2.841046  [ DEG:    17.2201    162.7799 ]
  Phi   =  -2.861625    0.279967  [ DEG:  -163.9590     16.0410 ]
 
# 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: T0301AL333_3-D2                               
REMARK     2: T0301_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301AL333_3-D2.T0301_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   40  191   5.0   30   2.92   10.00   9.643
REMARK  ---------------------------------------------------------- 
MOLECULE T0301AL333_3-D2
REMARK Aligment from pdb entry: 1lv3_A
ATOM     97  N   PRO   219      88.929  11.729  -3.501  1.00  0.00              
ATOM     98  CA  PRO   219      90.220  11.922  -2.810  1.00  0.00              
ATOM     99  C   PRO   219      90.926  10.566  -2.652  1.00  0.00              
ATOM    100  O   PRO   219      90.393   9.658  -2.041  1.00  0.00              
ATOM    101  N   THR   220      92.110  10.426  -3.215  1.00  0.00              
ATOM    102  CA  THR   220      92.872   9.128  -3.132  1.00  0.00              
ATOM    103  C   THR   220      92.151   8.042  -3.943  1.00  0.00              
ATOM    104  O   THR   220      90.970   8.140  -4.224  1.00  0.00              
ATOM    105  N   GLY   256      92.857   7.003  -4.319  1.00  0.00              
ATOM    106  CA  GLY   256      92.222   5.902  -5.109  1.00  0.00              
ATOM    107  C   GLY   256      91.658   4.832  -4.160  1.00  0.00              
ATOM    108  O   GLY   256      90.626   4.243  -4.429  1.00  0.00              
ATOM    109  N   ALA   257      92.324   4.581  -3.054  1.00  0.00              
ATOM    110  CA  ALA   257      91.833   3.556  -2.080  1.00  0.00              
ATOM    111  C   ALA   257      91.901   4.126  -0.656  1.00  0.00              
ATOM    112  O   ALA   257      92.542   5.135  -0.411  1.00  0.00              
ATOM    113  N   LEU   258      91.246   3.482   0.283  1.00  0.00              
ATOM    114  CA  LEU   258      91.268   3.973   1.697  1.00  0.00              
ATOM    115  C   LEU   258      92.645   3.708   2.321  1.00  0.00              
ATOM    116  O   LEU   258      93.139   4.517   3.080  1.00  0.00              
ATOM    117  N   ARG   259      93.276   2.594   1.997  1.00  0.00              
ATOM    118  CA  ARG   259      94.633   2.300   2.566  1.00  0.00              
ATOM    119  C   ARG   259      95.592   3.430   2.170  1.00  0.00              
ATOM    120  O   ARG   259      96.464   3.805   2.933  1.00  0.00              
ATOM    121  N   MET   260      95.420   3.983   0.989  1.00  0.00              
ATOM    122  CA  MET   260      96.300   5.102   0.541  1.00  0.00              
ATOM    123  C   MET   260      96.028   6.323   1.421  1.00  0.00              
ATOM    124  O   MET   260      96.926   6.851   2.054  1.00  0.00              
ATOM    125  N   GLY   261      94.788   6.760   1.483  1.00  0.00              
ATOM    126  CA  GLY   261      94.432   7.933   2.340  1.00  0.00              
ATOM    127  C   GLY   261      94.825   7.631   3.793  1.00  0.00              
ATOM    128  O   GLY   261      95.228   8.513   4.529  1.00  0.00              
ATOM    129  N   LEU   262      94.723   6.382   4.197  1.00  0.00              
ATOM    130  CA  LEU   262      95.101   5.991   5.587  1.00  0.00              
ATOM    131  C   LEU   262      96.595   6.265   5.786  1.00  0.00              
ATOM    132  O   LEU   262      96.972   7.125   6.558  1.00  0.00              
ATOM    133  N   ILE   263      97.441   5.552   5.078  1.00  0.00              
ATOM    134  CA  ILE   263      98.920   5.761   5.203  1.00  0.00              
ATOM    135  C   ILE   263      99.260   7.260   5.083  1.00  0.00              
ATOM    136  O   ILE   263     100.242   7.719   5.637  1.00  0.00              
ATOM    137  N   LYS   264      98.456   8.020   4.366  1.00  0.00              
ATOM    138  CA  LYS   264      98.731   9.483   4.209  1.00  0.00              
ATOM    139  C   LYS   264      98.754  10.175   5.580  1.00  0.00              
ATOM    140  O   LYS   264      99.582  11.034   5.824  1.00  0.00              
ATOM    141  N   THR   265      97.865   9.801   6.475  1.00  0.00              
ATOM    142  CA  THR   265      97.851  10.431   7.833  1.00  0.00              
ATOM    143  C   THR   265      99.164  10.089   8.550  1.00  0.00              
ATOM    144  O   THR   265      99.932  10.967   8.903  1.00  0.00              
ATOM    145  N   PRO   266      99.431   8.817   8.750  1.00  0.00              
ATOM    146  CA  PRO   266     100.704   8.405   9.424  1.00  0.00              
ATOM    147  C   PRO   266     100.420   7.802  10.807  1.00  0.00              
ATOM    148  O   PRO   266     101.275   7.813  11.674  1.00  0.00              
ATOM    149  N   GLU   267      99.236   7.272  11.022  1.00  0.00              
ATOM    150  CA  GLU   267      98.906   6.663  12.349  1.00  0.00              
ATOM    151  C   GLU   267      98.407   5.224  12.135  1.00  0.00              
ATOM    152  O   GLU   267      97.467   4.779  12.770  1.00  0.00              
ATOM    153  N   GLU   268      99.034   4.499  11.235  1.00  0.00              
ATOM    154  CA  GLU   268      98.607   3.089  10.951  1.00  0.00              
ATOM    155  C   GLU   268      99.845   2.192  10.813  1.00  0.00              
ATOM    156  O   GLU   268     100.970   2.644  10.948  1.00  0.00              
ATOM    157  N   ALA   269      99.645   0.921  10.545  1.00  0.00              
ATOM    158  CA  ALA   269     100.800  -0.016  10.394  1.00  0.00              
ATOM    159  C   ALA   269     101.081  -0.250   8.901  1.00  0.00              
ATOM    160  O   ALA   269     100.611  -1.211   8.313  1.00  0.00              
ATOM    161  N   ALA   270     101.845   0.622   8.284  1.00  0.00              
ATOM    162  CA  ALA   270     102.162   0.459   6.831  1.00  0.00              
ATOM    163  C   ALA   270     103.381   1.326   6.471  1.00  0.00              
ATOM    164  O   ALA   270     103.310   2.197   5.622  1.00  0.00              
ATOM    165  N   THR   271     104.503   1.082   7.116  1.00  0.00              
ATOM    166  CA  THR   271     105.744   1.875   6.833  1.00  0.00              
ATOM    167  C   THR   271     105.448   3.377   6.999  1.00  0.00              
ATOM    168  O   THR   271     105.271   4.096   6.028  1.00  0.00              
ATOM    169  N   ARG   272     105.391   3.854   8.223  1.00  0.00              
ATOM    170  CA  ARG   272     105.103   5.308   8.449  1.00  0.00              
ATOM    171  C   ARG   272     105.383   5.700   9.909  1.00  0.00              
ATOM    172  O   ARG   272     105.890   6.775  10.174  1.00  0.00              
ATOM    173  N   GLN   273     105.056   4.848  10.852  1.00  0.00              
ATOM    174  CA  GLN   273     105.302   5.179  12.289  1.00  0.00              
ATOM    175  C   GLN   273     105.839   3.941  13.019  1.00  0.00              
ATOM    176  O   GLN   273     105.179   2.922  13.097  1.00  0.00              
ATOM    177  N   HIS   274     107.044   4.025  13.541  1.00  0.00              
ATOM    178  CA  HIS   274     107.638   2.855  14.260  1.00  0.00              
ATOM    179  C   HIS   274     107.393   2.986  15.767  1.00  0.00              
ATOM    180  O   HIS   274     107.686   4.006  16.370  1.00  0.00              
ATOM    181  N   THR   275     106.850   1.954  16.373  1.00  0.00              
ATOM    182  CA  THR   275     106.564   1.988  17.841  1.00  0.00              
ATOM    183  C   THR   275     107.372   0.883  18.551  1.00  0.00              
ATOM    184  O   THR   275     106.970  -0.268  18.556  1.00  0.00              
ATOM    185  N   PRO   276     108.490   1.271  19.137  1.00  0.00              
ATOM    186  CA  PRO   276     109.382   0.337  19.871  1.00  0.00              
ATOM    187  C   PRO   276     108.804  -0.049  21.246  1.00  0.00              
ATOM    188  O   PRO   276     107.823   0.511  21.706  1.00  0.00              
ATOM    189  N   GLY   292     109.426  -1.010  21.898  1.00  0.00              
ATOM    190  CA  GLY   292     108.959  -1.467  23.247  1.00  0.00              
ATOM    191  C   GLY   292     109.101  -0.326  24.266  1.00  0.00              
ATOM    192  O   GLY   292     108.308  -0.212  25.180  1.00  0.00              
ATOM    193  N   LYS   293     110.099   0.523  24.116  1.00  0.00              
ATOM    194  CA  LYS   293     110.273   1.660  25.076  1.00  0.00              
ATOM    195  C   LYS   293     109.000   2.512  25.068  1.00  0.00              
ATOM    196  O   LYS   293     108.522   2.948  26.099  1.00  0.00              
ATOM    197  N   LEU   294     108.445   2.739  23.899  1.00  0.00              
ATOM    198  CA  LEU   294     107.196   3.548  23.787  1.00  0.00              
ATOM    199  C   LEU   294     107.064   4.067  22.352  1.00  0.00              
ATOM    200  O   LEU   294     106.733   3.322  21.445  1.00  0.00              
ATOM    201  N   VAL   295     107.334   5.335  22.143  1.00  0.00              
ATOM    202  CA  VAL   295     107.241   5.910  20.764  1.00  0.00              
ATOM    203  C   VAL   295     108.544   6.651  20.423  1.00  0.00              
ATOM    204  O   VAL   295     108.977   7.530  21.148  1.00  0.00              
ATOM    205  N   ALA   296     109.180   6.286  19.329  1.00  0.00              
ATOM    206  CA  ALA   296     110.468   6.948  18.943  1.00  0.00              
ATOM    207  C   ALA   296     110.400   7.478  17.505  1.00  0.00              
ATOM    208  O   ALA   296     109.883   6.825  16.617  1.00  0.00              
ATOM    209  N   ALA   297     110.945   8.656  17.276  1.00  0.00              
ATOM    210  CA  ALA   297     110.950   9.256  15.905  1.00  0.00              
ATOM    211  C   ALA   297     109.522   9.300  15.334  1.00  0.00              
ATOM    212  O   ALA   297     109.125   8.455  14.547  1.00  0.00              
ATOM    213  N   GLY   298     108.757  10.292  15.719  1.00  0.00              
ATOM    214  CA  GLY   298     107.361  10.419  15.199  1.00  0.00              
ATOM    215  C   GLY   298     107.412  11.122  13.838  1.00  0.00              
ATOM    216  O   GLY   298     108.043  12.155  13.692  1.00  0.00              
ATOM    217  N   ASP   299     106.765  10.560  12.841  1.00  0.00              
ATOM    218  CA  ASP   299     106.772  11.169  11.472  1.00  0.00              
ATOM    219  C   ASP   299     108.190  11.089  10.877  1.00  0.00              
ATOM    220  O   ASP   299     108.856  12.091  10.681  1.00  0.00              
ATOM    221  N   ILE   300     108.650   9.892  10.583  1.00  0.00              
ATOM    222  CA  ILE   300     110.016   9.723   9.993  1.00  0.00              
ATOM    223  C   ILE   300     109.945   8.695   8.857  1.00  0.00              
ATOM    224  O   ILE   300     109.705   7.522   9.087  1.00  0.00              
ATOM    225  N   ASP   301     110.143   9.136   7.633  1.00  0.00              
ATOM    226  CA  ASP   301     110.083   8.212   6.452  1.00  0.00              
ATOM    227  C   ASP   301     108.647   7.698   6.276  1.00  0.00              
ATOM    228  O   ASP   301     108.238   6.729   6.895  1.00  0.00              
ATOM    229  N   ALA   362     107.880   8.347   5.434  1.00  0.00              
ATOM    230  CA  ALA   362     106.465   7.915   5.200  1.00  0.00              
ATOM    231  C   ALA   362     106.377   7.116   3.900  1.00  0.00              
ATOM    232  O   ALA   362     107.295   7.112   3.096  1.00  0.00              
ATOM    233  N   SER   363     105.264   6.459   3.674  1.00  0.00              
ATOM    234  CA  SER   363     105.098   5.678   2.410  1.00  0.00              
ATOM    235  C   SER   363     105.039   6.656   1.231  1.00  0.00              
ATOM    236  O   SER   363     105.604   6.404   0.183  1.00  0.00              
ATOM    237  N   GLN   364     104.372   7.779   1.405  1.00  0.00              
ATOM    238  CA  GLN   364     104.284   8.791   0.305  1.00  0.00              
ATOM    239  C   GLN   364     105.666   9.402   0.073  1.00  0.00              
ATOM    240  O   GLN   364     106.202   9.370  -1.021  1.00  0.00              
ATOM    241  N   ALA   365     106.223   9.981   1.108  1.00  0.00              
ATOM    242  CA  ALA   365     107.551  10.639   1.003  1.00  0.00              
ATOM    243  C   ALA   365     108.510  10.051   2.052  1.00  0.00              
ATOM    244  O   ALA   365     108.378  10.323   3.229  1.00  0.00              
ATOM    245  N   ASN   366     109.455   9.264   1.595  1.00  0.00              
ATOM    246  CA  ASN   366     110.452   8.634   2.478  1.00  0.00              
ATOM    247  C   ASN   366     111.515   9.654   2.917  1.00  0.00              
ATOM    248  O   ASN   366     111.809   9.766   4.091  1.00  0.00              
ATOM    249  N   GLY   367     112.084  10.401   1.991  1.00  0.00              
ATOM    250  CA  GLY   367     113.127  11.415   2.368  1.00  0.00              
ATOM    251  C   GLY   367     113.175  12.546   1.322  1.00  0.00              
ATOM    252  O   GLY   367     113.198  12.299   0.132  1.00  0.00              
ATOM    253  N   GLU   368     113.196  13.786   1.770  1.00  0.00              
ATOM    254  CA  GLU   368     113.248  14.950   0.817  1.00  0.00              
ATOM    255  C   GLU   368     114.438  15.858   1.166  1.00  0.00              
ATOM    256  O   GLU   368     115.216  16.143   0.271  1.00  0.00              
END
