
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0301AL044_2-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected  191 , name T0301_D2.pdb
# PARAMETERS: T0301AL044_2-D2.T0301_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T     194      D     187           -
LGA    G     195      G     188           -
LGA    -       -      G     189           -
LGA    -       -      A     190           -
LGA    -       -      I     191           -
LGA    -       -      F     192           -
LGA    -       -      P     193           -
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    N     196      F     209           #
LGA    L     197      K     210          4.281
LGA    V     198      A     211          1.835
LGA    D     199      T     212          2.420
LGA    D     200      M     213          3.018
LGA    V     203      I     214          2.686
LGA    P     204      N     215          2.605
LGA    -       -      A     216           -
LGA    G     205      G     217          2.362
LGA    V     206      I     218          2.415
LGA    T     208      P     219          2.159
LGA    K     210      T     220          3.061
LGA    T     212      V     221          1.387
LGA    M     213      F     222          2.311
LGA    -       -      V     223           -
LGA    -       -      N     224           -
LGA    -       -      A     225           -
LGA    -       -      E     226           -
LGA    -       -      E     227           -
LGA    -       -      I     228           -
LGA    -       -      G     229           -
LGA    -       -      Y     230           -
LGA    -       -      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     247           -
LGA    -       -      R     248           -
LGA    -       -      F     249           -
LGA    -       -      E     250           -
LGA    -       -      R     251           -
LGA    -       -      I     252           -
LGA    -       -      R     253           -
LGA    -       -      V     254           -
LGA    -       -      A     255           -
LGA    -       -      G     256           -
LGA    -       -      A     257           -
LGA    -       -      L     258           -
LGA    -       -      R     259           -
LGA    -       -      M     260           -
LGA    -       -      G     261           -
LGA    -       -      L     262           -
LGA    -       -      I     263           -
LGA    -       -      K     264           -
LGA    -       -      T     265           -
LGA    -       -      P     266           -
LGA    -       -      E     267           -
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    I     214      F     280          1.970
LGA    N     215      V     281          1.730
LGA    A     216      A     282          1.610
LGA    G     217      P     283          1.959
LGA    I     218      P     284          1.620
LGA    P     219      R     285          2.110
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    T     220      A     297          1.921
LGA    E     227      G     298          3.296
LGA    -       -      D     299           -
LGA    -       -      I     300           -
LGA    I     228      D     301          2.302
LGA    G     229      L     302          1.144
LGA    Y     230      L     303          3.175
LGA    R     231      V     304          1.242
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)   27  191    5.0     24    2.39     8.33      9.542     0.966

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.594029 * X  +  -0.797619 * Y  +  -0.104558 * Z  +  94.367783
  Y_new =  -0.300893 * X  +  -0.340846 * Y  +   0.890667 * Z  + -21.294891
  Z_new =  -0.746051 * X  +  -0.497621 * Y  +  -0.442471 * Z  + 119.619682 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.297597    0.843996  [ DEG:  -131.6426     48.3574 ]
  Theta =   0.842112    2.299480  [ DEG:    48.2495    131.7505 ]
  Phi   =  -0.468857    2.672736  [ DEG:   -26.8635    153.1365 ]
 
# 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: T0301AL044_2-D2                               
REMARK     2: T0301_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301AL044_2-D2.T0301_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27  191   5.0   24   2.39    8.33   9.542
REMARK  ---------------------------------------------------------- 
MOLECULE T0301AL044_2-D2
REMARK Aligment from pdb entry: 1tm0_A
ATOM    269  N   THR   194     100.075  -3.240  21.089  1.00  0.00              
ATOM    270  CA  THR   194     101.009  -2.932  20.016  1.00  0.00              
ATOM    271  C   THR   194     101.735  -1.621  20.301  1.00  0.00              
ATOM    272  O   THR   194     101.218  -0.758  21.003  1.00  0.00              
ATOM    273  N   GLY   195     102.939  -1.481  19.756  1.00  0.00              
ATOM    274  CA  GLY   195     103.741  -0.273  19.936  1.00  0.00              
ATOM    275  C   GLY   195     104.361   0.127  18.603  1.00  0.00              
ATOM    276  O   GLY   195     104.944  -0.706  17.915  1.00  0.00              
ATOM    277  N   ASN   196     104.243   1.401  18.240  1.00  0.00              
ATOM    278  CA  ASN   196     104.805   1.881  16.979  1.00  0.00              
ATOM    279  C   ASN   196     104.503   0.894  15.859  1.00  0.00              
ATOM    280  O   ASN   196     105.397   0.203  15.372  1.00  0.00              
ATOM    281  N   LEU   197     103.240   0.812  15.463  1.00  0.00              
ATOM    282  CA  LEU   197     102.855  -0.085  14.389  1.00  0.00              
ATOM    283  C   LEU   197     102.205   0.740  13.292  1.00  0.00              
ATOM    284  O   LEU   197     101.460   1.677  13.569  1.00  0.00              
ATOM    285  N   VAL   198     102.494   0.413  12.027  1.00  0.00              
ATOM    286  CA  VAL   198     101.906   1.163  10.915  1.00  0.00              
ATOM    287  C   VAL   198     100.388   1.097  10.990  1.00  0.00              
ATOM    288  O   VAL   198      99.836   0.188  11.604  1.00  0.00              
ATOM    289  N   ASP   199      99.722   2.063  10.365  1.00  0.00              
ATOM    290  CA  ASP   199      98.263   2.113  10.371  1.00  0.00              
ATOM    291  C   ASP   199      97.721   2.770   9.100  1.00  0.00              
ATOM    292  O   ASP   199      97.796   3.987   8.935  1.00  0.00              
ATOM    293  N   ASP   200      97.173   1.952   8.205  1.00  0.00              
ATOM    294  CA  ASP   200      96.616   2.435   6.942  1.00  0.00              
ATOM    295  C   ASP   200      95.320   3.221   7.151  1.00  0.00              
ATOM    296  O   ASP   200      94.226   2.657   7.142  1.00  0.00              
ATOM    297  N   VAL   203      95.454   4.530   7.334  1.00  0.00              
ATOM    298  CA  VAL   203      94.300   5.391   7.541  1.00  0.00              
ATOM    299  C   VAL   203      93.836   6.018   6.229  1.00  0.00              
ATOM    300  O   VAL   203      94.582   6.753   5.581  1.00  0.00              
ATOM    301  N   PRO   204      92.600   5.724   5.840  1.00  0.00              
ATOM    302  CA  PRO   204      92.054   6.266   4.604  1.00  0.00              
ATOM    303  C   PRO   204      92.004   7.793   4.662  1.00  0.00              
ATOM    304  O   PRO   204      91.744   8.450   3.655  1.00  0.00              
ATOM    305  N   GLY   205      92.258   8.355   5.842  1.00  0.00              
ATOM    306  CA  GLY   205      92.234   9.800   5.995  1.00  0.00              
ATOM    307  C   GLY   205      93.293  10.497   5.158  1.00  0.00              
ATOM    308  O   GLY   205      92.974  11.185   4.189  1.00  0.00              
ATOM    309  N   VAL   206      94.555  10.327   5.542  1.00  0.00              
ATOM    310  CA  VAL   206      95.668  10.924   4.815  1.00  0.00              
ATOM    311  C   VAL   206      96.986  10.340   5.306  1.00  0.00              
ATOM    312  O   VAL   206      97.251  10.300   6.506  1.00  0.00              
ATOM    313  N   THR   208      97.801   9.881   4.362  1.00  0.00              
ATOM    314  CA  THR   208      99.086   9.302   4.699  1.00  0.00              
ATOM    315  C   THR   208      98.972   8.101   5.616  1.00  0.00              
ATOM    316  O   THR   208      97.874   7.620   5.902  1.00  0.00              
ATOM    317  N   LYS   210     100.118   7.604   6.065  1.00  0.00              
ATOM    318  CA  LYS   210     100.152   6.467   6.969  1.00  0.00              
ATOM    319  C   LYS   210     100.913   6.912   8.212  1.00  0.00              
ATOM    320  O   LYS   210     101.937   7.590   8.104  1.00  0.00              
ATOM    321  N   THR   212     100.405   6.544   9.387  1.00  0.00              
ATOM    322  CA  THR   212     101.034   6.908  10.658  1.00  0.00              
ATOM    323  C   THR   212     101.198   5.693  11.558  1.00  0.00              
ATOM    324  O   THR   212     100.484   4.702  11.410  1.00  0.00              
ATOM    325  N   MET   213     102.138   5.771  12.494  1.00  0.00              
ATOM    326  CA  MET   213     102.372   4.671  13.421  1.00  0.00              
ATOM    327  C   MET   213     101.686   4.981  14.745  1.00  0.00              
ATOM    328  O   MET   213     101.724   6.118  15.207  1.00  0.00              
ATOM    329  N   ILE   214     101.059   3.975  15.349  1.00  0.00              
ATOM    330  CA  ILE   214     100.374   4.157  16.626  1.00  0.00              
ATOM    331  C   ILE   214     100.633   2.993  17.578  1.00  0.00              
ATOM    332  O   ILE   214     101.267   2.003  17.207  1.00  0.00              
ATOM    333  N   ASN   215     100.144   3.123  18.810  1.00  0.00              
ATOM    334  CA  ASN   215     100.294   2.083  19.826  1.00  0.00              
ATOM    335  C   ASN   215      98.964   1.813  20.529  1.00  0.00              
ATOM    336  O   ASN   215      98.218   2.744  20.826  1.00  0.00              
ATOM    337  N   ALA   216      98.665   0.539  20.779  1.00  0.00              
ATOM    338  CA  ALA   216      97.420   0.165  21.453  1.00  0.00              
ATOM    339  C   ALA   216      97.716  -0.287  22.877  1.00  0.00              
ATOM    340  O   ALA   216      98.673  -1.015  23.115  1.00  0.00              
ATOM    341  N   GLY   217      96.896   0.158  23.822  1.00  0.00              
ATOM    342  CA  GLY   217      97.087  -0.205  25.222  1.00  0.00              
ATOM    343  C   GLY   217      95.766  -0.492  25.929  1.00  0.00              
ATOM    344  O   GLY   217      94.699  -0.352  25.341  1.00  0.00              
ATOM    345  N   ILE   218      95.850  -0.899  27.192  1.00  0.00              
ATOM    346  CA  ILE   218      94.667  -1.200  27.998  1.00  0.00              
ATOM    347  C   ILE   218      94.928  -0.877  29.452  1.00  0.00              
ATOM    348  O   ILE   218      95.810  -1.460  30.073  1.00  0.00              
ATOM    349  N   PRO   219      94.157   0.057  29.989  1.00  0.00              
ATOM    350  CA  PRO   219      94.310   0.441  31.375  1.00  0.00              
ATOM    351  C   PRO   219      92.928   0.621  31.946  1.00  0.00              
ATOM    352  O   PRO   219      92.614   1.651  32.526  1.00  0.00              
ATOM    353  N   THR   220      92.099  -0.403  31.775  1.00  0.00              
ATOM    354  CA  THR   220      90.735  -0.343  32.252  1.00  0.00              
ATOM    355  C   THR   220      89.831  -0.351  31.038  1.00  0.00              
ATOM    356  O   THR   220      88.652  -0.671  31.126  1.00  0.00              
ATOM    357  N   GLU   227      90.397   0.011  29.893  1.00  0.00              
ATOM    358  CA  GLU   227      89.658   0.027  28.640  1.00  0.00              
ATOM    359  C   GLU   227      90.668   0.022  27.487  1.00  0.00              
ATOM    360  O   GLU   227      91.845   0.364  27.674  1.00  0.00              
ATOM    361  N   ILE   228      90.212  -0.382  26.304  1.00  0.00              
ATOM    362  CA  ILE   228      91.080  -0.457  25.133  1.00  0.00              
ATOM    363  C   ILE   228      91.234   0.889  24.454  1.00  0.00              
ATOM    364  O   ILE   228      90.253   1.536  24.113  1.00  0.00              
ATOM    365  N   GLY   229      92.477   1.308  24.264  1.00  0.00              
ATOM    366  CA  GLY   229      92.760   2.584  23.637  1.00  0.00              
ATOM    367  C   GLY   229      93.804   2.425  22.560  1.00  0.00              
ATOM    368  O   GLY   229      94.548   1.445  22.516  1.00  0.00              
ATOM    369  N   TYR   230      93.853   3.420  21.685  1.00  0.00              
ATOM    370  CA  TYR   230      94.825   3.459  20.611  1.00  0.00              
ATOM    371  C   TYR   230      95.409   4.868  20.713  1.00  0.00              
ATOM    372  O   TYR   230      94.768   5.850  20.340  1.00  0.00              
ATOM    373  N   ARG   231      96.614   4.953  21.278  1.00  0.00              
ATOM    374  CA  ARG   231      97.293   6.229  21.477  1.00  0.00              
ATOM    375  C   ARG   231      98.021   6.654  20.206  1.00  0.00              
ATOM    376  O   ARG   231      98.708   5.852  19.564  1.00  0.00              
END
