
#######################################################
#                                                     #
#                        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   42 (  207),  selected   42 , name T0386TS103_4-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS103_4-D2.T0386_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N     219           -
LGA    -       -      P     220           -
LGA    -       -      E     221           -
LGA    -       -      K     222           -
LGA    -       -      I     223           -
LGA    I     223      R     224          2.936
LGA    R     224      L     225          4.468
LGA    L     225      -       -           -
LGA    L     226      L     226          1.184
LGA    K     227      K     227          4.287
LGA    E     228      E     228           #
LGA    F     229      F     229           #
LGA    M     230      M     230           #
LGA    H     231      -       -           -
LGA    T     232      H     231           #
LGA    -       -      T     232           -
LGA    M     233      M     233           #
LGA    A     248      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    K     249      V     240           #
LGA    E     250      N     241          2.849
LGA    -       -      D     242           -
LGA    G     251      R     243          3.729
LGA    E     252      P     244          2.690
LGA    T     253      V     245          0.852
LGA    Y     254      M     246          4.094
LGA    T     255      V     247          3.105
LGA    -       -      A     248           -
LGA    -       -      K     249           -
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    -       -      Y     254           -
LGA    -       -      T     255           -
LGA    -       -      G     256           -
LGA    -       -      T     257           -
LGA    -       -      Y     258           -
LGA    -       -      R     259           -
LGA    -       -      G     260           -
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      G     265           -
LGA    -       -      F     266           -
LGA    -       -      A     267           -
LGA    -       -      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    L     268      G     277          2.783
LGA    N     269      N     278          3.187
LGA    V     270      I     279          3.069
LGA    K     271      D     280          3.054
LGA    -       -      H     281           -
LGA    G     272      L     282          5.082
LGA    A     273      P     283          4.927
LGA    Y     274      -       -           -
LGA    I     275      P     284          4.851
LGA    I     276      E     285          2.214
LGA    G     277      Q     286           -
LGA    -       -      L     287           -
LGA    N     278      K     288           #
LGA    I     279      I     289           -
LGA    D     280      L     290           -
LGA    H     281      K     291           -
LGA    L     282      P     292           -
LGA    P     283      G     293           -
LGA    P     284      D     294           -
LGA    E     285      K     295           -
LGA    Q     286      I     296           -
LGA    L     287      T     297           -
LGA    K     288      F     298           -
LGA    F     298      T     299           -
LGA    T     299      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   42   81    5.0     18    3.50    16.67     14.793     0.501

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.352630 * X  +  -0.864650 * Y  +   0.357817 * Z  +  -0.551125
  Y_new =   0.376752 * X  +   0.481204 * Y  +   0.791518 * Z  +  53.927036
  Z_new =  -0.856569 * X  +  -0.144305 * Y  +   0.495445 * Z  +  78.798592 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.283423    2.858170  [ DEG:   -16.2389    163.7611 ]
  Theta =   1.028584    2.113009  [ DEG:    58.9335    121.0665 ]
  Phi   =   0.818457   -2.323135  [ DEG:    46.8941   -133.1059 ]
 
# 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: T0386TS103_4-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS103_4-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   42   81   5.0   18   3.50   16.67  14.793
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS103_4-D2
PFRMAT TS
TARGET T0386
MODEL 4
PARENT 1uls_A
ATOM    694  N   ILE   223       7.059  64.712  81.024  1.00  1.00
ATOM    695  CA  ILE   223       6.942  63.497  80.215  1.00  1.00
ATOM    696  C   ILE   223       6.594  63.889  78.765  1.00  1.00
ATOM    697  O   ILE   223       7.113  63.309  77.805  1.00  1.00
ATOM    698  CB  ILE   223       5.853  62.553  80.775  1.00  1.00
ATOM    699  N   ARG   224       5.712  64.877  78.623  1.00  1.00
ATOM    700  CA  ARG   224       5.321  65.343  77.310  1.00  1.00
ATOM    701  C   ARG   224       6.485  66.054  76.641  1.00  1.00
ATOM    702  O   ARG   224       6.645  65.989  75.418  1.00  1.00
ATOM    703  CB  ARG   224       4.163  66.346  77.471  1.00  1.00
ATOM    704  N   LEU   225       7.302  66.735  77.443  1.00  1.00
ATOM    705  CA  LEU   225       8.462  67.447  76.915  1.00  1.00
ATOM    706  C   LEU   225       9.468  66.416  76.401  1.00  1.00
ATOM    707  O   LEU   225       9.960  66.505  75.267  1.00  1.00
ATOM    708  CB  LEU   225       9.100  68.315  78.015  1.00  1.00
ATOM    709  N   LEU   226       9.769  65.434  77.245  1.00  1.00
ATOM    710  CA  LEU   226      10.705  64.377  76.885  1.00  1.00
ATOM    711  C   LEU   226      10.309  63.713  75.564  1.00  1.00
ATOM    712  O   LEU   226      11.143  63.542  74.688  1.00  1.00
ATOM    713  CB  LEU   226      10.784  63.286  77.978  1.00  1.00
ATOM    714  N   LYS   227       9.038  63.349  75.415  1.00  1.00
ATOM    715  CA  LYS   227       8.600  62.706  74.186  1.00  1.00
ATOM    716  C   LYS   227       8.762  63.601  72.968  1.00  1.00
ATOM    717  O   LYS   227       9.131  63.139  71.888  1.00  1.00
ATOM    718  CB  LYS   227       7.149  62.250  74.322  1.00  1.00
ATOM    719  N   GLU   228       8.487  64.885  73.138  1.00  1.00
ATOM    720  CA  GLU   228       8.621  65.828  72.038  1.00  1.00
ATOM    721  C   GLU   228      10.091  65.942  71.651  1.00  1.00
ATOM    722  O   GLU   228      10.451  65.836  70.476  1.00  1.00
ATOM    723  CB  GLU   228       8.100  67.203  72.447  1.00  1.00
ATOM    724  N   PHE   229      10.946  66.143  72.646  1.00  1.00
ATOM    725  CA  PHE   229      12.375  66.273  72.389  1.00  1.00
ATOM    726  C   PHE   229      12.924  65.031  71.702  1.00  1.00
ATOM    727  O   PHE   229      13.715  65.124  70.756  1.00  1.00
ATOM    728  CB  PHE   229      13.121  66.532  73.702  1.00  1.00
ATOM    729  N   MET   230      12.492  63.864  72.162  1.00  1.00
ATOM    730  CA  MET   230      12.971  62.622  71.576  1.00  1.00
ATOM    731  C   MET   230      12.668  62.584  70.078  1.00  1.00
ATOM    732  O   MET   230      13.514  62.188  69.281  1.00  1.00
ATOM    733  CB  MET   230      12.348  61.415  72.288  1.00  1.00
ATOM    734  N   HIS   231      11.470  63.016  69.705  1.00  1.00
ATOM    735  CA  HIS   231      11.069  63.034  68.305  1.00  1.00
ATOM    736  C   HIS   231      11.908  64.020  67.496  1.00  1.00
ATOM    737  O   HIS   231      12.278  63.751  66.350  1.00  1.00
ATOM    738  CB  HIS   231       9.589  63.416  68.185  1.00  1.00
ATOM    739  N   THR   232      12.216  65.163  68.095  1.00  1.00
ATOM    740  CA  THR   232      12.985  66.180  67.397  1.00  1.00
ATOM    741  C   THR   232      14.479  65.918  67.290  1.00  1.00
ATOM    742  O   THR   232      15.100  66.303  66.300  1.00  1.00
ATOM    743  CB  THR   232      12.745  67.548  68.047  1.00  1.00
ATOM    744  N   MET   233      15.054  65.253  68.290  1.00  1.00
ATOM    745  CA  MET   233      16.494  64.997  68.298  1.00  1.00
ATOM    746  C   MET   233      16.945  63.626  67.826  1.00  1.00
ATOM    747  O   MET   233      18.142  63.379  67.689  1.00  1.00
ATOM    748  CB  MET   233      17.044  65.242  69.700  1.00  1.00
ATOM    749  N   ALA   248      15.998  62.733  67.575  1.00  1.00
ATOM    750  CA  ALA   248      16.364  61.399  67.137  1.00  1.00
ATOM    751  C   ALA   248      17.312  61.364  65.955  1.00  1.00
ATOM    752  O   ALA   248      18.277  60.606  65.942  1.00  1.00
ATOM    753  CB  ALA   248      15.069  60.681  66.712  1.00  1.00
ATOM    754  N   LYS   249      17.034  62.187  64.954  1.00  1.00
ATOM    755  CA  LYS   249      17.851  62.238  63.749  1.00  1.00
ATOM    756  C   LYS   249      19.262  62.727  64.018  1.00  1.00
ATOM    757  O   LYS   249      20.160  62.515  63.205  1.00  1.00
ATOM    758  CB  LYS   249      17.199  63.156  62.723  1.00  1.00
ATOM    759  N   GLU   250      19.465  63.392  65.146  1.00  1.00
ATOM    760  CA  GLU   250      20.791  63.901  65.471  1.00  1.00
ATOM    761  C   GLU   250      21.516  62.968  66.414  1.00  1.00
ATOM    762  O   GLU   250      22.525  63.345  67.002  1.00  1.00
ATOM    763  CB  GLU   250      20.696  65.288  66.105  1.00  1.00
ATOM    764  N   GLY   251      20.998  61.752  66.553  1.00  1.00
ATOM    765  CA  GLY   251      21.613  60.772  67.435  1.00  1.00
ATOM    766  C   GLY   251      21.520  61.131  68.912  1.00  1.00
ATOM    767  O   GLY   251      22.295  60.624  69.729  1.00  1.00
ATOM    768  N   GLU   252      20.578  62.005  69.262  1.00  1.00
ATOM    769  CA  GLU   252      20.407  62.414  70.651  1.00  1.00
ATOM    770  C   GLU   252      19.151  61.807  71.255  1.00  1.00
ATOM    771  O   GLU   252      18.032  62.068  70.796  1.00  1.00
ATOM    772  CB  GLU   252      20.328  63.953  70.789  1.00  1.00
ATOM    773  N   THR   253      19.341  61.001  72.294  1.00  1.00
ATOM    774  CA  THR   253      18.220  60.361  72.967  1.00  1.00
ATOM    775  C   THR   253      17.727  61.188  74.161  1.00  1.00
ATOM    776  O   THR   253      18.506  61.856  74.838  1.00  1.00
ATOM    777  CB  THR   253      18.625  58.949  73.417  1.00  1.00
ATOM    778  N   TYR   254      16.422  61.152  74.392  1.00  1.00
ATOM    779  CA  TYR   254      15.799  61.862  75.500  1.00  1.00
ATOM    780  C   TYR   254      14.858  60.879  76.192  1.00  1.00
ATOM    781  O   TYR   254      13.922  60.358  75.583  1.00  1.00
ATOM    782  CB  TYR   254      14.975  63.062  75.012  1.00  1.00
ATOM    783  N   THR   255      15.120  60.618  77.464  1.00  1.00
ATOM    784  CA  THR   255      14.318  59.685  78.230  1.00  1.00
ATOM    785  C   THR   255      14.018  60.285  79.590  1.00  1.00
ATOM    786  O   THR   255      14.760  61.137  80.066  1.00  1.00
ATOM    787  CB  THR   255      15.079  58.363  78.409  1.00  1.00
ATOM    788  N   LEU   268      12.943  59.835  80.226  1.00  1.00
ATOM    789  CA  LEU   268      12.595  60.365  81.536  1.00  1.00
ATOM    790  C   LEU   268      12.429  59.311  82.629  1.00  1.00
ATOM    791  O   LEU   268      11.815  58.261  82.418  1.00  1.00
ATOM    792  CB  LEU   268      11.305  61.230  81.457  1.00  1.00
ATOM    793  N   ASN   269      13.001  59.597  83.795  1.00  1.00
ATOM    794  CA  ASN   269      12.911  58.714  84.954  1.00  1.00
ATOM    795  C   ASN   269      11.660  59.076  85.751  1.00  1.00
ATOM    796  O   ASN   269      11.301  60.256  85.860  1.00  1.00
ATOM    797  CB  ASN   269      14.127  58.903  85.865  1.00  1.00
ATOM    798  N   VAL   270      10.997  58.071  86.307  1.00  1.00
ATOM    799  CA  VAL   270       9.810  58.312  87.112  1.00  1.00
ATOM    800  C   VAL   270       9.968  57.567  88.432  1.00  1.00
ATOM    801  O   VAL   270       9.378  56.505  88.635  1.00  1.00
ATOM    802  CB  VAL   270       8.572  57.833  86.385  1.00  1.00
ATOM    803  N   LYS   271      10.786  58.110  89.346  1.00  1.00
ATOM    804  CA  LYS   271      11.005  57.469  90.648  1.00  1.00
ATOM    805  C   LYS   271       9.743  57.468  91.495  1.00  1.00
ATOM    806  O   LYS   271       8.839  58.280  91.289  1.00  1.00
ATOM    807  CB  LYS   271      12.120  58.309  91.266  1.00  1.00
ATOM    808  N   GLY   272       9.678  56.540  92.438  1.00  1.00
ATOM    809  CA  GLY   272       8.522  56.462  93.305  1.00  1.00
ATOM    810  C   GLY   272       8.879  57.028  94.658  1.00  1.00
ATOM    811  O   GLY   272       9.346  58.166  94.757  1.00  1.00
ATOM    812  N   ALA   273       8.656  56.237  95.703  1.00  1.00
ATOM    813  CA  ALA   273       8.978  56.669  97.046  1.00  1.00
ATOM    814  C   ALA   273      10.445  56.355  97.283  1.00  1.00
ATOM    815  O   ALA   273      10.827  55.196  97.465  1.00  1.00
ATOM    816  CB  ALA   273       8.115  55.945  98.090  1.00  1.00
ATOM    817  N   TYR   274      11.269  57.395  97.271  1.00  1.00
ATOM    818  CA  TYR   274      12.696  57.220  97.480  1.00  1.00
ATOM    819  C   TYR   274      13.101  57.714  98.851  1.00  1.00
ATOM    820  O   TYR   274      12.789  58.840  99.235  1.00  1.00
ATOM    821  CB  TYR   274      13.517  57.972  96.413  1.00  1.00
ATOM    822  N   ILE   275      13.800  56.854  99.580  1.00  1.00
ATOM    823  CA  ILE   275      14.270  57.169 100.917  1.00  1.00
ATOM    824  C   ILE   275      15.306  58.280 100.830  1.00  1.00
ATOM    825  O   ILE   275      16.424  58.066 100.366  1.00  1.00
ATOM    826  CB  ILE   275      14.893  55.926 101.555  1.00  1.00
ATOM    827  N   ILE   276      14.922  59.473 101.266  1.00  1.00
ATOM    828  CA  ILE   276      15.816  60.620 101.236  1.00  1.00
ATOM    829  C   ILE   276      15.778  61.354 102.570  1.00  1.00
ATOM    830  O   ILE   276      15.122  60.913 103.522  1.00  1.00
ATOM    831  CB  ILE   276      15.421  61.621 100.113  1.00  1.00
ATOM    832  N   GLY   277      16.492  62.473 102.633  1.00  1.00
ATOM    833  CA  GLY   277      16.529  63.290 103.836  1.00  1.00
ATOM    834  C   GLY   277      15.364  64.268 103.738  1.00  1.00
ATOM    835  O   GLY   277      15.390  65.348 104.330  1.00  1.00
ATOM    836  N   ASN   278      14.351  63.875 102.967  1.00  1.00
ATOM    837  CA  ASN   278      13.144  64.673 102.759  1.00  1.00
ATOM    838  C   ASN   278      11.922  63.825 103.110  1.00  1.00
ATOM    839  O   ASN   278      10.923  64.331 103.625  1.00  1.00
ATOM    840  CB  ASN   278      13.045  65.128 101.298  1.00  1.00
ATOM    841  N   ILE   279      12.017  62.530 102.822  1.00  1.00
ATOM    842  CA  ILE   279      10.937  61.594 103.106  1.00  1.00
ATOM    843  C   ILE   279      11.031  61.086 104.541  1.00  1.00
ATOM    844  O   ILE   279      10.087  60.495 105.062  1.00  1.00
ATOM    845  CB  ILE   279      10.984  60.386 102.146  1.00  1.00
ATOM    846  N   ASP   280      12.172  61.323 105.177  1.00  1.00
ATOM    847  CA  ASP   280      12.388  60.890 106.553  1.00  1.00
ATOM    848  C   ASP   280      11.394  61.556 107.499  1.00  1.00
ATOM    849  O   ASP   280      10.839  60.902 108.383  1.00  1.00
ATOM    850  CB  ASP   280      13.814  61.210 106.981  1.00  1.00
ATOM    851  N   HIS   281      11.177  62.856 107.310  1.00  1.00
ATOM    852  CA  HIS   281      10.246  63.610 108.145  1.00  1.00
ATOM    853  C   HIS   281       8.787  63.314 107.812  1.00  1.00
ATOM    854  O   HIS   281       7.890  63.630 108.593  1.00  1.00
ATOM    855  CB  HIS   281      10.502  65.114 108.019  1.00  1.00
ATOM    856  N   LEU   282       8.549  62.715 106.652  1.00  1.00
ATOM    857  CA  LEU   282       7.193  62.369 106.256  1.00  1.00
ATOM    858  C   LEU   282       6.562  61.547 107.372  1.00  1.00
ATOM    859  O   LEU   282       7.171  60.605 107.878  1.00  1.00
ATOM    860  CB  LEU   282       7.187  61.545 104.958  1.00  1.00
ATOM    861  N   PRO   283       5.329  61.894 107.773  1.00  1.00
ATOM    862  CA  PRO   283       4.612  61.186 108.839  1.00  1.00
ATOM    863  C   PRO   283       4.411  59.704 108.537  1.00  1.00
ATOM    864  O   PRO   283       4.250  59.318 107.379  1.00  1.00
ATOM    865  CB  PRO   283       3.292  61.948 108.925  1.00  1.00
ATOM    866  N   PRO   284       4.421  58.880 109.583  1.00  1.00
ATOM    867  CA  PRO   284       4.246  57.442 109.418  1.00  1.00
ATOM    868  C   PRO   284       2.972  57.103 108.674  1.00  1.00
ATOM    869  O   PRO   284       2.918  56.109 107.948  1.00  1.00
ATOM    870  CB  PRO   284       4.255  56.729 110.772  1.00  1.00
ATOM    871  N   GLU   285       1.942  57.923 108.860  1.00  1.00
ATOM    872  CA  GLU   285       0.681  57.708 108.165  1.00  1.00
ATOM    873  C   GLU   285       1.013  57.487 106.694  1.00  1.00
ATOM    874  O   GLU   285       0.612  56.491 106.094  1.00  1.00
ATOM    875  CB  GLU   285      -0.223  58.935 108.317  1.00  1.00
ATOM    876  N   GLN   286       1.775  58.421 106.133  1.00  1.00
ATOM    877  CA  GLN   286       2.185  58.354 104.738  1.00  1.00
ATOM    878  C   GLN   286       3.046  57.128 104.452  1.00  1.00
ATOM    879  O   GLN   286       2.735  56.351 103.552  1.00  1.00
ATOM    880  CB  GLN   286       2.970  59.619 104.330  1.00  1.00
ATOM    881  N   LEU   287       4.126  56.958 105.212  1.00  1.00
ATOM    882  CA  LEU   287       5.021  55.817 105.023  1.00  1.00
ATOM    883  C   LEU   287       4.269  54.493 104.881  1.00  1.00
ATOM    884  O   LEU   287       4.408  53.804 103.869  1.00  1.00
ATOM    885  CB  LEU   287       6.022  55.725 106.180  1.00  1.00
ATOM    886  N   LYS   288       3.477  54.139 105.891  1.00  1.00
ATOM    887  CA  LYS   288       2.699  52.899 105.865  1.00  1.00
ATOM    888  C   LYS   288       1.872  52.793 104.587  1.00  1.00
ATOM    889  O   LYS   288       1.793  51.732 103.970  1.00  1.00
ATOM    890  CB  LYS   288       1.759  52.831 107.073  1.00  1.00
ATOM    891  N   PHE   298       1.252  53.905 104.204  1.00  1.00
ATOM    892  CA  PHE   298       0.416  53.972 103.011  1.00  1.00
ATOM    893  C   PHE   298       1.234  53.774 101.730  1.00  1.00
ATOM    894  O   PHE   298       0.785  53.108 100.793  1.00  1.00
ATOM    895  CB  PHE   298      -0.295  55.328 102.964  1.00  1.00
ATOM    896  N   THR   299       2.430  54.356 101.693  1.00  1.00
ATOM    897  CA  THR   299       3.296  54.240 100.524  1.00  1.00
ATOM    898  C   THR   299       3.846  52.821 100.371  1.00  1.00
ATOM    899  O   THR   299       3.726  52.202  99.311  1.00  1.00
ATOM    900  CB  THR   299       4.442  55.236 100.630  1.00  1.00
TER
END
