
#######################################################
#                                                     #
#                        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   71 (   71),  selected   71 , name T0347TS599_2-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347TS599_2-D2.T0347_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    D     134      -       -           -
LGA    P     135      -       -           -
LGA    F     136      -       -           -
LGA    R     137      D     134          3.797
LGA    S     138      P     135           -
LGA    -       -      F     136           -
LGA    L     139      R     137          4.134
LGA    -       -      S     138           -
LGA    -       -      L     139           -
LGA    -       -      A     140           -
LGA    A     140      G     141           #
LGA    G     141      A     142           -
LGA    -       -      L     143           -
LGA    -       -      R     144           -
LGA    -       -      M     145           -
LGA    -       -      A     146           -
LGA    -       -      G     147           -
LGA    -       -      G     148           -
LGA    -       -      Y     149           -
LGA    -       -      A     150           -
LGA    -       -      K     151           -
LGA    -       -      V     152           -
LGA    -       -      I     153           -
LGA    -       -      I     154           -
LGA    -       -      P     155           -
LGA    A     142      F     156          3.698
LGA    L     143      S     157          4.720
LGA    R     144      E     158           #
LGA    M     145      F     159          4.220
LGA    A     146      G     160          2.821
LGA    G     147      W     161          4.918
LGA    G     148      A     162           #
LGA    Y     149      D     163           #
LGA    A     150      F     164          3.943
LGA    K     151      L     165          1.679
LGA    -       -      R     166           -
LGA    -       -      R     167           -
LGA    -       -      R     168           -
LGA    V     152      I     169          3.886
LGA    I     153      D     170          2.712
LGA    -       -      R     171           -
LGA    I     154      D     172           #
LGA    P     155      L     173          0.975
LGA    F     156      L     174          2.912
LGA    -       -      S     175           -
LGA    S     157      D     176          1.490
LGA    E     158      S     177          2.347
LGA    F     159      F     178          2.575
LGA    -       -      D     179           -
LGA    G     160      D     180          2.307
LGA    -       -      A     181           -
LGA    W     161      L     182          1.030
LGA    A     162      A     183          2.992
LGA    D     163      E     184          2.505
LGA    F     164      A     185          1.956
LGA    L     165      M     186          3.364
LGA    R     166      K     187          2.829
LGA    R     167      L     188          1.793
LGA    R     168      A     189          4.759
LGA    -       -      K     190           -
LGA    -       -      S     191           -
LGA    -       -      R     192           -
LGA    -       -      E     193           -
LGA    I     169      A     194          2.423
LGA    D     170      R     195          4.443
LGA    R     171      H     196           -
LGA    D     172      L     197           -
LGA    -       -      P     198           -
LGA    -       -      G     199           -
LGA    L     173      W     200          2.202
LGA    L     174      C     201          3.590
LGA    S     175      G     202          5.305
LGA    D     176      V     203           -
LGA    S     177      E     204           -
LGA    F     178      -       -           -
LGA    D     179      -       -           -
LGA    D     180      -       -           -
LGA    A     181      -       -           -
LGA    L     182      -       -           -
LGA    A     183      -       -           -
LGA    E     184      -       -           -
LGA    A     185      -       -           -
LGA    M     186      -       -           -
LGA    K     187      -       -           -
LGA    L     188      -       -           -
LGA    A     189      -       -           -
LGA    K     190      -       -           -
LGA    S     191      -       -           -
LGA    R     192      -       -           -
LGA    E     193      -       -           -
LGA    A     194      -       -           -
LGA    R     195      -       -           -
LGA    H     196      -       -           -
LGA    L     197      -       -           -
LGA    P     198      -       -           -
LGA    G     199      -       -           -
LGA    W     200      -       -           -
LGA    C     201      -       -           -
LGA    G     202      -       -           -
LGA    V     203      -       -           -
LGA    E     204      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   71   71    5.0     30    3.29     6.67     25.615     0.886

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.063316 * X  +   0.069109 * Y  +  -0.995598 * Z  +  16.623106
  Y_new =   0.997994 * X  +   0.004318 * Y  +  -0.063168 * Z  +  53.711624
  Z_new =  -0.000067 * X  +  -0.997600 * Y  +  -0.069244 * Z  + -16.967693 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.640096    1.501497  [ DEG:   -93.9706     86.0294 ]
  Theta =   0.000067    3.141526  [ DEG:     0.0038    179.9962 ]
  Phi   =   1.634154   -1.507438  [ DEG:    93.6301    -86.3699 ]
 
# 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: T0347TS599_2-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS599_2-D2.T0347_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   71   71   5.0   30   3.29    6.67  25.615
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS599_2-D2
PFRMAT TS                                                                       
TARGET T0347                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM    134  CA  ASP   134       6.210  49.354  -7.933  1.00  0.00              
ATOM    135  CA  PRO   135       9.949  49.285  -7.716  1.00  0.00              
ATOM    136  CA  PHE   136      10.302  52.690  -6.066  1.00  0.00              
ATOM    137  CA  ARG   137       7.641  52.278  -3.380  1.00  0.00              
ATOM    138  CA  SER   138       9.197  48.986  -2.399  1.00  0.00              
ATOM    139  CA  LEU   139      12.654  50.363  -2.054  1.00  0.00              
ATOM    140  CA  ALA   140      11.534  53.232   0.131  1.00  0.00              
ATOM    141  CA  GLY   141       9.592  50.901   2.367  1.00  0.00              
ATOM    142  CA  ALA   142      12.550  48.519   2.769  1.00  0.00              
ATOM    143  CA  LEU   143      14.871  51.379   3.650  1.00  0.00              
ATOM    144  CA  ARG   144      12.368  52.868   6.146  1.00  0.00              
ATOM    145  CA  MET   145      11.699  49.637   7.957  1.00  0.00              
ATOM    146  CA  ALA   146      15.356  48.760   8.232  1.00  0.00              
ATOM    147  CA  GLY   147      16.379  52.224   9.503  1.00  0.00              
ATOM    148  CA  GLY   148      18.688  53.240   6.695  1.00  0.00              
ATOM    149  CA  TYR   149      17.789  56.873   6.330  1.00  0.00              
ATOM    150  CA  ALA   150      14.630  57.499   4.323  1.00  0.00              
ATOM    151  CA  LYS   151      13.190  60.443   6.197  1.00  0.00              
ATOM    152  CA  VAL   152      10.927  62.019   3.584  1.00  0.00              
ATOM    153  CA  ILE   153      12.027  65.612   3.628  1.00  0.00              
ATOM    154  CA  ILE   154      12.611  66.803   0.117  1.00  0.00              
ATOM    155  CA  PRO   155       9.771  68.748  -1.490  1.00  0.00              
ATOM    156  CA  PHE   156       8.900  66.875  -4.630  1.00  0.00              
ATOM    157  CA  SER   157       9.821  69.471  -7.195  1.00  0.00              
ATOM    158  CA  GLU   158      13.211  70.075  -5.610  1.00  0.00              
ATOM    159  CA  PHE   159      14.549  66.580  -5.233  1.00  0.00              
ATOM    160  CA  GLY   160      17.629  66.289  -2.981  1.00  0.00              
ATOM    161  CA  TRP   161      19.050  62.842  -2.634  1.00  0.00              
ATOM    162  CA  ALA   162      22.692  63.330  -1.806  1.00  0.00              
ATOM    163  CA  ASP   163      22.119  65.854   0.966  1.00  0.00              
ATOM    164  CA  PHE   164      19.312  64.001   2.523  1.00  0.00              
ATOM    165  CA  LEU   165      21.107  60.645   2.711  1.00  0.00              
ATOM    166  CA  ARG   166      24.358  62.157   3.968  1.00  0.00              
ATOM    167  CA  ARG   167      22.649  64.139   6.644  1.00  0.00              
ATOM    168  CA  ARG   168      20.643  61.191   7.964  1.00  0.00              
ATOM    169  CA  ILE   169      23.333  58.579   7.818  1.00  0.00              
ATOM    170  CA  ASP   170      26.819  58.830   9.003  1.00  0.00              
ATOM    171  CA  ARG   171      29.400  59.446   6.344  1.00  0.00              
ATOM    172  CA  ASP   172      31.081  56.044   6.355  1.00  0.00              
ATOM    173  CA  LEU   173      27.776  54.166   5.974  1.00  0.00              
ATOM    174  CA  LEU   174      26.825  56.413   3.088  1.00  0.00              
ATOM    175  CA  SER   175      30.082  55.922   1.312  1.00  0.00              
ATOM    176  CA  ASP   176      29.973  52.126   1.589  1.00  0.00              
ATOM    177  CA  SER   177      26.401  51.921   0.231  1.00  0.00              
ATOM    178  CA  PHE   178      27.206  54.152  -2.688  1.00  0.00              
ATOM    179  CA  ASP   179      30.023  52.041  -4.017  1.00  0.00              
ATOM    180  CA  ASP   180      27.970  48.899  -3.855  1.00  0.00              
ATOM    181  CA  ALA   181      25.114  50.417  -5.658  1.00  0.00              
ATOM    182  CA  LEU   182      27.315  51.739  -8.430  1.00  0.00              
ATOM    183  CA  ALA   183      28.941  48.423  -8.940  1.00  0.00              
ATOM    184  CA  GLU   184      25.486  46.882  -9.178  1.00  0.00              
ATOM    185  CA  ALA   185      24.441  49.507 -11.692  1.00  0.00              
ATOM    186  CA  MET   186      27.446  48.855 -13.877  1.00  0.00              
ATOM    187  CA  LYS   187      26.834  45.195 -13.835  1.00  0.00              
ATOM    188  CA  LEU   188      23.225  45.686 -14.885  1.00  0.00              
ATOM    189  CA  ALA   189      24.338  47.968 -17.649  1.00  0.00              
ATOM    190  CA  LYS   190      26.748  45.419 -19.073  1.00  0.00              
ATOM    191  CA  SER   191      24.247  42.560 -19.094  1.00  0.00              
ATOM    192  CA  ARG   192      20.701  42.068 -20.150  1.00  0.00              
ATOM    193  CA  GLU   193      20.480  43.420 -23.659  1.00  0.00              
ATOM    194  CA  ALA   194      23.678  41.701 -24.698  1.00  0.00              
ATOM    195  CA  ARG   195      22.297  38.245 -23.802  1.00  0.00              
ATOM    196  CA  HIS   196      18.910  38.429 -25.440  1.00  0.00              
ATOM    197  CA  LEU   197      19.880  39.559 -28.927  1.00  0.00              
ATOM    198  CA  PRO   198      19.406  36.944 -31.589  1.00  0.00              
ATOM    199  CA  GLY   199      22.669  35.362 -32.692  1.00  0.00              
ATOM    200  CA  TRP   200      24.710  36.879 -29.828  1.00  0.00              
ATOM    201  CA  CYS   201      25.167  33.694 -27.902  1.00  0.00              
ATOM    202  CA  GLY   202      26.371  31.721 -30.987  1.00  0.00              
ATOM    203  CA  VAL   203      29.057  34.624 -32.169  1.00  0.00              
ATOM    204  CA  GLU   204      30.887  31.191 -33.075  1.00  0.00              
TER                                                                             
END
