
#######################################################
#                                                     #
#                        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  101 (  101),  selected  101 , name T0323TS393_3-D1
# Molecule2: number of CA atoms  101 (  777),  selected  101 , name T0323_D1.pdb
# PARAMETERS: T0323TS393_3-D1.T0323_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    R       2      R       2           -
LGA    Y       3      Y       3           -
LGA    F       4      F       4           -
LGA    S       5      S       5           -
LGA    T       6      T       6           -
LGA    D       7      D       7           -
LGA    S       8      S       8           -
LGA    P       9      P       9           -
LGA    E      10      E      10           -
LGA    V      11      V      11           -
LGA    K      12      K      12           -
LGA    T      13      T      13           -
LGA    I      14      I      14           -
LGA    V      15      V      15           -
LGA    A      16      A      16           -
LGA    Q      17      Q      17           -
LGA    D      18      D      18           -
LGA    S      19      S      19           -
LGA    R      20      R      20           -
LGA    L      21      L      21           -
LGA    F      22      F      22           -
LGA    Q      23      Q      23           -
LGA    F      24      F      24           -
LGA    I      25      I      25           -
LGA    E      26      E      26           -
LGA    I      27      I      27           -
LGA    A      28      A      28           -
LGA    G      29      G      29           -
LGA    E      30      E      30           -
LGA    V      31      V      31           -
LGA    Q      32      -       -           -
LGA    L      33      -       -           -
LGA    L     150      Q      32          4.651
LGA    D     151      L      33           -
LGA    V     152      L     150           -
LGA    -       -      D     151           -
LGA    -       -      V     152           -
LGA    -       -      L     153           -
LGA    -       -      S     154           -
LGA    -       -      V     155           -
LGA    -       -      G     156           -
LGA    -       -      D     157           -
LGA    L     153      V     158           #
LGA    S     154      G     159          2.211
LGA    V     155      L     160          4.225
LGA    G     156      Q     161          1.784
LGA    -       -      R     162           -
LGA    D     157      G     163           #
LGA    V     158      A     164          1.041
LGA    G     159      K     165           #
LGA    L     160      W     166           -
LGA    -       -      L     167           -
LGA    -       -      Y     168           -
LGA    -       -      G     169           -
LGA    -       -      N     170           -
LGA    -       -      G     171           -
LGA    -       -      E     172           -
LGA    -       -      G     173           -
LGA    -       -      D     174           -
LGA    -       -      G     175           -
LGA    -       -      K     176           -
LGA    -       -      K     177           -
LGA    Q     161      L     178          4.136
LGA    -       -      L     179           -
LGA    -       -      I     180           -
LGA    -       -      Y     181           -
LGA    R     162      H     182          3.953
LGA    G     163      G     183          1.685
LGA    A     164      K     184          2.455
LGA    K     165      A     185          2.737
LGA    W     166      W     186          2.592
LGA    L     167      -       -           -
LGA    Y     168      -       -           -
LGA    G     169      -       -           -
LGA    N     170      -       -           -
LGA    G     171      -       -           -
LGA    E     172      -       -           -
LGA    G     173      -       -           -
LGA    D     174      -       -           -
LGA    G     175      -       -           -
LGA    K     176      -       -           -
LGA    K     177      -       -           -
LGA    L     178      -       -           -
LGA    L     179      -       -           -
LGA    I     180      -       -           -
LGA    Y     181      -       -           -
LGA    H     182      A     187          4.894
LGA    G     183      P     188          2.423
LGA    K     184      -       -           -
LGA    A     185      -       -           -
LGA    W     186      Y     189          2.311
LGA    A     187      E     190          1.421
LGA    P     188      T     191          0.598
LGA    Y     189      V     192          1.927
LGA    E     190      A     193          2.076
LGA    T     191      C     194          0.777
LGA    V     192      L     195          1.031
LGA    A     193      Y     196          1.596
LGA    C     194      L     197          0.881
LGA    L     195      W     198          1.004
LGA    Y     196      K     199          1.235
LGA    L     197      A     200          0.202
LGA    W     198      A     201          1.441
LGA    K     199      G     202          2.316
LGA    A     200      T     203          2.614
LGA    A     201      F     204          3.342
LGA    -       -      A     205           -
LGA    -       -      E     206           -
LGA    -       -      E     207           -
LGA    G     202      Y     208          4.700
LGA    -       -      R     209           -
LGA    -       -      S     210           -
LGA    T     203      L     211          3.365
LGA    F     204      E     212          4.828
LGA    -       -      E     213           -
LGA    A     205      L     214          2.860
LGA    E     206      L     215          4.541
LGA    E     207      H     216           -
LGA    Y     208      H     217           -
LGA    R     209      -       -           -
LGA    S     210      -       -           -
LGA    L     211      -       -           -
LGA    E     212      -       -           -
LGA    E     213      -       -           -
LGA    L     214      -       -           -
LGA    L     215      -       -           -
LGA    H     216      -       -           -
LGA    H     217      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  101  101    5.0     34    2.81     5.88     23.986     1.168

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.244461 * X  +   0.423078 * Y  +   0.872493 * Z  +  13.201685
  Y_new =   0.768732 * X  +   0.632984 * Y  +  -0.091550 * Z  +  43.451347
  Z_new =  -0.591007 * X  +   0.648333 * Y  +  -0.479974 * Z  +  12.835818 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.208073   -0.933519  [ DEG:   126.5133    -53.4867 ]
  Theta =   0.632307    2.509285  [ DEG:    36.2285    143.7715 ]
  Phi   =   1.878688   -1.262904  [ DEG:   107.6409    -72.3591 ]
 
# 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: T0323TS393_3-D1                               
REMARK     2: T0323_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0323TS393_3-D1.T0323_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  101  101   5.0   34   2.81    5.88  23.986
REMARK  ---------------------------------------------------------- 
MOLECULE T0323TS393_3-D1
PFRMAT TS
TARGET T0323
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1     -12.250  30.935   6.386  1.00 25.00           C
ATOM      2  CA  ARG     2     -11.301  32.835   3.246  1.00 25.00           C
ATOM      3  CA  TYR     3      -8.448  35.222   2.642  1.00 25.00           C
ATOM      4  CA  PHE     4      -9.069  38.097   5.026  1.00 25.00           C
ATOM      5  CA  SER     5     -11.408  41.050   4.782  1.00 25.00           C
ATOM      6  CA  THR     6     -13.844  40.388   7.674  1.00 25.00           C
ATOM      7  CA  ASP     7     -10.893  41.602   9.844  1.00 25.00           C
ATOM      8  CA  SER     8      -9.566  42.778  13.254  1.00 25.00           C
ATOM      9  CA  PRO     9      -9.439  39.474  15.184  1.00 25.00           C
ATOM     10  CA  GLU    10      -5.619  39.689  15.352  1.00 25.00           C
ATOM     11  CA  VAL    11      -5.855  43.286  16.645  1.00 25.00           C
ATOM     12  CA  LYS    12      -8.375  42.187  19.312  1.00 25.00           C
ATOM     13  CA  THR    13      -6.045  39.339  20.375  1.00 25.00           C
ATOM     14  CA  ILE    14      -3.116  41.794  20.622  1.00 25.00           C
ATOM     15  CA  VAL    15      -5.244  44.155  22.757  1.00 25.00           C
ATOM     16  CA  ALA    16      -6.216  41.247  25.051  1.00 25.00           C
ATOM     17  CA  GLN    17      -4.566  38.377  26.985  1.00 25.00           C
ATOM     18  CA  ASP    18      -0.951  39.489  26.910  1.00 25.00           C
ATOM     19  CA  SER    19      -0.447  35.808  26.067  1.00 25.00           C
ATOM     20  CA  ARG    20      -1.788  36.711  22.595  1.00 25.00           C
ATOM     21  CA  LEU    21       1.411  35.359  20.981  1.00 25.00           C
ATOM     22  CA  PHE    22       1.075  32.109  22.978  1.00 25.00           C
ATOM     23  CA  GLN    23      -2.574  31.773  21.864  1.00 25.00           C
ATOM     24  CA  PHE    24      -1.537  32.323  18.218  1.00 25.00           C
ATOM     25  CA  ILE    25       1.185  29.652  18.564  1.00 25.00           C
ATOM     26  CA  GLU    26      -1.363  27.212  20.054  1.00 25.00           C
ATOM     27  CA  ILE    27      -3.767  27.913  17.156  1.00 25.00           C
ATOM     28  CA  ALA    28      -1.631  25.274  15.388  1.00 25.00           C
ATOM     29  CA  GLY    29      -0.751  21.590  15.686  1.00 25.00           C
ATOM     30  CA  GLU    30      -0.038  20.880  11.980  1.00 25.00           C
ATOM     31  CA  VAL    31      -0.027  23.634   9.336  1.00 25.00           C
ATOM     32  CA  GLN    32       3.445  22.663   8.133  1.00 25.00           C
ATOM     33  CA  LEU    33       5.374  24.360   5.392  1.00 25.00           C
ATOM    150  CA  LEU   150      16.652  26.863   9.023  1.00 25.00           C
ATOM    151  CA  ASP   151      13.072  27.785  10.116  1.00 25.00           C
ATOM    152  CA  VAL   152      12.553  31.001  12.092  1.00 25.00           C
ATOM    153  CA  LEU   153      11.776  33.845  14.469  1.00 25.00           C
ATOM    154  CA  SER   154      12.910  36.265  17.157  1.00 25.00           C
ATOM    155  CA  VAL   155      14.292  37.443  20.485  1.00 25.00           C
ATOM    156  CA  GLY   156      15.004  40.416  18.177  1.00 25.00           C
ATOM    157  CA  ASP   157      16.386  42.414  21.137  1.00 25.00           C
ATOM    158  CA  VAL   158      18.627  39.466  22.113  1.00 25.00           C
ATOM    159  CA  GLY   159      19.900  39.209  18.510  1.00 25.00           C
ATOM    160  CA  LEU   160      20.650  42.965  18.481  1.00 25.00           C
ATOM    161  CA  GLN   161      22.551  42.635  21.790  1.00 25.00           C
ATOM    162  CA  ARG   162      24.574  39.712  20.365  1.00 25.00           C
ATOM    163  CA  GLY   163      25.404  41.776  17.247  1.00 25.00           C
ATOM    164  CA  ALA   164      26.526  44.700  19.451  1.00 25.00           C
ATOM    165  CA  LYS   165      28.739  42.340  21.499  1.00 25.00           C
ATOM    166  CA  TRP   166      30.283  40.954  18.280  1.00 25.00           C
ATOM    167  CA  LEU   167      30.966  44.513  17.045  1.00 25.00           C
ATOM    168  CA  TYR   168      34.385  42.971  16.561  1.00 25.00           C
ATOM    169  CA  GLY   169      36.052  44.225  19.753  1.00 25.00           C
ATOM    170  CA  ASN   170      34.723  47.732  20.191  1.00 25.00           C
ATOM    171  CA  GLY   171      38.238  49.233  19.708  1.00 25.00           C
ATOM    172  CA  GLU   172      39.111  52.478  17.953  1.00 25.00           C
ATOM    173  CA  GLY   173      40.174  50.710  14.711  1.00 25.00           C
ATOM    174  CA  ASP   174      39.197  51.243  11.031  1.00 25.00           C
ATOM    175  CA  GLY   175      38.784  48.991   8.035  1.00 25.00           C
ATOM    176  CA  LYS   176      37.157  48.783   4.572  1.00 25.00           C
ATOM    177  CA  LYS   177      35.445  46.146   2.384  1.00 25.00           C
ATOM    178  CA  LEU   178      36.825  43.360   4.620  1.00 25.00           C
ATOM    179  CA  LEU   179      35.540  45.185   7.731  1.00 25.00           C
ATOM    180  CA  ILE   180      32.087  45.559   6.116  1.00 25.00           C
ATOM    181  CA  TYR   181      32.054  41.825   5.265  1.00 25.00           C
ATOM    182  CA  HIS   182      33.000  40.969   8.877  1.00 25.00           C
ATOM    183  CA  GLY   183      30.186  43.222  10.173  1.00 25.00           C
ATOM    184  CA  LYS   184      27.700  41.515   7.812  1.00 25.00           C
ATOM    185  CA  ALA   185      28.858  38.077   9.036  1.00 25.00           C
ATOM    186  CA  TRP   186      28.424  39.198  12.672  1.00 25.00           C
ATOM    187  CA  ALA   187      24.898  40.469  11.885  1.00 25.00           C
ATOM    188  CA  PRO   188      24.038  37.128  10.223  1.00 25.00           C
ATOM    189  CA  TYR   189      25.345  35.239  13.288  1.00 25.00           C
ATOM    190  CA  GLU   190      23.232  37.458  15.586  1.00 25.00           C
ATOM    191  CA  THR   191      20.141  36.797  13.423  1.00 25.00           C
ATOM    192  CA  VAL   192      20.809  33.029  13.576  1.00 25.00           C
ATOM    193  CA  ALA   193      21.149  33.219  17.386  1.00 25.00           C
ATOM    194  CA  CYS   194      17.846  35.143  17.610  1.00 25.00           C
ATOM    195  CA  LEU   195      16.134  32.505  15.422  1.00 25.00           C
ATOM    196  CA  TYR   196      17.514  29.719  17.659  1.00 25.00           C
ATOM    197  CA  LEU   197      16.228  31.545  20.770  1.00 25.00           C
ATOM    198  CA  TRP   198      12.776  31.918  19.154  1.00 25.00           C
ATOM    199  CA  LYS   199      12.743  28.184  18.304  1.00 25.00           C
ATOM    200  CA  ALA   200      13.688  27.329  21.916  1.00 25.00           C
ATOM    201  CA  ALA   201      10.874  29.582  23.211  1.00 25.00           C
ATOM    202  CA  GLY   202      13.737  30.851  25.311  1.00 25.00           C
ATOM    203  CA  THR   203      17.219  29.986  26.522  1.00 25.00           C
ATOM    204  CA  PHE   204      19.626  28.447  29.059  1.00 25.00           C
ATOM    205  CA  ALA   205      17.797  28.750  32.410  1.00 25.00           C
ATOM    206  CA  GLU   206      20.691  30.818  33.830  1.00 25.00           C
ATOM    207  CA  GLU   207      20.595  33.106  30.761  1.00 25.00           C
ATOM    208  CA  TYR   208      16.815  33.553  31.180  1.00 25.00           C
ATOM    209  CA  ARG   209      17.304  34.420  34.879  1.00 25.00           C
ATOM    210  CA  SER   210      19.994  36.981  33.948  1.00 25.00           C
ATOM    211  CA  LEU   211      17.651  38.535  31.348  1.00 25.00           C
ATOM    212  CA  GLU   212      14.855  38.743  33.956  1.00 25.00           C
ATOM    213  CA  GLU   213      17.249  40.427  36.425  1.00 25.00           C
ATOM    214  CA  LEU   214      18.295  42.943  33.734  1.00 25.00           C
ATOM    215  CA  LEU   215      14.617  43.694  32.974  1.00 25.00           C
ATOM    216  CA  HIS   216      13.929  44.227  36.704  1.00 25.00           C
ATOM    217  CA  HIS   217      11.064  46.222  38.291  1.00 25.00           C
TER
END
