
#######################################################
#                                                     #
#                        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 T0323TS168_5-D1
# Molecule2: number of CA atoms  101 (  777),  selected  101 , name T0323_D1.pdb
# PARAMETERS: T0323TS168_5-D1.T0323_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    R       2      -       -           -
LGA    Y       3      -       -           -
LGA    F       4      -       -           -
LGA    S       5      -       -           -
LGA    T       6      -       -           -
LGA    D       7      -       -           -
LGA    S       8      -       -           -
LGA    P       9      -       -           -
LGA    E      10      -       -           -
LGA    V      11      -       -           -
LGA    K      12      -       -           -
LGA    T      13      -       -           -
LGA    I      14      -       -           -
LGA    V      15      -       -           -
LGA    A      16      -       -           -
LGA    Q      17      -       -           -
LGA    D      18      -       -           -
LGA    S      19      -       -           -
LGA    R      20      -       -           -
LGA    L      21      -       -           -
LGA    F      22      -       -           -
LGA    Q      23      -       -           -
LGA    F      24      -       -           -
LGA    I      25      -       -           -
LGA    E      26      -       -           -
LGA    I      27      -       -           -
LGA    A      28      -       -           -
LGA    G      29      -       -           -
LGA    E      30      -       -           -
LGA    V      31      -       -           -
LGA    Q      32      -       -           -
LGA    L      33      -       -           -
LGA    L     150      -       -           -
LGA    D     151      -       -           -
LGA    V     152      -       -           -
LGA    L     153      -       -           -
LGA    S     154      M       1           #
LGA    V     155      R       2           #
LGA    G     156      Y       3          4.800
LGA    D     157      F       4           #
LGA    V     158      -       -           -
LGA    G     159      -       -           -
LGA    L     160      S       5          4.996
LGA    -       -      T       6           -
LGA    -       -      D       7           -
LGA    -       -      S       8           -
LGA    Q     161      P       9          1.218
LGA    R     162      E      10          1.473
LGA    G     163      V      11          1.116
LGA    A     164      K      12          1.320
LGA    K     165      T      13          1.552
LGA    W     166      I      14          1.686
LGA    L     167      V      15          1.882
LGA    Y     168      A      16          2.167
LGA    G     169      Q      17          2.111
LGA    N     170      D      18           -
LGA    G     171      S      19           -
LGA    E     172      R      20           -
LGA    G     173      L      21           -
LGA    D     174      F      22           -
LGA    G     175      Q      23           -
LGA    K     176      F      24           -
LGA    K     177      I      25           -
LGA    L     178      E      26           -
LGA    L     179      I      27           -
LGA    I     180      A      28           -
LGA    Y     181      G      29           -
LGA    H     182      E      30           -
LGA    -       -      V      31           -
LGA    -       -      Q      32           -
LGA    -       -      L      33           -
LGA    G     183      L     150          5.347
LGA    K     184      D     151          2.104
LGA    A     185      V     152           -
LGA    -       -      L     153           -
LGA    -       -      S     154           -
LGA    -       -      V     155           -
LGA    -       -      G     156           -
LGA    -       -      D     157           -
LGA    -       -      V     158           -
LGA    -       -      G     159           -
LGA    -       -      L     160           -
LGA    -       -      Q     161           -
LGA    -       -      R     162           -
LGA    -       -      G     163           -
LGA    -       -      A     164           -
LGA    -       -      K     165           -
LGA    -       -      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    -       -      L     178           -
LGA    -       -      L     179           -
LGA    -       -      I     180           -
LGA    -       -      Y     181           -
LGA    -       -      H     182           -
LGA    -       -      G     183           -
LGA    -       -      K     184           -
LGA    -       -      A     185           -
LGA    -       -      W     186           -
LGA    -       -      A     187           -
LGA    -       -      P     188           -
LGA    W     186      Y     189          3.277
LGA    A     187      E     190          1.854
LGA    P     188      T     191          1.923
LGA    Y     189      V     192          2.318
LGA    E     190      A     193          1.492
LGA    T     191      C     194          1.311
LGA    V     192      L     195          1.757
LGA    A     193      Y     196          1.395
LGA    C     194      L     197          1.498
LGA    L     195      W     198          1.605
LGA    Y     196      K     199          1.621
LGA    L     197      A     200          1.561
LGA    W     198      A     201          1.768
LGA    K     199      G     202          1.454
LGA    A     200      T     203          2.292
LGA    -       -      F     204           -
LGA    A     201      A     205          1.793
LGA    -       -      E     206           -
LGA    -       -      E     207           -
LGA    G     202      Y     208          5.613
LGA    T     203      R     209           #
LGA    F     204      -       -           -
LGA    A     205      -       -           -
LGA    E     206      -       -           -
LGA    E     207      S     210          2.811
LGA    Y     208      L     211          2.120
LGA    R     209      E     212          1.039
LGA    S     210      E     213          3.076
LGA    L     211      L     214          3.673
LGA    E     212      L     215          2.469
LGA    E     213      H     216          2.535
LGA    L     214      H     217          3.280
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     38    2.58     5.26     29.214     1.419

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.120323 * X  +   0.961781 * Y  +  -0.245967 * Z  +  25.714636
  Y_new =  -0.613858 * X  +   0.122639 * Y  +   0.779832 * Z  +  23.389202
  Z_new =   0.780193 * X  +   0.244820 * Y  +   0.575640 * Z  +   7.569025 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.402125   -2.739467  [ DEG:    23.0401   -156.9599 ]
  Theta =  -0.894974   -2.246618  [ DEG:   -51.2783   -128.7217 ]
  Phi   =  -1.764353    1.377239  [ DEG:  -101.0900     78.9100 ]
 
# 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: T0323TS168_5-D1                               
REMARK     2: T0323_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0323TS168_5-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   38   2.58    5.26  29.214
REMARK  ---------------------------------------------------------- 
MOLECULE T0323TS168_5-D1
PFRMAT TS
TARGET T0323
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      -1.078  25.809  -5.585  1.00 25.00           C
ATOM      2  CA  ARG     2       0.208  26.249  -9.165  1.00 25.00           C
ATOM      3  CA  TYR     3       3.865  25.420 -10.077  1.00 25.00           C
ATOM      4  CA  PHE     4       5.419  21.960  -9.455  1.00 25.00           C
ATOM      5  CA  SER     5       4.096  18.647 -10.856  1.00 25.00           C
ATOM      6  CA  THR     6       5.172  16.302  -8.089  1.00 25.00           C
ATOM      7  CA  ASP     7       7.415  13.662  -9.673  1.00 25.00           C
ATOM      8  CA  SER     8      11.028  14.545  -8.765  1.00 25.00           C
ATOM      9  CA  PRO     9      11.178  10.830  -7.843  1.00 25.00           C
ATOM     10  CA  GLU    10      14.049  11.526  -5.406  1.00 25.00           C
ATOM     11  CA  VAL    11      12.043  14.375  -3.817  1.00 25.00           C
ATOM     12  CA  LYS    12       9.009  12.066  -3.448  1.00 25.00           C
ATOM     13  CA  THR    13      11.210   9.396  -1.808  1.00 25.00           C
ATOM     14  CA  ILE    14      12.620  12.008   0.611  1.00 25.00           C
ATOM     15  CA  VAL    15       9.071  13.148   1.488  1.00 25.00           C
ATOM     16  CA  ALA    16       8.035   9.516   2.121  1.00 25.00           C
ATOM     17  CA  GLN    17       7.393   9.861   5.850  1.00 25.00           C
ATOM     18  CA  ASP    18       9.821  12.352   7.478  1.00 25.00           C
ATOM     19  CA  SER    19       9.581  13.391  11.144  1.00 25.00           C
ATOM     20  CA  ARG    20       9.820  16.218  13.717  1.00 25.00           C
ATOM     21  CA  LEU    21      11.401  18.510  11.087  1.00 25.00           C
ATOM     22  CA  PHE    22       8.596  17.658   8.623  1.00 25.00           C
ATOM     23  CA  GLN    23       5.973  18.433  11.302  1.00 25.00           C
ATOM     24  CA  PHE    24       7.672  21.787  12.031  1.00 25.00           C
ATOM     25  CA  ILE    25       7.689  22.619   8.292  1.00 25.00           C
ATOM     26  CA  GLU    26       3.968  21.748   8.056  1.00 25.00           C
ATOM     27  CA  ILE    27       3.226  23.991  11.070  1.00 25.00           C
ATOM     28  CA  ALA    28       3.346  27.609   9.910  1.00 25.00           C
ATOM     29  CA  GLY    29       1.114  29.277   7.390  1.00 25.00           C
ATOM     30  CA  GLU    30       2.046  30.669   4.016  1.00 25.00           C
ATOM     31  CA  VAL    31       5.589  30.997   2.666  1.00 25.00           C
ATOM     32  CA  GLN    32       7.020  33.500   0.182  1.00 25.00           C
ATOM     33  CA  LEU    33      10.031  32.280  -1.700  1.00 25.00           C
ATOM    150  CA  LEU   150      15.878  36.595   5.834  1.00 25.00           C
ATOM    151  CA  ASP   151      18.876  38.772   5.031  1.00 25.00           C
ATOM    152  CA  VAL   152      21.122  35.728   5.041  1.00 25.00           C
ATOM    153  CA  LEU   153      23.771  33.042   4.490  1.00 25.00           C
ATOM    154  CA  SER   154      27.517  32.700   4.156  1.00 25.00           C
ATOM    155  CA  VAL   155      30.005  30.143   2.704  1.00 25.00           C
ATOM    156  CA  GLY   156      28.867  27.616   5.347  1.00 25.00           C
ATOM    157  CA  ASP   157      32.451  27.351   6.673  1.00 25.00           C
ATOM    158  CA  VAL   158      32.689  31.169   6.861  1.00 25.00           C
ATOM    159  CA  GLY   159      29.367  31.307   8.762  1.00 25.00           C
ATOM    160  CA  LEU   160      30.627  28.640  11.206  1.00 25.00           C
ATOM    161  CA  GLN   161      33.856  30.627  11.749  1.00 25.00           C
ATOM    162  CA  ARG   162      31.820  33.802  12.410  1.00 25.00           C
ATOM    163  CA  GLY   163      29.642  31.911  14.930  1.00 25.00           C
ATOM    164  CA  ALA   164      32.779  30.591  16.686  1.00 25.00           C
ATOM    165  CA  LYS   165      34.211  34.140  16.848  1.00 25.00           C
ATOM    166  CA  TRP   166      30.922  35.426  18.328  1.00 25.00           C
ATOM    167  CA  LEU   167      30.977  32.630  20.944  1.00 25.00           C
ATOM    168  CA  TYR   168      33.371  35.156  22.447  1.00 25.00           C
ATOM    169  CA  GLY   169      34.121  38.543  20.798  1.00 25.00           C
ATOM    170  CA  ASN   170      34.869  40.242  17.430  1.00 25.00           C
ATOM    171  CA  GLY   171      37.678  42.652  18.155  1.00 25.00           C
ATOM    172  CA  GLU   172      40.648  43.899  16.079  1.00 25.00           C
ATOM    173  CA  GLY   173      41.627  45.924  13.053  1.00 25.00           C
ATOM    174  CA  ASP   174      39.592  44.712  10.097  1.00 25.00           C
ATOM    175  CA  GLY   175      39.685  43.156   6.609  1.00 25.00           C
ATOM    176  CA  LYS   176      37.936  42.712   3.224  1.00 25.00           C
ATOM    177  CA  LYS   177      34.750  41.877   1.270  1.00 25.00           C
ATOM    178  CA  LEU   178      35.105  38.184   2.220  1.00 25.00           C
ATOM    179  CA  LEU   179      35.550  39.149   5.900  1.00 25.00           C
ATOM    180  CA  ILE   180      32.424  41.355   5.726  1.00 25.00           C
ATOM    181  CA  TYR   181      30.447  38.472   4.161  1.00 25.00           C
ATOM    182  CA  HIS   182      31.643  36.116   6.934  1.00 25.00           C
ATOM    183  CA  GLY   183      30.588  38.665   9.590  1.00 25.00           C
ATOM    184  CA  LYS   184      27.141  38.985   7.950  1.00 25.00           C
ATOM    185  CA  ALA   185      26.777  35.172   7.917  1.00 25.00           C
ATOM    186  CA  TRP   186      27.732  35.025  11.624  1.00 25.00           C
ATOM    187  CA  ALA   187      25.148  37.737  12.423  1.00 25.00           C
ATOM    188  CA  PRO   188      22.473  35.789  10.494  1.00 25.00           C
ATOM    189  CA  TYR   189      23.370  32.603  12.420  1.00 25.00           C
ATOM    190  CA  GLU   190      23.116  34.504  15.734  1.00 25.00           C
ATOM    191  CA  THR   191      19.691  35.879  14.712  1.00 25.00           C
ATOM    192  CA  VAL   192      18.517  32.348  13.808  1.00 25.00           C
ATOM    193  CA  ALA   193      19.733  31.047  17.198  1.00 25.00           C
ATOM    194  CA  CYS   194      17.868  33.878  18.980  1.00 25.00           C
ATOM    195  CA  LEU   195      14.682  33.044  17.025  1.00 25.00           C
ATOM    196  CA  TYR   196      15.037  29.350  17.976  1.00 25.00           C
ATOM    197  CA  LEU   197      15.483  30.316  21.655  1.00 25.00           C
ATOM    198  CA  TRP   198      12.356  32.522  21.481  1.00 25.00           C
ATOM    199  CA  LYS   199      10.379  29.638  19.917  1.00 25.00           C
ATOM    200  CA  ALA   200      11.575  27.283  22.689  1.00 25.00           C
ATOM    201  CA  ALA   201      10.520  29.832  25.345  1.00 25.00           C
ATOM    202  CA  GLY   202      11.578  33.373  26.346  1.00 25.00           C
ATOM    203  CA  THR   203      13.444  36.667  25.935  1.00 25.00           C
ATOM    204  CA  PHE   204      17.115  37.697  26.155  1.00 25.00           C
ATOM    205  CA  ALA   205      18.589  37.330  29.671  1.00 25.00           C
ATOM    206  CA  GLU   206      15.910  34.737  30.548  1.00 25.00           C
ATOM    207  CA  GLU   207      16.697  32.803  27.338  1.00 25.00           C
ATOM    208  CA  TYR   208      20.431  32.865  28.186  1.00 25.00           C
ATOM    209  CA  ARG   209      19.677  31.575  31.711  1.00 25.00           C
ATOM    210  CA  SER   210      17.535  28.758  30.250  1.00 25.00           C
ATOM    211  CA  LEU   211      20.362  27.824  27.841  1.00 25.00           C
ATOM    212  CA  GLU   212      22.852  27.763  30.751  1.00 25.00           C
ATOM    213  CA  GLU   213      20.489  25.516  32.759  1.00 25.00           C
ATOM    214  CA  LEU   214      20.149  23.154  29.762  1.00 25.00           C
ATOM    215  CA  LEU   215      23.960  23.019  29.406  1.00 25.00           C
ATOM    216  CA  HIS   216      24.307  22.224  33.135  1.00 25.00           C
ATOM    217  CA  HIS   217      22.752  18.760  33.836  1.00 25.00           C
TER
END
