
#######################################################
#                                                     #
#                        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  104 (  104),  selected  104 , name T0341TS393_5-D2
# Molecule2: number of CA atoms  104 (  810),  selected  104 , name T0341_D2.pdb
# PARAMETERS: T0341TS393_5-D2.T0341_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      75      S      75          2.213
LGA    L      76      L      76          2.829
LGA    T      77      T      77          3.116
LGA    A      78      A      78          2.270
LGA    A      79      A      79          1.969
LGA    R      80      R      80          2.244
LGA    N      81      N      81          2.032
LGA    L      82      L      82          2.827
LGA    I      83      I      83          3.285
LGA    E      84      E      84          2.240
LGA    Q      85      Q      85          3.129
LGA    K      86      -       -           -
LGA    Q      87      K      86          4.922
LGA    V      88      Q      87          2.865
LGA    R      89      V      88          2.508
LGA    P      90      R      89          3.813
LGA    M      91      P      90          2.963
LGA    L      92      M      91          4.223
LGA    L      93      L      92          3.935
LGA    L      94      L      93          3.372
LGA    D      95      L      94          1.419
LGA    D      96      D      95          1.394
LGA    R      97      D      96          1.297
LGA    A      98      R      97          4.468
LGA    L      99      A      98          4.981
LGA    P     100      L      99          4.259
LGA    E     101      P     100          4.364
LGA    -       -      E     101           -
LGA    F     102      F     102          1.597
LGA    T     103      T     103          3.471
LGA    -       -      G     104           -
LGA    -       -      V     105           -
LGA    G     104      Q     106          4.407
LGA    V     105      T     107          1.684
LGA    Q     106      Q     108          2.427
LGA    T     107      D     109          2.120
LGA    Q     108      P     110          2.239
LGA    D     109      N     111          1.100
LGA    P     110      A     112          2.467
LGA    N     111      -       -           -
LGA    A     112      -       -           -
LGA    V     113      V     113           #
LGA    V     114      V     114          2.611
LGA    I     115      I     115          4.428
LGA    G     116      -       -           -
LGA    L     117      G     116          2.453
LGA    A     118      L     117          2.849
LGA    P     119      A     118          3.462
LGA    E     120      P     119          1.934
LGA    H     121      E     120          1.274
LGA    F     122      H     121          4.187
LGA    H     123      F     122          4.154
LGA    Y     124      H     123          1.808
LGA    -       -      Y     124           -
LGA    Q     125      Q     125          4.302
LGA    L     126      L     126          4.056
LGA    L     127      L     127          3.270
LGA    N     128      N     128          3.644
LGA    Q     129      Q     129          3.866
LGA    A     130      A     130          3.713
LGA    F     131      F     131          3.199
LGA    R     132      R     132          3.671
LGA    L     133      L     133          4.033
LGA    L     134      L     134          3.530
LGA    L     135      L     135          3.202
LGA    D     136      D     136          2.968
LGA    G     137      G     137          2.579
LGA    A     138      A     138          1.807
LGA    P     139      P     139          0.456
LGA    L     140      L     140          0.912
LGA    I     141      I     141          2.754
LGA    A     142      A     142          3.324
LGA    I     143      I     143          0.580
LGA    H     144      H     144          1.633
LGA    K     145      K     145          3.571
LGA    A     146      A     146          1.834
LGA    R     147      R     147          3.263
LGA    Y     148      Y     148          4.676
LGA    Y     149      Y     149          4.350
LGA    K     150      K     150          2.077
LGA    R     151      R     151          1.405
LGA    K     152      K     152          1.680
LGA    D     153      D     153          1.067
LGA    G     154      G     154          0.466
LGA    L     155      L     155          2.871
LGA    A     156      A     156          2.824
LGA    L     157      L     157          2.149
LGA    G     158      G     158          4.698
LGA    P     159      P     159          3.893
LGA    G     160      G     160          1.340
LGA    P     161      P     161          2.517
LGA    F     162      F     162          3.246
LGA    V     163      V     163          1.794
LGA    T     164      T     164          2.022
LGA    A     165      A     165          3.567
LGA    L     166      L     166          2.123
LGA    E     167      E     167          1.701
LGA    Y     168      Y     168          3.521
LGA    A     169      A     169          3.523
LGA    T     170      T     170          2.158
LGA    D     171      D     171          4.964
LGA    T     172      T     172          4.146
LGA    K     173      K     173          2.696
LGA    A     174      -       -           -
LGA    M     175      A     174          2.501
LGA    V     176      M     175           #
LGA    V     177      V     176           #
LGA    G     178      V     177           #
LGA    -       -      G     178           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  104  104    5.0     95    3.05    71.58     49.846     3.017

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.938658 * X  +   0.083714 * Y  +   0.334534 * Z  +  28.972340
  Y_new =  -0.034136 * X  +  -0.942767 * Y  +   0.331701 * Z  +  32.110203
  Z_new =   0.343155 * X  +  -0.322773 * Y  +  -0.882078 * Z  +  84.788490 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.790803    0.350789  [ DEG:  -159.9012     20.0988 ]
  Theta =  -0.350274   -2.791318  [ DEG:   -20.0692   -159.9308 ]
  Phi   =  -0.036351    3.105242  [ DEG:    -2.0828    177.9173 ]
 
# 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: T0341TS393_5-D2                               
REMARK     2: T0341_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0341TS393_5-D2.T0341_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  104  104   5.0   95   3.05   71.58  49.846
REMARK  ---------------------------------------------------------- 
MOLECULE T0341TS393_5-D2
PFRMAT TS
TARGET T0341
MODEL 5
PARENT N/A
ATOM     75  CA  SER    75      21.686  29.550  86.994  1.00 25.00           C
ATOM     76  CA  LEU    76      18.977  27.972  84.795  1.00 25.00           C
ATOM     77  CA  THR    77      16.402  28.434  87.590  1.00 25.00           C
ATOM     78  CA  ALA    78      17.434  32.103  87.968  1.00 25.00           C
ATOM     79  CA  ALA    79      17.081  32.617  84.190  1.00 25.00           C
ATOM     80  CA  ARG    80      13.601  31.020  84.273  1.00 25.00           C
ATOM     81  CA  ASN    81      12.593  33.312  87.172  1.00 25.00           C
ATOM     82  CA  LEU    82      13.852  36.363  85.230  1.00 25.00           C
ATOM     83  CA  ILE    83      11.853  35.263  82.154  1.00 25.00           C
ATOM     84  CA  GLU    84       8.717  34.844  84.313  1.00 25.00           C
ATOM     85  CA  GLN    85       9.236  38.341  85.787  1.00 25.00           C
ATOM     86  CA  LYS    86       8.646  39.409  82.148  1.00 25.00           C
ATOM     87  CA  GLN    87       6.498  39.230  79.014  1.00 25.00           C
ATOM     88  CA  VAL    88       5.863  35.543  78.184  1.00 25.00           C
ATOM     89  CA  ARG    89       7.833  32.432  79.163  1.00 25.00           C
ATOM     90  CA  PRO    90      10.703  29.991  79.415  1.00 25.00           C
ATOM     91  CA  MET    91      14.025  28.082  79.000  1.00 25.00           C
ATOM     92  CA  LEU    92      16.937  25.954  77.810  1.00 25.00           C
ATOM     93  CA  LEU    93      19.448  24.923  75.140  1.00 25.00           C
ATOM     94  CA  LEU    94      22.290  24.504  77.710  1.00 25.00           C
ATOM     95  CA  ASP    95      22.938  21.292  79.657  1.00 25.00           C
ATOM     96  CA  ASP    96      22.719  17.606  80.494  1.00 25.00           C
ATOM     97  CA  ARG    97      19.931  17.372  83.051  1.00 25.00           C
ATOM     98  CA  ALA    98      19.208  20.401  85.281  1.00 25.00           C
ATOM     99  CA  LEU    99      18.105  22.422  82.221  1.00 25.00           C
ATOM    100  CA  PRO   100      15.801  19.564  81.131  1.00 25.00           C
ATOM    101  CA  GLU   101      14.293  19.406  84.649  1.00 25.00           C
ATOM    102  CA  PHE   102      13.710  23.192  84.595  1.00 25.00           C
ATOM    103  CA  THR   103       9.933  23.064  84.294  1.00 25.00           C
ATOM    104  CA  GLY   104       8.311  20.415  82.138  1.00 25.00           C
ATOM    105  CA  VAL   105       9.592  22.361  79.119  1.00 25.00           C
ATOM    106  CA  GLN   106       6.548  23.144  77.025  1.00 25.00           C
ATOM    107  CA  THR   107       6.325  24.704  73.511  1.00 25.00           C
ATOM    108  CA  GLN   108       8.644  25.324  70.577  1.00 25.00           C
ATOM    109  CA  ASP   109       9.271  29.014  71.443  1.00 25.00           C
ATOM    110  CA  PRO   110      11.567  28.863  74.523  1.00 25.00           C
ATOM    111  CA  ASN   111      12.762  32.309  75.480  1.00 25.00           C
ATOM    112  CA  ALA   112      15.307  34.034  77.767  1.00 25.00           C
ATOM    113  CA  VAL   113      17.888  31.463  78.744  1.00 25.00           C
ATOM    114  CA  VAL   114      20.828  29.445  77.470  1.00 25.00           C
ATOM    115  CA  ILE   115      24.314  30.264  76.139  1.00 25.00           C
ATOM    116  CA  GLY   116      26.589  27.179  76.042  1.00 25.00           C
ATOM    117  CA  LEU   117      27.047  25.022  79.173  1.00 25.00           C
ATOM    118  CA  ALA   118      27.814  22.312  76.611  1.00 25.00           C
ATOM    119  CA  PRO   119      28.849  20.025  79.490  1.00 25.00           C
ATOM    120  CA  GLU   120      29.309  16.557  77.856  1.00 25.00           C
ATOM    121  CA  HIS   121      26.240  14.597  76.704  1.00 25.00           C
ATOM    122  CA  PHE   122      27.221  15.968  73.274  1.00 25.00           C
ATOM    123  CA  HIS   123      28.792  16.550  69.858  1.00 25.00           C
ATOM    124  CA  TYR   124      25.556  15.062  68.521  1.00 25.00           C
ATOM    125  CA  GLN   125      21.803  15.129  69.281  1.00 25.00           C
ATOM    126  CA  LEU   126      22.371  17.788  71.977  1.00 25.00           C
ATOM    127  CA  LEU   127      24.419  19.886  69.513  1.00 25.00           C
ATOM    128  CA  ASN   128      21.631  19.585  66.903  1.00 25.00           C
ATOM    129  CA  GLN   129      19.044  20.680  69.505  1.00 25.00           C
ATOM    130  CA  ALA   130      21.221  23.687  70.442  1.00 25.00           C
ATOM    131  CA  PHE   131      21.544  24.635  66.745  1.00 25.00           C
ATOM    132  CA  ARG   132      17.746  24.385  66.324  1.00 25.00           C
ATOM    133  CA  LEU   133      17.234  26.611  69.399  1.00 25.00           C
ATOM    134  CA  LEU   134      19.701  29.176  67.983  1.00 25.00           C
ATOM    135  CA  LEU   135      17.849  29.146  64.632  1.00 25.00           C
ATOM    136  CA  ASP   136      14.162  29.237  63.833  1.00 25.00           C
ATOM    137  CA  GLY   137      13.891  31.875  66.497  1.00 25.00           C
ATOM    138  CA  ALA   138      14.654  30.884  70.140  1.00 25.00           C
ATOM    139  CA  PRO   139      15.935  33.926  71.947  1.00 25.00           C
ATOM    140  CA  LEU   140      19.272  33.024  73.528  1.00 25.00           C
ATOM    141  CA  ILE   141      21.251  34.574  76.402  1.00 25.00           C
ATOM    142  CA  ALA   142      23.050  33.819  79.589  1.00 25.00           C
ATOM    143  CA  ILE   143      24.062  30.558  81.208  1.00 25.00           C
ATOM    144  CA  HIS   144      27.651  29.551  80.579  1.00 25.00           C
ATOM    145  CA  LYS   145      31.047  28.178  79.440  1.00 25.00           C
ATOM    146  CA  ALA   146      34.208  29.158  77.587  1.00 25.00           C
ATOM    147  CA  ARG   147      34.774  25.444  76.992  1.00 25.00           C
ATOM    148  CA  TYR   148      33.201  22.689  78.989  1.00 25.00           C
ATOM    149  CA  TYR   149      34.230  20.767  82.048  1.00 25.00           C
ATOM    150  CA  LYS   150      37.833  20.358  83.192  1.00 25.00           C
ATOM    151  CA  ARG   151      38.591  16.706  83.924  1.00 25.00           C
ATOM    152  CA  LYS   152      40.617  13.630  84.917  1.00 25.00           C
ATOM    153  CA  ASP   153      42.478  13.565  81.665  1.00 25.00           C
ATOM    154  CA  GLY   154      42.648  17.208  80.620  1.00 25.00           C
ATOM    155  CA  LEU   155      40.452  18.396  77.701  1.00 25.00           C
ATOM    156  CA  ALA   156      36.791  17.248  77.423  1.00 25.00           C
ATOM    157  CA  LEU   157      35.900  20.116  75.091  1.00 25.00           C
ATOM    158  CA  GLY   158      33.001  22.114  73.660  1.00 25.00           C
ATOM    159  CA  PRO   159      30.522  24.919  73.174  1.00 25.00           C
ATOM    160  CA  GLY   160      30.689  28.639  74.070  1.00 25.00           C
ATOM    161  CA  PRO   161      32.484  29.378  70.768  1.00 25.00           C
ATOM    162  CA  PHE   162      29.805  27.429  68.846  1.00 25.00           C
ATOM    163  CA  VAL   163      27.052  29.394  70.643  1.00 25.00           C
ATOM    164  CA  THR   164      28.798  32.688  69.768  1.00 25.00           C
ATOM    165  CA  ALA   165      29.056  31.606  66.103  1.00 25.00           C
ATOM    166  CA  LEU   166      25.332  30.714  66.078  1.00 25.00           C
ATOM    167  CA  GLU   167      24.477  34.133  67.578  1.00 25.00           C
ATOM    168  CA  TYR   168      26.610  35.864  64.909  1.00 25.00           C
ATOM    169  CA  ALA   169      24.834  33.870  62.163  1.00 25.00           C
ATOM    170  CA  THR   170      21.430  34.859  63.613  1.00 25.00           C
ATOM    171  CA  ASP   171      19.987  37.980  65.219  1.00 25.00           C
ATOM    172  CA  THR   172      18.866  35.511  67.884  1.00 25.00           C
ATOM    173  CA  LYS   173      21.417  37.203  70.120  1.00 25.00           C
ATOM    174  CA  ALA   174      23.879  37.148  73.006  1.00 25.00           C
ATOM    175  CA  MET   175      25.043  33.481  73.055  1.00 25.00           C
ATOM    176  CA  VAL   176      26.734  34.734  76.223  1.00 25.00           C
ATOM    177  CA  VAL   177      29.412  33.034  78.341  1.00 25.00           C
ATOM    178  CA  GLY   178      28.430  34.074  81.844  1.00 25.00           C
TER
END
