
#######################################################
#                                                     #
#                        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 T0341TS168_3-D2
# Molecule2: number of CA atoms  104 (  810),  selected  104 , name T0341_D2.pdb
# PARAMETERS: T0341TS168_3-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          2.638
LGA    L      76      L      76          3.423
LGA    T      77      T      77          2.937
LGA    A      78      A      78          1.710
LGA    A      79      A      79          2.179
LGA    R      80      R      80          2.263
LGA    N      81      N      81          1.849
LGA    L      82      L      82          1.944
LGA    I      83      I      83          2.265
LGA    E      84      E      84          1.687
LGA    Q      85      Q      85          2.467
LGA    K      86      K      86          4.690
LGA    Q      87      Q      87          5.645
LGA    V      88      V      88           #
LGA    R      89      R      89           #
LGA    P      90      P      90           #
LGA    -       -      M      91           -
LGA    -       -      L      92           -
LGA    -       -      L      93           -
LGA    -       -      L      94           -
LGA    -       -      D      95           -
LGA    -       -      D      96           -
LGA    -       -      R      97           -
LGA    -       -      A      98           -
LGA    -       -      L      99           -
LGA    -       -      P     100           -
LGA    -       -      E     101           -
LGA    -       -      F     102           -
LGA    -       -      T     103           -
LGA    -       -      G     104           -
LGA    -       -      V     105           -
LGA    -       -      Q     106           -
LGA    -       -      T     107           -
LGA    -       -      Q     108           -
LGA    -       -      D     109           -
LGA    -       -      P     110           -
LGA    M      91      N     111          5.134
LGA    L      92      A     112          3.486
LGA    L      93      V     113          3.897
LGA    L      94      V     114          4.142
LGA    D      95      I     115           #
LGA    D      96      -       -           -
LGA    R      97      -       -           -
LGA    A      98      -       -           -
LGA    L      99      -       -           -
LGA    P     100      -       -           -
LGA    E     101      -       -           -
LGA    F     102      -       -           -
LGA    T     103      -       -           -
LGA    G     104      -       -           -
LGA    V     105      -       -           -
LGA    Q     106      -       -           -
LGA    T     107      -       -           -
LGA    Q     108      -       -           -
LGA    D     109      -       -           -
LGA    P     110      -       -           -
LGA    N     111      -       -           -
LGA    A     112      -       -           -
LGA    V     113      -       -           -
LGA    V     114      -       -           -
LGA    I     115      -       -           -
LGA    G     116      G     116          3.738
LGA    L     117      L     117          1.887
LGA    A     118      A     118          2.703
LGA    P     119      P     119          3.559
LGA    E     120      E     120          3.959
LGA    H     121      H     121          3.390
LGA    F     122      F     122          1.706
LGA    H     123      H     123          1.903
LGA    Y     124      Y     124          2.216
LGA    Q     125      Q     125          2.215
LGA    L     126      L     126          2.266
LGA    L     127      L     127          1.294
LGA    N     128      N     128          1.275
LGA    Q     129      Q     129          1.750
LGA    A     130      A     130          1.352
LGA    F     131      F     131          0.854
LGA    R     132      R     132          1.769
LGA    L     133      L     133          1.879
LGA    L     134      L     134          1.370
LGA    L     135      L     135          2.095
LGA    D     136      D     136          1.212
LGA    G     137      G     137          0.430
LGA    A     138      A     138          2.635
LGA    P     139      P     139          2.370
LGA    L     140      L     140          4.698
LGA    I     141      I     141           #
LGA    A     142      A     142          4.737
LGA    I     143      I     143          4.567
LGA    H     144      H     144          3.352
LGA    K     145      K     145          3.322
LGA    A     146      A     146          2.063
LGA    R     147      R     147          2.165
LGA    Y     148      Y     148          1.659
LGA    Y     149      Y     149          1.350
LGA    K     150      K     150          2.041
LGA    R     151      R     151          2.096
LGA    K     152      K     152          1.273
LGA    D     153      D     153          2.032
LGA    G     154      G     154          1.088
LGA    L     155      L     155          2.324
LGA    A     156      A     156          1.803
LGA    L     157      L     157          1.547
LGA    G     158      G     158          1.433
LGA    P     159      P     159          1.994
LGA    G     160      G     160          1.784
LGA    P     161      P     161          1.425
LGA    F     162      F     162          0.970
LGA    V     163      V     163          1.417
LGA    T     164      T     164          1.502
LGA    A     165      A     165          0.936
LGA    L     166      L     166          1.085
LGA    E     167      E     167          1.457
LGA    Y     168      Y     168          0.905
LGA    A     169      A     169          1.052
LGA    T     170      T     170          2.029
LGA    D     171      D     171          3.773
LGA    T     172      T     172          1.738
LGA    K     173      K     173           #
LGA    A     174      -       -           -
LGA    M     175      A     174          4.419
LGA    V     176      M     175          3.047
LGA    V     177      V     176          4.533
LGA    G     178      V     177          2.793
LGA    -       -      G     178           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  104  104    5.0     77    2.64    90.91     50.735     2.809

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.920570 * X  +  -0.275995 * Y  +   0.276364 * Z  +  27.524757
  Y_new =  -0.390094 * X  +  -0.614526 * Y  +   0.685700 * Z  +  32.495350
  Z_new =  -0.019417 * X  +  -0.739043 * Y  +  -0.673378 * Z  +  84.494881 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.309737    0.831856  [ DEG:  -132.3382     47.6618 ]
  Theta =   0.019419    3.122174  [ DEG:     1.1126    178.8874 ]
  Phi   =  -0.400813    2.740779  [ DEG:   -22.9649    157.0351 ]
 
# 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: T0341TS168_3-D2                               
REMARK     2: T0341_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0341TS168_3-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   77   2.64   90.91  50.735
REMARK  ---------------------------------------------------------- 
MOLECULE T0341TS168_3-D2
PFRMAT TS
TARGET T0341
MODEL 3
PARENT N/A
ATOM     75  CA  SER    75      22.435  30.419  85.060  1.00 25.00           C
ATOM     76  CA  LEU    76      19.746  28.074  83.667  1.00 25.00           C
ATOM     77  CA  THR    77      17.604  28.635  86.791  1.00 25.00           C
ATOM     78  CA  ALA    78      17.997  32.426  86.411  1.00 25.00           C
ATOM     79  CA  ALA    79      16.964  32.189  82.731  1.00 25.00           C
ATOM     80  CA  ARG    80      13.890  30.121  83.701  1.00 25.00           C
ATOM     81  CA  ASN    81      12.953  32.716  86.357  1.00 25.00           C
ATOM     82  CA  LEU    82      13.313  35.523  83.776  1.00 25.00           C
ATOM     83  CA  ILE    83      11.088  33.592  81.329  1.00 25.00           C
ATOM     84  CA  GLU    84       8.461  33.096  84.072  1.00 25.00           C
ATOM     85  CA  GLN    85       8.560  36.839  84.879  1.00 25.00           C
ATOM     86  CA  LYS    86       6.459  37.422  81.723  1.00 25.00           C
ATOM     87  CA  GLN    87       4.778  38.590  78.487  1.00 25.00           C
ATOM     88  CA  VAL    88       4.610  35.441  76.352  1.00 25.00           C
ATOM     89  CA  ARG    89       7.975  33.649  76.120  1.00 25.00           C
ATOM     90  CA  PRO    90      11.208  32.373  74.437  1.00 25.00           C
ATOM     91  CA  MET    91      14.714  31.199  73.478  1.00 25.00           C
ATOM     92  CA  LEU    92      16.483  27.929  74.365  1.00 25.00           C
ATOM     93  CA  LEU    93      18.284  24.938  75.874  1.00 25.00           C
ATOM     94  CA  LEU    94      20.592  24.370  78.844  1.00 25.00           C
ATOM     95  CA  ASP    95      22.561  21.281  79.751  1.00 25.00           C
ATOM     96  CA  ASP    96      21.786  17.602  79.704  1.00 25.00           C
ATOM     97  CA  ARG    97      19.779  17.560  82.991  1.00 25.00           C
ATOM     98  CA  ALA    98      18.023  19.868  85.492  1.00 25.00           C
ATOM     99  CA  LEU    99      17.353  22.414  82.710  1.00 25.00           C
ATOM    100  CA  PRO   100      15.915  19.645  80.488  1.00 25.00           C
ATOM    101  CA  GLU   101      13.656  18.484  83.355  1.00 25.00           C
ATOM    102  CA  PHE   102      12.452  22.080  83.894  1.00 25.00           C
ATOM    103  CA  THR   103       9.015  22.568  82.445  1.00 25.00           C
ATOM    104  CA  GLY   104       7.492  19.372  81.066  1.00 25.00           C
ATOM    105  CA  VAL   105       8.295  20.517  77.513  1.00 25.00           C
ATOM    106  CA  GLN   106       7.384  20.207  73.903  1.00 25.00           C
ATOM    107  CA  THR   107       6.448  23.728  72.900  1.00 25.00           C
ATOM    108  CA  GLN   108       7.600  23.572  69.302  1.00 25.00           C
ATOM    109  CA  ASP   109       8.205  27.309  68.684  1.00 25.00           C
ATOM    110  CA  PRO   110      10.101  27.911  71.912  1.00 25.00           C
ATOM    111  CA  ASN   111      11.371  27.460  75.470  1.00 25.00           C
ATOM    112  CA  ALA   112      12.976  29.521  78.158  1.00 25.00           C
ATOM    113  CA  VAL   113      16.375  31.120  78.220  1.00 25.00           C
ATOM    114  CA  VAL   114      19.655  29.285  78.794  1.00 25.00           C
ATOM    115  CA  ILE   115      22.072  28.246  76.051  1.00 25.00           C
ATOM    116  CA  GLY   116      25.636  27.011  76.622  1.00 25.00           C
ATOM    117  CA  LEU   117      26.787  24.176  78.784  1.00 25.00           C
ATOM    118  CA  ALA   118      26.593  21.332  76.279  1.00 25.00           C
ATOM    119  CA  PRO   119      28.806  19.521  78.845  1.00 25.00           C
ATOM    120  CA  GLU   120      28.712  16.688  76.244  1.00 25.00           C
ATOM    121  CA  HIS   121      25.467  14.934  75.325  1.00 25.00           C
ATOM    122  CA  PHE   122      25.672  17.193  72.276  1.00 25.00           C
ATOM    123  CA  HIS   123      26.405  15.117  69.211  1.00 25.00           C
ATOM    124  CA  TYR   124      25.667  18.307  67.291  1.00 25.00           C
ATOM    125  CA  GLN   125      21.998  17.215  67.396  1.00 25.00           C
ATOM    126  CA  LEU   126      21.422  19.362  70.515  1.00 25.00           C
ATOM    127  CA  LEU   127      23.047  22.364  68.778  1.00 25.00           C
ATOM    128  CA  ASN   128      20.813  21.831  65.713  1.00 25.00           C
ATOM    129  CA  GLN   129      17.720  21.670  67.966  1.00 25.00           C
ATOM    130  CA  ALA   130      18.783  24.915  69.700  1.00 25.00           C
ATOM    131  CA  PHE   131      19.262  26.605  66.297  1.00 25.00           C
ATOM    132  CA  ARG   132      15.788  25.430  65.196  1.00 25.00           C
ATOM    133  CA  LEU   133      14.270  26.805  68.432  1.00 25.00           C
ATOM    134  CA  LEU   134      16.027  30.160  67.861  1.00 25.00           C
ATOM    135  CA  LEU   135      14.690  30.275  64.274  1.00 25.00           C
ATOM    136  CA  ASP   136      11.394  32.162  64.478  1.00 25.00           C
ATOM    137  CA  GLY   137      13.230  34.804  66.482  1.00 25.00           C
ATOM    138  CA  ALA   138      14.409  34.923  70.086  1.00 25.00           C
ATOM    139  CA  PRO   139      15.995  36.111  73.385  1.00 25.00           C
ATOM    140  CA  LEU   140      19.658  36.960  72.816  1.00 25.00           C
ATOM    141  CA  ILE   141      23.231  35.785  73.449  1.00 25.00           C
ATOM    142  CA  ALA   142      25.943  33.323  74.402  1.00 25.00           C
ATOM    143  CA  ILE   143      26.575  31.260  77.568  1.00 25.00           C
ATOM    144  CA  HIS   144      30.278  30.684  78.219  1.00 25.00           C
ATOM    145  CA  LYS   145      33.935  31.523  77.659  1.00 25.00           C
ATOM    146  CA  ALA   146      35.253  28.239  78.872  1.00 25.00           C
ATOM    147  CA  ARG   147      37.126  26.543  76.046  1.00 25.00           C
ATOM    148  CA  TYR   148      38.202  24.104  78.709  1.00 25.00           C
ATOM    149  CA  TYR   149      36.085  23.270  81.834  1.00 25.00           C
ATOM    150  CA  LYS   150      37.827  20.386  83.529  1.00 25.00           C
ATOM    151  CA  ARG   151      37.582  17.048  85.216  1.00 25.00           C
ATOM    152  CA  LYS   152      40.088  14.303  84.217  1.00 25.00           C
ATOM    153  CA  ASP   153      40.589  14.512  80.438  1.00 25.00           C
ATOM    154  CA  GLY   154      41.897  18.097  80.911  1.00 25.00           C
ATOM    155  CA  LEU   155      40.133  19.332  77.829  1.00 25.00           C
ATOM    156  CA  ALA   156      36.453  18.700  78.252  1.00 25.00           C
ATOM    157  CA  LEU   157      34.344  21.436  76.565  1.00 25.00           C
ATOM    158  CA  GLY   158      32.117  23.644  78.734  1.00 25.00           C
ATOM    159  CA  PRO   159      30.473  24.532  75.419  1.00 25.00           C
ATOM    160  CA  GLY   160      32.461  27.675  74.503  1.00 25.00           C
ATOM    161  CA  PRO   161      32.965  26.350  70.946  1.00 25.00           C
ATOM    162  CA  PHE   162      29.213  25.640  70.652  1.00 25.00           C
ATOM    163  CA  VAL   163      28.421  29.184  71.867  1.00 25.00           C
ATOM    164  CA  THR   164      30.858  30.636  69.294  1.00 25.00           C
ATOM    165  CA  ALA   165      29.213  28.559  66.528  1.00 25.00           C
ATOM    166  CA  LEU   166      25.758  29.802  67.617  1.00 25.00           C
ATOM    167  CA  GLU   167      27.013  33.420  67.560  1.00 25.00           C
ATOM    168  CA  TYR   168      28.442  32.894  64.046  1.00 25.00           C
ATOM    169  CA  ALA   169      25.100  31.431  62.879  1.00 25.00           C
ATOM    170  CA  THR   170      23.241  34.438  64.353  1.00 25.00           C
ATOM    171  CA  ASP   171      20.861  37.380  64.519  1.00 25.00           C
ATOM    172  CA  THR   172      21.782  37.646  68.206  1.00 25.00           C
ATOM    173  CA  LYS   173      20.295  34.211  68.585  1.00 25.00           C
ATOM    174  CA  ALA   174      21.969  31.688  70.794  1.00 25.00           C
ATOM    175  CA  MET   175      19.597  32.603  73.613  1.00 25.00           C
ATOM    176  CA  VAL   176      21.411  33.624  76.848  1.00 25.00           C
ATOM    177  CA  VAL   177      20.348  33.970  80.467  1.00 25.00           C
ATOM    178  CA  GLY   178      23.935  32.994  81.314  1.00 25.00           C
TER
END
