
#######################################################
#                                                     #
#                        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_4-D2
# Molecule2: number of CA atoms  104 (  810),  selected  104 , name T0341_D2.pdb
# PARAMETERS: T0341TS393_4-D2.T0341_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      S      75           -
LGA    -       -      L      76           -
LGA    -       -      T      77           -
LGA    S      75      A      78          2.161
LGA    L      76      A      79          2.728
LGA    T      77      R      80          2.014
LGA    A      78      N      81          0.933
LGA    A      79      L      82          1.777
LGA    R      80      I      83          2.807
LGA    N      81      E      84          2.551
LGA    L      82      Q      85          0.993
LGA    I      83      K      86          2.219
LGA    E      84      Q      87          3.919
LGA    Q      85      -       -           -
LGA    K      86      -       -           -
LGA    Q      87      -       -           -
LGA    V      88      -       -           -
LGA    R      89      V      88          3.313
LGA    P      90      R      89          3.015
LGA    M      91      P      90          3.257
LGA    L      92      M      91           #
LGA    L      93      L      92          3.981
LGA    L      94      L      93          1.806
LGA    D      95      L      94          1.993
LGA    D      96      D      95          2.451
LGA    R      97      D      96          2.635
LGA    -       -      R      97           -
LGA    -       -      A      98           -
LGA    A      98      L      99          2.677
LGA    L      99      P     100           -
LGA    P     100      E     101           -
LGA    E     101      F     102          4.677
LGA    F     102      T     103          4.989
LGA    -       -      G     104           -
LGA    T     103      V     105          3.240
LGA    G     104      Q     106          4.182
LGA    V     105      T     107          1.220
LGA    Q     106      Q     108          2.072
LGA    T     107      D     109          1.543
LGA    Q     108      P     110          3.223
LGA    D     109      N     111          3.419
LGA    P     110      -       -           -
LGA    N     111      A     112          1.974
LGA    A     112      V     113          3.429
LGA    V     113      V     114          3.335
LGA    V     114      I     115          2.330
LGA    I     115      -       -           -
LGA    G     116      G     116          2.336
LGA    L     117      L     117          1.188
LGA    A     118      A     118          3.162
LGA    P     119      P     119          3.679
LGA    E     120      E     120          4.291
LGA    H     121      H     121          4.073
LGA    F     122      F     122          1.814
LGA    H     123      H     123          2.035
LGA    Y     124      Y     124          3.321
LGA    Q     125      Q     125          3.362
LGA    L     126      L     126          2.770
LGA    L     127      L     127          1.607
LGA    N     128      N     128          2.322
LGA    Q     129      Q     129          2.749
LGA    A     130      A     130          2.317
LGA    F     131      F     131          1.539
LGA    R     132      R     132          2.347
LGA    L     133      L     133          2.872
LGA    L     134      L     134          2.195
LGA    L     135      L     135          1.712
LGA    D     136      D     136          0.873
LGA    G     137      G     137          1.931
LGA    A     138      A     138          2.601
LGA    P     139      P     139          2.493
LGA    L     140      L     140          3.686
LGA    I     141      I     141          1.433
LGA    A     142      A     142          2.158
LGA    I     143      I     143          2.370
LGA    H     144      H     144          2.385
LGA    K     145      K     145          1.773
LGA    A     146      A     146          1.244
LGA    R     147      R     147          1.181
LGA    Y     148      Y     148          1.194
LGA    Y     149      Y     149          1.717
LGA    K     150      K     150          2.947
LGA    R     151      R     151          2.476
LGA    K     152      K     152          1.781
LGA    D     153      D     153          1.431
LGA    G     154      G     154          1.359
LGA    L     155      L     155          1.437
LGA    A     156      A     156          1.486
LGA    L     157      L     157          1.254
LGA    G     158      G     158          1.233
LGA    P     159      P     159          0.912
LGA    G     160      G     160          1.429
LGA    P     161      P     161          1.200
LGA    F     162      F     162          0.432
LGA    V     163      V     163          1.124
LGA    T     164      T     164          1.360
LGA    A     165      A     165          0.828
LGA    L     166      L     166          0.702
LGA    E     167      E     167          0.889
LGA    Y     168      Y     168          1.519
LGA    A     169      A     169          1.642
LGA    T     170      T     170          0.985
LGA    D     171      D     171          0.456
LGA    T     172      T     172          1.274
LGA    K     173      K     173          3.881
LGA    A     174      A     174          1.477
LGA    M     175      M     175          2.685
LGA    V     176      V     176          2.002
LGA    V     177      V     177          1.605
LGA    G     178      G     178          1.522

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  104  104    5.0     95    2.41    71.58     62.280     3.777

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.951266 * X  +  -0.129164 * Y  +  -0.280016 * Z  +  27.125626
  Y_new =   0.147437 * X  +  -0.607033 * Y  +   0.780880 * Z  +  31.705601
  Z_new =  -0.270840 * X  +  -0.784109 * Y  +  -0.558407 * Z  +  85.212433 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.189633    0.951959  [ DEG:  -125.4567     54.5433 ]
  Theta =   0.274266    2.867326  [ DEG:    15.7143    164.2857 ]
  Phi   =   0.153766   -2.987826  [ DEG:     8.8102   -171.1898 ]
 
# 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_4-D2                               
REMARK     2: T0341_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0341TS393_4-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   2.41   71.58  62.280
REMARK  ---------------------------------------------------------- 
MOLECULE T0341TS393_4-D2
PFRMAT TS
TARGET T0341
MODEL 4
PARENT N/A
ATOM     75  CA  SER    75      19.617  31.017  86.544  1.00 25.00           C
ATOM     76  CA  LEU    76      17.016  28.918  84.675  1.00 25.00           C
ATOM     77  CA  THR    77      14.434  29.640  87.409  1.00 25.00           C
ATOM     78  CA  ALA    78      15.198  33.385  87.177  1.00 25.00           C
ATOM     79  CA  ALA    79      14.782  33.259  83.373  1.00 25.00           C
ATOM     80  CA  ARG    80      11.428  31.455  83.774  1.00 25.00           C
ATOM     81  CA  ASN    81      10.275  34.104  86.287  1.00 25.00           C
ATOM     82  CA  LEU    82      11.295  36.885  83.861  1.00 25.00           C
ATOM     83  CA  ILE    83       9.360  35.166  81.038  1.00 25.00           C
ATOM     84  CA  GLU    84       6.278  34.879  83.294  1.00 25.00           C
ATOM     85  CA  GLN    85       6.551  38.594  84.182  1.00 25.00           C
ATOM     86  CA  LYS    86       6.460  39.605  80.499  1.00 25.00           C
ATOM     87  CA  GLN    87       5.613  39.463  76.775  1.00 25.00           C
ATOM     88  CA  VAL    88       6.080  35.776  75.962  1.00 25.00           C
ATOM     89  CA  ARG    89       6.304  31.979  75.936  1.00 25.00           C
ATOM     90  CA  PRO    90       9.757  30.590  76.562  1.00 25.00           C
ATOM     91  CA  MET    91      13.275  29.834  77.652  1.00 25.00           C
ATOM     92  CA  LEU    92      16.719  28.350  78.526  1.00 25.00           C
ATOM     93  CA  LEU    93      19.553  25.924  79.012  1.00 25.00           C
ATOM     94  CA  LEU    94      19.056  23.374  76.239  1.00 25.00           C
ATOM     95  CA  ASP    95      22.042  21.684  77.915  1.00 25.00           C
ATOM     96  CA  ASP    96      21.266  18.705  80.034  1.00 25.00           C
ATOM     97  CA  ARG    97      18.131  17.231  81.543  1.00 25.00           C
ATOM     98  CA  ALA    98      17.791  20.705  83.119  1.00 25.00           C
ATOM     99  CA  LEU    99      16.001  21.980  79.982  1.00 25.00           C
ATOM    100  CA  PRO   100      13.617  18.983  80.096  1.00 25.00           C
ATOM    101  CA  GLU   101      12.890  19.671  83.792  1.00 25.00           C
ATOM    102  CA  PHE   102      12.181  23.349  82.995  1.00 25.00           C
ATOM    103  CA  THR   103       8.707  22.092  82.187  1.00 25.00           C
ATOM    104  CA  GLY   104       6.884  20.054  79.499  1.00 25.00           C
ATOM    105  CA  VAL   105       8.171  22.649  77.051  1.00 25.00           C
ATOM    106  CA  GLN   106       5.098  23.245  74.890  1.00 25.00           C
ATOM    107  CA  THR   107       5.826  25.094  71.710  1.00 25.00           C
ATOM    108  CA  GLN   108       8.850  23.660  70.005  1.00 25.00           C
ATOM    109  CA  ASP   109       9.496  27.290  69.076  1.00 25.00           C
ATOM    110  CA  PRO   110      11.738  27.274  72.146  1.00 25.00           C
ATOM    111  CA  ASN   111      12.577  30.986  72.410  1.00 25.00           C
ATOM    112  CA  ALA   112      16.232  31.278  73.184  1.00 25.00           C
ATOM    113  CA  VAL   113      19.286  29.291  74.244  1.00 25.00           C
ATOM    114  CA  VAL   114      22.257  26.881  74.589  1.00 25.00           C
ATOM    115  CA  ILE   115      25.186  29.188  75.537  1.00 25.00           C
ATOM    116  CA  GLY   116      25.441  26.953  78.604  1.00 25.00           C
ATOM    117  CA  LEU   117      26.986  23.616  79.561  1.00 25.00           C
ATOM    118  CA  ALA   118      27.684  21.463  76.541  1.00 25.00           C
ATOM    119  CA  PRO   119      29.326  19.208  79.114  1.00 25.00           C
ATOM    120  CA  GLU   120      29.123  16.638  76.319  1.00 25.00           C
ATOM    121  CA  HIS   121      26.434  14.632  74.555  1.00 25.00           C
ATOM    122  CA  PHE   122      26.748  17.155  71.741  1.00 25.00           C
ATOM    123  CA  HIS   123      27.446  17.224  67.958  1.00 25.00           C
ATOM    124  CA  TYR   124      23.849  15.998  67.826  1.00 25.00           C
ATOM    125  CA  GLN   125      20.103  16.222  68.594  1.00 25.00           C
ATOM    126  CA  LEU   126      20.801  18.752  71.383  1.00 25.00           C
ATOM    127  CA  LEU   127      22.950  20.833  68.991  1.00 25.00           C
ATOM    128  CA  ASN   128      20.152  20.763  66.376  1.00 25.00           C
ATOM    129  CA  GLN   129      17.620  21.889  69.020  1.00 25.00           C
ATOM    130  CA  ALA   130      19.943  24.752  70.060  1.00 25.00           C
ATOM    131  CA  PHE   131      20.313  25.814  66.400  1.00 25.00           C
ATOM    132  CA  ARG   132      16.508  25.766  65.975  1.00 25.00           C
ATOM    133  CA  LEU   133      16.105  27.903  69.127  1.00 25.00           C
ATOM    134  CA  LEU   134      18.696  30.392  67.802  1.00 25.00           C
ATOM    135  CA  LEU   135      16.844  30.574  64.454  1.00 25.00           C
ATOM    136  CA  ASP   136      13.229  31.784  64.331  1.00 25.00           C
ATOM    137  CA  GLY   137      12.052  33.345  67.571  1.00 25.00           C
ATOM    138  CA  ALA   138      14.924  34.692  69.718  1.00 25.00           C
ATOM    139  CA  PRO   139      15.782  36.356  73.030  1.00 25.00           C
ATOM    140  CA  LEU   140      18.703  35.198  75.156  1.00 25.00           C
ATOM    141  CA  ILE   141      19.439  32.753  77.891  1.00 25.00           C
ATOM    142  CA  ALA   142      22.220  30.705  79.450  1.00 25.00           C
ATOM    143  CA  ILE   143      25.826  31.564  80.121  1.00 25.00           C
ATOM    144  CA  HIS   144      29.213  30.249  78.802  1.00 25.00           C
ATOM    145  CA  LYS   145      31.682  32.622  77.220  1.00 25.00           C
ATOM    146  CA  ALA   146      34.322  30.592  78.941  1.00 25.00           C
ATOM    147  CA  ARG   147      36.248  27.642  77.394  1.00 25.00           C
ATOM    148  CA  TYR   148      37.812  24.517  78.932  1.00 25.00           C
ATOM    149  CA  TYR   149      36.063  22.658  81.809  1.00 25.00           C
ATOM    150  CA  LYS   150      37.387  19.451  83.259  1.00 25.00           C
ATOM    151  CA  ARG   151      37.704  16.220  85.150  1.00 25.00           C
ATOM    152  CA  LYS   152      40.357  13.527  84.444  1.00 25.00           C
ATOM    153  CA  ASP   153      41.570  14.761  81.047  1.00 25.00           C
ATOM    154  CA  GLY   154      42.251  18.452  81.670  1.00 25.00           C
ATOM    155  CA  LEU   155      40.409  19.722  78.613  1.00 25.00           C
ATOM    156  CA  ALA   156      36.940  18.758  77.371  1.00 25.00           C
ATOM    157  CA  LEU   157      34.551  21.421  76.209  1.00 25.00           C
ATOM    158  CA  GLY   158      32.312  23.447  78.428  1.00 25.00           C
ATOM    159  CA  PRO   159      30.262  25.744  76.208  1.00 25.00           C
ATOM    160  CA  GLY   160      32.279  28.416  74.346  1.00 25.00           C
ATOM    161  CA  PRO   161      32.202  26.290  71.162  1.00 25.00           C
ATOM    162  CA  PHE   162      28.411  25.867  71.507  1.00 25.00           C
ATOM    163  CA  VAL   163      28.004  29.649  71.949  1.00 25.00           C
ATOM    164  CA  THR   164      30.135  30.268  68.828  1.00 25.00           C
ATOM    165  CA  ALA   165      28.001  27.780  66.848  1.00 25.00           C
ATOM    166  CA  LEU   166      24.810  29.534  68.034  1.00 25.00           C
ATOM    167  CA  GLU   167      26.252  32.921  66.980  1.00 25.00           C
ATOM    168  CA  TYR   168      27.142  31.500  63.536  1.00 25.00           C
ATOM    169  CA  ALA   169      23.590  30.115  63.164  1.00 25.00           C
ATOM    170  CA  THR   170      22.133  33.527  64.114  1.00 25.00           C
ATOM    171  CA  ASP   171      24.595  36.466  63.780  1.00 25.00           C
ATOM    172  CA  THR   172      23.730  37.491  67.322  1.00 25.00           C
ATOM    173  CA  LYS   173      21.287  35.040  68.924  1.00 25.00           C
ATOM    174  CA  ALA   174      22.944  34.408  72.287  1.00 25.00           C
ATOM    175  CA  MET   175      23.301  37.399  74.610  1.00 25.00           C
ATOM    176  CA  VAL   176      23.434  35.256  77.684  1.00 25.00           C
ATOM    177  CA  VAL   177      22.563  35.362  81.391  1.00 25.00           C
ATOM    178  CA  GLY   178      24.905  34.806  84.394  1.00 25.00           C
TER
END
