
#######################################################
#                                                     #
#                        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  121 (  121),  selected  121 , name T0371TS168_4-D2
# Molecule2: number of CA atoms  121 (  915),  selected  121 , name T0371_D2.pdb
# PARAMETERS: T0371TS168_4-D2.T0371_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      82      S      82           #
LGA    G      83      G      83          4.467
LGA    M      84      -       -           -
LGA    I      85      M      84          4.713
LGA    T      86      I      85          3.823
LGA    K      87      T      86          2.509
LGA    E      88      K      87          1.772
LGA    Y      89      E      88          1.510
LGA    I      90      Y      89          1.105
LGA    D      91      I      90          2.181
LGA    L      92      D      91          3.178
LGA    K      93      L      92          1.846
LGA    V      94      K      93           #
LGA    D      95      -       -           -
LGA    G      96      -       -           -
LGA    G      97      V      94          2.362
LGA    I      98      D      95           #
LGA    -       -      G      96           -
LGA    -       -      G      97           -
LGA    -       -      I      98           -
LGA    V      99      V      99          5.028
LGA    A     100      A     100           #
LGA    Y     101      Y     101          3.368
LGA    L     102      L     102          3.847
LGA    G     103      G     103          2.698
LGA    T     104      T     104          2.691
LGA    A     105      A     105          3.555
LGA    N     106      N     106          2.126
LGA    S     107      S     107          1.548
LGA    A     108      A     108          3.001
LGA    N     109      N     109          3.495
LGA    Y     110      Y     110          3.383
LGA    L     111      L     111          3.794
LGA    V     112      V     112          4.234
LGA    S     113      S     113           #
LGA    D     114      D     114           #
LGA    G     115      G     115           #
LGA    I     116      I     116           #
LGA    K     117      K     117          2.844
LGA    M     118      M     118          3.664
LGA    L     119      L     119          3.467
LGA    P     120      P     120          3.159
LGA    V     121      V     121          3.461
LGA    S     122      S     122          3.963
LGA    A     123      A     123          1.813
LGA    I     124      I     124          1.825
LGA    D     125      D     125          4.524
LGA    D     126      D     126           #
LGA    S     127      S     127           #
LGA    N     128      N     128          4.192
LGA    I     129      I     129          2.835
LGA    G     130      G     130          1.303
LGA    -       -      E     131           -
LGA    E     131      V     132          3.694
LGA    V     132      N     133          1.177
LGA    N     133      A     134          3.706
LGA    A     134      L     135          2.133
LGA    L     135      V     136          3.247
LGA    V     136      -       -           -
LGA    L     137      L     137          3.386
LGA    L     138      L     138          4.425
LGA    D     139      D     139          0.826
LGA    D     140      D     140          1.211
LGA    E     141      E     141          2.843
LGA    G     142      G     142          4.676
LGA    F     143      F     143          4.167
LGA    N     144      N     144          4.355
LGA    W     145      W     145          3.271
LGA    F     146      F     146           #
LGA    H     147      H     147          4.433
LGA    D     148      D     148          2.024
LGA    L     149      L     149          3.736
LGA    N     150      N     150          4.209
LGA    K     151      K     151          2.139
LGA    T     152      T     152          2.408
LGA    V     153      V     153          3.985
LGA    N     154      N     154          2.785
LGA    L     155      L     155          1.115
LGA    L     156      L     156          2.661
LGA    R     157      R     157          3.133
LGA    K     158      K     158          1.443
LGA    R     159      R     159          4.287
LGA    T     160      T     160          1.610
LGA    I     161      I     161          1.141
LGA    P     162      P     162          2.012
LGA    A     163      A     163          1.005
LGA    I     164      I     164          2.674
LGA    V     165      V     165          2.891
LGA    A     166      A     166          3.077
LGA    N     167      N     167          4.007
LGA    T     168      T     168          1.046
LGA    D     169      D     169          1.579
LGA    N     170      N     170          2.860
LGA    T     171      T     171          2.995
LGA    Y     172      Y     172          5.301
LGA    P     173      -       -           -
LGA    L     174      P     173          5.279
LGA    T     175      L     174          2.473
LGA    K     176      T     175          3.329
LGA    T     177      K     176          4.589
LGA    -       -      T     177           -
LGA    D     178      D     178          3.513
LGA    V     179      V     179          2.823
LGA    A     180      A     180          3.355
LGA    I     181      I     181          2.120
LGA    A     182      A     182          1.770
LGA    I     183      I     183          2.587
LGA    G     184      G     184           #
LGA    G     185      G     185          4.818
LGA    V     186      V     186          0.846
LGA    A     187      A     187          3.625
LGA    T     188      T     188           #
LGA    M     189      M     189          4.137
LGA    I     190      I     190          0.383
LGA    E     191      E     191          4.681
LGA    S     192      S     192           #
LGA    I     193      -       -           -
LGA    L     194      I     193          1.655
LGA    G     195      L     194          3.790
LGA    R     196      G     195           #
LGA    R     197      R     196           #
LGA    F     198      R     197          3.124
LGA    I     199      -       -           -
LGA    R     200      -       -           -
LGA    F     201      -       -           -
LGA    G     202      F     198          3.802
LGA    -       -      I     199           -
LGA    -       -      R     200           -
LGA    -       -      F     201           -
LGA    -       -      G     202           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  121  121    5.0     96    3.20    76.04     42.242     2.913

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.024936 * X  +   0.773615 * Y  +   0.633165 * Z  +  38.031391
  Y_new =  -0.944723 * X  +  -0.188886 * Y  +   0.267992 * Z  +   7.958029
  Z_new =   0.326919 * X  +  -0.604848 * Y  +   0.726142 * Z  + -53.016827 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.694519    2.447074  [ DEG:   -39.7930    140.2070 ]
  Theta =  -0.333041   -2.808551  [ DEG:   -19.0819   -160.9181 ]
  Phi   =  -1.544407    1.597185  [ DEG:   -88.4880     91.5120 ]
 
# 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: T0371TS168_4-D2                               
REMARK     2: T0371_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0371TS168_4-D2.T0371_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  121  121   5.0   96   3.20   76.04  42.242
REMARK  ---------------------------------------------------------- 
MOLECULE T0371TS168_4-D2
PFRMAT TS
TARGET T0371
MODEL 4
PARENT N/A
ATOM     82  CA  SER    82      33.504  -1.460 -56.466  1.00 25.00           C
ATOM     83  CA  GLY    83      36.885  -0.064 -55.332  1.00 25.00           C
ATOM     84  CA  MET    84      38.680  -2.230 -57.932  1.00 25.00           C
ATOM     85  CA  ILE    85      36.292  -0.982 -60.654  1.00 25.00           C
ATOM     86  CA  THR    86      36.945   2.642 -59.601  1.00 25.00           C
ATOM     87  CA  LYS    87      40.722   2.027 -59.736  1.00 25.00           C
ATOM     88  CA  GLU    88      40.375   0.507 -63.234  1.00 25.00           C
ATOM     89  CA  TYR    89      38.334   3.540 -64.375  1.00 25.00           C
ATOM     90  CA  ILE    90      41.007   5.897 -62.972  1.00 25.00           C
ATOM     91  CA  ASP    91      43.736   3.937 -64.809  1.00 25.00           C
ATOM     92  CA  LEU    92      41.732   4.151 -68.066  1.00 25.00           C
ATOM     93  CA  LYS    93      44.970   5.276 -69.681  1.00 25.00           C
ATOM     94  CA  VAL    94      46.797   2.651 -71.773  1.00 25.00           C
ATOM     95  CA  ASP    95      50.624   2.845 -71.385  1.00 25.00           C
ATOM     96  CA  GLY    96      52.335   1.965 -68.063  1.00 25.00           C
ATOM     97  CA  GLY    97      50.515   0.942 -64.871  1.00 25.00           C
ATOM     98  CA  ILE    98      48.206   0.107 -61.915  1.00 25.00           C
ATOM     99  CA  VAL    99      45.687   0.912 -59.181  1.00 25.00           C
ATOM    100  CA  ALA   100      43.639  -1.034 -56.623  1.00 25.00           C
ATOM    101  CA  TYR   101      41.930  -3.840 -54.763  1.00 25.00           C
ATOM    102  CA  LEU   102      42.043  -1.688 -51.678  1.00 25.00           C
ATOM    103  CA  GLY   103      41.756  -4.767 -49.487  1.00 25.00           C
ATOM    104  CA  THR   104      39.843  -7.966 -50.058  1.00 25.00           C
ATOM    105  CA  ALA   105      38.084 -11.200 -51.162  1.00 25.00           C
ATOM    106  CA  ASN   106      35.472 -10.016 -53.700  1.00 25.00           C
ATOM    107  CA  SER   107      37.503  -6.832 -54.340  1.00 25.00           C
ATOM    108  CA  ALA   108      40.666  -8.926 -54.863  1.00 25.00           C
ATOM    109  CA  ASN   109      38.793 -11.185 -57.324  1.00 25.00           C
ATOM    110  CA  TYR   110      37.537  -8.110 -59.229  1.00 25.00           C
ATOM    111  CA  LEU   111      41.103  -6.722 -59.390  1.00 25.00           C
ATOM    112  CA  VAL   112      42.377 -10.083 -60.712  1.00 25.00           C
ATOM    113  CA  SER   113      39.625 -10.107 -63.376  1.00 25.00           C
ATOM    114  CA  ASP   114      38.647  -8.469 -66.706  1.00 25.00           C
ATOM    115  CA  GLY   115      42.336  -7.763 -67.308  1.00 25.00           C
ATOM    116  CA  ILE   116      42.364  -5.579 -64.159  1.00 25.00           C
ATOM    117  CA  LYS   117      45.930  -6.622 -63.313  1.00 25.00           C
ATOM    118  CA  MET   118      45.528  -4.401 -60.287  1.00 25.00           C
ATOM    119  CA  LEU   119      46.410  -6.097 -56.941  1.00 25.00           C
ATOM    120  CA  PRO   120      47.919  -6.273 -53.460  1.00 25.00           C
ATOM    121  CA  VAL   121      45.788  -8.157 -50.928  1.00 25.00           C
ATOM    122  CA  SER   122      47.161 -11.742 -51.274  1.00 25.00           C
ATOM    123  CA  ALA   123      50.677 -13.191 -51.023  1.00 25.00           C
ATOM    124  CA  ILE   124      53.165 -10.474 -51.895  1.00 25.00           C
ATOM    125  CA  ASP   125      55.861 -12.817 -53.164  1.00 25.00           C
ATOM    126  CA  ASP   126      56.016 -12.224 -56.905  1.00 25.00           C
ATOM    127  CA  SER   127      56.813 -11.548 -60.539  1.00 25.00           C
ATOM    128  CA  ASN   128      55.039  -8.250 -59.821  1.00 25.00           C
ATOM    129  CA  ILE   129      56.735  -5.762 -57.543  1.00 25.00           C
ATOM    130  CA  GLY   130      58.650  -2.449 -57.991  1.00 25.00           C
ATOM    131  CA  GLU   131      55.904   0.035 -57.180  1.00 25.00           C
ATOM    132  CA  VAL   132      52.310  -0.260 -58.505  1.00 25.00           C
ATOM    133  CA  ASN   133      50.537  -1.876 -55.501  1.00 25.00           C
ATOM    134  CA  ALA   134      48.542   1.315 -55.757  1.00 25.00           C
ATOM    135  CA  LEU   135      46.422   0.694 -52.626  1.00 25.00           C
ATOM    136  CA  VAL   136      45.310   2.804 -49.705  1.00 25.00           C
ATOM    137  CA  LEU   137      41.791   1.976 -48.577  1.00 25.00           C
ATOM    138  CA  LEU   138      38.942  -0.483 -47.921  1.00 25.00           C
ATOM    139  CA  ASP   139      36.788  -3.646 -48.190  1.00 25.00           C
ATOM    140  CA  ASP   140      38.463  -4.876 -44.974  1.00 25.00           C
ATOM    141  CA  GLU   141      35.365  -6.582 -43.562  1.00 25.00           C
ATOM    142  CA  GLY   142      35.601 -10.349 -44.155  1.00 25.00           C
ATOM    143  CA  PHE   143      39.283 -10.676 -43.040  1.00 25.00           C
ATOM    144  CA  ASN   144      40.925  -8.843 -40.119  1.00 25.00           C
ATOM    145  CA  TRP   145      42.294  -6.381 -42.704  1.00 25.00           C
ATOM    146  CA  PHE   146      43.738  -3.303 -40.940  1.00 25.00           C
ATOM    147  CA  HIS   147      47.236  -4.859 -41.036  1.00 25.00           C
ATOM    148  CA  ASP   148      46.835  -5.589 -44.774  1.00 25.00           C
ATOM    149  CA  LEU   149      45.734  -1.973 -45.387  1.00 25.00           C
ATOM    150  CA  ASN   150      48.776  -0.692 -43.444  1.00 25.00           C
ATOM    151  CA  LYS   151      51.079  -2.946 -45.514  1.00 25.00           C
ATOM    152  CA  THR   152      49.496  -1.636 -48.746  1.00 25.00           C
ATOM    153  CA  VAL   153      50.001   1.971 -47.562  1.00 25.00           C
ATOM    154  CA  ASN   154      53.666   1.215 -46.749  1.00 25.00           C
ATOM    155  CA  LEU   155      54.146  -0.322 -50.223  1.00 25.00           C
ATOM    156  CA  LEU   156      52.572   2.775 -51.837  1.00 25.00           C
ATOM    157  CA  ARG   157      54.897   5.044 -49.810  1.00 25.00           C
ATOM    158  CA  LYS   158      57.922   2.968 -50.908  1.00 25.00           C
ATOM    159  CA  ARG   159      59.415   5.950 -52.736  1.00 25.00           C
ATOM    160  CA  THR   160      57.322   5.328 -55.850  1.00 25.00           C
ATOM    161  CA  ILE   161      53.663   4.454 -56.141  1.00 25.00           C
ATOM    162  CA  PRO   162      50.542   6.157 -54.915  1.00 25.00           C
ATOM    163  CA  ALA   163      47.283   5.640 -52.929  1.00 25.00           C
ATOM    164  CA  ILE   164      45.163   4.960 -55.961  1.00 25.00           C
ATOM    165  CA  VAL   165      42.198   3.680 -53.958  1.00 25.00           C
ATOM    166  CA  ALA   166      38.923   3.283 -52.033  1.00 25.00           C
ATOM    167  CA  ASN   167      37.276   4.502 -48.909  1.00 25.00           C
ATOM    168  CA  THR   168      33.677   4.821 -47.803  1.00 25.00           C
ATOM    169  CA  ASP   169      33.508   6.393 -44.368  1.00 25.00           C
ATOM    170  CA  ASN   170      31.875   5.167 -41.122  1.00 25.00           C
ATOM    171  CA  THR   171      31.423   2.005 -43.164  1.00 25.00           C
ATOM    172  CA  TYR   172      30.068   1.076 -46.595  1.00 25.00           C
ATOM    173  CA  PRO   173      26.705   0.276 -45.144  1.00 25.00           C
ATOM    174  CA  LEU   174      28.053  -2.711 -43.307  1.00 25.00           C
ATOM    175  CA  THR   175      28.281  -4.535 -39.980  1.00 25.00           C
ATOM    176  CA  LYS   176      25.992  -6.115 -37.390  1.00 25.00           C
ATOM    177  CA  THR   177      24.160  -2.785 -37.709  1.00 25.00           C
ATOM    178  CA  ASP   178      26.717  -0.288 -36.581  1.00 25.00           C
ATOM    179  CA  VAL   179      29.545   0.868 -38.830  1.00 25.00           C
ATOM    180  CA  ALA   180      33.071   1.125 -37.329  1.00 25.00           C
ATOM    181  CA  ILE   181      34.158  -1.929 -39.400  1.00 25.00           C
ATOM    182  CA  ALA   182      35.254  -1.017 -42.925  1.00 25.00           C
ATOM    183  CA  ILE   183      36.528   2.192 -44.514  1.00 25.00           C
ATOM    184  CA  GLY   184      36.933   2.963 -40.785  1.00 25.00           C
ATOM    185  CA  GLY   185      39.292  -0.027 -40.396  1.00 25.00           C
ATOM    186  CA  VAL   186      41.349   1.175 -43.394  1.00 25.00           C
ATOM    187  CA  ALA   187      41.557   4.685 -41.876  1.00 25.00           C
ATOM    188  CA  THR   188      42.710   3.200 -38.539  1.00 25.00           C
ATOM    189  CA  MET   189      45.384   1.141 -40.350  1.00 25.00           C
ATOM    190  CA  ILE   190      46.584   4.277 -42.193  1.00 25.00           C
ATOM    191  CA  GLU   191      46.775   6.182 -38.875  1.00 25.00           C
ATOM    192  CA  SER   192      48.791   3.322 -37.320  1.00 25.00           C
ATOM    193  CA  ILE   193      51.182   3.347 -40.311  1.00 25.00           C
ATOM    194  CA  LEU   194      51.618   7.135 -39.962  1.00 25.00           C
ATOM    195  CA  GLY   195      54.920   7.404 -41.772  1.00 25.00           C
ATOM    196  CA  ARG   196      54.118   8.220 -45.390  1.00 25.00           C
ATOM    197  CA  ARG   197      51.180   8.508 -47.787  1.00 25.00           C
ATOM    198  CA  PHE   198      47.670   8.202 -46.391  1.00 25.00           C
ATOM    199  CA  ILE   199      46.571   9.490 -42.996  1.00 25.00           C
ATOM    200  CA  ARG   200      43.120   9.028 -44.632  1.00 25.00           C
ATOM    201  CA  PHE   201      39.761   8.582 -46.360  1.00 25.00           C
ATOM    202  CA  GLY   202      41.405   7.164 -49.496  1.00 25.00           C
TER
END
