
#######################################################
#                                                     #
#                        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_2-D2
# Molecule2: number of CA atoms  121 (  915),  selected  121 , name T0371_D2.pdb
# PARAMETERS: T0371TS168_2-D2.T0371_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      S      82           -
LGA    S      82      G      83          2.700
LGA    G      83      M      84          2.212
LGA    M      84      I      85          1.834
LGA    I      85      T      86          1.547
LGA    T      86      K      87          1.045
LGA    K      87      E      88          0.781
LGA    E      88      Y      89          0.381
LGA    Y      89      I      90          0.767
LGA    I      90      D      91          1.156
LGA    D      91      L      92          1.301
LGA    L      92      K      93          1.262
LGA    K      93      V      94           #
LGA    V      94      D      95          4.956
LGA    D      95      G      96           #
LGA    G      96      -       -           -
LGA    G      97      -       -           -
LGA    I      98      G      97           #
LGA    -       -      I      98           -
LGA    V      99      V      99           #
LGA    A     100      A     100           #
LGA    Y     101      -       -           -
LGA    L     102      Y     101           #
LGA    G     103      L     102          4.594
LGA    -       -      G     103           -
LGA    T     104      T     104          3.868
LGA    -       -      A     105           -
LGA    -       -      N     106           -
LGA    -       -      S     107           -
LGA    A     105      A     108          3.973
LGA    N     106      N     109          4.270
LGA    S     107      Y     110           -
LGA    A     108      L     111           -
LGA    N     109      V     112          4.237
LGA    Y     110      S     113          4.750
LGA    L     111      -       -           -
LGA    V     112      D     114           #
LGA    S     113      G     115          2.527
LGA    D     114      I     116          4.189
LGA    G     115      K     117           #
LGA    I     116      -       -           -
LGA    K     117      -       -           -
LGA    M     118      -       -           -
LGA    L     119      -       -           -
LGA    P     120      M     118           #
LGA    V     121      L     119          4.613
LGA    S     122      P     120           -
LGA    A     123      V     121           -
LGA    -       -      S     122           -
LGA    -       -      A     123           -
LGA    I     124      I     124          3.296
LGA    D     125      D     125          1.503
LGA    D     126      D     126          3.806
LGA    S     127      S     127          4.810
LGA    N     128      -       -           -
LGA    I     129      N     128           #
LGA    G     130      I     129           -
LGA    E     131      G     130           -
LGA    V     132      E     131           -
LGA    N     133      V     132           #
LGA    -       -      N     133           -
LGA    A     134      A     134          4.579
LGA    L     135      L     135           #
LGA    V     136      V     136          4.843
LGA    L     137      L     137           #
LGA    L     138      L     138           #
LGA    D     139      D     139          2.055
LGA    D     140      D     140          2.465
LGA    E     141      E     141          2.422
LGA    G     142      G     142          2.898
LGA    F     143      F     143           #
LGA    N     144      N     144          4.463
LGA    W     145      W     145          3.452
LGA    F     146      F     146           #
LGA    H     147      H     147          4.494
LGA    D     148      D     148          2.431
LGA    L     149      L     149          3.719
LGA    N     150      N     150          4.223
LGA    K     151      K     151          2.434
LGA    T     152      T     152          2.475
LGA    V     153      V     153          3.966
LGA    N     154      N     154          3.015
LGA    L     155      L     155          1.323
LGA    L     156      L     156          2.668
LGA    R     157      R     157          3.254
LGA    K     158      K     158          1.826
LGA    R     159      R     159          4.380
LGA    T     160      T     160          1.808
LGA    I     161      I     161          3.201
LGA    P     162      -       -           -
LGA    A     163      P     162          2.237
LGA    I     164      A     163          2.343
LGA    V     165      I     164          2.674
LGA    A     166      V     165          1.701
LGA    N     167      A     166          4.368
LGA    T     168      N     167          4.866
LGA    D     169      T     168           #
LGA    N     170      D     169          1.777
LGA    T     171      N     170          2.874
LGA    Y     172      T     171          4.075
LGA    P     173      Y     172          2.260
LGA    L     174      P     173          4.118
LGA    T     175      L     174          1.458
LGA    K     176      T     175          2.722
LGA    -       -      K     176           -
LGA    T     177      T     177          2.849
LGA    D     178      D     178          2.600
LGA    V     179      V     179          2.343
LGA    A     180      A     180          2.923
LGA    I     181      I     181          3.490
LGA    A     182      A     182          2.896
LGA    I     183      I     183          3.325
LGA    G     184      -       -           -
LGA    G     185      -       -           -
LGA    V     186      G     184          3.631
LGA    A     187      G     185          2.933
LGA    T     188      V     186          3.600
LGA    M     189      A     187          3.296
LGA    I     190      T     188          2.911
LGA    E     191      M     189          2.968
LGA    S     192      I     190          2.856
LGA    I     193      E     191          3.110
LGA    L     194      S     192          3.422
LGA    -       -      I     193           -
LGA    G     195      L     194          2.562
LGA    R     196      G     195          4.954
LGA    R     197      R     196          4.473
LGA    F     198      R     197          0.757
LGA    I     199      F     198          1.875
LGA    R     200      I     199           #
LGA    F     201      R     200          3.152
LGA    G     202      F     201           #
LGA    -       -      G     202           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  121  121    5.0     83    3.20    45.78     37.086     2.518

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.496026 * X  +   0.634475 * Y  +   0.592789 * Z  +  36.622559
  Y_new =  -0.172282 * X  +  -0.597209 * Y  +   0.783365 * Z  +   5.523058
  Z_new =   0.851045 * X  +  -0.490696 * Y  +  -0.186923 * Z  + -54.383492 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.934759    1.206834  [ DEG:  -110.8535     69.1465 ]
  Theta =  -1.017972   -2.123621  [ DEG:   -58.3255   -121.6745 ]
  Phi   =  -0.334289    2.807304  [ DEG:   -19.1533    160.8467 ]
 
# 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_2-D2                               
REMARK     2: T0371_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0371TS168_2-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   83   3.20   45.78  37.086
REMARK  ---------------------------------------------------------- 
MOLECULE T0371TS168_2-D2
PFRMAT TS
TARGET T0371
MODEL 2
PARENT N/A
ATOM     82  CA  SER    82      36.287   0.006 -57.586  1.00 25.00           C
ATOM     83  CA  GLY    83      34.982   1.348 -60.928  1.00 25.00           C
ATOM     84  CA  MET    84      36.772   4.678 -60.317  1.00 25.00           C
ATOM     85  CA  ILE    85      40.019   2.813 -59.514  1.00 25.00           C
ATOM     86  CA  THR    86      39.667   0.765 -62.731  1.00 25.00           C
ATOM     87  CA  LYS    87      39.107   3.974 -64.744  1.00 25.00           C
ATOM     88  CA  GLU    88      42.219   5.542 -63.156  1.00 25.00           C
ATOM     89  CA  TYR    89      44.263   2.422 -64.021  1.00 25.00           C
ATOM     90  CA  ILE    90      43.006   2.571 -67.636  1.00 25.00           C
ATOM     91  CA  ASP    91      43.964   6.273 -67.842  1.00 25.00           C
ATOM     92  CA  LEU    92      47.454   5.472 -66.483  1.00 25.00           C
ATOM     93  CA  LYS    93      50.171   4.612 -68.953  1.00 25.00           C
ATOM     94  CA  VAL    94      48.738   1.695 -70.896  1.00 25.00           C
ATOM     95  CA  ASP    95      49.289  -1.487 -72.937  1.00 25.00           C
ATOM     96  CA  GLY    96      45.947  -3.203 -72.163  1.00 25.00           C
ATOM     97  CA  GLY    97      44.591  -3.326 -68.584  1.00 25.00           C
ATOM     98  CA  ILE    98      42.534  -2.292 -65.552  1.00 25.00           C
ATOM     99  CA  VAL    99      44.026  -1.653 -62.093  1.00 25.00           C
ATOM    100  CA  ALA   100      41.871  -1.816 -58.894  1.00 25.00           C
ATOM    101  CA  TYR   101      41.225  -3.340 -55.451  1.00 25.00           C
ATOM    102  CA  LEU   102      37.651  -3.947 -54.240  1.00 25.00           C
ATOM    103  CA  GLY   103      39.366  -6.228 -51.725  1.00 25.00           C
ATOM    104  CA  THR   104      41.805  -8.911 -52.873  1.00 25.00           C
ATOM    105  CA  ALA   105      42.334  -9.828 -56.496  1.00 25.00           C
ATOM    106  CA  ASN   106      41.250  -7.160 -59.021  1.00 25.00           C
ATOM    107  CA  SER   107      44.514  -5.245 -58.436  1.00 25.00           C
ATOM    108  CA  ALA   108      46.525  -8.461 -58.966  1.00 25.00           C
ATOM    109  CA  ASN   109      44.624  -9.143 -62.219  1.00 25.00           C
ATOM    110  CA  TYR   110      45.334  -5.573 -63.411  1.00 25.00           C
ATOM    111  CA  LEU   111      49.050  -6.014 -62.596  1.00 25.00           C
ATOM    112  CA  VAL   112      49.110  -9.314 -64.539  1.00 25.00           C
ATOM    113  CA  SER   113      47.434  -7.610 -67.533  1.00 25.00           C
ATOM    114  CA  ASP   114      49.457  -4.734 -68.864  1.00 25.00           C
ATOM    115  CA  GLY   115      51.732  -1.899 -67.589  1.00 25.00           C
ATOM    116  CA  ILE   116      49.422   0.090 -65.386  1.00 25.00           C
ATOM    117  CA  LYS   117      49.862   3.278 -63.365  1.00 25.00           C
ATOM    118  CA  MET   118      49.723   1.253 -60.131  1.00 25.00           C
ATOM    119  CA  LEU   119      50.060  -0.748 -56.993  1.00 25.00           C
ATOM    120  CA  PRO   120      50.781  -2.721 -53.852  1.00 25.00           C
ATOM    121  CA  VAL   121      50.551  -5.915 -55.865  1.00 25.00           C
ATOM    122  CA  SER   122      54.060  -5.501 -57.356  1.00 25.00           C
ATOM    123  CA  ALA   123      57.550  -6.519 -56.276  1.00 25.00           C
ATOM    124  CA  ILE   124      55.964  -6.465 -52.820  1.00 25.00           C
ATOM    125  CA  ASP   125      58.461  -9.122 -51.944  1.00 25.00           C
ATOM    126  CA  ASP   126      60.807 -11.789 -53.167  1.00 25.00           C
ATOM    127  CA  SER   127      58.780 -14.941 -53.803  1.00 25.00           C
ATOM    128  CA  ASN   128      55.467 -13.100 -53.509  1.00 25.00           C
ATOM    129  CA  ILE   129      52.570 -10.623 -53.346  1.00 25.00           C
ATOM    130  CA  GLY   130      49.223 -11.230 -54.918  1.00 25.00           C
ATOM    131  CA  GLU   131      47.824  -8.673 -52.488  1.00 25.00           C
ATOM    132  CA  VAL   132      46.435  -5.144 -53.099  1.00 25.00           C
ATOM    133  CA  ASN   133      45.939  -1.465 -54.106  1.00 25.00           C
ATOM    134  CA  ALA   134      45.089   1.715 -56.010  1.00 25.00           C
ATOM    135  CA  LEU   135      41.814   1.144 -54.169  1.00 25.00           C
ATOM    136  CA  VAL   136      39.612  -0.415 -51.529  1.00 25.00           C
ATOM    137  CA  LEU   137      35.890  -0.577 -50.806  1.00 25.00           C
ATOM    138  CA  LEU   138      32.843  -0.952 -48.562  1.00 25.00           C
ATOM    139  CA  ASP   139      35.489  -3.446 -47.489  1.00 25.00           C
ATOM    140  CA  ASP   140      38.487  -5.663 -46.788  1.00 25.00           C
ATOM    141  CA  GLU   141      36.776  -9.070 -47.310  1.00 25.00           C
ATOM    142  CA  GLY   142      37.992 -11.128 -44.353  1.00 25.00           C
ATOM    143  CA  PHE   143      37.235  -8.750 -41.468  1.00 25.00           C
ATOM    144  CA  ASN   144      40.632  -9.673 -40.080  1.00 25.00           C
ATOM    145  CA  TRP   145      41.731  -6.670 -42.191  1.00 25.00           C
ATOM    146  CA  PHE   146      43.256  -3.667 -40.368  1.00 25.00           C
ATOM    147  CA  HIS   147      46.734  -5.251 -40.618  1.00 25.00           C
ATOM    148  CA  ASP   148      46.218  -5.851 -44.365  1.00 25.00           C
ATOM    149  CA  LEU   149      45.137  -2.206 -44.825  1.00 25.00           C
ATOM    150  CA  ASN   150      48.246  -1.019 -42.929  1.00 25.00           C
ATOM    151  CA  LYS   151      50.465  -3.223 -45.140  1.00 25.00           C
ATOM    152  CA  THR   152      48.803  -1.792 -48.279  1.00 25.00           C
ATOM    153  CA  VAL   153      49.379   1.768 -46.990  1.00 25.00           C
ATOM    154  CA  ASN   154      53.058   0.954 -46.310  1.00 25.00           C
ATOM    155  CA  LEU   155      53.422  -0.471 -49.846  1.00 25.00           C
ATOM    156  CA  LEU   156      51.834   2.693 -51.309  1.00 25.00           C
ATOM    157  CA  ARG   157      54.240   4.870 -49.276  1.00 25.00           C
ATOM    158  CA  LYS   158      57.210   2.804 -50.530  1.00 25.00           C
ATOM    159  CA  ARG   159      58.672   6.126 -51.671  1.00 25.00           C
ATOM    160  CA  THR   160      56.009   7.405 -54.051  1.00 25.00           C
ATOM    161  CA  ILE   161      52.283   7.341 -54.377  1.00 25.00           C
ATOM    162  CA  PRO   162      50.631   4.324 -55.969  1.00 25.00           C
ATOM    163  CA  ALA   163      47.511   5.827 -54.488  1.00 25.00           C
ATOM    164  CA  ILE   164      45.193   4.567 -51.662  1.00 25.00           C
ATOM    165  CA  VAL   165      41.676   5.796 -52.255  1.00 25.00           C
ATOM    166  CA  ALA   166      38.330   4.111 -52.159  1.00 25.00           C
ATOM    167  CA  ASN   167      37.237   3.064 -48.621  1.00 25.00           C
ATOM    168  CA  THR   168      36.167   5.609 -45.984  1.00 25.00           C
ATOM    169  CA  ASP   169      36.184   7.666 -42.735  1.00 25.00           C
ATOM    170  CA  ASN   170      32.459   7.651 -43.247  1.00 25.00           C
ATOM    171  CA  THR   171      32.020   4.578 -41.129  1.00 25.00           C
ATOM    172  CA  TYR   172      31.319   2.778 -44.452  1.00 25.00           C
ATOM    173  CA  PRO   173      27.815   1.749 -43.355  1.00 25.00           C
ATOM    174  CA  LEU   174      27.990  -1.912 -42.338  1.00 25.00           C
ATOM    175  CA  THR   175      25.717  -2.675 -39.405  1.00 25.00           C
ATOM    176  CA  LYS   176      23.150  -1.624 -36.795  1.00 25.00           C
ATOM    177  CA  THR   177      25.555  -1.842 -33.911  1.00 25.00           C
ATOM    178  CA  ASP   178      29.047  -0.986 -34.965  1.00 25.00           C
ATOM    179  CA  VAL   179      29.961   0.536 -38.321  1.00 25.00           C
ATOM    180  CA  ALA   180      33.782   0.436 -38.755  1.00 25.00           C
ATOM    181  CA  ILE   181      33.576  -3.222 -39.713  1.00 25.00           C
ATOM    182  CA  ALA   182      32.999  -2.029 -43.289  1.00 25.00           C
ATOM    183  CA  ILE   183      35.449   0.868 -43.508  1.00 25.00           C
ATOM    184  CA  GLY   184      37.903  -0.516 -40.913  1.00 25.00           C
ATOM    185  CA  GLY   185      40.452  -1.245 -43.675  1.00 25.00           C
ATOM    186  CA  VAL   186      40.048   2.318 -45.022  1.00 25.00           C
ATOM    187  CA  ALA   187      40.572   3.734 -41.502  1.00 25.00           C
ATOM    188  CA  THR   188      43.729   1.605 -41.089  1.00 25.00           C
ATOM    189  CA  MET   189      45.042   2.853 -44.463  1.00 25.00           C
ATOM    190  CA  ILE   190      44.363   6.473 -43.416  1.00 25.00           C
ATOM    191  CA  GLU   191      46.220   5.893 -40.116  1.00 25.00           C
ATOM    192  CA  SER   192      49.187   4.399 -42.021  1.00 25.00           C
ATOM    193  CA  ILE   193      49.235   7.424 -44.369  1.00 25.00           C
ATOM    194  CA  LEU   194      49.184   9.793 -41.361  1.00 25.00           C
ATOM    195  CA  GLY   195      52.973   9.706 -41.698  1.00 25.00           C
ATOM    196  CA  ARG   196      53.746   9.546 -45.363  1.00 25.00           C
ATOM    197  CA  ARG   197      50.823  10.151 -47.730  1.00 25.00           C
ATOM    198  CA  PHE   198      47.310   9.502 -49.163  1.00 25.00           C
ATOM    199  CA  ILE   199      43.599   8.927 -49.373  1.00 25.00           C
ATOM    200  CA  ARG   200      40.137   8.097 -48.089  1.00 25.00           C
ATOM    201  CA  PHE   201      37.461   8.174 -50.787  1.00 25.00           C
ATOM    202  CA  GLY   202      34.129   6.387 -50.841  1.00 25.00           C
TER
END
