
#######################################################
#                                                     #
#                        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  155 (  155),  selected  155 , name T0321TS393_3-D2
# Molecule2: number of CA atoms  148 ( 1130),  selected  148 , name T0321_D2.pdb
# PARAMETERS: T0321TS393_3-D2.T0321_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V      97      V      97           -
LGA    I      98      I      98           -
LGA    F      99      F      99           -
LGA    S     100      S     100           -
LGA    D     101      D     101           -
LGA    A     102      A     102           -
LGA    K     103      N     110           -
LGA    R     104      D     111           -
LGA    V     105      P     112           -
LGA    E     106      F     113           -
LGA    D     107      I     114           -
LGA    R     108      M     115           -
LGA    M     109      S     116           -
LGA    N     110      Q     117           -
LGA    D     111      N     118           -
LGA    P     112      E     119           -
LGA    F     113      V     120           -
LGA    I     114      K     121           -
LGA    M     115      G     122           -
LGA    S     116      K     123           -
LGA    Q     117      K     124           -
LGA    N     118      V     125           -
LGA    E     119      G     126           -
LGA    V     120      V     127           -
LGA    K     121      -       -           -
LGA    G     122      -       -           -
LGA    K     123      -       -           -
LGA    K     124      -       -           -
LGA    V     125      -       -           -
LGA    G     126      -       -           -
LGA    V     127      -       -           -
LGA    V     128      -       -           -
LGA    G     129      -       -           -
LGA    H     130      -       -           -
LGA    F     131      -       -           -
LGA    P     132      -       -           -
LGA    H     133      -       -           -
LGA    L     134      -       -           -
LGA    E     135      -       -           -
LGA    S     136      -       -           -
LGA    L     137      -       -           -
LGA    L     138      -       -           -
LGA    E     139      -       -           -
LGA    P     140      -       -           -
LGA    I     141      -       -           -
LGA    C     142      -       -           -
LGA    D     143      -       -           -
LGA    L     144      -       -           -
LGA    S     145      -       -           -
LGA    I     146      -       -           -
LGA    L     147      -       -           -
LGA    E     148      V     128          1.596
LGA    W     149      G     129          4.051
LGA    S     150      H     130           -
LGA    P     151      F     131           #
LGA    -       -      P     132           -
LGA    -       -      H     133           -
LGA    E     152      L     134          1.292
LGA    -       -      E     135           -
LGA    -       -      S     136           -
LGA    -       -      L     137           -
LGA    -       -      L     138           -
LGA    E     153      E     139          3.495
LGA    G     154      P     140           -
LGA    -       -      I     141           -
LGA    -       -      C     142           -
LGA    -       -      D     143           -
LGA    -       -      L     144           -
LGA    -       -      S     145           -
LGA    -       -      I     146           -
LGA    -       -      L     147           -
LGA    -       -      E     148           -
LGA    -       -      W     149           -
LGA    -       -      S     150           -
LGA    -       -      P     151           -
LGA    -       -      E     152           -
LGA    -       -      E     153           -
LGA    D     155      G     154          3.603
LGA    Y     156      D     155          1.515
LGA    P     157      Y     156          5.126
LGA    L     158      P     157           -
LGA    P     159      L     158           -
LGA    -       -      P     159           -
LGA    -       -      A     160           -
LGA    A     160      S     161           #
LGA    S     161      E     162           #
LGA    E     162      F     163          6.292
LGA    F     163      I     164          4.434
LGA    I     164      L     165          2.017
LGA    L     165      P     166          3.045
LGA    P     166      E     167           -
LGA    E     167      C     168           -
LGA    C     168      D     169           -
LGA    D     169      Y     170           -
LGA    Y     170      V     171           -
LGA    V     171      -       -           -
LGA    Y     172      Y     172           #
LGA    I     173      I     173          3.885
LGA    T     174      T     174          3.137
LGA    C     175      C     175           #
LGA    A     176      A     176          3.145
LGA    S     177      -       -           -
LGA    V     178      S     177          2.040
LGA    V     179      V     178          4.215
LGA    D     180      V     179           #
LGA    -       -      D     180           -
LGA    K     181      K     181          2.772
LGA    T     182      T     182          3.445
LGA    L     183      L     183          3.101
LGA    P     184      P     184          2.424
LGA    R     185      R     185          2.553
LGA    L     186      L     186          4.069
LGA    L     187      L     187          5.073
LGA    E     188      -       -           -
LGA    L     189      -       -           -
LGA    S     190      -       -           -
LGA    R     191      -       -           -
LGA    N     192      -       -           -
LGA    A     193      -       -           -
LGA    R     194      -       -           -
LGA    R     195      E     188          2.959
LGA    I     196      L     189          1.672
LGA    T     197      S     190          3.644
LGA    L     198      R     191           -
LGA    V     199      N     192           -
LGA    G     200      A     193           -
LGA    P     201      R     194           -
LGA    G     202      -       -           -
LGA    T     203      -       -           -
LGA    P     204      -       -           -
LGA    L     205      -       -           -
LGA    A     206      -       -           -
LGA    P     207      -       -           -
LGA    V     208      -       -           -
LGA    L     209      -       -           -
LGA    F     210      -       -           -
LGA    E     211      -       -           -
LGA    H     212      -       -           -
LGA    G     213      R     195          1.986
LGA    L     214      -       -           -
LGA    Q     215      -       -           -
LGA    E     216      -       -           -
LGA    L     217      -       -           -
LGA    S     218      -       -           -
LGA    G     219      I     196          2.581
LGA    F     220      T     197          2.285
LGA    M     221      L     198          1.771
LGA    V     222      V     199          1.488
LGA    K     223      G     200          1.596
LGA    D     224      P     201          2.057
LGA    N     225      -       -           -
LGA    A     226      G     202          5.468
LGA    R     227      T     203          2.072
LGA    A     228      P     204          3.605
LGA    F     229      L     205          0.895
LGA    R     230      A     206          3.522
LGA    I     231      -       -           -
LGA    V     232      P     207          4.008
LGA    A     233      V     208          2.725
LGA    G     234      L     209          0.731
LGA    A     235      F     210          1.231
LGA    E     236      -       -           -
LGA    K     237      -       -           -
LGA    V     238      E     211          1.959
LGA    K     239      -       -           -
LGA    I     240      -       -           -
LGA    Y     241      -       -           -
LGA    S     242      -       -           -
LGA    A     243      -       -           -
LGA    G     244      H     212           #
LGA    Q     245      G     213           -
LGA    K     246      L     214           -
LGA    V     247      Q     215           -
LGA    T     248      E     216           -
LGA    I     249      L     217           -
LGA    K     250      S     218           -
LGA    K     251      G     219           -
LGA    -       -      F     220           -
LGA    -       -      M     221           -
LGA    -       -      V     222           -
LGA    -       -      K     223           -
LGA    -       -      D     224           -
LGA    -       -      N     225           -
LGA    -       -      A     226           -
LGA    -       -      R     227           -
LGA    -       -      A     228           -
LGA    -       -      F     229           -
LGA    -       -      R     230           -
LGA    -       -      I     231           -
LGA    -       -      V     232           -
LGA    -       -      A     233           -
LGA    -       -      G     234           -
LGA    -       -      A     235           -
LGA    -       -      E     236           -
LGA    -       -      K     237           -
LGA    -       -      V     238           -
LGA    -       -      K     239           -
LGA    -       -      I     240           -
LGA    -       -      Y     241           -
LGA    -       -      S     242           -
LGA    -       -      A     243           -
LGA    -       -      G     244           -
LGA    -       -      Q     245           -
LGA    -       -      K     246           -
LGA    -       -      V     247           -
LGA    -       -      T     248           -
LGA    -       -      I     249           -
LGA    -       -      K     250           -
LGA    -       -      K     251           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  155  148    5.0     43    3.16    30.23     17.365     1.318

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.439815 * X  +  -0.577261 * Y  +  -0.687991 * Z  +  10.986067
  Y_new =   0.631914 * X  +   0.743257 * Y  +  -0.219666 * Z  +  41.687038
  Z_new =   0.638159 * X  +  -0.338139 * Y  +   0.691676 * Z  +  54.978527 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.454704    2.686889  [ DEG:   -26.0526    153.9474 ]
  Theta =  -0.692105   -2.449488  [ DEG:   -39.6547   -140.3453 ]
  Phi   =   0.962757   -2.178836  [ DEG:    55.1619   -124.8381 ]
 
# 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: T0321TS393_3-D2                               
REMARK     2: T0321_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS393_3-D2.T0321_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  155  148   5.0   43   3.16   30.23  17.365
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS393_3-D2
PFRMAT TS
TARGET T0321
MODEL 3
PARENT N/A
ATOM     97  CA  VAL    97      29.981  59.000  45.925  1.00 25.00           C
ATOM     98  CA  ILE    98      29.951  55.707  47.930  1.00 25.00           C
ATOM     99  CA  PHE    99      28.290  52.279  47.823  1.00 25.00           C
ATOM    100  CA  SER   100      29.110  52.546  44.092  1.00 25.00           C
ATOM    101  CA  ASP   101      26.261  50.125  43.267  1.00 25.00           C
ATOM    102  CA  ALA   102      23.851  52.191  45.409  1.00 25.00           C
ATOM    103  CA  LYS   103      24.959  55.388  43.616  1.00 25.00           C
ATOM    104  CA  ARG   104      24.404  53.704  40.220  1.00 25.00           C
ATOM    105  CA  VAL   105      20.910  52.585  41.318  1.00 25.00           C
ATOM    106  CA  GLU   106      20.098  56.151  42.457  1.00 25.00           C
ATOM    107  CA  ASP   107      21.295  57.524  39.089  1.00 25.00           C
ATOM    108  CA  ARG   108      19.112  54.975  37.245  1.00 25.00           C
ATOM    109  CA  MET   109      20.985  51.811  36.341  1.00 25.00           C
ATOM    110  CA  ASN   110      18.404  50.144  34.121  1.00 25.00           C
ATOM    111  CA  ASP   111      15.987  47.341  34.941  1.00 25.00           C
ATOM    112  CA  PRO   112      16.851  45.079  31.973  1.00 25.00           C
ATOM    113  CA  PHE   113      13.536  43.209  32.403  1.00 25.00           C
ATOM    114  CA  ILE   114      11.642  46.537  32.490  1.00 25.00           C
ATOM    115  CA  MET   115      12.161  46.550  28.744  1.00 25.00           C
ATOM    116  CA  SER   116       8.368  46.774  28.413  1.00 25.00           C
ATOM    117  CA  GLN   117       5.919  49.636  28.145  1.00 25.00           C
ATOM    118  CA  ASN   118       4.307  50.789  31.449  1.00 25.00           C
ATOM    119  CA  GLU   119       3.542  50.074  35.092  1.00 25.00           C
ATOM    120  CA  VAL   120       1.918  51.415  38.305  1.00 25.00           C
ATOM    121  CA  LYS   121       0.766  53.572  41.272  1.00 25.00           C
ATOM    122  CA  GLY   122       3.001  51.542  43.531  1.00 25.00           C
ATOM    123  CA  LYS   123       2.418  48.168  45.252  1.00 25.00           C
ATOM    124  CA  LYS   124       5.054  48.518  47.925  1.00 25.00           C
ATOM    125  CA  VAL   125       6.956  45.513  46.625  1.00 25.00           C
ATOM    126  CA  GLY   126       7.716  41.780  46.920  1.00 25.00           C
ATOM    127  CA  VAL   127       9.831  39.244  48.870  1.00 25.00           C
ATOM    128  CA  VAL   128      11.630  38.191  45.658  1.00 25.00           C
ATOM    129  CA  GLY   129      13.611  41.168  44.350  1.00 25.00           C
ATOM    130  CA  HIS   130      12.833  44.236  46.490  1.00 25.00           C
ATOM    131  CA  PHE   131      14.526  47.473  45.239  1.00 25.00           C
ATOM    132  CA  PRO   132      12.621  50.361  46.858  1.00 25.00           C
ATOM    133  CA  HIS   133      10.043  52.913  48.064  1.00 25.00           C
ATOM    134  CA  LEU   134       6.525  53.325  46.676  1.00 25.00           C
ATOM    135  CA  GLU   135       6.569  55.342  43.453  1.00 25.00           C
ATOM    136  CA  SER   136       8.948  53.524  41.155  1.00 25.00           C
ATOM    137  CA  LEU   137       8.071  49.879  41.436  1.00 25.00           C
ATOM    138  CA  LEU   138       5.450  47.420  40.050  1.00 25.00           C
ATOM    139  CA  GLU   139       2.199  45.620  39.467  1.00 25.00           C
ATOM    140  CA  PRO   140       3.347  43.236  42.194  1.00 25.00           C
ATOM    141  CA  ILE   141      -0.061  43.467  43.902  1.00 25.00           C
ATOM    142  CA  CYS   142       0.802  41.109  46.669  1.00 25.00           C
ATOM    143  CA  ASP   143       2.479  43.406  49.157  1.00 25.00           C
ATOM    144  CA  LEU   144       3.387  45.889  51.861  1.00 25.00           C
ATOM    145  CA  SER   145       5.957  47.085  54.444  1.00 25.00           C
ATOM    146  CA  ILE   146       8.643  46.610  57.080  1.00 25.00           C
ATOM    147  CA  LEU   147      10.915  46.861  60.119  1.00 25.00           C
ATOM    148  CA  GLU   148      13.330  44.028  60.570  1.00 25.00           C
ATOM    149  CA  TRP   149      15.685  46.677  61.813  1.00 25.00           C
ATOM    150  CA  SER   150      15.607  44.660  65.035  1.00 25.00           C
ATOM    151  CA  PRO   151      16.890  46.294  68.219  1.00 25.00           C
ATOM    152  CA  GLU   152      19.568  48.429  69.899  1.00 25.00           C
ATOM    153  CA  GLU   153      22.466  46.700  68.270  1.00 25.00           C
ATOM    154  CA  GLY   154      20.678  46.744  64.924  1.00 25.00           C
ATOM    155  CA  ASP   155      21.934  48.526  61.761  1.00 25.00           C
ATOM    156  CA  TYR   156      20.350  46.436  58.946  1.00 25.00           C
ATOM    157  CA  PRO   157      22.696  43.742  60.248  1.00 25.00           C
ATOM    158  CA  LEU   158      22.639  40.079  61.257  1.00 25.00           C
ATOM    159  CA  PRO   159      20.238  38.523  63.802  1.00 25.00           C
ATOM    160  CA  ALA   160      17.241  39.637  61.693  1.00 25.00           C
ATOM    161  CA  SER   161      18.842  38.109  58.566  1.00 25.00           C
ATOM    162  CA  GLU   162      19.439  34.827  60.448  1.00 25.00           C
ATOM    163  CA  PHE   163      15.790  34.797  61.607  1.00 25.00           C
ATOM    164  CA  ILE   164      14.617  35.393  58.010  1.00 25.00           C
ATOM    165  CA  LEU   165      16.364  32.176  57.091  1.00 25.00           C
ATOM    166  CA  PRO   166      13.263  31.411  55.041  1.00 25.00           C
ATOM    167  CA  GLU   167      10.042  31.059  53.050  1.00 25.00           C
ATOM    168  CA  CYS   168       7.432  33.614  52.038  1.00 25.00           C
ATOM    169  CA  ASP   169       7.520  37.384  52.455  1.00 25.00           C
ATOM    170  CA  TYR   170       7.920  37.943  56.241  1.00 25.00           C
ATOM    171  CA  VAL   171       7.567  38.427  59.996  1.00 25.00           C
ATOM    172  CA  TYR   172       7.274  41.086  62.716  1.00 25.00           C
ATOM    173  CA  ILE   173       8.036  44.366  60.992  1.00 25.00           C
ATOM    174  CA  THR   174       6.920  47.973  61.640  1.00 25.00           C
ATOM    175  CA  CYS   175       5.159  51.341  61.807  1.00 25.00           C
ATOM    176  CA  ALA   176       2.323  49.491  63.597  1.00 25.00           C
ATOM    177  CA  SER   177       0.662  48.731  60.231  1.00 25.00           C
ATOM    178  CA  VAL   178       3.984  47.405  58.862  1.00 25.00           C
ATOM    179  CA  VAL   179       4.401  45.186  61.955  1.00 25.00           C
ATOM    180  CA  ASP   180       0.843  43.843  61.502  1.00 25.00           C
ATOM    181  CA  LYS   181       1.571  43.089  57.818  1.00 25.00           C
ATOM    182  CA  THR   182       4.785  41.255  58.803  1.00 25.00           C
ATOM    183  CA  LEU   183       2.851  39.206  61.396  1.00 25.00           C
ATOM    184  CA  PRO   184       0.218  38.313  58.763  1.00 25.00           C
ATOM    185  CA  ARG   185       2.976  37.232  56.336  1.00 25.00           C
ATOM    186  CA  LEU   186       4.561  35.062  59.065  1.00 25.00           C
ATOM    187  CA  LEU   187       1.162  33.456  59.796  1.00 25.00           C
ATOM    188  CA  GLU   188       0.667  32.745  56.064  1.00 25.00           C
ATOM    189  CA  LEU   189       4.148  31.159  55.880  1.00 25.00           C
ATOM    190  CA  SER   190       3.343  28.981  58.927  1.00 25.00           C
ATOM    191  CA  ARG   191       3.423  26.141  56.413  1.00 25.00           C
ATOM    192  CA  ASN   192       5.586  24.971  53.595  1.00 25.00           C
ATOM    193  CA  ALA   193       9.192  26.105  53.870  1.00 25.00           C
ATOM    194  CA  ARG   194       8.261  26.956  57.419  1.00 25.00           C
ATOM    195  CA  ARG   195       8.481  30.611  58.657  1.00 25.00           C
ATOM    196  CA  ILE   196       9.235  33.811  56.808  1.00 25.00           C
ATOM    197  CA  THR   197      10.829  35.972  59.422  1.00 25.00           C
ATOM    198  CA  LEU   198      12.211  39.415  60.447  1.00 25.00           C
ATOM    199  CA  VAL   199      12.138  40.532  64.098  1.00 25.00           C
ATOM    200  CA  GLY   200      10.620  43.677  65.708  1.00 25.00           C
ATOM    201  CA  PRO   201      10.542  47.384  65.083  1.00 25.00           C
ATOM    202  CA  GLY   202      10.143  50.950  66.202  1.00 25.00           C
ATOM    203  CA  THR   203      10.391  51.141  70.034  1.00 25.00           C
ATOM    204  CA  PRO   204       8.704  48.836  72.560  1.00 25.00           C
ATOM    205  CA  LEU   205       8.715  45.032  72.600  1.00 25.00           C
ATOM    206  CA  ALA   206      11.775  45.743  70.410  1.00 25.00           C
ATOM    207  CA  PRO   207      14.039  44.017  72.973  1.00 25.00           C
ATOM    208  CA  VAL   208      11.705  40.981  73.025  1.00 25.00           C
ATOM    209  CA  LEU   209      11.765  40.837  69.200  1.00 25.00           C
ATOM    210  CA  PHE   210      15.592  40.999  69.229  1.00 25.00           C
ATOM    211  CA  GLU   211      15.716  38.162  71.799  1.00 25.00           C
ATOM    212  CA  HIS   212      13.360  36.060  69.631  1.00 25.00           C
ATOM    213  CA  GLY   213      11.008  33.139  69.102  1.00 25.00           C
ATOM    214  CA  LEU   214       8.107  31.831  67.008  1.00 25.00           C
ATOM    215  CA  GLN   215       9.570  29.453  64.487  1.00 25.00           C
ATOM    216  CA  GLU   216      12.362  31.126  62.631  1.00 25.00           C
ATOM    217  CA  LEU   217      12.191  34.627  64.090  1.00 25.00           C
ATOM    218  CA  SER   218       8.618  34.766  62.671  1.00 25.00           C
ATOM    219  CA  GLY   219       8.062  36.955  65.711  1.00 25.00           C
ATOM    220  CA  PHE   220       7.041  40.218  67.402  1.00 25.00           C
ATOM    221  CA  MET   221       5.967  43.825  66.877  1.00 25.00           C
ATOM    222  CA  VAL   222       6.697  47.213  68.449  1.00 25.00           C
ATOM    223  CA  LYS   223       5.185  50.608  67.954  1.00 25.00           C
ATOM    224  CA  ASP   224       2.538  50.091  70.643  1.00 25.00           C
ATOM    225  CA  ASN   225      -0.912  49.977  72.347  1.00 25.00           C
ATOM    226  CA  ALA   226      -3.806  48.752  70.157  1.00 25.00           C
ATOM    227  CA  ARG   227      -1.319  47.138  67.731  1.00 25.00           C
ATOM    228  CA  ALA   228       0.452  45.414  70.657  1.00 25.00           C
ATOM    229  CA  PHE   229      -2.908  44.117  71.958  1.00 25.00           C
ATOM    230  CA  ARG   230      -3.771  42.783  68.473  1.00 25.00           C
ATOM    231  CA  ILE   231      -0.370  41.033  68.275  1.00 25.00           C
ATOM    232  CA  VAL   232      -0.947  39.465  71.721  1.00 25.00           C
ATOM    233  CA  ALA   233      -4.407  38.250  70.616  1.00 25.00           C
ATOM    234  CA  GLY   234      -2.887  36.730  67.446  1.00 25.00           C
ATOM    235  CA  ALA   235      -0.213  34.963  69.545  1.00 25.00           C
ATOM    236  CA  GLU   236      -2.921  33.587  71.878  1.00 25.00           C
ATOM    237  CA  LYS   237      -4.912  32.321  68.862  1.00 25.00           C
ATOM    238  CA  VAL   238      -1.772  30.627  67.469  1.00 25.00           C
ATOM    239  CA  LYS   239      -1.130  28.972  70.862  1.00 25.00           C
ATOM    240  CA  ILE   240      -4.751  27.731  70.969  1.00 25.00           C
ATOM    241  CA  TYR   241      -4.394  26.308  67.431  1.00 25.00           C
ATOM    242  CA  SER   242      -5.066  28.183  64.242  1.00 25.00           C
ATOM    243  CA  ALA   243      -5.618  31.874  63.614  1.00 25.00           C
ATOM    244  CA  GLY   244      -6.621  35.293  62.292  1.00 25.00           C
ATOM    245  CA  GLN   245      -8.425  38.579  61.798  1.00 25.00           C
ATOM    246  CA  LYS   246      -7.327  42.100  61.211  1.00 25.00           C
ATOM    247  CA  VAL   247      -8.581  44.497  63.844  1.00 25.00           C
ATOM    248  CA  THR   248     -11.561  46.841  64.161  1.00 25.00           C
ATOM    249  CA  ILE   249     -11.192  50.448  65.382  1.00 25.00           C
ATOM    250  CA  LYS   250     -14.754  50.741  66.803  1.00 25.00           C
ATOM    251  CA  LYS   251     -17.690  50.733  64.366  1.00 25.00           C
TER
END
