
#######################################################
#                                                     #
#                        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  157 (  157),  selected  157 , name T0356TS677_1-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected  192 , name T0356_D2.pdb
# PARAMETERS: T0356TS677_1-D2.T0356_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T     122      T     122           -
LGA    K     123      K     123           -
LGA    R     124      R     124           -
LGA    L     125      L     125           -
LGA    R     126      R     126           -
LGA    G     127      G     127           -
LGA    A     128      A     128           -
LGA    P     129      P     129           -
LGA    N     143      C     130           -
LGA    R     144      Q     131           -
LGA    I     145      Q     132           -
LGA    P     146      K     133           -
LGA    I     147      I     134           -
LGA    M     148      V     135           -
LGA    T     149      S     136           -
LGA    C     150      G     137           -
LGA    W     151      D     138           -
LGA    P     152      D     139           -
LGA    P     157      V     140           -
LGA    L     158      D     141           -
LGA    I     159      L     142           -
LGA    T     160      N     143           -
LGA    W     161      R     144           -
LGA    G     162      I     145           -
LGA    L     163      P     146           -
LGA    T     164      I     147           -
LGA    V     165      M     148           -
LGA    T     166      T     149          4.492
LGA    R     167      C     150          3.101
LGA    P     169      W     151           -
LGA    H     170      P     152           -
LGA    K     171      E     153           -
LGA    E     172      D     154           -
LGA    R     173      A     155           -
LGA    Q     174      A     156           -
LGA    N     175      P     157           -
LGA    L     176      L     158           -
LGA    G     177      I     159           -
LGA    I     178      T     160           -
LGA    Y     179      W     161           -
LGA    R     180      G     162           -
LGA    Q     181      L     163           -
LGA    Q     182      T     164           -
LGA    L     183      V     165           -
LGA    I     184      T     166           -
LGA    I     190      R     167           -
LGA    M     191      G     168           -
LGA    R     192      P     169           -
LGA    W     193      H     170           -
LGA    L     194      K     171           -
LGA    S     195      E     172           -
LGA    H     196      R     173           -
LGA    R     197      Q     174           -
LGA    G     198      N     175           -
LGA    G     199      L     176           -
LGA    A     200      G     177           -
LGA    L     201      I     178           -
LGA    D     202      Y     179           -
LGA    Y     203      R     180           -
LGA    Q     204      Q     181           -
LGA    E     205      Q     182           -
LGA    W     206      L     183           -
LGA    C     207      I     184           -
LGA    A     208      G     185           -
LGA    A     209      K     186           -
LGA    H     210      N     187           -
LGA    V     217      K     188           -
LGA    S     218      L     189           -
LGA    -       -      I     190           -
LGA    -       -      M     191           -
LGA    -       -      R     192           -
LGA    -       -      W     193           -
LGA    -       -      L     194           -
LGA    -       -      S     195           -
LGA    -       -      H     196           -
LGA    -       -      R     197           -
LGA    -       -      G     198           -
LGA    -       -      G     199           -
LGA    -       -      A     200           -
LGA    -       -      L     201           -
LGA    -       -      D     202           -
LGA    -       -      Y     203           -
LGA    -       -      Q     204           -
LGA    -       -      E     205           -
LGA    -       -      W     206           -
LGA    -       -      C     207           -
LGA    -       -      A     208           -
LGA    -       -      A     209           -
LGA    -       -      H     210           -
LGA    -       -      P     211           -
LGA    -       -      G     212           -
LGA    -       -      E     213           -
LGA    -       -      R     214           -
LGA    -       -      F     215           -
LGA    -       -      P     216           -
LGA    -       -      V     217           -
LGA    -       -      S     218           -
LGA    -       -      V     219           -
LGA    -       -      A     220           -
LGA    -       -      L     221           -
LGA    -       -      G     222           -
LGA    -       -      A     223           -
LGA    -       -      D     224           -
LGA    V     219      P     225          5.977
LGA    A     220      A     226           -
LGA    -       -      T     227           -
LGA    -       -      I     228           -
LGA    -       -      L     229           -
LGA    -       -      G     230           -
LGA    -       -      A     231           -
LGA    L     221      V     232          4.244
LGA    G     222      T     233          3.385
LGA    A     223      -       -           -
LGA    D     224      -       -           -
LGA    P     225      -       -           -
LGA    A     226      P     234          1.649
LGA    T     227      V     235          1.763
LGA    I     228      P     236          1.646
LGA    L     229      D     237           #
LGA    G     230      T     238           -
LGA    A     231      L     239          3.467
LGA    V     232      -       -           -
LGA    T     233      -       -           -
LGA    P     234      -       -           -
LGA    V     235      -       -           -
LGA    P     236      -       -           -
LGA    D     237      -       -           -
LGA    T     238      -       -           -
LGA    L     239      -       -           -
LGA    S     240      -       -           -
LGA    E     241      -       -           -
LGA    Y     242      S     240          2.475
LGA    A     243      E     241          2.017
LGA    F     244      Y     242          2.422
LGA    A     245      A     243          2.344
LGA    G     246      F     244          2.309
LGA    L     247      A     245          2.664
LGA    L     248      G     246          3.196
LGA    R     249      L     247          3.212
LGA    G     250      L     248          2.811
LGA    T     251      R     249          3.346
LGA    K     252      G     250           -
LGA    -       -      T     251           -
LGA    -       -      K     252           -
LGA    -       -      T     253           -
LGA    -       -      E     254           -
LGA    -       -      V     255           -
LGA    -       -      V     256           -
LGA    -       -      K     257           -
LGA    -       -      C     258           -
LGA    -       -      I     259           -
LGA    -       -      S     260           -
LGA    -       -      N     261           -
LGA    -       -      D     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      V     265           -
LGA    T     253      P     266          4.338
LGA    -       -      A     267           -
LGA    -       -      S     268           -
LGA    E     254      A     269           #
LGA    V     255      E     270           -
LGA    V     256      I     271           -
LGA    K     257      V     272           -
LGA    C     258      -       -           -
LGA    D     262      L     273           #
LGA    L     263      E     274           -
LGA    E     264      -       -           -
LGA    V     265      -       -           -
LGA    P     266      -       -           -
LGA    S     268      -       -           -
LGA    A     269      -       -           -
LGA    E     270      -       -           -
LGA    I     271      -       -           -
LGA    V     272      -       -           -
LGA    L     273      -       -           -
LGA    E     274      -       -           -
LGA    G     275      -       -           -
LGA    E     278      -       -           -
LGA    Q     279      -       -           -
LGA    G     280      -       -           -
LGA    E     281      -       -           -
LGA    T     282      -       -           -
LGA    A     283      -       -           -
LGA    P     284      -       -           -
LGA    E     285      G     275           #
LGA    G     286      Y     276          2.767
LGA    P     287      I     277          3.997
LGA    Y     288      E     278          2.508
LGA    G     289      Q     279          3.724
LGA    -       -      G     280           -
LGA    D     290      E     281          4.211
LGA    H     291      T     282          4.454
LGA    T     292      A     283          2.727
LGA    G     293      -       -           -
LGA    Y     294      -       -           -
LGA    Y     295      -       -           -
LGA    N     296      -       -           -
LGA    E     297      -       -           -
LGA    V     298      -       -           -
LGA    D     299      -       -           -
LGA    S     300      -       -           -
LGA    F     301      P     284           #
LGA    P     302      E     285          5.773
LGA    V     303      G     286          3.530
LGA    -       -      P     287           -
LGA    -       -      Y     288           -
LGA    -       -      G     289           -
LGA    -       -      D     290           -
LGA    -       -      H     291           -
LGA    -       -      T     292           -
LGA    -       -      G     293           -
LGA    -       -      Y     294           -
LGA    -       -      Y     295           -
LGA    -       -      N     296           -
LGA    -       -      E     297           -
LGA    -       -      V     298           -
LGA    F     304      D     299          4.019
LGA    T     305      S     300          3.119
LGA    V     306      F     301          3.384
LGA    T     307      -       -           -
LGA    H     308      P     302          3.533
LGA    I     309      V     303           #
LGA    T     310      F     304          3.261
LGA    Q     311      T     305          3.364
LGA    R     312      V     306          3.996
LGA    E     313      T     307          1.693
LGA    -       -      H     308           -
LGA    -       -      I     309           -
LGA    -       -      T     310           -
LGA    -       -      Q     311           -
LGA    -       -      R     312           -
LGA    -       -      E     313           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  157  192    5.0     37    3.42     5.41     11.431     1.051

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.869513 * X  +   0.374913 * Y  +  -0.321539 * Z  +  44.178288
  Y_new =   0.417254 * X  +  -0.905930 * Y  +   0.072038 * Z  +  70.824455
  Z_new =  -0.264284 * X  +  -0.196802 * Y  +  -0.944152 * Z  +  96.763428 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.936092    0.205500  [ DEG:  -168.2257     11.7743 ]
  Theta =   0.267461    2.874131  [ DEG:    15.3244    164.6756 ]
  Phi   =   0.447415   -2.694178  [ DEG:    25.6350   -154.3650 ]
 
# 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: T0356TS677_1-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS677_1-D2.T0356_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  157  192   5.0   37   3.42    5.41  11.431
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS677_1-D2
PFRMAT TS
TARGET T0356
MODEL  1
PARENT 2D1Q_A
ATOM    184  CA  THR   122      37.267  63.391  92.501  1.00 94.00
ATOM    185  CA  LYS   123      40.428  61.385  91.710  1.00 99.00
ATOM    186  CA  ARG   124      40.501  57.699  92.659  1.00 83.00
ATOM    187  CA  LEU   125      43.054  56.559  95.251  1.00 63.00
ATOM    188  CA  ARG   126      44.812  53.349  94.358  1.00 70.00
ATOM    189  CA  GLY   127      47.295  50.908  95.852  1.00 75.00
ATOM    190  CA  ALA   128      50.384  52.727  94.637  1.00 44.00
ATOM    191  CA  PRO   129      52.984  49.970  94.505  1.00 67.00
ATOM    192  CA  ASN   143      50.573  47.539  92.780  1.00 99.00
ATOM    193  CA  ARG   144      48.329  49.615  90.425  1.00 99.00
ATOM    194  CA  ILE   145      49.572  49.692  86.819  1.00 99.00
ATOM    195  CA  PRO   146      49.392  53.239  85.439  1.00 99.00
ATOM    196  CA  ILE   147      51.047  52.900  82.018  1.00 97.00
ATOM    197  CA  MET   148      51.884  50.111  79.571  1.00 86.00
ATOM    198  CA  THR   149      54.934  51.224  77.609  1.00 92.00
ATOM    199  CA  CYS   150      56.816  49.885  74.608  1.00 77.00
ATOM    200  CA  TRP   151      60.557  50.437  74.074  1.00 83.00
ATOM    201  CA  PRO   152      62.076  51.722  70.764  1.00 73.00
ATOM    206  CA  PRO   157      58.078  42.442  68.713  1.00 84.00
ATOM    211  CA  LEU   158      54.097  47.814  83.310  1.00 74.00
ATOM    212  CA  ILE   159      54.734  50.979  85.278  1.00 61.00
ATOM    213  CA  THR   160      52.951  51.712  88.549  1.00 52.00
ATOM    214  CA  TRP   161      51.795  54.888  90.341  1.00 86.00
ATOM    215  CA  GLY   162      54.783  54.512  92.669  1.00 66.00
ATOM    216  CA  LEU   163      57.181  54.550  89.682  1.00 84.00
ATOM    217  CA  THR   164      55.508  57.747  88.459  1.00 99.00
ATOM    218  CA  VAL   165      55.338  59.684  91.750  1.00 99.00
ATOM    219  CA  THR   166      59.095  59.042  92.107  1.00 99.00
ATOM    220  CA  ARG   167      59.742  60.638  88.721  1.00 99.00
ATOM    232  CA  PRO   169      63.286  74.414  89.282  1.00 91.00
ATOM    233  CA  HIS   170      59.571  75.154  89.436  1.00 92.00
ATOM    234  CA  LYS   171      58.974  78.340  87.367  1.00 99.00
ATOM    235  CA  GLU   172      55.459  78.615  85.816  1.00 99.00
ATOM    236  CA  ARG   173      55.274  80.202  82.375  1.00 91.00
ATOM    237  CA  GLN   174      58.827  79.141  81.456  1.00 99.00
ATOM    238  CA  ASN   175      58.704  77.760  77.884  1.00 78.00
ATOM    239  CA  LEU   176      60.443  74.460  77.019  1.00 51.00
ATOM    240  CA  GLY   177      60.855  73.117  73.470  1.00 31.00
ATOM    241  CA  ILE   178      60.372  69.368  72.980  1.00 50.00
ATOM    242  CA  TYR   179      60.916  67.273  69.842  1.00 41.00
ATOM    243  CA  ARG   180      60.787  63.856  71.578  1.00 61.00
ATOM    244  CA  GLN   181      58.010  61.261  70.944  1.00 64.00
ATOM    245  CA  GLN   182      55.281  61.367  73.603  1.00 73.00
ATOM    246  CA  LEU   183      54.328  57.655  73.452  1.00 83.00
ATOM    247  CA  ILE   184      57.841  56.661  74.503  1.00 99.00
ATOM    263  CA  ILE   190      54.777  75.893  78.878  1.00 90.00
ATOM    264  CA  MET   191      55.378  72.847  76.694  1.00 83.00
ATOM    265  CA  ARG   192      56.231  73.903  73.171  1.00 93.00
ATOM    266  CA  TRP   193      55.857  70.926  70.895  1.00 71.00
ATOM    267  CA  LEU   194      57.368  70.554  67.442  1.00 62.00
ATOM    268  CA  SER   195      56.084  67.531  65.512  1.00 62.00
ATOM    269  CA  HIS   196      58.100  67.461  62.341  1.00 63.00
ATOM    270  CA  ARG   197      61.622  68.844  62.657  1.00 47.00
ATOM    271  CA  GLY   198      62.763  71.596  60.321  1.00 47.00
ATOM    272  CA  GLY   199      65.932  73.700  60.715  1.00 53.00
ATOM    273  CA  ALA   200      64.327  77.115  60.148  1.00 60.00
ATOM    274  CA  LEU   201      61.124  76.249  62.080  1.00 57.00
ATOM    275  CA  ASP   202      63.209  74.876  64.937  1.00 74.00
ATOM    276  CA  TYR   203      65.155  78.167  65.267  1.00 89.00
ATOM    277  CA  GLN   204      62.086  80.417  64.723  1.00 83.00
ATOM    278  CA  GLU   205      60.293  78.506  67.482  1.00 97.00
ATOM    279  CA  TRP   206      63.185  78.881  69.981  1.00 99.00
ATOM    280  CA  CYS   207      63.162  82.606  69.320  1.00 99.00
ATOM    281  CA  ALA   208      59.383  83.264  69.127  1.00 99.00
ATOM    282  CA  ALA   209      58.548  81.453  72.356  1.00 83.00
ATOM    283  CA  HIS   210      61.697  82.565  74.173  1.00 72.00
ATOM    284  CA  VAL   217      62.361  78.951  75.070  1.00 90.00
ATOM    285  CA  SER   218      64.516  78.485  78.132  1.00 97.00
ATOM    286  CA  VAL   219      65.324  74.894  77.464  1.00 99.00
ATOM    287  CA  ALA   220      65.177  72.313  74.699  1.00 99.00
ATOM    288  CA  LEU   221      65.089  68.528  74.802  1.00 94.00
ATOM    289  CA  GLY   222      66.322  66.547  71.797  1.00 69.00
ATOM    290  CA  ALA   223      67.264  63.175  70.401  1.00 63.00
ATOM    291  CA  ASP   224      70.989  62.943  69.488  1.00 54.00
ATOM    292  CA  PRO   225      70.342  62.821  65.718  1.00 75.00
ATOM    293  CA  ALA   226      69.390  66.497  65.769  1.00 95.00
ATOM    294  CA  THR   227      72.724  67.722  67.158  1.00 99.00
ATOM    295  CA  ILE   228      74.312  66.884  63.798  1.00 99.00
ATOM    296  CA  LEU   229      72.046  69.415  62.109  1.00 91.00
ATOM    297  CA  GLY   230      72.715  72.164  64.761  1.00 99.00
ATOM    298  CA  ALA   231      76.498  71.786  64.555  1.00 86.00
ATOM    299  CA  VAL   232      76.449  72.396  60.778  1.00 67.00
ATOM    300  CA  THR   233      73.695  75.058  60.772  1.00 99.00
ATOM    301  CA  PRO   234      74.551  78.397  59.147  1.00 99.00
ATOM    302  CA  VAL   235      71.322  79.943  60.408  1.00 81.00
ATOM    303  CA  PRO   236      72.015  80.125  64.200  1.00 91.00
ATOM    304  CA  ASP   237      73.135  83.727  63.998  1.00 80.00
ATOM    305  CA  THR   238      70.026  85.151  62.290  1.00 54.00
ATOM    322  CA  LEU   239      79.082  62.031  70.395  1.00 78.00
ATOM    323  CA  SER   240      81.030  63.890  73.112  1.00 60.00
ATOM    324  CA  GLU   241      82.785  65.983  70.403  1.00 67.00
ATOM    325  CA  TYR   242      79.573  66.987  68.604  1.00 99.00
ATOM    326  CA  ALA   243      77.889  67.720  71.966  1.00 99.00
ATOM    327  CA  PHE   244      80.798  69.953  73.047  1.00 74.00
ATOM    328  CA  ALA   245      80.767  71.800  69.704  1.00 82.00
ATOM    329  CA  GLY   246      76.982  72.403  69.989  1.00 90.00
ATOM    330  CA  LEU   247      77.359  73.637  73.587  1.00 59.00
ATOM    331  CA  LEU   248      80.060  76.000  72.308  1.00 40.00
ATOM    332  CA  ARG   249      77.873  77.294  69.454  1.00 60.00
ATOM    333  CA  GLY   250      74.976  78.144  71.838  1.00 66.00
ATOM    334  CA  THR   251      77.363  79.591  74.449  1.00 51.00
ATOM    335  CA  LYS   252      76.409  77.077  77.141  1.00 60.00
ATOM    336  CA  THR   253      78.618  75.176  79.637  1.00 97.00
ATOM    337  CA  GLU   254      77.560  71.743  78.376  1.00 99.00
ATOM    338  CA  VAL   255      74.768  69.406  77.351  1.00 99.00
ATOM    339  CA  VAL   256      72.413  68.048  79.975  1.00 99.00
ATOM    340  CA  LYS   257      72.137  64.288  79.416  1.00 99.00
ATOM    341  CA  CYS   258      69.691  61.776  80.846  1.00 99.00
ATOM    365  CA  ASP   262      75.511  62.198  84.592  1.00 99.00
ATOM    366  CA  LEU   263      75.084  60.828  88.084  1.00 99.00
ATOM    367  CA  GLU   264      72.811  58.396  89.893  1.00 99.00
ATOM    368  CA  VAL   265      69.416  59.969  90.650  1.00 99.00
ATOM    369  CA  PRO   266      68.075  60.202  94.224  1.00 99.00
ATOM    370  CA  SER   268      66.808  56.881  95.660  1.00 99.00
ATOM    371  CA  ALA   269      68.704  54.733  93.145  1.00 76.00
ATOM    372  CA  GLU   270      71.741  52.479  93.246  1.00 83.00
ATOM    373  CA  ILE   271      74.037  51.570  90.366  1.00 74.00
ATOM    374  CA  VAL   272      76.882  49.125  89.774  1.00 64.00
ATOM    375  CA  LEU   273      79.090  48.073  86.881  1.00 43.00
ATOM    376  CA  GLU   274      79.637  44.303  86.489  1.00 58.00
ATOM    377  CA  GLY   275      82.382  42.399  84.701  1.00 57.00
ATOM    379  CA  GLU   278      82.927  37.429  82.319  1.00 50.00
ATOM    380  CA  GLN   279      82.862  37.077  86.128  1.00 55.00
ATOM    381  CA  GLY   280      79.677  39.030  87.090  1.00 75.00
ATOM    382  CA  GLU   281      81.774  40.791  89.768  1.00 66.00
ATOM    383  CA  THR   282      81.487  44.494  90.656  1.00 61.00
ATOM    384  CA  ALA   283      84.026  46.920  89.212  1.00 77.00
ATOM    385  CA  PRO   284      85.795  50.030  90.507  1.00 56.00
ATOM    386  CA  GLU   285      86.018  53.288  88.510  1.00 49.00
ATOM    387  CA  GLY   286      87.349  53.379  84.911  1.00 67.00
ATOM    388  CA  PRO   287      86.569  49.723  84.151  1.00 50.00
ATOM    389  CA  TYR   288      83.960  48.973  81.442  1.00 49.00
ATOM    390  CA  GLY   289      81.155  46.492  82.103  1.00 50.00
ATOM    391  CA  ASP   290      77.395  46.053  82.269  1.00 57.00
ATOM    392  CA  HIS   291      75.372  48.724  84.084  1.00 27.00
ATOM    393  CA  THR   292      72.893  47.421  86.684  1.00 24.00
ATOM    402  CA  GLY   293      57.088  43.476  85.062  1.00 59.00
ATOM    403  CA  TYR   294      56.284  42.577  81.448  1.00 71.00
ATOM    404  CA  TYR   295      52.597  41.832  80.761  1.00 67.00
ATOM    405  CA  ASN   296      52.136  38.025  80.635  1.00 99.00
ATOM    406  CA  GLU   297      55.906  37.467  80.301  1.00 99.00
ATOM    407  CA  VAL   298      57.263  36.222  83.672  1.00 90.00
ATOM    408  CA  ASP   299      60.169  34.584  81.787  1.00 99.00
ATOM    417  CA  SER   300      68.865  40.291  94.244  1.00 99.00
ATOM    418  CA  PHE   301      66.547  42.845  92.648  1.00 99.00
ATOM    419  CA  PRO   302      69.122  44.409  90.270  1.00 99.00
ATOM    420  CA  VAL   303      67.960  45.175  86.728  1.00 99.00
ATOM    421  CA  PHE   304      70.519  44.377  84.024  1.00 99.00
ATOM    422  CA  THR   305      70.451  47.171  81.451  1.00 99.00
ATOM    423  CA  VAL   306      72.213  45.322  78.641  1.00 77.00
ATOM    424  CA  THR   307      74.214  48.578  78.330  1.00 75.00
ATOM    425  CA  HIS   308      77.951  48.946  78.573  1.00 65.00
ATOM    426  CA  ILE   309      79.474  51.772  80.567  1.00 48.00
ATOM    427  CA  THR   310      81.767  52.906  83.376  1.00 58.00
ATOM    428  CA  GLN   311      82.092  55.542  86.103  1.00 78.00
ATOM    429  CA  ARG   312      85.070  57.695  86.965  1.00 90.00
ATOM    430  CA  GLU   313      86.692  58.632  90.304  1.00 98.00
TER
END
