
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0338TS474_1-D2
# Molecule2: number of CA atoms  113 (  914),  selected  113 , name T0338_D2.pdb
# PARAMETERS: T0338TS474_1-D2.T0338_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      E     144           -
LGA    -       -      H     145           -
LGA    -       -      P     146           -
LGA    -       -      H     147           -
LGA    -       -      T     148           -
LGA    -       -      D     149           -
LGA    -       -      V     150           -
LGA    -       -      V     151           -
LGA    -       -      K     152           -
LGA    -       -      C     153           -
LGA    -       -      T     154           -
LGA    -       -      Q     155           -
LGA    -       -      L     156           -
LGA    -       -      V     157           -
LGA    -       -      R     158           -
LGA    -       -      A     159           -
LGA    E     144      S     160          1.046
LGA    H     145      K     161          3.383
LGA    P     146      D     162          3.640
LGA    H     147      L     163          4.261
LGA    -       -      A     164           -
LGA    T     148      Q     165          1.553
LGA    D     149      T     166          3.161
LGA    -       -      S     167           -
LGA    V     150      Y     168          1.153
LGA    V     151      F     169          2.277
LGA    -       -      M     170           -
LGA    -       -      A     171           -
LGA    K     152      T     172          2.229
LGA    C     153      N     173          4.086
LGA    -       -      S     174           -
LGA    T     154      L     175          3.324
LGA    Q     155      H     176          3.732
LGA    L     156      L     177           #
LGA    V     157      T     178          3.762
LGA    R     158      T     179          2.470
LGA    A     159      F     180          3.208
LGA    S     160      C     181          3.606
LGA    -       -      L     182           -
LGA    K     161      Q     183          2.761
LGA    D     162      Y     184          3.589
LGA    L     163      K     185           -
LGA    A     164      P     186           -
LGA    Q     165      T     187           -
LGA    T     166      V     188           -
LGA    S     167      I     189          3.936
LGA    Y     168      A     190          3.525
LGA    F     169      C     191          5.057
LGA    M     170      V     192           #
LGA    -       -      C     193           -
LGA    -       -      I     194           -
LGA    -       -      H     195           -
LGA    -       -      L     196           -
LGA    -       -      A     197           -
LGA    -       -      C     198           -
LGA    -       -      K     199           -
LGA    -       -      W     200           -
LGA    -       -      S     201           -
LGA    -       -      N     202           -
LGA    -       -      W     203           -
LGA    -       -      E     204           -
LGA    -       -      I     205           -
LGA    -       -      P     206           -
LGA    -       -      V     207           -
LGA    -       -      S     208           -
LGA    -       -      T     209           -
LGA    -       -      D     210           -
LGA    -       -      G     211           -
LGA    -       -      K     212           -
LGA    -       -      H     213           -
LGA    -       -      W     214           -
LGA    -       -      W     215           -
LGA    -       -      E     216           -
LGA    -       -      Y     217           -
LGA    A     171      V     218          2.274
LGA    T     172      D     219          1.841
LGA    N     173      P     220          2.776
LGA    S     174      T     221           #
LGA    L     175      V     222           -
LGA    H     176      T     223           -
LGA    -       -      L     224           -
LGA    -       -      E     225           -
LGA    -       -      L     226           -
LGA    -       -      L     227           -
LGA    -       -      D     228           -
LGA    -       -      E     229           -
LGA    -       -      L     230           -
LGA    -       -      T     231           -
LGA    -       -      H     232           -
LGA    -       -      E     233           -
LGA    -       -      F     234           -
LGA    -       -      L     235           -
LGA    -       -      Q     236           -
LGA    -       -      I     237           -
LGA    -       -      L     238           -
LGA    -       -      E     239           -
LGA    -       -      K     240           -
LGA    -       -      T     241           -
LGA    -       -      P     242           -
LGA    -       -      N     243           -
LGA    -       -      R     244           -
LGA    -       -      L     245           -
LGA    -       -      K     246           -
LGA    -       -      K     247           -
LGA    -       -      I     248           -
LGA    -       -      R     249           -
LGA    -       -      N     250           -
LGA    -       -      W     251           -
LGA    -       -      R     252           -
LGA    -       -      A     253           -
LGA    -       -      N     254           -
LGA    -       -      Q     255           -
LGA    -       -      A     256           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   33  113    5.0     24    3.18     0.00     12.120     0.731

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.993946 * X  +  -0.106485 * Y  +  -0.027064 * Z  + -91.411186
  Y_new =  -0.035103 * X  +  -0.074359 * Y  +  -0.996614 * Z  +  47.458473
  Z_new =   0.104112 * X  +   0.991530 * Y  +  -0.077646 * Z  +  29.944487 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.648947   -1.492646  [ DEG:    94.4777    -85.5223 ]
  Theta =  -0.104301   -3.037292  [ DEG:    -5.9760   -174.0240 ]
  Phi   =  -0.035302    3.106291  [ DEG:    -2.0226    177.9774 ]
 
# 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: T0338TS474_1-D2                               
REMARK     2: T0338_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0338TS474_1-D2.T0338_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   33  113   5.0   24   3.18    0.00  12.120
REMARK  ---------------------------------------------------------- 
MOLECULE T0338TS474_1-D2
PFRMAT TS
TARGET T0338
MODEL 1
PARENT N/A
ATOM    573  N   GLU   144     -33.889  18.375  81.783  1.00 18.46
ATOM    574  CA  GLU   144     -33.392  17.516  82.846  1.00 21.33
ATOM    575  C   GLU   144     -32.077  18.053  83.463  1.00 17.80
ATOM    576  O   GLU   144     -31.540  17.483  84.401  1.00 24.44
ATOM    577  N   HIS   145     -31.574  19.148  82.914  1.00 19.89
ATOM    578  CA  HIS   145     -30.322  19.773  83.369  1.00 19.35
ATOM    579  C   HIS   145     -29.163  19.114  82.625  1.00 19.59
ATOM    580  O   HIS   145     -29.064  19.227  81.406  1.00 21.97
ATOM    581  N   PRO   146     -28.247  18.439  83.345  1.00 17.87
ATOM    582  CA  PRO   146     -27.138  17.799  82.630  1.00 21.70
ATOM    583  C   PRO   146     -26.190  18.735  81.893  1.00 28.52
ATOM    584  O   PRO   146     -25.382  18.286  81.083  1.00 23.07
ATOM    585  N   HIS   147     -26.308  20.035  82.143  1.00 16.22
ATOM    586  CA  HIS   147     -25.421  20.996  81.492  1.00 28.05
ATOM    587  C   HIS   147     -26.040  21.708  80.290  1.00 28.78
ATOM    588  O   HIS   147     -25.435  22.620  79.737  1.00 24.83
ATOM    589  N   THR   148     -27.225  21.298  79.858  1.00 24.83
ATOM    590  CA  THR   148     -27.864  22.020  78.754  1.00 25.20
ATOM    591  C   THR   148     -27.678  21.469  77.343  1.00 13.90
ATOM    592  O   THR   148     -28.372  21.896  76.422  1.00 21.58
ATOM    593  N   ASP   149     -26.765  20.529  77.147  1.00 18.21
ATOM    594  CA  ASP   149     -26.599  19.986  75.800  1.00 22.90
ATOM    595  C   ASP   149     -26.327  21.016  74.723  1.00 31.52
ATOM    596  O   ASP   149     -25.697  22.047  74.981  1.00 22.10
ATOM    597  N   VAL   150     -26.800  20.730  73.508  1.00 21.29
ATOM    598  CA  VAL   150     -26.485  21.588  72.373  1.00 27.37
ATOM    599  C   VAL   150     -25.068  21.093  72.088  1.00 33.30
ATOM    600  O   VAL   150     -24.845  19.877  72.015  1.00 21.95
ATOM    601  N   VAL   151     -24.117  22.016  71.950  1.00 23.79
ATOM    602  CA  VAL   151     -22.715  21.648  71.751  1.00 23.83
ATOM    603  C   VAL   151     -22.273  21.693  70.305  1.00 26.09
ATOM    604  O   VAL   151     -22.484  22.682  69.607  1.00 22.49
ATOM    605  N   LYS   152     -21.633  20.617  69.880  1.00 16.95
ATOM    606  CA  LYS   152     -21.137  20.473  68.514  1.00 22.70
ATOM    607  C   LYS   152     -19.998  21.486  68.304  1.00 33.28
ATOM    608  O   LYS   152     -19.226  21.722  69.224  1.00 21.52
ATOM    609  N   CYS   153     -19.885  22.095  67.124  1.00 26.58
ATOM    610  CA  CYS   153     -18.794  23.048  66.920  1.00 27.49
ATOM    611  C   CYS   153     -17.462  22.322  66.781  1.00 29.15
ATOM    612  O   CYS   153     -17.405  21.097  66.571  1.00 19.41
ATOM    613  N   THR   154     -16.388  23.091  66.887  1.00 24.42
ATOM    614  CA  THR   154     -15.045  22.541  66.827  1.00 28.20
ATOM    615  C   THR   154     -14.784  21.804  65.537  1.00 31.58
ATOM    616  O   THR   154     -14.310  20.671  65.568  1.00 33.89
ATOM    617  N   GLN   155     -15.112  22.418  64.396  1.00 25.98
ATOM    618  CA  GLN   155     -14.833  21.765  63.119  1.00 29.83
ATOM    619  C   GLN   155     -15.642  20.512  62.832  1.00 37.45
ATOM    620  O   GLN   155     -15.144  19.593  62.175  1.00 28.36
ATOM    621  N   LEU   156     -16.892  20.454  63.285  1.00 31.09
ATOM    622  CA  LEU   156     -17.651  19.235  63.020  1.00 36.98
ATOM    623  C   LEU   156     -17.204  18.156  63.998  1.00 22.35
ATOM    624  O   LEU   156     -17.248  16.968  63.682  1.00 43.54
ATOM    625  N   VAL   157     -16.750  18.572  65.173  1.00 33.48
ATOM    626  CA  VAL   157     -16.274  17.617  66.164  1.00 40.32
ATOM    627  C   VAL   157     -15.070  16.851  65.608  1.00 51.27
ATOM    628  O   VAL   157     -15.108  15.627  65.462  1.00 48.17
ATOM    629  N   ARG   158     -14.011  17.573  65.259  1.00 54.74
ATOM    630  CA  ARG   158     -12.807  16.912  64.760  1.00 63.54
ATOM    631  C   ARG   158     -12.983  16.234  63.401  1.00 57.11
ATOM    632  O   ARG   158     -12.234  15.327  63.052  1.00 65.77
ATOM    633  N   ALA   159     -13.977  16.663  62.640  1.00 52.52
ATOM    634  CA  ALA   159     -14.252  16.073  61.336  1.00 52.55
ATOM    635  C   ALA   159     -15.197  14.855  61.462  1.00 63.71
ATOM    636  O   ALA   159     -15.490  14.178  60.473  1.00 62.49
ATOM    637  N   SER   160     -15.643  14.568  62.686  1.00 60.38
ATOM    638  CA  SER   160     -16.574  13.462  62.942  1.00 58.15
ATOM    639  C   SER   160     -15.985  12.057  62.871  1.00 63.82
ATOM    640  O   SER   160     -14.945  11.782  63.476  1.00 63.98
ATOM    641  N   LYS   161     -16.675  11.167  62.155  1.00 59.23
ATOM    642  CA  LYS   161     -16.238   9.778  62.018  1.00 68.12
ATOM    643  C   LYS   161     -17.189   8.776  62.677  1.00 67.33
ATOM    644  O   LYS   161     -17.121   7.577  62.414  1.00 68.15
ATOM    645  N   ASP   162     -18.076   9.281  63.529  1.00 63.69
ATOM    646  CA  ASP   162     -19.025   8.447  64.261  1.00 60.16
ATOM    647  C   ASP   162     -18.720   8.642  65.736  1.00 48.51
ATOM    648  O   ASP   162     -18.628   9.772  66.211  1.00 51.04
ATOM    649  N   LEU   163     -18.553   7.547  66.460  1.00 41.95
ATOM    650  CA  LEU   163     -18.257   7.642  67.882  1.00 47.13
ATOM    651  C   LEU   163     -19.558   7.739  68.683  1.00 41.22
ATOM    652  O   LEU   163     -20.528   7.062  68.361  1.00 40.78
ATOM    653  N   ALA   164     -19.614   8.616  69.705  1.00 42.34
ATOM    654  CA  ALA   164     -18.576   9.544  70.190  1.00 50.26
ATOM    655  C   ALA   164     -18.490  10.742  69.238  1.00 43.69
ATOM    656  O   ALA   164     -19.508  11.270  68.805  1.00 40.71
ATOM    657  N   GLN   165     -17.275  11.163  68.917  1.00 38.17
ATOM    658  CA  GLN   165     -17.071  12.244  67.962  1.00 43.31
ATOM    659  C   GLN   165     -17.623  13.607  68.336  1.00 37.38
ATOM    660  O   GLN   165     -17.947  14.412  67.455  1.00 34.10
ATOM    661  N   THR   166     -17.750  13.873  69.626  1.00 29.93
ATOM    662  CA  THR   166     -18.249  15.178  70.035  1.00 42.34
ATOM    663  C   THR   166     -19.763  15.248  70.249  1.00 37.65
ATOM    664  O   THR   166     -20.270  16.293  70.665  1.00 35.86
ATOM    665  N   SER   167     -20.498  14.160  69.979  1.00 28.64
ATOM    666  CA  SER   167     -21.950  14.227  70.174  1.00 22.87
ATOM    667  C   SER   167     -22.569  15.017  69.021  1.00 26.06
ATOM    668  O   SER   167     -22.202  14.837  67.858  1.00 28.24
ATOM    669  N   TYR   168     -23.499  15.902  69.346  1.00 22.71
ATOM    670  CA  TYR   168     -24.158  16.709  68.331  1.00 21.55
ATOM    671  C   TYR   168     -25.035  15.818  67.424  1.00 27.43
ATOM    672  O   TYR   168     -25.186  16.072  66.216  1.00 20.64
ATOM    673  N   PHE   169     -25.580  14.755  68.008  1.00 20.92
ATOM    674  CA  PHE   169     -26.484  13.866  67.282  1.00 25.94
ATOM    675  C   PHE   169     -26.199  12.388  67.491  1.00 26.09
ATOM    676  O   PHE   169     -25.544  12.004  68.451  1.00 25.42
ATOM    677  N   MET   170     -26.726  11.562  66.594  1.00 24.47
ATOM    678  CA  MET   170     -26.558  10.113  66.676  1.00 24.94
ATOM    679  C   MET   170     -27.877   9.396  66.371  1.00 34.26
ATOM    680  O   MET   170     -28.810   9.976  65.801  1.00 23.39
ATOM    681  N   ALA   171     -27.936   8.128  66.758  1.00 28.05
ATOM    682  CA  ALA   171     -29.113   7.298  66.570  1.00 23.66
ATOM    683  C   ALA   171     -28.757   6.166  65.605  1.00 28.52
ATOM    684  O   ALA   171     -27.779   5.443  65.812  1.00 30.83
ATOM    685  N   THR   172     -29.548   6.015  64.547  1.00 29.99
ATOM    686  CA  THR   172     -29.301   4.977  63.551  1.00 30.02
ATOM    687  C   THR   172     -30.588   4.206  63.262  1.00 28.26
ATOM    688  O   THR   172     -31.705   4.693  63.516  1.00 24.19
ATOM    689  N   ASN   173     -30.419   3.012  62.708  1.00 27.90
ATOM    690  CA  ASN   173     -31.540   2.143  62.373  1.00 19.60
ATOM    691  C   ASN   173     -32.485   2.035  63.552  1.00 24.98
ATOM    692  O   ASN   173     -33.699   2.106  63.396  1.00 24.74
ATOM    693  N   SER   174     -31.915   1.851  64.737  1.00 22.22
ATOM    694  CA  SER   174     -32.722   1.735  65.937  1.00 17.93
ATOM    695  C   SER   174     -33.190   0.312  66.068  1.00 32.80
ATOM    696  O   SER   174     -32.371  -0.632  66.019  1.00 22.03
ATOM    697  N   LEU   175     -34.497   0.153  66.242  1.00 19.16
ATOM    698  CA  LEU   175     -35.067  -1.174  66.404  1.00 35.16
ATOM    699  C   LEU   175     -34.627  -1.696  67.780  1.00 32.16
ATOM    700  O   LEU   175     -34.476  -2.892  67.972  1.00 26.88
ATOM    701  N   HIS   176     -34.405  -0.783  68.724  1.00 29.22
ATOM    702  CA  HIS   176     -33.980  -1.150  70.068  1.00 31.28
ATOM    703  C   HIS   176     -32.485  -1.064  70.303  1.00 29.96
ATOM    704  O   HIS   176     -31.785  -0.244  69.694  1.00 24.52
TER
END
