
#######################################################
#                                                     #
#                        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   36 (  177),  selected   36 , name T0321TS261_1_2-D2
# Molecule2: number of CA atoms  148 ( 1130),  selected  148 , name T0321_D2.pdb
# PARAMETERS: T0321TS261_1_2-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    -       -      P     112           -
LGA    -       -      F     113           -
LGA    -       -      I     114           -
LGA    -       -      M     115           -
LGA    -       -      S     116           -
LGA    -       -      Q     117           -
LGA    -       -      N     118           -
LGA    -       -      E     119           -
LGA    -       -      V     120           -
LGA    V     105      K     121          3.785
LGA    E     106      G     122          1.601
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    D     107      C     142          1.069
LGA    R     108      D     143          1.596
LGA    M     109      L     144          2.921
LGA    V     120      S     145          3.987
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    K     121      G     154          3.569
LGA    G     122      D     155          4.592
LGA    -       -      Y     156           -
LGA    -       -      P     157           -
LGA    -       -      L     158           -
LGA    -       -      P     159           -
LGA    -       -      A     160           -
LGA    -       -      S     161           -
LGA    -       -      E     162           -
LGA    -       -      F     163           -
LGA    -       -      I     164           -
LGA    -       -      L     165           -
LGA    -       -      P     166           -
LGA    -       -      E     167           -
LGA    -       -      C     168           -
LGA    -       -      D     169           -
LGA    -       -      Y     170           -
LGA    -       -      V     171           -
LGA    -       -      Y     172           -
LGA    -       -      I     173           -
LGA    -       -      T     174           -
LGA    -       -      C     175           -
LGA    -       -      A     176           -
LGA    -       -      S     177           -
LGA    -       -      V     178           -
LGA    -       -      V     179           -
LGA    -       -      D     180           -
LGA    -       -      K     181           -
LGA    L     183      T     182          1.520
LGA    P     207      L     183           -
LGA    V     208      P     184          4.256
LGA    L     209      R     185          3.436
LGA    -       -      L     186           -
LGA    F     210      L     187          1.784
LGA    E     211      E     188          2.807
LGA    H     212      L     189          2.073
LGA    G     213      S     190          3.084
LGA    L     214      R     191           #
LGA    -       -      N     192           -
LGA    Q     215      A     193          2.111
LGA    -       -      R     194           -
LGA    -       -      R     195           -
LGA    -       -      I     196           -
LGA    -       -      T     197           -
LGA    -       -      L     198           -
LGA    E     216      V     199          1.742
LGA    L     217      G     200          1.331
LGA    S     218      P     201          2.382
LGA    G     219      G     202          2.273
LGA    F     220      T     203          2.340
LGA    M     221      P     204          2.853
LGA    V     222      L     205           -
LGA    K     223      -       -           -
LGA    D     224      -       -           -
LGA    N     225      A     206          3.417
LGA    -       -      P     207           -
LGA    -       -      V     208           -
LGA    -       -      L     209           -
LGA    -       -      F     210           -
LGA    -       -      E     211           -
LGA    -       -      H     212           -
LGA    -       -      G     213           -
LGA    -       -      L     214           -
LGA    -       -      Q     215           -
LGA    -       -      E     216           -
LGA    -       -      L     217           -
LGA    -       -      S     218           -
LGA    -       -      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)   36  148    5.0     23    2.81     8.70      9.810     0.791

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.696385 * X  +   0.212041 * Y  +  -0.685629 * Z  +  95.571075
  Y_new =  -0.545256 * X  +   0.464852 * Y  +   0.697573 * Z  +   6.603138
  Z_new =   0.466630 * X  +   0.859623 * Y  +  -0.208099 * Z  +  65.164169 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.808309   -1.333284  [ DEG:   103.6085    -76.3915 ]
  Theta =  -0.485477   -2.656116  [ DEG:   -27.8158   -152.1842 ]
  Phi   =  -2.477316    0.664277  [ DEG:  -141.9397     38.0603 ]
 
# 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: T0321TS261_1_2-D2                             
REMARK     2: T0321_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS261_1_2-D2.T0321_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36  148   5.0   23   2.81    8.70   9.810
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS261_1_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0321
PARENT 1qp8_A
ATOM    872  N   VAL    97      22.540  38.579  87.891  1.00  3.21
ATOM    873  CA  VAL    97      21.880  38.673  89.186  1.00  3.21
ATOM    874  C   VAL    97      21.754  37.331  89.883  1.00  3.21
ATOM    875  O   VAL    97      21.938  37.252  91.093  1.00  3.21
ATOM    876  CB  VAL    97      20.488  39.278  89.041  1.00  3.21
ATOM    877  N   ILE    98      21.448  36.277  89.127  1.00  3.86
ATOM    878  CA  ILE    98      21.271  34.966  89.739  1.00  3.86
ATOM    879  C   ILE    98      22.571  34.206  89.970  1.00  3.86
ATOM    880  O   ILE    98      22.556  33.081  90.468  1.00  3.86
ATOM    881  CB  ILE    98      20.284  34.113  88.933  1.00  3.86
ATOM    882  N   PHE    99      23.696  34.824  89.624  1.00  4.50
ATOM    883  CA  PHE    99      24.982  34.186  89.839  1.00  4.50
ATOM    884  C   PHE    99      25.549  33.492  88.624  1.00  4.50
ATOM    885  O   PHE    99      26.706  33.076  88.624  1.00  4.50
ATOM    886  CB  PHE    99      24.841  33.191  91.003  1.00  4.50
ATOM    887  N   SER   100      24.734  33.354  87.587  1.00  5.36
ATOM    888  CA  SER   100      25.174  32.708  86.359  1.00  5.36
ATOM    889  C   SER   100      26.095  33.678  85.594  1.00  5.36
ATOM    890  O   SER   100      25.667  34.748  85.156  1.00  5.36
ATOM    891  CB  SER   100      23.945  32.344  85.525  1.00  5.36
ATOM    892  N   ASP   101      27.362  33.312  85.442  1.00  6.29
ATOM    893  CA  ASP   101      28.316  34.177  84.745  1.00  6.29
ATOM    894  C   ASP   101      28.785  33.576  83.424  1.00  6.29
ATOM    895  O   ASP   101      29.829  33.948  82.901  1.00  6.29
ATOM    896  CB  ASP   101      29.532  34.452  85.640  1.00  6.29
ATOM    897  N   ALA   102      28.012  32.647  82.886  1.00  4.84
ATOM    898  CA  ALA   102      28.395  32.038  81.631  1.00  4.84
ATOM    899  C   ALA   102      28.109  32.967  80.475  1.00  4.84
ATOM    900  O   ALA   102      27.286  33.880  80.590  1.00  4.84
ATOM    901  CB  ALA   102      27.655  30.699  81.469  1.00  4.84
ATOM    902  N   LYS   103      28.800  32.737  79.364  1.00  4.15
ATOM    903  CA  LYS   103      28.628  33.529  78.158  1.00  4.15
ATOM    904  C   LYS   103      28.089  32.579  77.107  1.00  4.15
ATOM    905  O   LYS   103      28.596  32.514  75.990  1.00  4.15
ATOM    906  CB  LYS   103      29.969  34.115  77.693  1.00  4.15
ATOM    907  N   ARG   104      27.053  31.839  77.478  1.00  4.02
ATOM    908  CA  ARG   104      26.444  30.867  76.577  1.00  4.02
ATOM    909  C   ARG   104      25.501  31.440  75.541  1.00  4.02
ATOM    910  O   ARG   104      25.130  30.742  74.607  1.00  4.02
ATOM    911  CB  ARG   104      25.666  29.838  77.379  1.00  4.02
ATOM    912  N   VAL   105      25.086  32.689  75.712  1.00  3.56
ATOM    913  CA  VAL   105      24.158  33.312  74.762  1.00  3.56
ATOM    914  C   VAL   105      24.920  34.214  73.802  1.00  3.56
ATOM    915  O   VAL   105      25.649  35.108  74.239  1.00  3.56
ATOM    916  CB  VAL   105      23.118  34.219  75.472  1.00  3.56
ATOM    917  N   GLU   106      24.761  34.002  72.500  1.00  5.10
ATOM    918  CA  GLU   106      25.466  34.862  71.560  1.00  5.10
ATOM    919  C   GLU   106      24.711  36.175  71.370  1.00  5.10
ATOM    920  O   GLU   106      23.475  36.209  71.322  1.00  5.10
ATOM    921  CB  GLU   106      25.677  34.175  70.208  1.00  5.10
ATOM    922  N   ASP   107      25.473  37.258  71.278  1.00  5.26
ATOM    923  CA  ASP   107      24.916  38.587  71.110  1.00  5.26
ATOM    924  C   ASP   107      24.758  38.949  69.642  1.00  5.26
ATOM    925  O   ASP   107      25.733  39.050  68.909  1.00  5.26
ATOM    926  CB  ASP   107      25.801  39.584  71.843  1.00  5.26
ATOM    927  N   ARG   108      23.514  39.117  69.183  1.00  4.53
ATOM    928  CA  ARG   108      23.237  39.460  67.790  1.00  4.53
ATOM    929  C   ARG   108      23.832  40.791  67.436  1.00  4.53
ATOM    930  O   ARG   108      24.038  41.638  68.305  1.00  4.53
ATOM    931  CB  ARG   108      21.719  39.542  67.735  1.00  4.53
ATOM    932  N   MET   109      24.115  40.980  66.158  1.00  2.25
ATOM    933  CA  MET   109      24.637  42.253  65.711  1.00  2.25
ATOM    934  C   MET   109      23.522  42.909  64.918  1.00  2.25
ATOM    935  O   MET   109      22.647  42.238  64.386  1.00  2.25
ATOM    936  CB  MET   109      25.888  42.051  64.857  1.00  2.25
ATOM    937  N   VAL   120      23.526  44.228  64.882  1.00  3.81
ATOM    938  CA  VAL   120      22.518  44.947  64.135  1.00  3.81
ATOM    939  C   VAL   120      23.085  45.141  62.731  1.00  3.81
ATOM    940  O   VAL   120      22.386  44.961  61.719  1.00  3.81
ATOM    941  CB  VAL   120      22.197  46.291  64.837  1.00  3.81
ATOM    942  N   LYS   121      24.372  45.471  62.693  1.00  4.32
ATOM    943  CA  LYS   121      25.093  45.674  61.446  1.00  4.32
ATOM    944  C   LYS   121      24.818  44.524  60.473  1.00  4.32
ATOM    945  O   LYS   121      24.884  43.349  60.844  1.00  4.32
ATOM    946  CB  LYS   121      26.588  45.742  61.735  1.00  4.32
ATOM    947  N   GLY   122      24.505  44.868  59.231  1.00  3.27
ATOM    948  CA  GLY   122      24.231  43.861  58.223  1.00  3.27
ATOM    949  C   GLY   122      23.015  42.994  58.492  1.00  3.27
ATOM    950  O   GLY   122      22.870  41.921  57.904  1.00  3.27
ATOM    951  N   LEU   183       3.705  43.994  53.858  1.00  3.53
ATOM    952  CA  LEU   183       4.224  43.797  55.209  1.00  3.53
ATOM    953  C   LEU   183       5.050  42.516  55.212  1.00  3.53
ATOM    954  O   LEU   183       6.140  42.473  55.792  1.00  3.53
ATOM    955  CB  LEU   183       3.083  43.675  56.234  1.00  3.53
ATOM    956  N   PRO   207      -0.062  35.643  62.392  1.00  4.70
ATOM    957  CA  PRO   207       0.846  34.551  62.725  1.00  4.70
ATOM    958  C   PRO   207       1.728  34.170  61.541  1.00  4.70
ATOM    959  O   PRO   207       2.959  34.151  61.630  1.00  4.70
ATOM    960  CB  PRO   207       0.053  33.324  63.181  1.00  4.70
ATOM    961  N   VAL   208       1.072  33.859  60.432  1.00  3.84
ATOM    962  CA  VAL   208       1.740  33.474  59.199  1.00  3.84
ATOM    963  C   VAL   208       2.834  34.459  58.812  1.00  3.84
ATOM    964  O   VAL   208       3.929  34.055  58.426  1.00  3.84
ATOM    965  CB  VAL   208       0.692  33.370  58.098  1.00  3.84
ATOM    966  N   LEU   209       2.540  35.752  58.927  1.00  4.12
ATOM    967  CA  LEU   209       3.509  36.787  58.580  1.00  4.12
ATOM    968  C   LEU   209       4.647  36.804  59.588  1.00  4.12
ATOM    969  O   LEU   209       5.822  36.759  59.211  1.00  4.12
ATOM    970  CB  LEU   209       2.828  38.148  58.519  1.00  4.12
ATOM    971  N   PHE   210       4.294  36.854  60.869  1.00  2.96
ATOM    972  CA  PHE   210       5.280  36.855  61.939  1.00  2.96
ATOM    973  C   PHE   210       6.228  35.673  61.760  1.00  2.96
ATOM    974  O   PHE   210       7.451  35.814  61.876  1.00  2.96
ATOM    975  CB  PHE   210       4.575  36.734  63.288  1.00  2.96
ATOM    976  N   GLU   211       5.642  34.513  61.467  1.00  4.39
ATOM    977  CA  GLU   211       6.389  33.274  61.271  1.00  4.39
ATOM    978  C   GLU   211       7.402  33.315  60.129  1.00  4.39
ATOM    979  O   GLU   211       8.195  32.395  59.974  1.00  4.39
ATOM    980  CB  GLU   211       5.425  32.139  61.056  1.00  4.39
ATOM    981  N   HIS   212       7.370  34.378  59.329  1.00  4.18
ATOM    982  CA  HIS   212       8.302  34.518  58.221  1.00  4.18
ATOM    983  C   HIS   212       9.615  35.083  58.747  1.00  4.18
ATOM    984  O   HIS   212      10.639  35.084  58.054  1.00  4.18
ATOM    985  CB  HIS   212       7.725  35.456  57.161  1.00  4.18
ATOM    986  N   GLY   213       9.583  35.578  59.980  1.00  5.45
ATOM    987  CA  GLY   213      10.779  36.147  60.579  1.00  5.45
ATOM    988  C   GLY   213      11.668  35.031  61.083  1.00  5.45
ATOM    989  O   GLY   213      11.281  33.873  61.066  1.00  5.45
ATOM    990  N   LEU   214      12.866  35.386  61.520  1.00  4.57
ATOM    991  CA  LEU   214      13.800  34.410  62.054  1.00  4.57
ATOM    992  C   LEU   214      13.205  33.859  63.352  1.00  4.57
ATOM    993  O   LEU   214      12.518  34.584  64.073  1.00  4.57
ATOM    994  CB  LEU   214      15.128  35.080  62.332  1.00  4.57
ATOM    995  N   GLN   215      13.455  32.590  63.662  1.00  4.64
ATOM    996  CA  GLN   215      12.898  32.026  64.887  1.00  4.64
ATOM    997  C   GLN   215      13.531  32.688  66.092  1.00  4.64
ATOM    998  O   GLN   215      13.092  32.512  67.222  1.00  4.64
ATOM    999  CB  GLN   215      13.116  30.516  64.935  1.00  4.64
ATOM   1000  N   GLU   216       6.587  46.447  68.972  1.00  4.69
ATOM   1001  CA  GLU   216       5.383  47.184  68.589  1.00  4.69
ATOM   1002  C   GLU   216       5.295  48.442  69.420  1.00  4.69
ATOM   1003  O   GLU   216       5.338  48.384  70.641  1.00  4.69
ATOM   1004  CB  GLU   216       4.110  46.379  68.798  1.00  4.69
ATOM   1005  N   LEU   217       5.156  49.585  68.764  1.00  5.67
ATOM   1006  CA  LEU   217       5.099  50.832  69.499  1.00  5.67
ATOM   1007  C   LEU   217       3.860  51.643  69.091  1.00  5.67
ATOM   1008  O   LEU   217       3.544  52.661  69.690  1.00  5.67
ATOM   1009  CB  LEU   217       6.435  51.619  69.298  1.00  5.67
ATOM   1010  N   SER   218       3.159  51.172  68.069  1.00  3.69
ATOM   1011  CA  SER   218       1.941  51.826  67.655  1.00  3.69
ATOM   1012  C   SER   218       0.825  50.929  68.137  1.00  3.69
ATOM   1013  O   SER   218       1.060  49.880  68.747  1.00  3.69
ATOM   1014  CB  SER   218       1.919  52.033  66.132  1.00  3.69
ATOM   1015  N   GLY   219      -0.408  51.316  67.846  1.00  5.32
ATOM   1016  CA  GLY   219      -1.561  50.515  68.266  1.00  5.32
ATOM   1017  C   GLY   219      -1.417  48.975  68.126  1.00  5.32
ATOM   1018  O   GLY   219      -0.993  48.452  67.100  1.00  5.32
ATOM   1019  N   PHE   220      -1.766  48.264  69.195  1.00  4.05
ATOM   1020  CA  PHE   220      -1.673  46.806  69.263  1.00  4.05
ATOM   1021  C   PHE   220      -2.598  46.051  68.301  1.00  4.05
ATOM   1022  O   PHE   220      -2.210  45.037  67.725  1.00  4.05
ATOM   1023  CB  PHE   220      -1.950  46.341  70.704  1.00  4.05
ATOM   1024  N   MET   221      -3.822  46.544  68.148  1.00  4.85
ATOM   1025  CA  MET   221      -4.834  45.933  67.288  1.00  4.85
ATOM   1026  C   MET   221      -4.335  45.612  65.883  1.00  4.85
ATOM   1027  O   MET   221      -4.930  44.797  65.175  1.00  4.85
ATOM   1028  CB  MET   221      -6.057  46.847  67.196  1.00  4.85
ATOM   1029  N   VAL   222      -3.235  46.254  65.495  1.00  4.30
ATOM   1030  CA  VAL   222      -2.619  46.059  64.186  1.00  4.30
ATOM   1031  C   VAL   222      -2.099  44.640  64.052  1.00  4.30
ATOM   1032  O   VAL   222      -1.896  44.135  62.948  1.00  4.30
ATOM   1033  CB  VAL   222      -1.460  47.041  63.999  1.00  4.30
ATOM   1034  N   LYS   223      -1.874  44.002  65.190  1.00  4.49
ATOM   1035  CA  LYS   223      -1.389  42.633  65.224  1.00  4.49
ATOM   1036  C   LYS   223      -2.518  41.743  65.718  1.00  4.49
ATOM   1037  O   LYS   223      -3.230  42.099  66.655  1.00  4.49
ATOM   1038  CB  LYS   223      -0.227  42.517  66.197  1.00  4.49
ATOM   1039  N   ASP   224      -2.692  40.590  65.089  1.00  5.00
ATOM   1040  CA  ASP   224      -3.725  39.670  65.521  1.00  5.00
ATOM   1041  C   ASP   224      -3.233  39.108  66.846  1.00  5.00
ATOM   1042  O   ASP   224      -2.268  38.333  66.881  1.00  5.00
ATOM   1043  CB  ASP   224      -3.904  38.568  64.464  1.00  5.00
ATOM   1044  N   ASN   225      -3.890  39.518  67.931  1.00  4.50
ATOM   1045  CA  ASN   225      -3.507  39.077  69.264  1.00  4.50
ATOM   1046  C   ASN   225      -3.245  37.569  69.365  1.00  4.50
ATOM   1047  O   ASN   225      -2.226  37.144  69.914  1.00  4.50
ATOM   1048  CB  ASN   225      -4.563  39.488  70.279  1.00  4.50
TER
END
