
#######################################################
#                                                     #
#                        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   22 (  167),  selected   22 , name T0385TS009_3_2-D1
# Molecule2: number of CA atoms  135 ( 1000),  selected  135 , name T0385_D1.pdb
# PARAMETERS: T0385TS009_3_2-D1.T0385_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      S      17           -
LGA    -       -      E      18           -
LGA    -       -      G      19           -
LGA    -       -      S      20           -
LGA    -       -      A      21           -
LGA    -       -      D      22           -
LGA    -       -      N      23           -
LGA    -       -      A      24           -
LGA    -       -      A      25           -
LGA    -       -      L      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      A      29           -
LGA    -       -      L      30           -
LGA    -       -      A      31           -
LGA    -       -      V      32           -
LGA    -       -      E      33           -
LGA    A     130      H      34          3.174
LGA    S     131      A      35           #
LGA    -       -      T      36           -
LGA    -       -      I      37           -
LGA    T     132      Y      38          4.179
LGA    -       -      G      39           -
LGA    -       -      Y      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      V      43           -
LGA    -       -      S      44           -
LGA    -       -      A      45           -
LGA    -       -      L      46           -
LGA    -       -      S      47           -
LGA    -       -      P      48           -
LGA    -       -      P      49           -
LGA    -       -      G      50           -
LGA    -       -      V      51           -
LGA    -       -      N      52           -
LGA    -       -      F      53           -
LGA    -       -      L      54           -
LGA    -       -      V      55           -
LGA    -       -      A      56           -
LGA    -       -      D      57           -
LGA    -       -      A      58           -
LGA    -       -      L      59           -
LGA    -       -      K      60           -
LGA    -       -      Q      61           -
LGA    -       -      H      62           -
LGA    -       -      R      63           -
LGA    -       -      H      64           -
LGA    -       -      R      65           -
LGA    -       -      R      66           -
LGA    -       -      D      67           -
LGA    -       -      D      68           -
LGA    -       -      V      69           -
LGA    -       -      I      70           -
LGA    -       -      V      71           -
LGA    -       -      M      72           -
LGA    -       -      L      73           -
LGA    -       -      S      74           -
LGA    -       -      A      75           -
LGA    -       -      R      76           -
LGA    -       -      G      77           -
LGA    -       -      V      78           -
LGA    -       -      T      79           -
LGA    -       -      A      80           -
LGA    -       -      P      81           -
LGA    -       -      I      82           -
LGA    -       -      A      83           -
LGA    A     133      A      84          4.583
LGA    L     134      A      85          4.103
LGA    T     135      G      86          4.358
LGA    E     136      Y      87          2.973
LGA    S     137      Q      88           #
LGA    A     138      L      89          4.339
LGA    V     139      P      90          4.740
LGA    M     140      M      91          4.872
LGA    -       -      Q      92           -
LGA    -       -      V      93           -
LGA    -       -      S      94           -
LGA    -       -      S      95           -
LGA    -       -      A      96           -
LGA    -       -      A      97           -
LGA    -       -      D      98           -
LGA    -       -      A      99           -
LGA    -       -      A     100           -
LGA    -       -      R     101           -
LGA    -       -      L     102           -
LGA    -       -      A     103           -
LGA    -       -      V     104           -
LGA    A     141      R     105          3.184
LGA    T     142      M     106          4.278
LGA    R     143      E     107          4.470
LGA    W     144      N     108          2.704
LGA    N     145      D     109          2.853
LGA    -       -      G     110           -
LGA    -       -      A     111           -
LGA    R     146      T     112          1.787
LGA    V     147      A     113          3.825
LGA    L     148      W     114          3.213
LGA    G     149      R     115          1.855
LGA    -       -      A     116           -
LGA    -       -      V     117           -
LGA    A     150      V     118          2.767
LGA    W     151      E     119          1.721
LGA    -       -      H     120           -
LGA    -       -      A     121           -
LGA    -       -      E     122           -
LGA    -       -      T     123           -
LGA    -       -      A     124           -
LGA    -       -      D     125           -
LGA    -       -      D     126           -
LGA    -       -      R     127           -
LGA    -       -      V     128           -
LGA    -       -      F     129           -
LGA    -       -      A     130           -
LGA    -       -      S     131           -
LGA    -       -      T     132           -
LGA    -       -      A     133           -
LGA    -       -      L     134           -
LGA    -       -      T     135           -
LGA    -       -      E     136           -
LGA    -       -      S     137           -
LGA    -       -      A     138           -
LGA    -       -      V     139           -
LGA    -       -      M     140           -
LGA    -       -      A     141           -
LGA    -       -      T     142           -
LGA    -       -      R     143           -
LGA    -       -      W     144           -
LGA    -       -      N     145           -
LGA    -       -      R     146           -
LGA    -       -      V     147           -
LGA    -       -      L     148           -
LGA    -       -      G     149           -
LGA    -       -      A     150           -
LGA    -       -      W     151           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   22  135    5.0     20    3.64    10.00      8.217     0.535

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.981448 * X  +  -0.171889 * Y  +  -0.084941 * Z  +  94.495041
  Y_new =  -0.081095 * X  +  -0.029286 * Y  +   0.996276 * Z  +  46.489651
  Z_new =  -0.173736 * X  +   0.984681 * Y  +   0.014804 * Z  +  98.264343 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.555763   -1.585829  [ DEG:    89.1387    -90.8613 ]
  Theta =   0.174622    2.966970  [ DEG:    10.0051    169.9949 ]
  Phi   =  -3.059152    0.082441  [ DEG:  -175.2765      4.7235 ]
 
# 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: T0385TS009_3_2-D1                             
REMARK     2: T0385_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0385TS009_3_2-D1.T0385_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   22  135   5.0   20   3.64   10.00   8.217
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS009_3_2-D1
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0385                                                                    
PARENT N/A                                                                      
ATOM    948  N   ALA   130      27.742   3.976  24.030  1.00  0.00              
ATOM    949  CA  ALA   130      28.741   4.955  23.617  1.00  0.00              
ATOM    950  C   ALA   130      28.455   5.474  22.212  1.00  0.00              
ATOM    951  O   ALA   130      27.859   6.538  22.043  1.00  0.00              
ATOM    952  CB  ALA   130      28.791   6.111  24.604  1.00  0.00              
ATOM    953  N   SER   131      28.884   4.718  21.208  1.00  0.00              
ATOM    954  CA  SER   131      28.676   5.100  19.816  1.00  0.00              
ATOM    955  C   SER   131      27.704   4.150  19.122  1.00  0.00              
ATOM    956  O   SER   131      26.646   4.565  18.650  1.00  0.00              
ATOM    957  CB  SER   131      28.159   6.538  19.728  1.00  0.00              
ATOM    958  OG  SER   131      28.625   7.175  18.552  1.00  0.00              
ATOM    959  N   THR   132      28.071   2.875  19.065  1.00  0.00              
ATOM    960  CA  THR   132      27.215   1.842  18.415  1.00  0.00              
ATOM    961  C   THR   132      26.631   0.881  19.446  1.00  0.00              
ATOM    962  O   THR   132      25.797   0.037  19.120  1.00  0.00              
ATOM    963  CB  THR   132      26.066   2.482  17.616  1.00  0.00              
ATOM    964  OG1 THR   132      25.563   3.620  18.326  1.00  0.00              
ATOM    965  CG2 THR   132      26.552   2.921  16.243  1.00  0.00              
ATOM    966  N   ALA   133      27.075   1.017  20.692  1.00  0.00              
ATOM    967  CA  ALA   133      26.598   0.162  21.772  1.00  0.00              
ATOM    968  C   ALA   133      25.225  -0.419  21.450  1.00  0.00              
ATOM    969  O   ALA   133      25.035  -1.044  20.407  1.00  0.00              
ATOM    970  CB  ALA   133      27.591  -0.958  22.041  1.00  0.00              
ATOM    971  N   LEU   134      24.273  -0.208  22.353  1.00  0.00              
ATOM    972  CA  LEU   134      22.917  -0.711  22.167  1.00  0.00              
ATOM    973  C   LEU   134      22.008   0.361  21.574  1.00  0.00              
ATOM    974  O   LEU   134      22.245   0.846  20.467  1.00  0.00              
ATOM    975  CB  LEU   134      22.923  -1.950  21.271  1.00  0.00              
ATOM    976  CG  LEU   134      21.989  -3.090  21.684  1.00  0.00              
ATOM    977  CD1 LEU   134      21.930  -4.156  20.601  1.00  0.00              
ATOM    978  CD2 LEU   134      20.599  -2.560  21.999  1.00  0.00              
ATOM    979  N   THR   135      20.969   0.727  22.316  1.00  0.00              
ATOM    980  CA  THR   135      20.002   1.764  21.855  1.00  0.00              
ATOM    981  C   THR   135      20.484   3.166  22.216  1.00  0.00              
ATOM    982  O   THR   135      20.324   4.106  21.438  1.00  0.00              
ATOM    983  CB  THR   135      19.773   1.686  20.335  1.00  0.00              
ATOM    984  OG1 THR   135      20.542   0.607  19.788  1.00  0.00              
ATOM    985  CG2 THR   135      18.301   1.460  20.028  1.00  0.00              
ATOM    986  N   GLU   136      21.073   3.297  23.400  1.00  0.00              
ATOM    987  CA  GLU   136      21.578   4.582  23.866  1.00  0.00              
ATOM    988  C   GLU   136      22.531   5.203  22.848  1.00  0.00              
ATOM    989  O   GLU   136      22.336   6.337  22.412  1.00  0.00              
ATOM    990  CB  GLU   136      20.420   5.540  24.154  1.00  0.00              
ATOM    991  CG  GLU   136      19.536   5.113  25.314  1.00  0.00              
ATOM    992  CD  GLU   136      18.642   6.233  25.808  1.00  0.00              
ATOM    993  OE1 GLU   136      18.131   7.001  24.966  1.00  0.00              
ATOM    994  OE2 GLU   136      18.452   6.343  27.037  1.00  0.00              
ATOM    995  N   SER   137      23.560   4.450  22.474  1.00  0.00              
ATOM    996  CA  SER   137      24.544   4.923  21.508  1.00  0.00              
ATOM    997  C   SER   137      23.897   5.820  20.457  1.00  0.00              
ATOM    998  O   SER   137      24.252   6.992  20.324  1.00  0.00              
ATOM    999  CB  SER   137      25.673   5.674  22.217  1.00  0.00              
ATOM   1000  OG  SER   137      26.867   4.911  22.224  1.00  0.00              
ATOM   1001  N   ALA   138      22.948   5.263  19.714  1.00  0.00              
ATOM   1002  CA  ALA   138      22.250   6.010  18.674  1.00  0.00              
ATOM   1003  C   ALA   138      21.344   7.078  19.276  1.00  0.00              
ATOM   1004  O   ALA   138      21.136   8.137  18.683  1.00  0.00              
ATOM   1005  CB  ALA   138      23.249   6.647  17.719  1.00  0.00              
ATOM   1006  N   VAL   139      20.806   6.792  20.458  1.00  0.00              
ATOM   1007  CA  VAL   139      19.900   7.749  21.158  1.00  0.00              
ATOM   1008  C   VAL   139      18.748   8.179  20.256  1.00  0.00              
ATOM   1009  O   VAL   139      18.590   7.665  19.149  1.00  0.00              
ATOM   1010  CB  VAL   139      19.327   7.140  22.451  1.00  0.00              
ATOM   1011  CG1 VAL   139      19.652   8.023  23.646  1.00  0.00              
ATOM   1012  CG2 VAL   139      19.863   5.731  22.659  1.00  0.00              
ATOM   1013  N   MET   140      17.947   9.123  20.737  1.00  0.00              
ATOM   1014  CA  MET   140      16.809   9.625  19.976  1.00  0.00              
ATOM   1015  C   MET   140      16.821  11.147  19.904  1.00  0.00              
ATOM   1016  O   MET   140      15.774  11.790  19.970  1.00  0.00              
ATOM   1017  CB  MET   140      16.805   9.030  18.565  1.00  0.00              
ATOM   1018  CG  MET   140      15.617   9.454  17.718  1.00  0.00              
ATOM   1019  SD  MET   140      15.226   8.262  16.423  1.00  0.00              
ATOM   1020  CE  MET   140      13.821   9.055  15.645  1.00  0.00              
ATOM   1021  N   ALA   141      18.014  11.719  19.765  1.00  0.00              
ATOM   1022  CA  ALA   141      18.165  13.166  19.683  1.00  0.00              
ATOM   1023  C   ALA   141      17.795  13.835  21.004  1.00  0.00              
ATOM   1024  O   ALA   141      17.346  13.175  21.940  1.00  0.00              
ATOM   1025  CB  ALA   141      19.588  13.530  19.292  1.00  0.00              
ATOM   1026  N   THR   142      17.990  15.148  21.071  1.00  0.00              
ATOM   1027  CA  THR   142      17.671  15.925  22.302  1.00  0.00              
ATOM   1028  C   THR   142      18.079  17.387  22.154  1.00  0.00              
ATOM   1029  O   THR   142      18.544  18.012  23.107  1.00  0.00              
ATOM   1030  CB  THR   142      16.170  15.853  22.644  1.00  0.00              
ATOM   1031  OG1 THR   142      15.500  15.026  21.685  1.00  0.00              
ATOM   1032  CG2 THR   142      15.968  15.274  24.036  1.00  0.00              
ATOM   1033  N   ARG   143      17.900  17.927  20.952  1.00  0.00              
ATOM   1034  CA  ARG   143      18.249  19.315  20.676  1.00  0.00              
ATOM   1035  C   ARG   143      19.360  19.799  21.601  1.00  0.00              
ATOM   1036  O   ARG   143      19.103  20.210  22.733  1.00  0.00              
ATOM   1037  CB  ARG   143      18.671  19.481  19.215  1.00  0.00              
ATOM   1038  CG  ARG   143      17.802  20.443  18.423  1.00  0.00              
ATOM   1039  CD  ARG   143      18.322  20.618  17.004  1.00  0.00              
ATOM   1040  NE  ARG   143      17.851  21.860  16.399  1.00  0.00              
ATOM   1041  CZ  ARG   143      18.572  22.973  16.319  1.00  0.00              
ATOM   1042  NH1 ARG   143      19.804  23.001  16.810  1.00  0.00              
ATOM   1043  NH2 ARG   143      18.060  24.055  15.750  1.00  0.00              
ATOM   1044  N   TRP   144      20.595  19.747  21.113  1.00  0.00              
ATOM   1045  CA  TRP   144      21.747  20.180  21.895  1.00  0.00              
ATOM   1046  C   TRP   144      21.920  19.320  23.143  1.00  0.00              
ATOM   1047  O   TRP   144      22.265  19.824  24.212  1.00  0.00              
ATOM   1048  CB  TRP   144      23.018  20.136  21.045  1.00  0.00              
ATOM   1049  CG  TRP   144      24.116  21.013  21.564  1.00  0.00              
ATOM   1050  CD1 TRP   144      25.311  21.276  20.958  1.00  0.00              
ATOM   1051  CD2 TRP   144      24.122  21.744  22.796  1.00  0.00              
ATOM   1052  NE1 TRP   144      26.061  22.125  21.734  1.00  0.00              
ATOM   1053  CE2 TRP   144      25.352  22.427  22.870  1.00  0.00              
ATOM   1054  CE3 TRP   144      23.205  21.887  23.843  1.00  0.00              
ATOM   1055  CZ2 TRP   144      25.690  23.242  23.949  1.00  0.00              
ATOM   1056  CZ3 TRP   144      23.543  22.694  24.912  1.00  0.00              
ATOM   1057  CH2 TRP   144      24.777  23.364  24.960  1.00  0.00              
ATOM   1058  N   ASN   145      21.680  18.021  22.999  1.00  0.00              
ATOM   1059  CA  ASN   145      21.809  17.090  24.114  1.00  0.00              
ATOM   1060  C   ASN   145      21.203  17.668  25.388  1.00  0.00              
ATOM   1061  O   ASN   145      21.560  17.264  26.494  1.00  0.00              
ATOM   1062  CB  ASN   145      21.148  15.753  23.773  1.00  0.00              
ATOM   1063  CG  ASN   145      22.066  14.571  24.015  1.00  0.00              
ATOM   1064  OD1 ASN   145      21.716  13.429  23.715  1.00  0.00              
ATOM   1065  ND2 ASN   145      23.246  14.841  24.559  1.00  0.00              
ATOM   1066  N   ARG   146      20.284  18.613  25.224  1.00  0.00              
ATOM   1067  CA  ARG   146      19.626  19.247  26.360  1.00  0.00              
ATOM   1068  C   ARG   146      20.641  19.695  27.405  1.00  0.00              
ATOM   1069  O   ARG   146      20.273  20.202  28.465  1.00  0.00              
ATOM   1070  CB  ARG   146      18.787  20.440  25.895  1.00  0.00              
ATOM   1071  CG  ARG   146      17.453  20.059  25.277  1.00  0.00              
ATOM   1072  CD  ARG   146      16.724  21.278  24.740  1.00  0.00              
ATOM   1073  NE  ARG   146      15.877  20.950  23.597  1.00  0.00              
ATOM   1074  CZ  ARG   146      14.794  20.181  23.665  1.00  0.00              
ATOM   1075  NH1 ARG   146      14.425  19.660  24.826  1.00  0.00              
ATOM   1076  NH2 ARG   146      14.085  19.937  22.573  1.00  0.00              
ATOM   1077  N   VAL   147      21.920  19.503  27.101  1.00  0.00              
ATOM   1078  CA  VAL   147      23.015  19.895  28.035  1.00  0.00              
ATOM   1079  C   VAL   147      22.584  19.731  29.488  1.00  0.00              
ATOM   1080  O   VAL   147      22.894  20.569  30.335  1.00  0.00              
ATOM   1081  CB  VAL   147      24.288  19.064  27.791  1.00  0.00              
ATOM   1082  CG1 VAL   147      25.430  19.962  27.336  1.00  0.00              
ATOM   1083  CG2 VAL   147      24.024  17.970  26.769  1.00  0.00              
ATOM   1084  N   LEU   148      21.868  18.648  29.771  1.00  0.00              
ATOM   1085  CA  LEU   148      21.394  18.373  31.122  1.00  0.00              
ATOM   1086  C   LEU   148      21.078  19.665  31.869  1.00  0.00              
ATOM   1087  O   LEU   148      21.467  19.837  33.024  1.00  0.00              
ATOM   1088  CB  LEU   148      20.159  17.471  31.083  1.00  0.00              
ATOM   1089  CG  LEU   148      18.980  17.972  30.246  1.00  0.00              
ATOM   1090  CD1 LEU   148      19.099  19.466  29.989  1.00  0.00              
ATOM   1091  CD2 LEU   148      17.660  17.644  30.926  1.00  0.00              
ATOM   1092  N   GLY   149      20.368  20.569  31.201  1.00  0.00              
ATOM   1093  CA  GLY   149      20.013  21.833  31.821  1.00  0.00              
ATOM   1094  C   GLY   149      21.083  22.335  32.770  1.00  0.00              
ATOM   1095  O   GLY   149      20.789  23.041  33.735  1.00  0.00              
ATOM   1096  N   ALA   150      22.331  21.969  32.500  1.00  0.00              
ATOM   1097  CA  ALA   150      23.451  22.387  33.336  1.00  0.00              
ATOM   1098  C   ALA   150      23.001  22.643  34.770  1.00  0.00              
ATOM   1099  O   ALA   150      23.824  22.778  35.676  1.00  0.00              
ATOM   1100  CB  ALA   150      24.551  21.336  33.312  1.00  0.00              
ATOM   1101  N   TRP   151      21.688  22.711  34.971  1.00  0.00              
ATOM   1102  CA  TRP   151      21.126  22.952  36.294  1.00  0.00              
ATOM   1103  C   TRP   151      22.216  22.972  37.361  1.00  0.00              
ATOM   1104  O   TRP   151      21.935  22.925  38.558  1.00  0.00              
ATOM   1105  CB  TRP   151      20.347  24.268  36.313  1.00  0.00              
ATOM   1106  CG  TRP   151      18.896  24.101  36.645  1.00  0.00              
ATOM   1107  CD1 TRP   151      17.931  25.066  36.615  1.00  0.00              
ATOM   1108  CD2 TRP   151      18.243  22.893  37.058  1.00  0.00              
ATOM   1109  NE1 TRP   151      16.717  24.537  36.983  1.00  0.00              
ATOM   1110  CE2 TRP   151      16.883  23.203  37.259  1.00  0.00              
ATOM   1111  CE3 TRP   151      18.678  21.582  37.274  1.00  0.00              
ATOM   1112  CZ2 TRP   151      15.953  22.248  37.669  1.00  0.00              
ATOM   1113  CZ3 TRP   151      17.753  20.638  37.680  1.00  0.00              
ATOM   1114  CH2 TRP   151      16.404  20.974  37.874  1.00  0.00              
TER
END
