
#######################################################
#                                                     #
#                        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   17 (  137),  selected   17 , name T0385TS009_4_2
# Molecule2: number of CA atoms  142 ( 1050),  selected  142 , name T0385.pdb
# PARAMETERS: T0385TS009_4_2.T0385.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    A     141      S      17          3.148
LGA    T     142      E      18          1.597
LGA    R     143      G      19          1.744
LGA    W     144      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    -       -      H      34           -
LGA    -       -      A      35           -
LGA    -       -      T      36           -
LGA    -       -      I      37           -
LGA    -       -      Y      38           -
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      84           -
LGA    -       -      A      85           -
LGA    -       -      G      86           -
LGA    -       -      Y      87           -
LGA    -       -      Q      88           -
LGA    -       -      L      89           -
LGA    -       -      P      90           -
LGA    -       -      M      91           -
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    -       -      R     105           -
LGA    -       -      M     106           -
LGA    -       -      E     107           -
LGA    -       -      N     108           -
LGA    -       -      D     109           -
LGA    -       -      G     110           -
LGA    -       -      A     111           -
LGA    -       -      T     112           -
LGA    -       -      A     113           -
LGA    -       -      W     114           -
LGA    -       -      R     115           -
LGA    -       -      A     116           -
LGA    -       -      V     117           -
LGA    -       -      V     118           -
LGA    N     145      E     119           #
LGA    R     146      H     120          3.853
LGA    V     147      A     121          1.067
LGA    L     148      E     122          3.043
LGA    G     149      T     123          1.211
LGA    A     150      A     124          2.760
LGA    W     151      D     125          2.191
LGA    P     152      D     126          2.145
LGA    -       -      R     127           -
LGA    -       -      V     128           -
LGA    I     153      F     129          1.674
LGA    T     154      A     130          2.084
LGA    A     155      S     131          2.321
LGA    -       -      T     132           -
LGA    -       -      A     133           -
LGA    -       -      L     134           -
LGA    A     156      T     135          0.665
LGA    F     157      E     136          1.380
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           -
LGA    -       -      P     152           -
LGA    -       -      I     153           -
LGA    -       -      T     154           -
LGA    -       -      A     155           -
LGA    -       -      A     156           -
LGA    -       -      F     157           -
LGA    -       -      P     158           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   17  142    5.0     15    2.22     6.67      8.196     0.646

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.554900 * X  +   0.347753 * Y  +  -0.755748 * Z  + -15.497847
  Y_new =  -0.831903 * X  +   0.237254 * Y  +  -0.501645 * Z  +  32.339691
  Z_new =   0.004856 * X  +   0.907072 * Y  +   0.420949 * Z  +  46.795044 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.136300   -2.005292  [ DEG:    65.1052   -114.8948 ]
  Theta =  -0.004856   -3.136737  [ DEG:    -0.2782   -179.7218 ]
  Phi   =  -0.982546    2.159047  [ DEG:   -56.2957    123.7043 ]
 
# 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_4_2                                
REMARK     2: T0385.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0385TS009_4_2.T0385.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   17  142   5.0   15   2.22    6.67   8.196
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS009_4_2
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0385                                                                    
PARENT N/A                                                                      
ATOM   1021  N   ALA   141      20.304  15.508  45.942  1.00  0.00              
ATOM   1022  CA  ALA   141      20.767  16.881  46.102  1.00  0.00              
ATOM   1023  C   ALA   141      21.621  17.032  47.357  1.00  0.00              
ATOM   1024  O   ALA   141      21.330  16.435  48.393  1.00  0.00              
ATOM   1025  CB  ALA   141      21.554  17.322  44.877  1.00  0.00              
ATOM   1026  N   THR   142      22.675  17.836  47.256  1.00  0.00              
ATOM   1027  CA  THR   142      23.592  18.072  48.407  1.00  0.00              
ATOM   1028  C   THR   142      25.029  18.270  47.936  1.00  0.00              
ATOM   1029  O   THR   142      25.789  19.031  48.535  1.00  0.00              
ATOM   1030  CB  THR   142      23.159  19.299  49.231  1.00  0.00              
ATOM   1031  OG1 THR   142      21.961  19.854  48.675  1.00  0.00              
ATOM   1032  CG2 THR   142      22.905  18.906  50.679  1.00  0.00              
ATOM   1033  N   ARG   143      25.393  17.581  46.861  1.00  0.00              
ATOM   1034  CA  ARG   143      26.739  17.678  46.307  1.00  0.00              
ATOM   1035  C   ARG   143      27.176  19.133  46.174  1.00  0.00              
ATOM   1036  O   ARG   143      27.667  19.550  45.125  1.00  0.00              
ATOM   1037  CB  ARG   143      27.734  16.909  47.178  1.00  0.00              
ATOM   1038  CG  ARG   143      28.340  15.692  46.498  1.00  0.00              
ATOM   1039  CD  ARG   143      29.608  15.239  47.206  1.00  0.00              
ATOM   1040  NE  ARG   143      30.351  14.257  46.422  1.00  0.00              
ATOM   1041  CZ  ARG   143      31.246  14.568  45.489  1.00  0.00              
ATOM   1042  NH1 ARG   143      31.510  15.839  45.222  1.00  0.00              
ATOM   1043  NH2 ARG   143      31.873  13.606  44.826  1.00  0.00              
ATOM   1044  N   TRP   144      26.992  19.902  47.243  1.00  0.00              
ATOM   1045  CA  TRP   144      27.365  21.311  47.247  1.00  0.00              
ATOM   1046  C   TRP   144      27.132  21.948  45.881  1.00  0.00              
ATOM   1047  O   TRP   144      28.080  22.302  45.179  1.00  0.00              
ATOM   1048  CB  TRP   144      26.585  22.069  48.322  1.00  0.00              
ATOM   1049  CG  TRP   144      27.458  22.698  49.365  1.00  0.00              
ATOM   1050  CD1 TRP   144      27.437  24.000  49.775  1.00  0.00              
ATOM   1051  CD2 TRP   144      28.481  22.051  50.132  1.00  0.00              
ATOM   1052  NE1 TRP   144      28.383  24.206  50.750  1.00  0.00              
ATOM   1053  CE2 TRP   144      29.037  23.023  50.987  1.00  0.00              
ATOM   1054  CE3 TRP   144      28.978  20.746  50.179  1.00  0.00              
ATOM   1055  CZ2 TRP   144      30.069  22.731  51.878  1.00  0.00              
ATOM   1056  CZ3 TRP   144      30.000  20.459  51.064  1.00  0.00              
ATOM   1057  CH2 TRP   144      30.537  21.446  51.903  1.00  0.00              
ATOM   1058  N   ASN   145      25.864  22.091  45.510  1.00  0.00              
ATOM   1059  CA  ASN   145      25.502  22.685  44.229  1.00  0.00              
ATOM   1060  C   ASN   145      25.787  21.728  43.078  1.00  0.00              
ATOM   1061  O   ASN   145      26.014  22.153  41.944  1.00  0.00              
ATOM   1062  CB  ASN   145      24.028  23.093  44.224  1.00  0.00              
ATOM   1063  CG  ASN   145      23.660  23.933  43.016  1.00  0.00              
ATOM   1064  OD1 ASN   145      22.981  24.952  43.141  1.00  0.00              
ATOM   1065  ND2 ASN   145      24.109  23.507  41.841  1.00  0.00              
ATOM   1066  N   ARG   146      25.772  20.432  43.375  1.00  0.00              
ATOM   1067  CA  ARG   146      26.027  19.411  42.365  1.00  0.00              
ATOM   1068  C   ARG   146      27.218  19.787  41.490  1.00  0.00              
ATOM   1069  O   ARG   146      28.290  19.191  41.593  1.00  0.00              
ATOM   1070  CB  ARG   146      26.269  18.052  43.026  1.00  0.00              
ATOM   1071  CG  ARG   146      24.998  17.290  43.361  1.00  0.00              
ATOM   1072  CD  ARG   146      25.295  16.068  44.215  1.00  0.00              
ATOM   1073  NE  ARG   146      24.155  15.691  45.045  1.00  0.00              
ATOM   1074  CZ  ARG   146      22.981  15.292  44.566  1.00  0.00              
ATOM   1075  NH1 ARG   146      22.790  15.220  43.256  1.00  0.00              
ATOM   1076  NH2 ARG   146      22.001  14.969  45.398  1.00  0.00              
ATOM   1077  N   VAL   147      27.023  20.780  40.628  1.00  0.00              
ATOM   1078  CA  VAL   147      28.103  21.248  39.713  1.00  0.00              
ATOM   1079  C   VAL   147      29.407  21.476  40.471  1.00  0.00              
ATOM   1080  O   VAL   147      30.212  22.330  40.097  1.00  0.00              
ATOM   1081  CB  VAL   147      28.352  20.243  38.574  1.00  0.00              
ATOM   1082  CG1 VAL   147      28.078  20.889  37.224  1.00  0.00              
ATOM   1083  CG2 VAL   147      27.496  19.000  38.762  1.00  0.00              
ATOM   1084  N   LEU   148      29.608  20.710  41.537  1.00  0.00              
ATOM   1085  CA  LEU   148      30.814  20.827  42.349  1.00  0.00              
ATOM   1086  C   LEU   148      31.441  22.210  42.207  1.00  0.00              
ATOM   1087  O   LEU   148      32.467  22.371  41.547  1.00  0.00              
ATOM   1088  CB  LEU   148      30.500  20.540  43.818  1.00  0.00              
ATOM   1089  CG  LEU   148      29.634  21.574  44.542  1.00  0.00              
ATOM   1090  CD1 LEU   148      29.385  22.782  43.653  1.00  0.00              
ATOM   1091  CD2 LEU   148      30.279  21.993  45.853  1.00  0.00              
ATOM   1092  N   GLY   149      30.817  23.204  42.831  1.00  0.00              
ATOM   1093  CA  GLY   149      31.332  24.559  42.760  1.00  0.00              
ATOM   1094  C   GLY   149      31.306  25.116  41.351  1.00  0.00              
ATOM   1095  O   GLY   149      32.323  25.581  40.837  1.00  0.00              
ATOM   1096  N   ALA   150      30.137  25.072  40.719  1.00  0.00              
ATOM   1097  CA  ALA   150      29.981  25.576  39.360  1.00  0.00              
ATOM   1098  C   ALA   150      30.859  24.805  38.381  1.00  0.00              
ATOM   1099  O   ALA   150      30.450  24.522  37.255  1.00  0.00              
ATOM   1100  CB  ALA   150      28.524  25.499  38.931  1.00  0.00              
ATOM   1101  N   TRP   151      32.067  24.465  38.818  1.00  0.00              
ATOM   1102  CA  TRP   151      33.005  23.726  37.982  1.00  0.00              
ATOM   1103  C   TRP   151      32.322  22.548  37.296  1.00  0.00              
ATOM   1104  O   TRP   151      32.979  21.661  36.751  1.00  0.00              
ATOM   1105  CB  TRP   151      33.635  24.650  36.937  1.00  0.00              
ATOM   1106  CG  TRP   151      34.682  25.563  37.499  1.00  0.00              
ATOM   1107  CD1 TRP   151      35.775  26.055  36.846  1.00  0.00              
ATOM   1108  CD2 TRP   151      34.734  26.095  38.828  1.00  0.00              
ATOM   1109  NE1 TRP   151      36.506  26.861  37.686  1.00  0.00              
ATOM   1110  CE2 TRP   151      35.887  26.901  38.909  1.00  0.00              
ATOM   1111  CE3 TRP   151      33.917  25.968  39.956  1.00  0.00              
ATOM   1112  CZ2 TRP   151      36.245  27.577  40.075  1.00  0.00              
ATOM   1113  CZ3 TRP   151      34.274  26.638  41.110  1.00  0.00              
ATOM   1114  CH2 TRP   151      35.428  27.435  41.164  1.00  0.00              
ATOM   1115  N   PRO   152      30.981  22.529  37.316  1.00  0.00              
ATOM   1116  CA  PRO   152      30.197  21.456  36.695  1.00  0.00              
ATOM   1117  C   PRO   152      30.571  21.257  35.230  1.00  0.00              
ATOM   1118  O   PRO   152      30.221  20.246  34.622  1.00  0.00              
ATOM   1119  CB  PRO   152      30.594  20.224  37.511  1.00  0.00              
ATOM   1120  CG  PRO   152      31.806  19.693  36.822  1.00  0.00              
ATOM   1121  CD  PRO   152      30.131  23.553  37.946  1.00  0.00              
ATOM   1122  N   ILE   153      31.283  22.229  34.669  1.00  0.00              
ATOM   1123  CA  ILE   153      31.714  22.162  33.243  1.00  0.00              
ATOM   1124  C   ILE   153      30.519  22.258  32.301  1.00  0.00              
ATOM   1125  O   ILE   153      29.521  21.557  32.473  1.00  0.00              
ATOM   1126  CB  ILE   153      32.715  23.280  32.902  1.00  0.00              
ATOM   1127  CG2 ILE   153      33.524  23.663  34.132  1.00  0.00              
ATOM   1128  CG1 ILE   153      31.983  24.497  32.336  1.00  0.00              
ATOM   1129  CD1 ILE   153      32.708  25.806  32.563  1.00  0.00              
ATOM   1130  N   THR   154      30.627  23.131  31.304  1.00  0.00              
ATOM   1131  CA  THR   154      29.532  23.325  30.311  1.00  0.00              
ATOM   1132  C   THR   154      29.394  24.793  29.921  1.00  0.00              
ATOM   1133  O   THR   154      29.933  25.675  30.589  1.00  0.00              
ATOM   1134  CB  THR   154      29.767  22.487  29.040  1.00  0.00              
ATOM   1135  OG1 THR   154      31.175  22.324  28.825  1.00  0.00              
ATOM   1136  CG2 THR   154      29.119  21.118  29.178  1.00  0.00              
ATOM   1137  N   ALA   155      28.669  25.047  28.837  1.00  0.00              
ATOM   1138  CA  ALA   155      28.459  26.408  28.358  1.00  0.00              
ATOM   1139  C   ALA   155      28.099  26.421  26.875  1.00  0.00              
ATOM   1140  O   ALA   155      28.714  27.135  26.085  1.00  0.00              
ATOM   1141  CB  ALA   155      27.369  27.093  29.168  1.00  0.00              
ATOM   1142  N   ALA   156      27.100  25.625  26.507  1.00  0.00              
ATOM   1143  CA  ALA   156      26.657  25.544  25.121  1.00  0.00              
ATOM   1144  C   ALA   156      27.840  25.601  24.160  1.00  0.00              
ATOM   1145  O   ALA   156      28.153  26.656  23.609  1.00  0.00              
ATOM   1146  CB  ALA   156      25.857  24.270  24.894  1.00  0.00              
ATOM   1147  N   PHE   157      28.491  24.460  23.963  1.00  0.00              
ATOM   1148  CA  PHE   157      29.639  24.378  23.069  1.00  0.00              
ATOM   1149  C   PHE   157      30.881  23.893  23.808  1.00  0.00              
ATOM   1150  O   PHE   157      30.940  23.919  25.038  1.00  0.00              
ATOM   1151  CB  PHE   157      29.335  23.451  21.889  1.00  0.00              
ATOM   1152  CG  PHE   157      30.545  22.753  21.338  1.00  0.00              
ATOM   1153  CD1 PHE   157      30.811  21.435  21.667  1.00  0.00              
ATOM   1154  CD2 PHE   157      31.418  23.413  20.492  1.00  0.00              
ATOM   1155  CE1 PHE   157      31.924  20.792  21.161  1.00  0.00              
ATOM   1156  CE2 PHE   157      32.533  22.771  19.986  1.00  0.00              
ATOM   1157  CZ  PHE   157      32.787  21.465  20.317  1.00  0.00              
TER
END
