
#######################################################
#                                                     #
#                        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   11 (   94),  selected   11 , name T0385TS009_4_2-D1
# Molecule2: number of CA atoms  135 ( 1000),  selected  135 , name T0385_D1.pdb
# PARAMETERS: T0385TS009_4_2-D1.T0385_D1.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    -       -      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    -       -      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    A     141      V     104          1.210
LGA    T     142      R     105          0.767
LGA    R     143      M     106          1.921
LGA    -       -      E     107           -
LGA    W     144      N     108          3.729
LGA    N     145      D     109          3.680
LGA    R     146      G     110          2.391
LGA    V     147      A     111          2.488
LGA    L     148      T     112          4.293
LGA    G     149      A     113          2.130
LGA    A     150      W     114          2.569
LGA    -       -      R     115           -
LGA    -       -      A     116           -
LGA    W     151      V     117          3.238
LGA    -       -      V     118           -
LGA    -       -      E     119           -
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)   11  135    5.0     11    2.78     0.00      5.529     0.382

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.446150 * X  +  -0.888319 * Y  +  -0.108811 * Z  +  11.233484
  Y_new =  -0.894957 * X  +  -0.443029 * Y  +  -0.052693 * Z  +  50.240852
  Z_new =  -0.001398 * X  +   0.120890 * Y  +  -0.992665 * Z  +  -4.260844 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.020406   -0.121186  [ DEG:   173.0565     -6.9435 ]
  Theta =   0.001398    3.140195  [ DEG:     0.0801    179.9199 ]
  Phi   =  -1.108338    2.033255  [ DEG:   -63.5031    116.4969 ]
 
# 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-D1                             
REMARK     2: T0385_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0385TS009_4_2-D1.T0385_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   11  135   5.0   11   2.78    0.00   5.529
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS009_4_2-D1
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0385                                                                    
PARENT N/A                                                                      
ATOM   1021  N   ALA   141      21.582  17.529  15.454  1.00  0.00              
ATOM   1022  CA  ALA   141      20.731  18.092  16.496  1.00  0.00              
ATOM   1023  C   ALA   141      19.603  17.134  16.865  1.00  0.00              
ATOM   1024  O   ALA   141      19.032  16.470  16.000  1.00  0.00              
ATOM   1025  CB  ALA   141      21.556  18.430  17.729  1.00  0.00              
ATOM   1026  N   THR   142      19.287  17.068  18.154  1.00  0.00              
ATOM   1027  CA  THR   142      18.204  16.172  18.650  1.00  0.00              
ATOM   1028  C   THR   142      18.530  15.628  20.037  1.00  0.00              
ATOM   1029  O   THR   142      17.636  15.414  20.856  1.00  0.00              
ATOM   1030  CB  THR   142      16.848  16.901  18.701  1.00  0.00              
ATOM   1031  OG1 THR   142      17.003  18.240  18.217  1.00  0.00              
ATOM   1032  CG2 THR   142      15.821  16.174  17.846  1.00  0.00              
ATOM   1033  N   ARG   143      19.815  15.407  20.293  1.00  0.00              
ATOM   1034  CA  ARG   143      20.261  14.887  21.580  1.00  0.00              
ATOM   1035  C   ARG   143      19.617  15.646  22.735  1.00  0.00              
ATOM   1036  O   ARG   143      20.298  16.073  23.667  1.00  0.00              
ATOM   1037  CB  ARG   143      19.948  13.394  21.693  1.00  0.00              
ATOM   1038  CG  ARG   143      21.180  12.504  21.740  1.00  0.00              
ATOM   1039  CD  ARG   143      20.844  11.126  22.286  1.00  0.00              
ATOM   1040  NE  ARG   143      22.044  10.354  22.598  1.00  0.00              
ATOM   1041  CZ  ARG   143      22.691  10.414  23.758  1.00  0.00              
ATOM   1042  NH1 ARG   143      22.252  11.213  24.720  1.00  0.00              
ATOM   1043  NH2 ARG   143      23.774   9.674  23.951  1.00  0.00              
ATOM   1044  N   TRP   144      18.300  15.812  22.666  1.00  0.00              
ATOM   1045  CA  TRP   144      17.561  16.521  23.704  1.00  0.00              
ATOM   1046  C   TRP   144      18.380  17.672  24.276  1.00  0.00              
ATOM   1047  O   TRP   144      18.809  17.630  25.429  1.00  0.00              
ATOM   1048  CB  TRP   144      16.231  17.042  23.155  1.00  0.00              
ATOM   1049  CG  TRP   144      15.031  16.481  23.856  1.00  0.00              
ATOM   1050  CD1 TRP   144      13.997  17.184  24.401  1.00  0.00              
ATOM   1051  CD2 TRP   144      14.743  15.096  24.088  1.00  0.00              
ATOM   1052  NE1 TRP   144      13.080  16.326  24.958  1.00  0.00              
ATOM   1053  CE2 TRP   144      13.516  15.038  24.778  1.00  0.00              
ATOM   1054  CE3 TRP   144      15.402  13.904  23.778  1.00  0.00              
ATOM   1055  CZ2 TRP   144      12.934  13.831  25.165  1.00  0.00              
ATOM   1056  CZ3 TRP   144      14.823  12.709  24.163  1.00  0.00              
ATOM   1057  CH2 TRP   144      13.600  12.678  24.850  1.00  0.00              
ATOM   1058  N   ASN   145      18.593  18.701  23.463  1.00  0.00              
ATOM   1059  CA  ASN   145      19.360  19.867  23.885  1.00  0.00              
ATOM   1060  C   ASN   145      20.849  19.549  23.959  1.00  0.00              
ATOM   1061  O   ASN   145      21.593  20.178  24.713  1.00  0.00              
ATOM   1062  CB  ASN   145      19.119  21.041  22.934  1.00  0.00              
ATOM   1063  CG  ASN   145      19.694  22.342  23.459  1.00  0.00              
ATOM   1064  OD1 ASN   145      19.036  23.382  23.420  1.00  0.00              
ATOM   1065  ND2 ASN   145      20.927  22.288  23.951  1.00  0.00              
ATOM   1066  N   ARG   146      21.280  18.568  23.172  1.00  0.00              
ATOM   1067  CA  ARG   146      22.681  18.164  23.147  1.00  0.00              
ATOM   1068  C   ARG   146      23.252  18.062  24.557  1.00  0.00              
ATOM   1069  O   ARG   146      23.501  16.967  25.060  1.00  0.00              
ATOM   1070  CB  ARG   146      22.842  16.829  22.417  1.00  0.00              
ATOM   1071  CG  ARG   146      22.932  16.955  20.906  1.00  0.00              
ATOM   1072  CD  ARG   146      22.858  15.593  20.233  1.00  0.00              
ATOM   1073  NE  ARG   146      22.327  15.683  18.875  1.00  0.00              
ATOM   1074  CZ  ARG   146      22.920  16.340  17.883  1.00  0.00              
ATOM   1075  NH1 ARG   146      24.067  16.969  18.098  1.00  0.00              
ATOM   1076  NH2 ARG   146      22.363  16.367  16.681  1.00  0.00              
ATOM   1077  N   VAL   147      23.456  19.212  25.192  1.00  0.00              
ATOM   1078  CA  VAL   147      24.008  19.256  26.576  1.00  0.00              
ATOM   1079  C   VAL   147      23.271  18.287  27.495  1.00  0.00              
ATOM   1080  O   VAL   147      23.156  18.523  28.698  1.00  0.00              
ATOM   1081  CB  VAL   147      25.511  18.922  26.594  1.00  0.00              
ATOM   1082  CG1 VAL   147      26.312  20.098  27.134  1.00  0.00              
ATOM   1083  CG2 VAL   147      25.989  18.537  25.202  1.00  0.00              
ATOM   1084  N   LEU   148      22.775  17.196  26.921  1.00  0.00              
ATOM   1085  CA  LEU   148      22.048  16.190  27.687  1.00  0.00              
ATOM   1086  C   LEU   148      21.453  16.789  28.958  1.00  0.00              
ATOM   1087  O   LEU   148      21.949  16.552  30.058  1.00  0.00              
ATOM   1088  CB  LEU   148      20.945  15.561  26.834  1.00  0.00              
ATOM   1089  CG  LEU   148      19.767  16.469  26.472  1.00  0.00              
ATOM   1090  CD1 LEU   148      19.880  17.807  27.186  1.00  0.00              
ATOM   1091  CD2 LEU   148      18.446  15.792  26.799  1.00  0.00              
ATOM   1092  N   GLY   149      20.385  17.564  28.796  1.00  0.00              
ATOM   1093  CA  GLY   149      19.742  18.183  29.940  1.00  0.00              
ATOM   1094  C   GLY   149      20.644  19.173  30.648  1.00  0.00              
ATOM   1095  O   GLY   149      20.857  19.081  31.857  1.00  0.00              
ATOM   1096  N   ALA   150      21.180  20.129  29.894  1.00  0.00              
ATOM   1097  CA  ALA   150      22.066  21.142  30.455  1.00  0.00              
ATOM   1098  C   ALA   150      23.322  20.511  31.045  1.00  0.00              
ATOM   1099  O   ALA   150      24.419  21.055  30.919  1.00  0.00              
ATOM   1100  CB  ALA   150      22.440  22.164  29.394  1.00  0.00              
ATOM   1101  N   TRP   151      23.155  19.360  31.688  1.00  0.00              
ATOM   1102  CA  TRP   151      24.275  18.653  32.298  1.00  0.00              
ATOM   1103  C   TRP   151      25.464  18.579  31.346  1.00  0.00              
ATOM   1104  O   TRP   151      26.408  17.821  31.566  1.00  0.00              
ATOM   1105  CB  TRP   151      24.688  19.331  33.606  1.00  0.00              
ATOM   1106  CG  TRP   151      23.751  19.059  34.743  1.00  0.00              
ATOM   1107  CD1 TRP   151      24.069  18.998  36.070  1.00  0.00              
ATOM   1108  CD2 TRP   151      22.343  18.812  34.656  1.00  0.00              
ATOM   1109  NE1 TRP   151      22.946  18.728  36.814  1.00  0.00              
ATOM   1110  CE2 TRP   151      21.873  18.610  35.968  1.00  0.00              
ATOM   1111  CE3 TRP   151      21.435  18.743  33.595  1.00  0.00              
ATOM   1112  CZ2 TRP   151      20.534  18.342  36.249  1.00  0.00              
ATOM   1113  CZ3 TRP   151      20.108  18.476  33.875  1.00  0.00              
ATOM   1114  CH2 TRP   151      19.667  18.279  35.192  1.00  0.00              
TER
END
