
#######################################################
#                                                     #
#                        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   14 (  112),  selected   14 , name T0318TS193_1_2-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected  154 , name T0318_D1.pdb
# PARAMETERS: T0318TS193_1_2-D1.T0318_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    -       -      T       2           -
LGA    -       -      Q       3           -
LGA    -       -      V       4           -
LGA    -       -      L       5           -
LGA    -       -      V       6           -
LGA    -       -      R       7           -
LGA    -       -      N       8           -
LGA    -       -      G       9           -
LGA    -       -      I      10           -
LGA    -       -      Q      11           -
LGA    -       -      A      12           -
LGA    -       -      V      13           -
LGA    -       -      G      14           -
LGA    -       -      D      15           -
LGA    -       -      G      16           -
LGA    -       -      L      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      L      20           -
LGA    -       -      I      21           -
LGA    -       -      I      22           -
LGA    -       -      V      23           -
LGA    -       -      G      24           -
LGA    -       -      K      25           -
LGA    -       -      K      26           -
LGA    -       -      S      27           -
LGA    -       -      V      28           -
LGA    -       -      L      29           -
LGA    -       -      K      30           -
LGA    -       -      N      31           -
LGA    -       -      V      32           -
LGA    -       -      T      33           -
LGA    -       -      F      34           -
LGA    -       -      E      35           -
LGA    -       -      G      36           -
LGA    -       -      K      37           -
LGA    -       -      F      38           -
LGA    -       -      K      39           -
LGA    -       -      E      40           -
LGA    -       -      V      41           -
LGA    -       -      A      42           -
LGA    -       -      Q      43           -
LGA    -       -      K      44           -
LGA    -       -      F      45           -
LGA    -       -      V      46           -
LGA    -       -      T      47           -
LGA    R     142      D      48          2.735
LGA    E     143      G      49          0.707
LGA    L     144      D      50          4.242
LGA    -       -      S      51           -
LGA    -       -      W      52           -
LGA    N     145      N      53          1.630
LGA    -       -      S      54           -
LGA    -       -      M      55           -
LGA    V     146      I      56          0.864
LGA    N     147      S      57          2.818
LGA    I     148      R      58          3.647
LGA    D     149      I      59          2.972
LGA    V     150      P      60          3.798
LGA    V     151      A      61          5.183
LGA    C     152      S      62          4.110
LGA    D     153      G      63          3.708
LGA    -       -      R      64           -
LGA    -       -      H      65           -
LGA    -       -      P      66           -
LGA    -       -      L      67           -
LGA    -       -      H      68           -
LGA    -       -      Y      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      A      72           -
LGA    -       -      H      73           -
LGA    -       -      L      74           -
LGA    -       -      I      75           -
LGA    -       -      T      76           -
LGA    -       -      V      77           -
LGA    K     154      P      78          1.986
LGA    L     155      D      79          2.231
LGA    -       -      A      80           -
LGA    -       -      S      81           -
LGA    -       -      S      82           -
LGA    -       -      R      83           -
LGA    -       -      G      84           -
LGA    -       -      N      85           -
LGA    -       -      T      86           -
LGA    -       -      P      87           -
LGA    -       -      T      88           -
LGA    -       -      N      89           -
LGA    -       -      A      90           -
LGA    -       -      H      91           -
LGA    -       -      S      92           -
LGA    -       -      I      93           -
LGA    -       -      Y      94           -
LGA    -       -      K      95           -
LGA    -       -      E      96           -
LGA    -       -      L      97           -
LGA    -       -      K      98           -
LGA    -       -      P      99           -
LGA    -       -      I     100           -
LGA    -       -      N     101           -
LGA    -       -      Y     102           -
LGA    -       -      P     103           -
LGA    -       -      E     104           -
LGA    -       -      D     105           -
LGA    -       -      T     106           -
LGA    -       -      K     107           -
LGA    -       -      N     108           -
LGA    -       -      V     109           -
LGA    -       -      H     110           -
LGA    -       -      F     111           -
LGA    -       -      V     112           -
LGA    -       -      L     113           -
LGA    -       -      F     114           -
LGA    -       -      A     115           -
LGA    -       -      E     116           -
LGA    -       -      Y     117           -
LGA    -       -      P     118           -
LGA    -       -      D     119           -
LGA    -       -      V     120           -
LGA    -       -      L     121           -
LGA    -       -      S     122           -
LGA    -       -      H     123           -
LGA    -       -      V     124           -
LGA    -       -      A     125           -
LGA    -       -      A     126           -
LGA    -       -      I     127           -
LGA    -       -      A     128           -
LGA    -       -      R     129           -
LGA    -       -      T     130           -
LGA    -       -      F     131           -
LGA    -       -      C     132           -
LGA    -       -      K     133           -
LGA    -       -      F     134           -
LGA    -       -      S     135           -
LGA    -       -      M     136           -
LGA    -       -      K     137           -
LGA    -       -      T     138           -
LGA    -       -      S     139           -
LGA    -       -      G     140           -
LGA    -       -      I     141           -
LGA    -       -      R     142           -
LGA    -       -      E     143           -
LGA    -       -      L     144           -
LGA    -       -      N     145           -
LGA    -       -      V     146           -
LGA    -       -      N     147           -
LGA    -       -      I     148           -
LGA    -       -      D     149           -
LGA    -       -      V     150           -
LGA    -       -      V     151           -
LGA    -       -      C     152           -
LGA    -       -      D     153           -
LGA    -       -      K     154           -
LGA    -       -      L     155           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   14  154    5.0     14    3.17     7.14      5.623     0.429

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.251878 * X  +   0.950549 * Y  +  -0.181698 * Z  +  56.632008
  Y_new =   0.782387 * X  +   0.089507 * Y  +  -0.616327 * Z  +  29.870089
  Z_new =  -0.569586 * X  +  -0.297397 * Y  +  -0.766242 * Z  +  33.581875 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.771366    0.370226  [ DEG:  -158.7876     21.2124 ]
  Theta =   0.606002    2.535591  [ DEG:    34.7213    145.2787 ]
  Phi   =   1.882253   -1.259339  [ DEG:   107.8452    -72.1548 ]
 
# 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: T0318TS193_1_2-D1                             
REMARK     2: T0318_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS193_1_2-D1.T0318_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   14  154   5.0   14   3.17    7.14   5.623
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS193_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0318
PARENT N/A
ATOM   1097  N   ARG   142      50.215  33.316  32.366  1.00  0.00
ATOM   1098  CA  ARG   142      49.616  34.568  32.814  1.00  0.00
ATOM   1099  C   ARG   142      48.109  34.429  32.982  1.00  0.00
ATOM   1100  O   ARG   142      47.409  33.990  32.070  1.00  0.00
ATOM   1101  CB  ARG   142      49.879  35.681  31.797  1.00  0.00
ATOM   1102  CG  ARG   142      51.348  36.032  31.627  1.00  0.00
ATOM   1103  CD  ARG   142      51.874  36.804  32.826  1.00  0.00
ATOM   1104  NE  ARG   142      53.272  37.194  32.655  1.00  0.00
ATOM   1105  CZ  ARG   142      53.953  37.933  33.525  1.00  0.00
ATOM   1106  NH1 ARG   142      55.221  38.239  33.285  1.00  0.00
ATOM   1107  NH2 ARG   142      53.364  38.366  34.631  1.00  0.00
ATOM   1108  N   GLU   143      47.613  34.805  34.157  1.00  0.00
ATOM   1109  CA  GLU   143      46.185  34.737  34.443  1.00  0.00
ATOM   1110  C   GLU   143      45.714  35.975  35.195  1.00  0.00
ATOM   1111  O   GLU   143      46.242  36.307  36.256  1.00  0.00
ATOM   1112  CB  GLU   143      45.867  33.512  35.301  1.00  0.00
ATOM   1113  CG  GLU   143      44.395  33.357  35.644  1.00  0.00
ATOM   1114  CD  GLU   143      44.099  32.065  36.378  1.00  0.00
ATOM   1115  OE1 GLU   143      45.032  31.250  36.547  1.00  0.00
ATOM   1116  OE2 GLU   143      42.936  31.865  36.786  1.00  0.00
ATOM   1117  N   LEU   144      44.718  36.656  34.639  1.00  0.00
ATOM   1118  CA  LEU   144      44.176  37.862  35.255  1.00  0.00
ATOM   1119  C   LEU   144      43.001  37.534  36.167  1.00  0.00
ATOM   1120  O   LEU   144      41.988  36.996  35.720  1.00  0.00
ATOM   1121  CB  LEU   144      43.687  38.837  34.183  1.00  0.00
ATOM   1122  CG  LEU   144      43.065  40.141  34.687  1.00  0.00
ATOM   1123  CD1 LEU   144      44.097  40.980  35.423  1.00  0.00
ATOM   1124  CD2 LEU   144      42.526  40.963  33.526  1.00  0.00
ATOM   1125  N   ASN   145      43.142  37.861  37.446  1.00  0.00
ATOM   1126  CA  ASN   145      42.085  37.618  38.420  1.00  0.00
ATOM   1127  C   ASN   145      41.021  38.707  38.364  1.00  0.00
ATOM   1128  O   ASN   145      41.317  39.887  38.552  1.00  0.00
ATOM   1129  CB  ASN   145      42.659  37.589  39.838  1.00  0.00
ATOM   1130  CG  ASN   145      43.496  36.352  40.103  1.00  0.00
ATOM   1131  OD1 ASN   145      43.327  35.325  39.445  1.00  0.00
ATOM   1132  ND2 ASN   145      44.400  36.448  41.070  1.00  0.00
ATOM   1133  N   VAL   146      39.782  38.304  38.105  1.00  0.00
ATOM   1134  CA  VAL   146      38.670  39.244  38.035  1.00  0.00
ATOM   1135  C   VAL   146      38.112  39.543  39.420  1.00  0.00
ATOM   1136  O   VAL   146      37.666  38.640  40.128  1.00  0.00
ATOM   1137  CB  VAL   146      37.515  38.690  37.179  1.00  0.00
ATOM   1138  CG1 VAL   146      36.341  39.656  37.180  1.00  0.00
ATOM   1139  CG2 VAL   146      37.968  38.485  35.742  1.00  0.00
ATOM   1140  N   ASN   147      38.138  40.815  39.801  1.00  0.00
ATOM   1141  CA  ASN   147      37.633  41.236  41.103  1.00  0.00
ATOM   1142  C   ASN   147      36.214  40.733  41.331  1.00  0.00
ATOM   1143  O   ASN   147      35.405  40.684  40.403  1.00  0.00
ATOM   1144  CB  ASN   147      37.617  42.762  41.203  1.00  0.00
ATOM   1145  CG  ASN   147      37.388  43.250  42.621  1.00  0.00
ATOM   1146  OD1 ASN   147      37.688  42.548  43.586  1.00  0.00
ATOM   1147  ND2 ASN   147      36.855  44.459  42.750  1.00  0.00
ATOM   1148  N   ILE   148      35.951  41.071  42.551  1.00  0.00
ATOM   1149  CA  ILE   148      34.619  40.770  43.062  1.00  0.00
ATOM   1150  C   ILE   148      33.582  41.734  42.498  1.00  0.00
ATOM   1151  O   ILE   148      32.498  41.323  42.085  1.00  0.00
ATOM   1152  CB  ILE   148      34.566  40.878  44.597  1.00  0.00
ATOM   1153  CG1 ILE   148      35.435  39.792  45.238  1.00  0.00
ATOM   1154  CG2 ILE   148      33.139  40.707  45.094  1.00  0.00
ATOM   1155  CD1 ILE   148      35.636  39.972  46.727  1.00  0.00
ATOM   1156  N   ASP   149      33.921  43.018  42.484  1.00  0.00
ATOM   1157  CA  ASP   149      33.019  44.043  41.975  1.00  0.00
ATOM   1158  C   ASP   149      32.780  43.874  40.480  1.00  0.00
ATOM   1159  O   ASP   149      31.663  44.063  39.995  1.00  0.00
ATOM   1160  CB  ASP   149      33.606  45.437  42.206  1.00  0.00
ATOM   1161  CG  ASP   149      32.657  46.545  41.792  1.00  0.00
ATOM   1162  OD1 ASP   149      31.504  46.234  41.427  1.00  0.00
ATOM   1163  OD2 ASP   149      33.069  47.724  41.831  1.00  0.00
ATOM   1164  N   VAL   150      33.902  44.001  39.782  1.00  0.00
ATOM   1165  CA  VAL   150      33.877  44.084  38.326  1.00  0.00
ATOM   1166  C   VAL   150      33.188  42.870  37.717  1.00  0.00
ATOM   1167  O   VAL   150      32.434  42.993  36.750  1.00  0.00
ATOM   1168  CB  VAL   150      35.300  44.151  37.740  1.00  0.00
ATOM   1169  CG1 VAL   150      35.258  44.036  36.224  1.00  0.00
ATOM   1170  CG2 VAL   150      35.963  45.471  38.104  1.00  0.00
ATOM   1171  N   VAL   151      33.451  41.699  38.286  1.00  0.00
ATOM   1172  CA  VAL   151      32.873  40.457  37.786  1.00  0.00
ATOM   1173  C   VAL   151      31.363  40.431  37.991  1.00  0.00
ATOM   1174  O   VAL   151      30.614  40.023  37.103  1.00  0.00
ATOM   1175  CB  VAL   151      33.460  39.230  38.507  1.00  0.00
ATOM   1176  CG1 VAL   151      32.712  37.968  38.107  1.00  0.00
ATOM   1177  CG2 VAL   151      34.927  39.053  38.147  1.00  0.00
ATOM   1178  N   CYS   152      30.923  40.868  39.165  1.00  0.00
ATOM   1179  CA  CYS   152      29.502  40.885  39.492  1.00  0.00
ATOM   1180  C   CYS   152      28.787  42.028  38.784  1.00  0.00
ATOM   1181  O   CYS   152      27.558  42.097  38.780  1.00  0.00
ATOM   1182  CB  CYS   152      29.301  41.061  40.998  1.00  0.00
ATOM   1183  SG  CYS   152      29.848  39.655  41.995  1.00  0.00
ATOM   1184  N   ASP   153      29.411  43.295  38.343  1.00  0.00
ATOM   1185  CA  ASP   153      28.786  44.091  37.293  1.00  0.00
ATOM   1186  C   ASP   153      28.534  43.255  36.046  1.00  0.00
ATOM   1187  O   ASP   153      27.699  43.604  35.210  1.00  0.00
ATOM   1188  CB  ASP   153      29.685  45.266  36.904  1.00  0.00
ATOM   1189  CG  ASP   153      29.000  46.236  35.961  1.00  0.00
ATOM   1190  OD1 ASP   153      27.820  46.004  35.623  1.00  0.00
ATOM   1191  OD2 ASP   153      29.644  47.228  35.560  1.00  0.00
ATOM   1192  N   LYS   154      25.947  43.929  36.585  1.00  0.00
ATOM   1193  CA  LYS   154      25.447  42.567  36.453  1.00  0.00
ATOM   1194  C   LYS   154      25.138  42.231  34.999  1.00  0.00
ATOM   1195  O   LYS   154      25.082  41.062  34.620  1.00  0.00
ATOM   1196  CB  LYS   154      24.164  42.386  37.266  1.00  0.00
ATOM   1197  CG  LYS   154      24.363  42.476  38.769  1.00  0.00
ATOM   1198  CD  LYS   154      23.055  42.258  39.513  1.00  0.00
ATOM   1199  CE  LYS   154      23.251  42.367  41.017  1.00  0.00
ATOM   1200  NZ  LYS   154      21.975  42.171  41.758  1.00  0.00
ATOM   1201  N   LEU   155      23.039  40.240  35.084  1.00  0.00
ATOM   1202  CA  LEU   155      23.530  39.256  36.041  1.00  0.00
ATOM   1203  C   LEU   155      24.395  38.205  35.356  1.00  0.00
ATOM   1204  O   LEU   155      25.448  37.824  35.867  1.00  0.00
ATOM   1205  CB  LEU   155      22.362  38.540  36.721  1.00  0.00
ATOM   1206  CG  LEU   155      22.729  37.486  37.768  1.00  0.00
ATOM   1207  CD1 LEU   155      23.501  38.115  38.917  1.00  0.00
ATOM   1208  CD2 LEU   155      21.477  36.835  38.336  1.00  0.00
TER
END
