
#######################################################
#                                                     #
#                        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_4_2-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected  154 , name T0318_D1.pdb
# PARAMETERS: T0318TS193_4_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    R     142      A      42          3.257
LGA    E     143      Q      43          3.838
LGA    -       -      K      44           -
LGA    L     144      F      45          2.087
LGA    N     145      V      46          2.563
LGA    V     146      T      47          2.461
LGA    N     147      D      48          1.277
LGA    I     148      G      49          2.927
LGA    -       -      D      50           -
LGA    -       -      S      51           -
LGA    D     149      W      52          2.161
LGA    -       -      N      53           -
LGA    -       -      S      54           -
LGA    V     150      M      55          1.316
LGA    V     151      I      56          3.919
LGA    -       -      S      57           -
LGA    -       -      R      58           -
LGA    -       -      I      59           -
LGA    -       -      P      60           -
LGA    -       -      A      61           -
LGA    -       -      S      62           -
LGA    -       -      G      63           -
LGA    C     152      R      64          5.273
LGA    D     153      H      65          0.938
LGA    K     154      P      66          4.398
LGA    L     155      L      67          2.032
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    -       -      P      78           -
LGA    -       -      D      79           -
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    3.01     7.14      6.179     0.451

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.777576 * X  +   0.519231 * Y  +   0.354647 * Z  +  43.385662
  Y_new =   0.551439 * X  +   0.292088 * Y  +   0.781409 * Z  +  47.502975
  Z_new =   0.302144 * X  +   0.803171 * Y  +  -0.513445 * Z  +  23.467854 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.139593   -1.002000  [ DEG:   122.5896    -57.4104 ]
  Theta =  -0.306941   -2.834652  [ DEG:   -17.5864   -162.4136 ]
  Phi   =   2.524734   -0.616859  [ DEG:   144.6566    -35.3434 ]
 
# 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_4_2-D1                             
REMARK     2: T0318_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS193_4_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   3.01    7.14   6.179
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS193_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0318
PARENT N/A
ATOM   1097  N   ARG   142      45.923  42.958  24.341  1.00  0.00
ATOM   1098  CA  ARG   142      44.467  42.923  24.408  1.00  0.00
ATOM   1099  C   ARG   142      43.987  42.646  25.827  1.00  0.00
ATOM   1100  O   ARG   142      43.004  43.228  26.286  1.00  0.00
ATOM   1101  CB  ARG   142      43.914  41.825  23.498  1.00  0.00
ATOM   1102  CG  ARG   142      42.397  41.742  23.477  1.00  0.00
ATOM   1103  CD  ARG   142      41.914  40.710  22.469  1.00  0.00
ATOM   1104  NE  ARG   142      40.458  40.589  22.466  1.00  0.00
ATOM   1105  CZ  ARG   142      39.782  39.724  21.716  1.00  0.00
ATOM   1106  NH1 ARG   142      38.459  39.684  21.779  1.00  0.00
ATOM   1107  NH2 ARG   142      40.433  38.901  20.904  1.00  0.00
ATOM   1108  N   GLU   143      44.689  41.755  26.520  1.00  0.00
ATOM   1109  CA  GLU   143      44.340  41.404  27.892  1.00  0.00
ATOM   1110  C   GLU   143      44.622  42.558  28.844  1.00  0.00
ATOM   1111  O   GLU   143      43.823  42.850  29.734  1.00  0.00
ATOM   1112  CB  GLU   143      45.152  40.193  28.358  1.00  0.00
ATOM   1113  CG  GLU   143      44.901  38.930  27.552  1.00  0.00
ATOM   1114  CD  GLU   143      45.821  37.792  27.952  1.00  0.00
ATOM   1115  OE1 GLU   143      46.671  38.001  28.842  1.00  0.00
ATOM   1116  OE2 GLU   143      45.690  36.692  27.374  1.00  0.00
ATOM   1117  N   LEU   144      45.184  44.639  29.841  1.00  0.00
ATOM   1118  CA  LEU   144      46.401  43.867  29.620  1.00  0.00
ATOM   1119  C   LEU   144      46.965  43.340  30.934  1.00  0.00
ATOM   1120  O   LEU   144      47.255  44.111  31.849  1.00  0.00
ATOM   1121  CB  LEU   144      47.473  44.734  28.958  1.00  0.00
ATOM   1122  CG  LEU   144      48.774  44.028  28.572  1.00  0.00
ATOM   1123  CD1 LEU   144      48.518  42.976  27.503  1.00  0.00
ATOM   1124  CD2 LEU   144      49.785  45.024  28.025  1.00  0.00
ATOM   1125  N   ASN   145      47.117  42.023  31.022  1.00  0.00
ATOM   1126  CA  ASN   145      47.628  41.389  32.231  1.00  0.00
ATOM   1127  C   ASN   145      48.644  40.305  31.897  1.00  0.00
ATOM   1128  O   ASN   145      48.654  39.769  30.789  1.00  0.00
ATOM   1129  CB  ASN   145      46.487  40.744  33.020  1.00  0.00
ATOM   1130  CG  ASN   145      45.504  41.763  33.563  1.00  0.00
ATOM   1131  OD1 ASN   145      44.463  42.019  32.957  1.00  0.00
ATOM   1132  ND2 ASN   145      45.833  42.349  34.708  1.00  0.00
ATOM   1133  N   VAL   146      49.498  39.984  32.864  1.00  0.00
ATOM   1134  CA  VAL   146      50.489  38.928  32.691  1.00  0.00
ATOM   1135  C   VAL   146      49.895  37.560  32.999  1.00  0.00
ATOM   1136  O   VAL   146      49.415  37.315  34.106  1.00  0.00
ATOM   1137  CB  VAL   146      51.698  39.130  33.623  1.00  0.00
ATOM   1138  CG1 VAL   146      52.720  38.023  33.417  1.00  0.00
ATOM   1139  CG2 VAL   146      52.371  40.464  33.341  1.00  0.00
ATOM   1140  N   ASN   147      48.106  35.699  33.248  1.00  0.00
ATOM   1141  CA  ASN   147      48.368  36.068  31.862  1.00  0.00
ATOM   1142  C   ASN   147      47.071  36.232  31.081  1.00  0.00
ATOM   1143  O   ASN   147      46.126  35.462  31.257  1.00  0.00
ATOM   1144  CB  ASN   147      49.206  34.991  31.169  1.00  0.00
ATOM   1145  CG  ASN   147      49.717  35.433  29.812  1.00  0.00
ATOM   1146  OD1 ASN   147      49.849  36.628  29.547  1.00  0.00
ATOM   1147  ND2 ASN   147      50.005  34.467  28.948  1.00  0.00
ATOM   1148  N   ILE   148      46.283  36.876  33.000  1.00  0.00
ATOM   1149  CA  ILE   148      44.841  37.028  33.151  1.00  0.00
ATOM   1150  C   ILE   148      44.475  38.454  33.543  1.00  0.00
ATOM   1151  O   ILE   148      45.334  39.234  33.956  1.00  0.00
ATOM   1152  CB  ILE   148      44.285  36.091  34.239  1.00  0.00
ATOM   1153  CG1 ILE   148      44.921  36.410  35.594  1.00  0.00
ATOM   1154  CG2 ILE   148      44.585  34.639  33.896  1.00  0.00
ATOM   1155  CD1 ILE   148      44.286  35.675  36.754  1.00  0.00
ATOM   1156  N   ASP   149      43.196  38.787  33.415  1.00  0.00
ATOM   1157  CA  ASP   149      42.701  40.097  33.824  1.00  0.00
ATOM   1158  C   ASP   149      41.966  40.017  35.156  1.00  0.00
ATOM   1159  O   ASP   149      41.343  39.004  35.472  1.00  0.00
ATOM   1160  CB  ASP   149      41.731  40.654  32.779  1.00  0.00
ATOM   1161  CG  ASP   149      41.483  42.139  32.949  1.00  0.00
ATOM   1162  OD1 ASP   149      40.856  42.526  33.957  1.00  0.00
ATOM   1163  OD2 ASP   149      41.915  42.917  32.072  1.00  0.00
ATOM   1164  N   VAL   150      42.042  41.092  35.933  1.00  0.00
ATOM   1165  CA  VAL   150      41.400  41.138  37.241  1.00  0.00
ATOM   1166  C   VAL   150      40.353  42.244  37.302  1.00  0.00
ATOM   1167  O   VAL   150      40.652  43.409  37.037  1.00  0.00
ATOM   1168  CB  VAL   150      42.422  41.403  38.363  1.00  0.00
ATOM   1169  CG1 VAL   150      41.795  41.148  39.725  1.00  0.00
ATOM   1170  CG2 VAL   150      43.629  40.490  38.210  1.00  0.00
ATOM   1171  N   VAL   151      38.785  43.740  38.249  1.00  0.00
ATOM   1172  CA  VAL   151      37.922  43.014  37.324  1.00  0.00
ATOM   1173  C   VAL   151      37.848  43.714  35.975  1.00  0.00
ATOM   1174  O   VAL   151      37.680  43.071  34.938  1.00  0.00
ATOM   1175  CB  VAL   151      36.485  42.899  37.867  1.00  0.00
ATOM   1176  CG1 VAL   151      35.567  42.289  36.818  1.00  0.00
ATOM   1177  CG2 VAL   151      36.452  42.017  39.105  1.00  0.00
ATOM   1178  N   CYS   152      37.203  44.927  36.118  1.00  0.00
ATOM   1179  CA  CYS   152      36.204  45.407  35.172  1.00  0.00
ATOM   1180  C   CYS   152      36.860  46.080  33.972  1.00  0.00
ATOM   1181  O   CYS   152      37.767  46.898  34.127  1.00  0.00
ATOM   1182  CB  CYS   152      35.279  46.426  35.840  1.00  0.00
ATOM   1183  SG  CYS   152      34.241  45.745  37.153  1.00  0.00
ATOM   1184  N   ASP   153      36.933  48.961  33.794  1.00  0.00
ATOM   1185  CA  ASP   153      35.975  48.533  32.781  1.00  0.00
ATOM   1186  C   ASP   153      36.682  48.103  31.502  1.00  0.00
ATOM   1187  O   ASP   153      37.690  48.691  31.111  1.00  0.00
ATOM   1188  CB  ASP   153      35.017  49.674  32.432  1.00  0.00
ATOM   1189  CG  ASP   153      33.859  49.218  31.568  1.00  0.00
ATOM   1190  OD1 ASP   153      33.732  47.997  31.339  1.00  0.00
ATOM   1191  OD2 ASP   153      33.077  50.083  31.118  1.00  0.00
ATOM   1192  N   LYS   154      36.268  47.083  30.437  1.00  0.00
ATOM   1193  CA  LYS   154      37.275  46.029  30.409  1.00  0.00
ATOM   1194  C   LYS   154      37.884  45.886  29.022  1.00  0.00
ATOM   1195  O   LYS   154      38.623  44.939  28.752  1.00  0.00
ATOM   1196  CB  LYS   154      36.655  44.685  30.796  1.00  0.00
ATOM   1197  CG  LYS   154      37.650  43.538  30.861  1.00  0.00
ATOM   1198  CD  LYS   154      36.982  42.252  31.320  1.00  0.00
ATOM   1199  CE  LYS   154      37.975  41.103  31.376  1.00  0.00
ATOM   1200  NZ  LYS   154      37.335  39.837  31.827  1.00  0.00
ATOM   1201  N   LEU   155      40.365  45.349  30.115  1.00  0.00
ATOM   1202  CA  LEU   155      40.926  46.396  29.269  1.00  0.00
ATOM   1203  C   LEU   155      41.519  45.814  27.992  1.00  0.00
ATOM   1204  O   LEU   155      42.410  44.966  28.040  1.00  0.00
ATOM   1205  CB  LEU   155      42.036  47.145  30.010  1.00  0.00
ATOM   1206  CG  LEU   155      41.617  47.907  31.269  1.00  0.00
ATOM   1207  CD1 LEU   155      42.827  48.530  31.947  1.00  0.00
ATOM   1208  CD2 LEU   155      40.640  49.020  30.923  1.00  0.00
TER
END
