
#######################################################
#                                                     #
#                        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   18 (  179),  selected   18 , name T0386TS083_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS083_2-D2.T0386_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219          3.819
LGA    P     220      P     220          5.187
LGA    E     221      E     221          5.337
LGA    -       -      K     222           -
LGA    K     222      I     223          2.887
LGA    I     223      R     224          2.919
LGA    R     224      L     225          1.936
LGA    L     225      L     226          0.590
LGA    L     226      K     227          1.259
LGA    K     227      E     228          0.816
LGA    E     228      F     229          0.720
LGA    F     229      M     230          0.728
LGA    M     230      H     231          0.344
LGA    H     231      T     232          0.344
LGA    T     232      M     233          1.586
LGA    M     233      K     234          2.314
LGA    K     234      N     235          3.171
LGA    N     235      T     236          1.803
LGA    T     236      G     237          3.884
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    -       -      V     240           -
LGA    -       -      N     241           -
LGA    -       -      D     242           -
LGA    -       -      R     243           -
LGA    -       -      P     244           -
LGA    -       -      V     245           -
LGA    -       -      M     246           -
LGA    -       -      V     247           -
LGA    -       -      A     248           -
LGA    -       -      K     249           -
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    -       -      Y     254           -
LGA    -       -      T     255           -
LGA    -       -      G     256           -
LGA    -       -      T     257           -
LGA    -       -      Y     258           -
LGA    -       -      R     259           -
LGA    -       -      G     260           -
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      G     265           -
LGA    -       -      F     266           -
LGA    -       -      A     267           -
LGA    -       -      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    -       -      G     277           -
LGA    -       -      N     278           -
LGA    -       -      I     279           -
LGA    -       -      D     280           -
LGA    -       -      H     281           -
LGA    -       -      L     282           -
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      Q     286           -
LGA    -       -      L     287           -
LGA    -       -      K     288           -
LGA    -       -      I     289           -
LGA    -       -      L     290           -
LGA    -       -      K     291           -
LGA    -       -      P     292           -
LGA    -       -      G     293           -
LGA    -       -      D     294           -
LGA    -       -      K     295           -
LGA    -       -      I     296           -
LGA    -       -      T     297           -
LGA    -       -      F     298           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   18   81    5.0     18    2.69    22.22     18.145     0.644

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.361664 * X  +   0.163015 * Y  +  -0.917946 * Z  +  -6.719537
  Y_new =  -0.286708 * X  +   0.917434 * Y  +   0.275885 * Z  +  11.882388
  Z_new =   0.887129 * X  +   0.362961 * Y  +  -0.285066 * Z  +  59.461266 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.236565   -0.905028  [ DEG:   128.1457    -51.8543 ]
  Theta =  -1.091086   -2.050507  [ DEG:   -62.5146   -117.4854 ]
  Phi   =  -2.471290    0.670302  [ DEG:  -141.5945     38.4055 ]
 
# 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: T0386TS083_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS083_2-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18   81   5.0   18   2.69   22.22  18.145
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS083_2-D2
PFRMAT TS
TARGET T0386
MODEL 2
PARENT 2G03_A
ATOM   1197  H   ASN   219       5.830  56.912  71.494  1.00  1.00              
ATOM   1198  N   ASN   219       6.262  57.601  71.968  1.00  6.04              
ATOM   1199  CA  ASN   219       5.690  58.036  73.267  1.00  3.75              
ATOM   1200  CB  ASN   219       6.600  57.601  74.421  1.00  1.14              
ATOM   1201  C   ASN   219       5.384  59.528  73.336  1.00  2.49              
ATOM   1202  O   ASN   219       5.918  60.248  74.182  1.00  1.00              
ATOM   1203  CG  ASN   219       5.894  57.608  75.763  1.00  1.16              
ATOM   1204  ND2 ASN   219       6.521  57.004  76.766  1.00  1.38              
ATOM   1205 HD21 ASN   219       7.359  56.608  76.600  1.00  1.00              
ATOM   1206 HD22 ASN   219       6.121  56.986  77.619  1.00  1.00              
ATOM   1207  OD1 ASN   219       4.775  58.111  75.890  1.00  2.49              
ATOM   1208  N   PRO   220       4.537  60.013  72.431  1.00  2.78              
ATOM   1209  CA  PRO   220       4.164  61.425  72.367  1.00  2.20              
ATOM   1210  CB  PRO   220       2.960  61.436  71.426  1.00  1.00              
ATOM   1211  C   PRO   220       3.844  62.154  73.671  1.00  2.61              
ATOM   1212  O   PRO   220       4.272  63.298  73.841  1.00  1.75              
ATOM   1213  CG  PRO   220       3.240  60.293  70.500  1.00  1.00              
ATOM   1214  CD  PRO   220       3.835  59.229  71.394  1.00  1.00              
ATOM   1215  H   GLU   221       2.804  60.671  74.458  1.00  1.00              
ATOM   1216  N   GLU   221       3.075  61.568  74.579  1.00  4.76              
ATOM   1217  CA  GLU   221       2.669  62.306  75.773  1.00  2.66              
ATOM   1218  CB  GLU   221       1.214  61.986  76.131  1.00  1.00              
ATOM   1219  C   GLU   221       3.559  62.133  77.001  1.00  2.29              
ATOM   1220  O   GLU   221       3.229  62.654  78.068  1.00  1.94              
ATOM   1221  CG  GLU   221       0.211  62.425  75.076  1.00  1.00              
ATOM   1222  CD  GLU   221      -1.219  62.043  75.415  1.00  1.00              
ATOM   1223  OE1 GLU   221      -1.434  61.396  76.464  1.00  1.00              
ATOM   1224  OE2 GLU   221      -2.134  62.396  74.636  1.00  1.00              
ATOM   1225  H   LYS   222       4.930  61.067  76.047  1.00  1.00              
ATOM   1226  N   LYS   222       4.671  61.418  76.892  1.00  1.67              
ATOM   1227  CA  LYS   222       5.514  61.181  78.062  1.00  1.05              
ATOM   1228  CB  LYS   222       6.711  60.308  77.676  1.00  1.00              
ATOM   1229  C   LYS   222       6.035  62.489  78.664  1.00  1.00              
ATOM   1230  O   LYS   222       6.623  63.315  77.959  1.00  1.00              
ATOM   1231  CG  LYS   222       7.627  59.969  78.841  1.00  1.00              
ATOM   1232  CD  LYS   222       8.782  59.080  78.401  1.00  1.00              
ATOM   1233  CE  LYS   222       9.706  58.743  79.564  1.00  1.00              
ATOM   1234  NZ  LYS   222      10.837  57.869  79.137  1.00  1.56              
ATOM   1235  H   ILE   223       5.557  61.924  80.494  1.00  1.00              
ATOM   1236  N   ILE   223       5.899  62.635  79.981  1.00  2.30              
ATOM   1237  CA  ILE   223       6.274  63.877  80.658  1.00  1.00              
ATOM   1238  CB  ILE   223       5.976  63.791  82.173  1.00  1.00              
ATOM   1239  C   ILE   223       7.755  64.162  80.441  1.00  1.00              
ATOM   1240  O   ILE   223       8.132  65.289  80.111  1.00  1.00              
ATOM   1241  CG1 ILE   223       4.466  63.698  82.417  1.00  2.49              
ATOM   1242  CD1 ILE   223       4.094  63.388  83.857  1.00  1.96              
ATOM   1243  CG2 ILE   223       6.576  64.989  82.908  1.00  1.59              
ATOM   1244  H   ARG   224       8.260  62.286  80.826  1.00  1.00              
ATOM   1245  N   ARG   224       8.597  63.148  80.605  1.00  2.65              
ATOM   1246  CA  ARG   224      10.034  63.349  80.466  1.00  1.00              
ATOM   1247  CB  ARG   224      10.793  62.080  80.867  1.00  1.00              
ATOM   1248  C   ARG   224      10.411  63.762  79.054  1.00  1.00              
ATOM   1249  O   ARG   224      11.202  64.689  78.880  1.00  1.00              
ATOM   1250  CG  ARG   224      10.707  61.765  82.354  1.00  1.00              
ATOM   1251  CD  ARG   224      11.469  60.495  82.716  1.00  1.00              
ATOM   1252  NE  ARG   224      11.377  60.207  84.145  1.00  1.00              
ATOM   1253  HE  ARG   224      10.877  60.812  84.681  1.00  1.00              
ATOM   1254  CZ  ARG   224      11.939  59.167  84.759  1.00  1.00              
ATOM   1255  NH1 ARG   224      12.677  58.297  84.076  1.00  1.00              
ATOM   1256  NH2 ARG   224      11.769  58.996  86.066  1.00  1.00              
ATOM   1257  H   LEU   225       9.226  62.420  78.191  1.00  1.00              
ATOM   1258  N   LEU   225       9.831  63.131  78.038  1.00  1.86              
ATOM   1259  CA  LEU   225      10.165  63.541  76.682  1.00  2.46              
ATOM   1260  CB  LEU   225       9.410  62.664  75.676  1.00  1.14              
ATOM   1261  C   LEU   225       9.719  64.981  76.535  1.00  1.38              
ATOM   1262  O   LEU   225      10.528  65.814  76.177  1.00  1.00              
ATOM   1263  CG  LEU   225       9.632  62.963  74.191  1.00  2.03              
ATOM   1264  CD1 LEU   225       9.366  61.712  73.366  1.00  1.00              
ATOM   1265  CD2 LEU   225       8.728  64.101  73.734  1.00  1.00              
ATOM   1266  H   LEU   226       7.931  64.659  77.321  1.00  1.00              
ATOM   1267  N   LEU   226       8.486  65.306  76.912  1.00  1.09              
ATOM   1268  CA  LEU   226       7.974  66.650  76.673  1.00  1.00              
ATOM   1269  CB  LEU   226       6.526  66.742  77.164  1.00  1.00              
ATOM   1270  C   LEU   226       8.809  67.722  77.374  1.00  1.00              
ATOM   1271  O   LEU   226       9.221  68.705  76.753  1.00  1.00              
ATOM   1272  CG  LEU   226       5.842  68.107  77.038  1.00  1.92              
ATOM   1273  CD1 LEU   226       5.732  68.506  75.573  1.00  1.30              
ATOM   1274  CD2 LEU   226       4.465  68.064  77.686  1.00  1.65              
ATOM   1275  H   LYS   227       8.820  66.737  79.085  1.00  1.00              
ATOM   1276  N   LYS   227       9.100  67.536  78.653  1.00  1.51              
ATOM   1277  CA  LYS   227       9.822  68.555  79.405  1.00  1.39              
ATOM   1278  CB  LYS   227       9.650  68.339  80.911  1.00  1.00              
ATOM   1279  C   LYS   227      11.299  68.673  79.063  1.00  1.18              
ATOM   1280  O   LYS   227      11.797  69.773  78.802  1.00  1.00              
ATOM   1281  CG  LYS   227      10.357  69.378  81.769  1.00  1.00              
ATOM   1282  CD  LYS   227      10.123  69.126  83.252  1.00  1.00              
ATOM   1283  CE  LYS   227      10.836  70.159  84.116  1.00  1.00              
ATOM   1284  NZ  LYS   227      10.607  69.918  85.570  1.00  1.00              
ATOM   1285  H   GLU   228      11.573  66.722  79.204  1.00  1.00              
ATOM   1286  N   GLU   228      11.997  67.547  79.020  1.00  1.00              
ATOM   1287  CA  GLU   228      13.406  67.574  78.668  1.00  1.00              
ATOM   1288  CB  GLU   228      14.012  66.170  78.688  1.00  1.00              
ATOM   1289  C   GLU   228      13.511  68.149  77.258  1.00  1.54              
ATOM   1290  O   GLU   228      14.462  68.876  76.937  1.00  1.00              
ATOM   1291  CG  GLU   228      14.115  65.538  80.067  1.00  1.00              
ATOM   1292  CD  GLU   228      14.673  64.127  80.017  1.00  1.00              
ATOM   1293  OE1 GLU   228      14.999  63.653  78.903  1.00  1.00              
ATOM   1294  OE2 GLU   228      14.795  63.491  81.088  1.00  1.30              
ATOM   1295  H   PHE   229      11.889  67.168  76.649  1.00  1.00              
ATOM   1296  N   PHE   229      12.556  67.791  76.392  1.00  5.37              
ATOM   1297  CA  PHE   229      12.562  68.331  75.038  1.00  6.21              
ATOM   1298  CB  PHE   229      11.585  67.700  74.033  1.00  5.65              
ATOM   1299  C   PHE   229      12.434  69.851  75.038  1.00  2.00              
ATOM   1300  O   PHE   229      13.227  70.538  74.382  1.00  1.00              
ATOM   1301  CG  PHE   229      10.554  68.621  73.438  1.00  3.45              
ATOM   1302  CD1 PHE   229      10.927  69.625  72.555  1.00  1.00              
ATOM   1303  CE1 PHE   229       9.977  70.488  72.017  1.00  1.00              
ATOM   1304  CZ  PHE   229       8.644  70.360  72.379  1.00  1.00              
ATOM   1305  CD2 PHE   229       9.205  68.447  73.723  1.00  1.00              
ATOM   1306  CE2 PHE   229       8.252  69.324  73.213  1.00  1.00              
ATOM   1307  H   MET   230      10.904  69.852  76.305  1.00  1.00              
ATOM   1308  N   MET   230      11.497  70.397  75.805  1.00  1.36              
ATOM   1309  CA  MET   230      11.342  71.847  75.839  1.00  1.00              
ATOM   1310  CB  MET   230      10.225  72.241  76.811  1.00  1.00              
ATOM   1311  C   MET   230      12.649  72.485  76.290  1.00  1.00              
ATOM   1312  O   MET   230      13.108  73.468  75.700  1.00  1.00              
ATOM   1313  CG  MET   230       8.825  71.889  76.331  1.00  1.00              
ATOM   1314  SD  MET   230       8.381  72.766  74.814  1.00  1.00              
ATOM   1315  CE  MET   230       8.286  74.444  75.417  1.00  1.00              
ATOM   1316  H   HIS   231      12.874  71.133  77.707  1.00  1.00              
ATOM   1317  N   HIS   231      13.276  71.886  77.294  1.00  1.00              
ATOM   1318  CA  HIS   231      14.547  72.391  77.795  1.00  1.00              
ATOM   1319  CB  HIS   231      15.022  71.505  78.953  1.00  1.00              
ATOM   1320  C   HIS   231      15.592  72.386  76.683  1.00  1.00              
ATOM   1321  O   HIS   231      16.257  73.400  76.446  1.00  1.00              
ATOM   1322  CG  HIS   231      16.345  71.918  79.520  1.00  1.00              
ATOM   1323  ND1 HIS   231      16.517  73.069  80.257  1.00  1.00              
ATOM   1324  HD1 HIS   231      15.833  73.685  80.499  1.00  1.00              
ATOM   1325  CE1 HIS   231      17.776  73.145  80.656  1.00  1.00              
ATOM   1326  NE2 HIS   231      18.429  72.098  80.181  1.00  1.00              
ATOM   1327  HE2 HIS   231      19.344  71.906  80.353  1.00  1.00              
ATOM   1328  CD2 HIS   231      17.552  71.299  79.492  1.00  1.00              
ATOM   1329  H   THR   232      15.201  70.508  76.164  1.00  1.00              
ATOM   1330  N   THR   232      15.707  71.274  75.962  1.00  1.00              
ATOM   1331  CA  THR   232      16.672  71.212  74.866  1.00  1.24              
ATOM   1332  CB  THR   232      16.895  69.808  74.290  1.00  1.00              
ATOM   1333  C   THR   232      16.343  72.210  73.758  1.00  1.00              
ATOM   1334  O   THR   232      17.247  72.830  73.182  1.00  1.00              
ATOM   1335  CG2 THR   232      18.085  69.894  73.341  1.00  1.00              
ATOM   1336  OG1 THR   232      17.263  68.941  75.371  1.00  1.00              
ATOM   1337  H   MET   233      14.403  71.782  73.799  1.00  1.00              
ATOM   1338  N   MET   233      15.063  72.341  73.410  1.00  1.10              
ATOM   1339  CA  MET   233      14.697  73.314  72.389  1.00  1.83              
ATOM   1340  CB  MET   233      13.252  73.222  71.901  1.00  2.05              
ATOM   1341  C   MET   233      15.092  74.734  72.788  1.00  1.00              
ATOM   1342  O   MET   233      15.695  75.463  71.994  1.00  1.00              
ATOM   1343  CG  MET   233      13.016  72.000  71.032  1.00  1.62              
ATOM   1344  SD  MET   233      14.180  71.907  69.652  1.00  1.44              
ATOM   1345  CE  MET   233      14.827  73.569  69.613  1.00  1.17              
ATOM   1346  H   LYS   234      14.359  74.549  74.619  1.00  1.00              
ATOM   1347  N   LYS   234      14.839  75.122  74.029  1.00  1.00              
ATOM   1348  CA  LYS   234      15.254  76.444  74.485  1.00  1.00              
ATOM   1349  CB  LYS   234      14.780  76.689  75.920  1.00  1.00              
ATOM   1350  C   LYS   234      16.770  76.598  74.407  1.00  1.00              
ATOM   1351  O   LYS   234      17.266  77.662  74.034  1.00  1.00              
ATOM   1352  CG  LYS   234      13.273  76.840  76.054  1.00  1.00              
ATOM   1353  CD  LYS   234      12.864  77.074  77.502  1.00  1.00              
ATOM   1354  CE  LYS   234      11.356  77.235  77.641  1.00  1.00              
ATOM   1355  NZ  LYS   234      10.950  77.459  79.059  1.00  1.00              
ATOM   1356  H   ASN   235      17.090  74.760  75.064  1.00  1.00              
ATOM   1357  N   ASN   235      17.509  75.546  74.748  1.00  1.00              
ATOM   1358  CA  ASN   235      18.968  75.609  74.698  1.00  1.00              
ATOM   1359  CB  ASN   235      19.622  74.344  75.262  1.00  1.00              
ATOM   1360  C   ASN   235      19.489  75.912  73.299  1.00  1.00              
ATOM   1361  O   ASN   235      20.449  76.672  73.148  1.00  1.76              
ATOM   1362  CG  ASN   235      19.531  74.263  76.774  1.00  1.00              
ATOM   1363  ND2 ASN   235      19.848  73.099  77.328  1.00  1.61              
ATOM   1364 HD21 ASN   235      20.110  72.389  76.768  1.00  1.00              
ATOM   1365 HD22 ASN   235      19.805  73.005  78.266  1.00  1.00              
ATOM   1366  OD1 ASN   235      19.231  75.255  77.443  1.00  1.65              
ATOM   1367  H   THR   236      18.164  74.737  72.419  1.00  1.00              
ATOM   1368  N   THR   236      18.887  75.318  72.273  1.00  1.00              
ATOM   1369  CA  THR   236      19.380  75.518  70.913  1.00  1.00              
ATOM   1370  CB  THR   236      18.511  74.733  69.914  1.00  1.00              
ATOM   1371  C   THR   236      19.363  76.990  70.534  1.00  1.00              
ATOM   1372  O   THR   236      20.247  77.385  69.747  1.00  1.00              
ATOM   1373  OXT THR   236      18.306  77.620  70.742  1.00  1.00              
ATOM   1374  CG2 THR   236      19.067  74.895  68.505  1.00  1.00              
ATOM   1375  OG1 THR   236      18.522  73.348  70.283  1.00  1.00              
TER
END
