
#######################################################
#                                                     #
#                        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   15 (  124),  selected   15 , name T0386TS389_3-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS389_3-D2.T0386_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    P     220      N     219          0.821
LGA    R     224      P     220          0.231
LGA    L     225      E     221          0.998
LGA    L     226      K     222          0.430
LGA    K     227      I     223          0.534
LGA    E     228      R     224          0.560
LGA    F     229      L     225          0.398
LGA    M     230      L     226          0.280
LGA    H     231      K     227          0.304
LGA    T     232      E     228          0.231
LGA    M     233      F     229          0.053
LGA    K     234      M     230          0.559
LGA    N     235      H     231          0.702
LGA    T     236      T     232          0.451
LGA    G     237      M     233          0.979
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
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)   15   81    5.0     15    0.57     6.67     18.519     2.241

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.458591 * X  +   0.817785 * Y  +   0.347739 * Z  +  15.143411
  Y_new =  -0.525069 * X  +  -0.066343 * Y  +   0.848470 * Z  +  65.780678
  Z_new =   0.716936 * X  +  -0.571687 * Y  +   0.398970 * Z  +  81.249710 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.961494    2.180099  [ DEG:   -55.0896    124.9104 ]
  Theta =  -0.799397   -2.342196  [ DEG:   -45.8021   -134.1979 ]
  Phi   =  -0.852878    2.288714  [ DEG:   -48.8663    131.1337 ]
 
# 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: T0386TS389_3-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS389_3-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15   81   5.0   15   0.57    6.67  18.519
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS389_3-D2
PFRMAT TS
TARGET T0386
MODEL  3
PARENT N/A
ATOM   1175  N   PRO   220       2.730  54.941  76.537  1.00  0.00
ATOM   1176  CA  PRO   220       3.102  55.657  75.299  1.00  0.00
ATOM   1177  CB  PRO   220       2.191  55.048  74.231  1.00  0.00
ATOM   1178  CG  PRO   220       1.939  53.656  74.706  1.00  0.00
ATOM   1179  CD  PRO   220       1.775  53.747  76.196  1.00  0.00
ATOM   1180  O   PRO   220       3.756  57.994  75.206  1.00  0.00
ATOM   1181  C   PRO   220       2.859  57.172  75.458  1.00  0.00
ATOM   1182  N   ARG   224       1.649  57.524  75.895  1.00  0.00
ATOM   1183  CA  ARG   224       1.266  58.903  76.182  1.00  0.00
ATOM   1184  CB  ARG   224      -0.142  58.955  76.780  1.00  0.00
ATOM   1185  CG  ARG   224      -1.250  58.634  75.791  1.00  0.00
ATOM   1186  CD  ARG   224      -2.611  58.632  76.466  1.00  0.00
ATOM   1187  NE  ARG   224      -3.684  58.295  75.533  1.00  0.00
ATOM   1188  CZ  ARG   224      -4.958  58.153  75.883  1.00  0.00
ATOM   1189  NH1 ARG   224      -5.866  57.848  74.965  1.00  0.00
ATOM   1190  NH2 ARG   224      -5.323  58.318  77.146  1.00  0.00
ATOM   1191  O   ARG   224       2.640  60.700  77.004  1.00  0.00
ATOM   1192  C   ARG   224       2.230  59.558  77.183  1.00  0.00
ATOM   1193  N   LEU   225       2.593  58.807  78.217  1.00  0.00
ATOM   1194  CA  LEU   225       3.456  59.305  79.269  1.00  0.00
ATOM   1195  CB  LEU   225       3.534  58.298  80.418  1.00  0.00
ATOM   1196  CG  LEU   225       2.261  58.109  81.242  1.00  0.00
ATOM   1197  CD1 LEU   225       2.422  56.962  82.227  1.00  0.00
ATOM   1198  CD2 LEU   225       1.938  59.370  82.030  1.00  0.00
ATOM   1199  O   LEU   225       5.486  60.569  79.077  1.00  0.00
ATOM   1200  C   LEU   225       4.876  59.550  78.758  1.00  0.00
ATOM   1201  N   LEU   226       5.385  58.630  77.946  1.00  0.00
ATOM   1202  CA  LEU   226       6.717  58.765  77.366  1.00  0.00
ATOM   1203  CB  LEU   226       7.101  57.498  76.601  1.00  0.00
ATOM   1204  CG  LEU   226       8.472  57.503  75.923  1.00  0.00
ATOM   1205  CD1 LEU   226       9.578  57.674  76.952  1.00  0.00
ATOM   1206  CD2 LEU   226       8.710  56.195  75.181  1.00  0.00
ATOM   1207  O   LEU   226       7.721  60.739  76.442  1.00  0.00
ATOM   1208  C   LEU   226       6.780  59.950  76.388  1.00  0.00
ATOM   1209  N   LYS   227       5.778  60.077  75.521  1.00  0.00
ATOM   1210  CA  LYS   227       5.656  61.252  74.659  1.00  0.00
ATOM   1211  CB  LYS   227       4.345  61.206  73.871  1.00  0.00
ATOM   1212  CG  LYS   227       4.313  60.147  72.781  1.00  0.00
ATOM   1213  CD  LYS   227       2.995  60.173  72.025  1.00  0.00
ATOM   1214  CE  LYS   227       2.961  59.110  70.938  1.00  0.00
ATOM   1215  NZ  LYS   227       1.656  59.091  70.221  1.00  0.00
ATOM   1216  O   LYS   227       6.324  63.520  75.084  1.00  0.00
ATOM   1217  C   LYS   227       5.670  62.547  75.465  1.00  0.00
ATOM   1218  N   GLU   228       4.961  62.538  76.591  1.00  0.00
ATOM   1219  CA  GLU   228       4.927  63.655  77.498  1.00  0.00
ATOM   1220  CB  GLU   228       4.015  63.352  78.688  1.00  0.00
ATOM   1221  CG  GLU   228       2.535  63.316  78.342  1.00  0.00
ATOM   1222  CD  GLU   228       1.674  62.879  79.510  1.00  0.00
ATOM   1223  OE1 GLU   228       2.239  62.526  80.566  1.00  0.00
ATOM   1224  OE2 GLU   228       0.432  62.888  79.371  1.00  0.00
ATOM   1225  O   GLU   228       6.706  65.176  78.042  1.00  0.00
ATOM   1226  C   GLU   228       6.293  64.003  78.060  1.00  0.00
ATOM   1227  N   PHE   229       7.005  62.998  78.556  1.00  0.00
ATOM   1228  CA  PHE   229       8.290  63.246  79.194  1.00  0.00
ATOM   1229  CB  PHE   229       8.779  61.992  79.923  1.00  0.00
ATOM   1230  CG  PHE   229       8.056  61.721  81.212  1.00  0.00
ATOM   1231  CD1 PHE   229       7.079  60.743  81.282  1.00  0.00
ATOM   1232  CD2 PHE   229       8.354  62.443  82.356  1.00  0.00
ATOM   1233  CE1 PHE   229       6.414  60.492  82.468  1.00  0.00
ATOM   1234  CE2 PHE   229       7.687  62.193  83.541  1.00  0.00
ATOM   1235  CZ  PHE   229       6.723  61.223  83.599  1.00  0.00
ATOM   1236  O   PHE   229      10.198  64.457  78.465  1.00  0.00
ATOM   1237  C   PHE   229       9.345  63.637  78.174  1.00  0.00
ATOM   1238  N   MET   230       9.274  63.071  76.970  1.00  0.00
ATOM   1239  CA  MET   230      10.167  63.453  75.890  1.00  0.00
ATOM   1240  CB  MET   230       9.846  62.659  74.622  1.00  0.00
ATOM   1241  CG  MET   230      10.751  62.979  73.444  1.00  0.00
ATOM   1242  SD  MET   230      10.329  62.034  71.967  1.00  0.00
ATOM   1243  CE  MET   230       8.815  62.848  71.464  1.00  0.00
ATOM   1244  O   MET   230      10.976  65.652  75.371  1.00  0.00
ATOM   1245  C   MET   230      10.001  64.950  75.599  1.00  0.00
ATOM   1246  N   HIS   231       8.769  65.443  75.625  1.00  0.00
ATOM   1247  CA  HIS   231       8.521  66.846  75.349  1.00  0.00
ATOM   1248  CB  HIS   231       7.020  67.103  75.189  1.00  0.00
ATOM   1249  CG  HIS   231       6.686  68.519  74.840  1.00  0.00
ATOM   1250  CD2 HIS   231       6.616  69.297  73.611  1.00  0.00
ATOM   1251  ND1 HIS   231       6.329  69.455  75.787  1.00  0.00
ATOM   1252  CE1 HIS   231       6.087  70.628  75.173  1.00  0.00
ATOM   1253  NE2 HIS   231       6.257  70.541  73.868  1.00  0.00
ATOM   1254  O   HIS   231       9.637  68.768  76.263  1.00  0.00
ATOM   1255  C   HIS   231       9.042  67.706  76.495  1.00  0.00
ATOM   1256  N   THR   232       8.840  67.234  77.728  1.00  0.00
ATOM   1257  CA  THR   232       9.349  67.922  78.894  1.00  0.00
ATOM   1258  CB  THR   232       9.109  67.108  80.179  1.00  0.00
ATOM   1259  CG2 THR   232       9.671  67.841  81.387  1.00  0.00
ATOM   1260  OG1 THR   232       7.702  66.913  80.368  1.00  0.00
ATOM   1261  O   THR   232      11.351  69.253  79.008  1.00  0.00
ATOM   1262  C   THR   232      10.862  68.152  78.750  1.00  0.00
ATOM   1263  N   MET   233      11.590  67.117  78.332  1.00  0.00
ATOM   1264  CA  MET   233      13.040  67.222  78.121  1.00  0.00
ATOM   1265  CB  MET   233      13.645  65.838  77.869  1.00  0.00
ATOM   1266  CG  MET   233      15.164  65.830  77.798  1.00  0.00
ATOM   1267  SD  MET   233      15.935  66.365  79.338  1.00  0.00
ATOM   1268  CE  MET   233      15.613  64.950  80.386  1.00  0.00
ATOM   1269  O   MET   233      14.413  68.784  76.911  1.00  0.00
ATOM   1270  C   MET   233      13.381  68.102  76.924  1.00  0.00
ATOM   1271  N   LYS   234      12.493  68.098  75.935  1.00  0.00
ATOM   1272  CA  LYS   234      12.640  68.969  74.797  1.00  0.00
ATOM   1273  CB  LYS   234      11.537  68.701  73.772  1.00  0.00
ATOM   1274  CG  LYS   234      11.668  67.369  73.052  1.00  0.00
ATOM   1275  CD  LYS   234      10.538  67.165  72.055  1.00  0.00
ATOM   1276  CE  LYS   234      10.667  65.831  71.340  1.00  0.00
ATOM   1277  NZ  LYS   234       9.549  65.605  70.382  1.00  0.00
ATOM   1278  O   LYS   234      13.209  71.280  74.547  1.00  0.00
ATOM   1279  C   LYS   234      12.561  70.444  75.186  1.00  0.00
ATOM   1280  N   ASN   235      11.771  70.754  76.227  1.00  0.00
ATOM   1281  CA  ASN   235      11.593  72.123  76.699  1.00  0.00
ATOM   1282  CB  ASN   235      10.589  72.164  77.853  1.00  0.00
ATOM   1283  CG  ASN   235       9.154  72.018  77.381  1.00  0.00
ATOM   1284  ND2 ASN   235       8.503  70.941  77.804  1.00  0.00
ATOM   1285  OD1 ASN   235       8.641  72.862  76.647  1.00  0.00
ATOM   1286  O   ASN   235      13.147  73.885  77.167  1.00  0.00
ATOM   1287  C   ASN   235      12.931  72.681  77.190  1.00  0.00
ATOM   1288  N   THR   236      13.799  71.783  77.663  1.00  0.00
ATOM   1289  CA  THR   236      15.102  72.130  78.185  1.00  0.00
ATOM   1290  CB  THR   236      15.549  71.147  79.284  1.00  0.00
ATOM   1291  CG2 THR   236      14.550  71.145  80.433  1.00  0.00
ATOM   1292  OG1 THR   236      15.634  69.824  78.741  1.00  0.00
ATOM   1293  O   THR   236      17.369  72.287  77.411  1.00  0.00
ATOM   1294  C   THR   236      16.189  72.110  77.101  1.00  0.00
ATOM   1295  N   GLY   237      15.798  71.888  75.839  1.00  0.00
ATOM   1296  CA  GLY   237      16.738  71.893  74.714  1.00  0.00
ATOM   1297  O   GLY   237      18.232  70.494  73.462  1.00  0.00
ATOM   1298  C   GLY   237      17.279  70.546  74.245  1.00  0.00
TER
END
