
#######################################################
#                                                     #
#                        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   13 (  115),  selected   13 , name T0386TS389_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS389_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           -
LGA    -       -      P     220           -
LGA    -       -      E     221           -
LGA    -       -      K     222           -
LGA    -       -      I     223           -
LGA    -       -      R     224           -
LGA    N     219      L     225          1.317
LGA    P     220      L     226          0.967
LGA    E     221      K     227          1.148
LGA    K     222      E     228          1.120
LGA    I     223      F     229          0.855
LGA    R     224      M     230          0.842
LGA    L     225      H     231          1.128
LGA    L     226      T     232          0.406
LGA    K     227      M     233          0.954
LGA    E     228      K     234          1.799
LGA    F     229      N     235          2.929
LGA    M     230      T     236          1.248
LGA    H     231      G     237          2.489
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)   13   81    5.0     13    1.48     0.00     15.308     0.821

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.226395 * X  +   0.955343 * Y  +   0.189906 * Z  +  20.682198
  Y_new =   0.062890 * X  +  -0.208899 * Y  +   0.975913 * Z  +  78.268639
  Z_new =   0.972003 * X  +  -0.208999 * Y  +  -0.107375 * Z  +  79.136780 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.045392    1.096201  [ DEG:  -117.1923     62.8077 ]
  Theta =  -1.333611   -1.807982  [ DEG:   -76.4103   -103.5897 ]
  Phi   =   0.270957   -2.870636  [ DEG:    15.5247   -164.4753 ]
 
# 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_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS389_2-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   13   81   5.0   13   1.48    0.00  15.308
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS389_2-D2
PFRMAT TS
TARGET T0386
MODEL  2
PARENT N/A
ATOM   1164  N   ASN   219       7.768  63.986  79.303  1.00  0.00
ATOM   1165  CA  ASN   219       9.226  64.029  79.426  1.00  0.00
ATOM   1166  CB  ASN   219       9.781  62.633  79.713  1.00  0.00
ATOM   1167  CG  ASN   219       9.494  62.171  81.129  1.00  0.00
ATOM   1168  ND2 ASN   219       9.562  60.864  81.350  1.00  0.00
ATOM   1169  OD1 ASN   219       9.215  62.983  82.012  1.00  0.00
ATOM   1170  O   ASN   219      10.876  65.323  78.247  1.00  0.00
ATOM   1171  C   ASN   219       9.936  64.540  78.154  1.00  0.00
ATOM   1172  N   PRO   220       9.473  64.124  76.980  1.00  0.00
ATOM   1173  CA  PRO   220      10.117  64.510  75.736  1.00  0.00
ATOM   1174  CB  PRO   220       9.432  63.640  74.679  1.00  0.00
ATOM   1175  CG  PRO   220       8.142  63.235  75.308  1.00  0.00
ATOM   1176  CD  PRO   220       8.409  63.145  76.785  1.00  0.00
ATOM   1177  O   PRO   220      10.879  66.692  75.010  1.00  0.00
ATOM   1178  C   PRO   220       9.930  66.001  75.423  1.00  0.00
ATOM   1179  N   GLU   221       8.714  66.504  75.632  1.00  0.00
ATOM   1180  CA  GLU   221       8.418  67.921  75.465  1.00  0.00
ATOM   1181  CB  GLU   221       6.929  68.189  75.696  1.00  0.00
ATOM   1182  CG  GLU   221       6.024  67.652  74.599  1.00  0.00
ATOM   1183  CD  GLU   221       4.553  67.814  74.928  1.00  0.00
ATOM   1184  OE1 GLU   221       4.240  68.270  76.046  1.00  0.00
ATOM   1185  OE2 GLU   221       3.713  67.484  74.064  1.00  0.00
ATOM   1186  O   GLU   221       9.807  69.762  76.087  1.00  0.00
ATOM   1187  C   GLU   221       9.221  68.745  76.462  1.00  0.00
ATOM   1188  N   LYS   222       9.261  68.321  77.724  1.00  0.00
ATOM   1189  CA  LYS   222      10.039  69.057  78.723  1.00  0.00
ATOM   1190  CB  LYS   222       9.898  68.404  80.100  1.00  0.00
ATOM   1191  CG  LYS   222       8.508  68.520  80.702  1.00  0.00
ATOM   1192  CD  LYS   222       8.447  67.875  82.078  1.00  0.00
ATOM   1193  CE  LYS   222       7.039  67.921  82.647  1.00  0.00
ATOM   1194  NZ  LYS   222       6.972  67.335  84.014  1.00  0.00
ATOM   1195  O   LYS   222      12.141  70.134  78.169  1.00  0.00
ATOM   1196  C   LYS   222      11.547  69.075  78.345  1.00  0.00
ATOM   1197  N   ILE   223      12.147  67.913  78.165  1.00  0.00
ATOM   1198  CA  ILE   223      13.589  67.855  77.964  1.00  0.00
ATOM   1199  CB  ILE   223      14.120  66.415  78.101  1.00  0.00
ATOM   1200  CG1 ILE   223      13.982  65.931  79.546  1.00  0.00
ATOM   1201  CG2 ILE   223      15.589  66.350  77.710  1.00  0.00
ATOM   1202  CD1 ILE   223      14.231  64.449  79.719  1.00  0.00
ATOM   1203  O   ILE   223      15.143  68.995  76.563  1.00  0.00
ATOM   1204  C   ILE   223      14.117  68.333  76.599  1.00  0.00
ATOM   1205  N   ARG   224      13.427  68.011  75.505  1.00  0.00
ATOM   1206  CA  ARG   224      13.785  68.560  74.195  1.00  0.00
ATOM   1207  CB  ARG   224      12.941  67.912  73.094  1.00  0.00
ATOM   1208  CG  ARG   224      13.293  66.459  72.819  1.00  0.00
ATOM   1209  CD  ARG   224      12.364  65.857  71.775  1.00  0.00
ATOM   1210  NE  ARG   224      12.682  64.457  71.505  1.00  0.00
ATOM   1211  CZ  ARG   224      11.948  63.660  70.737  1.00  0.00
ATOM   1212  NH1 ARG   224      12.313  62.399  70.547  1.00  0.00
ATOM   1213  NH2 ARG   224      10.850  64.124  70.157  1.00  0.00
ATOM   1214  O   ARG   224      14.244  70.790  73.455  1.00  0.00
ATOM   1215  C   ARG   224      13.544  70.064  74.166  1.00  0.00
ATOM   1216  N   LEU   225      12.563  70.525  74.945  1.00  0.00
ATOM   1217  CA  LEU   225      12.269  71.935  75.099  1.00  0.00
ATOM   1218  CB  LEU   225      10.980  72.131  75.900  1.00  0.00
ATOM   1219  CG  LEU   225       9.680  71.717  75.204  1.00  0.00
ATOM   1220  CD1 LEU   225       8.508  71.785  76.171  1.00  0.00
ATOM   1221  CD2 LEU   225       9.383  72.638  74.031  1.00  0.00
ATOM   1222  O   LEU   225      13.737  73.787  75.396  1.00  0.00
ATOM   1223  C   LEU   225      13.356  72.703  75.822  1.00  0.00
ATOM   1224  N   LEU   226      13.829  72.167  76.946  1.00  0.00
ATOM   1225  CA  LEU   226      14.975  72.714  77.672  1.00  0.00
ATOM   1226  CB  LEU   226      15.314  71.834  78.877  1.00  0.00
ATOM   1227  CG  LEU   226      14.316  71.856  80.036  1.00  0.00
ATOM   1228  CD1 LEU   226      14.673  70.803  81.072  1.00  0.00
ATOM   1229  CD2 LEU   226      14.314  73.214  80.719  1.00  0.00
ATOM   1230  O   LEU   226      16.901  73.792  76.741  1.00  0.00
ATOM   1231  C   LEU   226      16.207  72.784  76.762  1.00  0.00
ATOM   1232  N   LYS   227      16.488  71.718  76.026  1.00  0.00
ATOM   1233  CA  LYS   227      17.580  71.762  75.059  1.00  0.00
ATOM   1234  CB  LYS   227      17.675  70.440  74.296  1.00  0.00
ATOM   1235  CG  LYS   227      18.171  69.273  75.136  1.00  0.00
ATOM   1236  CD  LYS   227      18.243  67.996  74.315  1.00  0.00
ATOM   1237  CE  LYS   227      18.715  66.823  75.163  1.00  0.00
ATOM   1238  NZ  LYS   227      18.759  65.556  74.381  1.00  0.00
ATOM   1239  O   LYS   227      18.413  73.502  73.652  1.00  0.00
ATOM   1240  C   LYS   227      17.430  72.867  74.007  1.00  0.00
ATOM   1241  N   GLU   228      16.216  73.080  73.508  1.00  0.00
ATOM   1242  CA  GLU   228      15.993  74.099  72.489  1.00  0.00
ATOM   1243  CB  GLU   228      14.590  73.966  71.897  1.00  0.00
ATOM   1244  CG  GLU   228      14.272  74.989  70.818  1.00  0.00
ATOM   1245  CD  GLU   228      15.110  74.797  69.569  1.00  0.00
ATOM   1246  OE1 GLU   228      15.787  73.752  69.463  1.00  0.00
ATOM   1247  OE2 GLU   228      15.089  75.690  68.697  1.00  0.00
ATOM   1248  O   GLU   228      16.788  76.348  72.546  1.00  0.00
ATOM   1249  C   GLU   228      16.135  75.488  73.108  1.00  0.00
ATOM   1250  N   PHE   229      15.536  75.692  74.279  1.00  0.00
ATOM   1251  CA  PHE   229      15.655  76.928  75.032  1.00  0.00
ATOM   1252  CB  PHE   229      15.026  76.773  76.418  1.00  0.00
ATOM   1253  CG  PHE   229      13.525  76.694  76.398  1.00  0.00
ATOM   1254  CD1 PHE   229      12.814  77.039  75.263  1.00  0.00
ATOM   1255  CD2 PHE   229      12.827  76.276  77.517  1.00  0.00
ATOM   1256  CE1 PHE   229      11.434  76.968  75.246  1.00  0.00
ATOM   1257  CE2 PHE   229      11.446  76.202  77.499  1.00  0.00
ATOM   1258  CZ  PHE   229      10.751  76.547  76.370  1.00  0.00
ATOM   1259  O   PHE   229      17.438  78.555  75.084  1.00  0.00
ATOM   1260  C   PHE   229      17.107  77.370  75.246  1.00  0.00
ATOM   1261  N   MET   230      17.959  76.423  75.629  1.00  0.00
ATOM   1262  CA  MET   230      19.385  76.681  75.872  1.00  0.00
ATOM   1263  CB  MET   230      20.039  75.478  76.555  1.00  0.00
ATOM   1264  CG  MET   230      21.476  75.717  76.989  1.00  0.00
ATOM   1265  SD  MET   230      21.626  77.040  78.204  1.00  0.00
ATOM   1266  CE  MET   230      20.939  76.247  79.655  1.00  0.00
ATOM   1267  O   MET   230      21.207  77.619  74.588  1.00  0.00
ATOM   1268  C   MET   230      20.159  76.949  74.578  1.00  0.00
ATOM   1269  N   HIS   231      19.639  76.421  73.473  1.00  0.00
ATOM   1270  CA  HIS   231      20.196  76.677  72.141  1.00  0.00
ATOM   1271  CB  HIS   231      19.581  75.728  71.110  1.00  0.00
ATOM   1272  CG  HIS   231      19.925  74.289  71.333  1.00  0.00
ATOM   1273  CD2 HIS   231      20.885  73.566  72.157  1.00  0.00
ATOM   1274  ND1 HIS   231      19.278  73.258  70.686  1.00  0.00
ATOM   1275  CE1 HIS   231      19.804  72.088  71.090  1.00  0.00
ATOM   1276  NE2 HIS   231      20.769  72.265  71.971  1.00  0.00
ATOM   1277  O   HIS   231      20.760  78.716  70.950  1.00  0.00
ATOM   1278  C   HIS   231      19.931  78.130  71.646  1.00  0.00
TER
END
