
#######################################################
#                                                     #
#                        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   41 (  164),  selected   41 , name T0316AL044_5-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316AL044_5-D2.T0316_D2.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    -       -      G     220           -
LGA    -       -      R     221           -
LGA    -       -      M     222           -
LGA    -       -      M     223           -
LGA    -       -      T     224           -
LGA    -       -      V     225           -
LGA    -       -      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    -       -      D     229           -
LGA    -       -      M     230           -
LGA    -       -      G     231           -
LGA    -       -      E     232           -
LGA    -       -      H     233           -
LGA    -       -      A     234           -
LGA    -       -      G     235           -
LGA    -       -      L     236           -
LGA    -       -      M     237           -
LGA    -       -      Y     238           -
LGA    -       -      Y     239           -
LGA    -       -      T     240           -
LGA    -       -      I     241           -
LGA    -       -      G     242           -
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    -       -      G     245           -
LGA    G     220      G     246          2.105
LGA    R     221      L     247          1.777
LGA    M     222      G     248          3.116
LGA    T     224      I     249          2.264
LGA    R     228      G     250          3.077
LGA    D     229      G     251          2.277
LGA    M     230      -       -           -
LGA    G     231      -       -           -
LGA    E     232      -       -           -
LGA    G     235      -       -           -
LGA    L     236      -       -           -
LGA    M     237      -       -           -
LGA    G     246      -       -           -
LGA    L     247      -       -           -
LGA    G     254      -       -           -
LGA    G     255      -       -           -
LGA    D     256      -       -           -
LGA    N     257      -       -           -
LGA    A     258      D     256           #
LGA    W     260      N     257          2.191
LGA    F     261      A     258          3.396
LGA    V     262      P     259          2.528
LGA    V     263      W     260          2.618
LGA    G     264      F     261          2.183
LGA    -       -      V     262           -
LGA    D     266      V     263          1.360
LGA    L     267      G     264          4.256
LGA    S     268      -       -           -
LGA    K     269      K     265          4.501
LGA    N     270      D     266          3.412
LGA    I     271      L     267          3.320
LGA    L     272      S     268           #
LGA    V     274      K     269          4.875
LGA    G     275      N     270           #
LGA    Q     276      -       -           -
LGA    G     277      -       -           -
LGA    F     278      -       -           -
LGA    Y     279      -       -           -
LGA    H     280      I     271          4.499
LGA    D     281      L     272          3.558
LGA    S     282      Y     273          1.409
LGA    L     283      V     274          0.723
LGA    -       -      G     275           -
LGA    -       -      Q     276           -
LGA    -       -      G     277           -
LGA    -       -      F     278           -
LGA    -       -      Y     279           -
LGA    -       -      H     280           -
LGA    -       -      D     281           -
LGA    -       -      S     282           -
LGA    -       -      L     283           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41   60    5.0     21    3.04     9.52     21.839     0.670

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.215418 * X  +  -0.818977 * Y  +  -0.531857 * Z  +  80.566444
  Y_new =   0.888841 * X  +   0.390005 * Y  +  -0.240539 * Z  + -95.178482
  Z_new =   0.404422 * X  +  -0.420920 * Y  +   0.811954 * Z  + -107.442261 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.478262    2.663330  [ DEG:   -27.4024    152.5976 ]
  Theta =  -0.416347   -2.725245  [ DEG:   -23.8549   -156.1451 ]
  Phi   =   1.333023   -1.808570  [ DEG:    76.3766   -103.6234 ]
 
# 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: T0316AL044_5-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL044_5-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41   60   5.0   21   3.04    9.52  21.839
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL044_5-D2
REMARK Aligment from pdb entry: 1gpm_A
ATOM    657  N   GLY   220      32.669  29.314 -18.561  1.00  0.00              
ATOM    658  CA  GLY   220      32.793  30.628 -19.196  1.00  0.00              
ATOM    659  C   GLY   220      33.957  30.655 -20.166  1.00  0.00              
ATOM    660  O   GLY   220      33.864  31.235 -21.250  1.00  0.00              
ATOM    661  N   ARG   221      35.063  30.043 -19.753  1.00  0.00              
ATOM    662  CA  ARG   221      36.267  29.989 -20.568  1.00  0.00              
ATOM    663  C   ARG   221      36.000  29.221 -21.850  1.00  0.00              
ATOM    664  O   ARG   221      36.194  29.739 -22.945  1.00  0.00              
ATOM    665  N   MET   222      35.483  28.007 -21.715  1.00  0.00              
ATOM    666  CA  MET   222      35.196  27.178 -22.876  1.00  0.00              
ATOM    667  C   MET   222      34.151  27.793 -23.797  1.00  0.00              
ATOM    668  O   MET   222      34.311  27.775 -25.018  1.00  0.00              
ATOM    669  N   THR   224      33.082  28.337 -23.217  1.00  0.00              
ATOM    670  CA  THR   224      32.024  28.929 -24.020  1.00  0.00              
ATOM    671  C   THR   224      32.576  30.083 -24.843  1.00  0.00              
ATOM    672  O   THR   224      32.340  30.158 -26.049  1.00  0.00              
ATOM    673  N   ARG   228      33.394  30.926 -24.209  1.00  0.00              
ATOM    674  CA  ARG   228      33.998  32.077 -24.877  1.00  0.00              
ATOM    675  C   ARG   228      34.772  31.652 -26.121  1.00  0.00              
ATOM    676  O   ARG   228      34.647  32.274 -27.182  1.00  0.00              
ATOM    677  N   ASP   229      34.350  28.800 -27.802  1.00  0.00              
ATOM    678  CA  ASP   229      33.384  28.264 -28.751  1.00  0.00              
ATOM    679  C   ASP   229      32.698  29.392 -29.553  1.00  0.00              
ATOM    680  O   ASP   229      32.552  29.287 -30.782  1.00  0.00              
ATOM    681  N   MET   230      33.850  32.613 -29.966  1.00  0.00              
ATOM    682  CA  MET   230      34.874  33.345 -30.720  1.00  0.00              
ATOM    683  C   MET   230      35.078  32.662 -32.074  1.00  0.00              
ATOM    684  O   MET   230      34.995  33.292 -33.143  1.00  0.00              
ATOM    685  N   GLY   231      35.281  31.350 -32.013  1.00  0.00              
ATOM    686  CA  GLY   231      35.494  30.548 -33.195  1.00  0.00              
ATOM    687  C   GLY   231      34.312  30.573 -34.152  1.00  0.00              
ATOM    688  O   GLY   231      34.499  30.688 -35.363  1.00  0.00              
ATOM    689  N   GLU   232      33.099  30.467 -33.620  1.00  0.00              
ATOM    690  CA  GLU   232      31.903  30.507 -34.459  1.00  0.00              
ATOM    691  C   GLU   232      31.854  31.814 -35.229  1.00  0.00              
ATOM    692  O   GLU   232      31.454  31.848 -36.399  1.00  0.00              
ATOM    693  N   GLY   235      32.231  32.898 -34.563  1.00  0.00              
ATOM    694  CA  GLY   235      32.209  34.207 -35.198  1.00  0.00              
ATOM    695  C   GLY   235      33.272  34.318 -36.281  1.00  0.00              
ATOM    696  O   GLY   235      32.965  34.671 -37.414  1.00  0.00              
ATOM    697  N   LEU   236      34.502  33.942 -35.946  1.00  0.00              
ATOM    698  CA  LEU   236      35.616  33.979 -36.887  1.00  0.00              
ATOM    699  C   LEU   236      35.265  33.178 -38.129  1.00  0.00              
ATOM    700  O   LEU   236      35.637  33.549 -39.241  1.00  0.00              
ATOM    701  N   MET   237      34.560  32.071 -37.914  1.00  0.00              
ATOM    702  CA  MET   237      34.164  31.162 -38.975  1.00  0.00              
ATOM    703  C   MET   237      32.892  31.558 -39.728  1.00  0.00              
ATOM    704  O   MET   237      32.422  30.811 -40.583  1.00  0.00              
ATOM    705  N   GLY   246      32.333  32.723 -39.410  1.00  0.00              
ATOM    706  CA  GLY   246      31.115  33.218 -40.066  1.00  0.00              
ATOM    707  C   GLY   246      29.979  32.201 -39.892  1.00  0.00              
ATOM    708  O   GLY   246      29.084  32.076 -40.731  1.00  0.00              
ATOM    709  N   LEU   247      30.021  31.480 -38.774  1.00  0.00              
ATOM    710  CA  LEU   247      29.023  30.467 -38.468  1.00  0.00              
ATOM    711  C   LEU   247      28.046  30.859 -37.361  1.00  0.00              
ATOM    712  O   LEU   247      27.030  30.195 -37.160  1.00  0.00              
ATOM    713  N   GLY   254      28.325  31.957 -36.671  1.00  0.00              
ATOM    714  CA  GLY   254      27.457  32.396 -35.588  1.00  0.00              
ATOM    715  C   GLY   254      25.997  32.574 -36.008  1.00  0.00              
ATOM    716  O   GLY   254      25.071  32.112 -35.316  1.00  0.00              
ATOM    717  N   GLY   255      25.784  33.252 -37.129  1.00  0.00              
ATOM    718  CA  GLY   255      24.430  33.478 -37.612  1.00  0.00              
ATOM    719  C   GLY   255      23.918  32.296 -38.433  1.00  0.00              
ATOM    720  O   GLY   255      22.821  32.336 -38.993  1.00  0.00              
ATOM    721  N   ASP   256      24.687  31.217 -38.466  1.00  0.00              
ATOM    722  CA  ASP   256      24.265  30.035 -39.208  1.00  0.00              
ATOM    723  C   ASP   256      23.515  29.066 -38.293  1.00  0.00              
ATOM    724  O   ASP   256      23.043  28.023 -38.744  1.00  0.00              
ATOM    725  N   ASN   257      23.420  29.410 -37.008  1.00  0.00              
ATOM    726  CA  ASN   257      22.730  28.586 -36.013  1.00  0.00              
ATOM    727  C   ASN   257      21.814  29.462 -35.156  1.00  0.00              
ATOM    728  O   ASN   257      22.098  30.649 -34.959  1.00  0.00              
ATOM    729  N   ALA   258      20.715  28.876 -34.673  1.00  0.00              
ATOM    730  CA  ALA   258      19.733  29.575 -33.830  1.00  0.00              
ATOM    731  C   ALA   258      20.290  29.796 -32.433  1.00  0.00              
ATOM    732  O   ALA   258      20.008  30.807 -31.789  1.00  0.00              
ATOM    733  N   TRP   260      21.038  28.812 -31.945  1.00  0.00              
ATOM    734  CA  TRP   260      21.666  28.915 -30.643  1.00  0.00              
ATOM    735  C   TRP   260      22.912  28.042 -30.598  1.00  0.00              
ATOM    736  O   TRP   260      23.023  27.063 -31.334  1.00  0.00              
ATOM    737  N   PHE   261      23.866  28.444 -29.773  1.00  0.00              
ATOM    738  CA  PHE   261      25.129  27.739 -29.627  1.00  0.00              
ATOM    739  C   PHE   261      25.683  28.084 -28.255  1.00  0.00              
ATOM    740  O   PHE   261      25.782  29.259 -27.906  1.00  0.00              
ATOM    741  N   VAL   262      25.977  27.059 -27.466  1.00  0.00              
ATOM    742  CA  VAL   262      26.505  27.237 -26.126  1.00  0.00              
ATOM    743  C   VAL   262      27.229  25.970 -25.681  1.00  0.00              
ATOM    744  O   VAL   262      27.264  24.966 -26.400  1.00  0.00              
ATOM    745  N   VAL   263      27.881  23.165 -22.401  1.00  0.00              
ATOM    746  CA  VAL   263      27.302  22.594 -21.195  1.00  0.00              
ATOM    747  C   VAL   263      28.438  21.926 -20.418  1.00  0.00              
ATOM    748  O   VAL   263      29.286  21.266 -21.002  1.00  0.00              
ATOM    749  N   GLY   264      28.480  22.114 -19.111  1.00  0.00              
ATOM    750  CA  GLY   264      29.529  21.504 -18.314  1.00  0.00              
ATOM    751  C   GLY   264      29.047  20.169 -17.741  1.00  0.00              
ATOM    752  O   GLY   264      27.996  20.107 -17.093  1.00  0.00              
ATOM    753  N   ASP   266      29.800  19.099 -17.994  1.00  0.00              
ATOM    754  CA  ASP   266      29.426  17.783 -17.468  1.00  0.00              
ATOM    755  C   ASP   266      30.371  17.435 -16.333  1.00  0.00              
ATOM    756  O   ASP   266      31.590  17.441 -16.507  1.00  0.00              
ATOM    757  N   LEU   267      29.818  17.118 -15.152  1.00  0.00              
ATOM    758  CA  LEU   267      30.641  16.765 -13.992  1.00  0.00              
ATOM    759  C   LEU   267      31.107  15.303 -14.059  1.00  0.00              
ATOM    760  O   LEU   267      30.827  14.510 -13.156  1.00  0.00              
ATOM    761  N   SER   268      31.782  14.938 -15.145  1.00  0.00              
ATOM    762  CA  SER   268      32.277  13.574 -15.314  1.00  0.00              
ATOM    763  C   SER   268      33.774  13.622 -15.568  1.00  0.00              
ATOM    764  O   SER   268      34.275  14.557 -16.190  1.00  0.00              
ATOM    765  N   LYS   269      37.505  12.462 -17.025  1.00  0.00              
ATOM    766  CA  LYS   269      38.176  11.971 -18.218  1.00  0.00              
ATOM    767  C   LYS   269      39.664  12.150 -17.943  1.00  0.00              
ATOM    768  O   LYS   269      40.070  13.194 -17.422  1.00  0.00              
ATOM    769  N   ASN   270      40.470  11.138 -18.271  1.00  0.00              
ATOM    770  CA  ASN   270      41.913  11.205 -18.042  1.00  0.00              
ATOM    771  C   ASN   270      42.475  12.585 -18.370  1.00  0.00              
ATOM    772  O   ASN   270      42.384  13.049 -19.503  1.00  0.00              
ATOM    773  N   ILE   271      43.034  13.224 -17.347  1.00  0.00              
ATOM    774  CA  ILE   271      43.607  14.553 -17.461  1.00  0.00              
ATOM    775  C   ILE   271      44.639  14.786 -18.548  1.00  0.00              
ATOM    776  O   ILE   271      45.230  13.851 -19.101  1.00  0.00              
ATOM    777  N   LEU   272      44.857  16.056 -18.856  1.00  0.00              
ATOM    778  CA  LEU   272      45.812  16.434 -19.878  1.00  0.00              
ATOM    779  C   LEU   272      47.210  16.551 -19.275  1.00  0.00              
ATOM    780  O   LEU   272      47.393  17.176 -18.223  1.00  0.00              
ATOM    781  N   VAL   274      48.189  15.919 -19.925  1.00  0.00              
ATOM    782  CA  VAL   274      49.573  15.967 -19.460  1.00  0.00              
ATOM    783  C   VAL   274      50.027  17.423 -19.466  1.00  0.00              
ATOM    784  O   VAL   274      50.287  18.011 -20.520  1.00  0.00              
ATOM    785  N   GLY   275      50.091  17.997 -18.273  1.00  0.00              
ATOM    786  CA  GLY   275      50.483  19.383 -18.113  1.00  0.00              
ATOM    787  C   GLY   275      49.678  19.931 -16.955  1.00  0.00              
ATOM    788  O   GLY   275      50.237  20.455 -15.992  1.00  0.00              
ATOM    789  N   GLN   276      48.365  19.726 -17.014  1.00  0.00              
ATOM    790  CA  GLN   276      47.456  20.184 -15.969  1.00  0.00              
ATOM    791  C   GLN   276      47.819  19.590 -14.611  1.00  0.00              
ATOM    792  O   GLN   276      47.532  20.172 -13.561  1.00  0.00              
ATOM    793  N   GLY   277      48.459  18.426 -14.638  1.00  0.00              
ATOM    794  CA  GLY   277      48.881  17.781 -13.409  1.00  0.00              
ATOM    795  C   GLY   277      47.826  16.969 -12.678  1.00  0.00              
ATOM    796  O   GLY   277      48.121  16.389 -11.628  1.00  0.00              
ATOM    797  N   PHE   278      46.600  16.947 -13.190  1.00  0.00              
ATOM    798  CA  PHE   278      45.543  16.173 -12.553  1.00  0.00              
ATOM    799  C   PHE   278      45.453  14.832 -13.266  1.00  0.00              
ATOM    800  O   PHE   278      45.737  14.747 -14.460  1.00  0.00              
ATOM    801  N   TYR   279      42.701  13.245 -13.582  1.00  0.00              
ATOM    802  CA  TYR   279      41.435  13.365 -14.292  1.00  0.00              
ATOM    803  C   TYR   279      40.967  14.818 -14.352  1.00  0.00              
ATOM    804  O   TYR   279      41.172  15.591 -13.411  1.00  0.00              
ATOM    805  N   HIS   280      40.337  15.177 -15.465  1.00  0.00              
ATOM    806  CA  HIS   280      39.792  16.509 -15.657  1.00  0.00              
ATOM    807  C   HIS   280      38.306  16.389 -15.990  1.00  0.00              
ATOM    808  O   HIS   280      37.735  15.300 -15.911  1.00  0.00              
ATOM    809  N   ASP   281      37.683  17.501 -16.365  1.00  0.00              
ATOM    810  CA  ASP   281      36.254  17.515 -16.684  1.00  0.00              
ATOM    811  C   ASP   281      35.935  17.514 -18.179  1.00  0.00              
ATOM    812  O   ASP   281      36.820  17.644 -19.037  1.00  0.00              
ATOM    813  N   SER   282      34.648  17.407 -18.476  1.00  0.00              
ATOM    814  CA  SER   282      34.161  17.363 -19.847  1.00  0.00              
ATOM    815  C   SER   282      33.098  18.438 -20.111  1.00  0.00              
ATOM    816  O   SER   282      32.359  18.843 -19.206  1.00  0.00              
ATOM    817  N   LEU   283      33.060  18.932 -21.342  1.00  0.00              
ATOM    818  CA  LEU   283      32.045  19.902 -21.732  1.00  0.00              
ATOM    819  C   LEU   283      31.445  19.439 -23.044  1.00  0.00              
ATOM    820  O   LEU   283      32.078  18.686 -23.798  1.00  0.00              
END
