
#######################################################
#                                                     #
#                        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 T0320AL044_1-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320AL044_1-D2.T0320_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    N     228      N     233          2.905
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    N     229      L     236          5.373
LGA    S     230      R     237           -
LGA    L     231      K     238           -
LGA    P     232      D     239           -
LGA    N     233      S     240           -
LGA    -       -      N     241           -
LGA    P     234      N     242          4.181
LGA    L     236      P     243          4.447
LGA    S     240      A     244          4.179
LGA    N     241      -       -           -
LGA    N     242      L     245          1.670
LGA    P     243      H     246          2.450
LGA    L     245      F     247          1.803
LGA    H     246      E     248          2.426
LGA    I     251      W     249          2.054
LGA    G     256      E     250          4.113
LGA    K     257      I     251          4.491
LGA    D     258      I     252          2.860
LGA    A     259      H     253          1.342
LGA    -       -      A     254           -
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    E     260      R     263           #
LGA    G     261      S     264          5.161
LGA    E     262      S     265          3.223
LGA    R     263      A     266          2.042
LGA    S     264      I     267          4.580
LGA    S     265      N     268          1.341
LGA    N     268      T     269          1.618
LGA    -       -      S     270           -
LGA    -       -      P     271           -
LGA    -       -      I     272           -
LGA    -       -      S     273           -
LGA    -       -      V     274           -
LGA    -       -      V     275           -
LGA    -       -      D     276           -
LGA    -       -      K     277           -
LGA    -       -      E     278           -
LGA    -       -      R     279           -
LGA    -       -      F     280           -
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    -       -      Y     283           -
LGA    -       -      H     284           -
LGA    -       -      D     285           -
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    -       -      G     290           -
LGA    T     269      W     291          2.109
LGA    V     274      Y     292          2.711
LGA    V     275      L     293          2.545
LGA    -       -      V     294           -
LGA    D     276      D     295          3.522
LGA    K     277      D     296          3.180
LGA    F     280      T     297          2.339
LGA    G     290      L     298           #
LGA    Y     292      E     299           -
LGA    V     294      R     300           -
LGA    T     297      A     301           -
LGA    L     298      G     302           -
LGA    E     299      R     303           -
LGA    R     300      I     304           -
LGA    A     301      -       -           -
LGA    G     302      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41   73    5.0     26    3.25     7.69     21.576     0.777

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.372879 * X  +   0.163051 * Y  +   0.913442 * Z  + -12.091949
  Y_new =  -0.320909 * X  +   0.901028 * Y  +  -0.291834 * Z  +  27.087740
  Z_new =  -0.870620 * X  +  -0.401950 * Y  +  -0.283650 * Z  + 162.204727 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.185327    0.956265  [ DEG:  -125.2100     54.7900 ]
  Theta =   1.056461    2.085132  [ DEG:    60.5308    119.4692 ]
  Phi   =  -2.430963    0.710630  [ DEG:  -139.2839     40.7161 ]
 
# 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: T0320AL044_1-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320AL044_1-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41   73   5.0   26   3.25    7.69  21.576
REMARK  ---------------------------------------------------------- 
MOLECULE T0320AL044_1-D2
REMARK Aligment from pdb entry: 1gpm_A
ATOM    685  N   ASN   228      16.251  13.752   4.236  1.00  0.00              
ATOM    686  CA  ASN   228      15.225  13.743   5.279  1.00  0.00              
ATOM    687  C   ASN   228      15.328  12.410   6.043  1.00  0.00              
ATOM    688  O   ASN   228      14.727  12.242   7.101  1.00  0.00              
ATOM    689  N   ASN   229      16.043  11.451   5.457  1.00  0.00              
ATOM    690  CA  ASN   229      16.275  10.139   6.061  1.00  0.00              
ATOM    691  C   ASN   229      17.743  10.148   6.502  1.00  0.00              
ATOM    692  O   ASN   229      18.654  10.164   5.662  1.00  0.00              
ATOM    693  N   SER   230      17.966  10.155   7.813  1.00  0.00              
ATOM    694  CA  SER   230      19.317  10.201   8.356  1.00  0.00              
ATOM    695  C   SER   230      20.115   8.967   8.025  1.00  0.00              
ATOM    696  O   SER   230      19.634   7.852   8.197  1.00  0.00              
ATOM    697  N   LEU   231      21.353   9.177   7.586  1.00  0.00              
ATOM    698  CA  LEU   231      22.214   8.071   7.217  1.00  0.00              
ATOM    699  C   LEU   231      21.767   7.351   5.948  1.00  0.00              
ATOM    700  O   LEU   231      21.252   7.965   5.003  1.00  0.00              
ATOM    701  N   PRO   232      21.987   6.042   5.926  1.00  0.00              
ATOM    702  CA  PRO   232      21.632   5.194   4.801  1.00  0.00              
ATOM    703  C   PRO   232      20.153   5.275   4.444  1.00  0.00              
ATOM    704  O   PRO   232      19.292   5.140   5.302  1.00  0.00              
ATOM    705  N   ASN   233      12.484   2.902   4.916  1.00  0.00              
ATOM    706  CA  ASN   233      12.485   4.177   5.614  1.00  0.00              
ATOM    707  C   ASN   233      11.788   5.260   4.805  1.00  0.00              
ATOM    708  O   ASN   233      11.059   6.091   5.355  1.00  0.00              
ATOM    709  N   PRO   234       7.141   8.980   4.107  1.00  0.00              
ATOM    710  CA  PRO   234       6.082   9.553   3.274  1.00  0.00              
ATOM    711  C   PRO   234       4.748   9.520   3.991  1.00  0.00              
ATOM    712  O   PRO   234       3.964  10.469   3.912  1.00  0.00              
ATOM    713  N   LEU   236       4.488   8.408   4.672  1.00  0.00              
ATOM    714  CA  LEU   236       3.246   8.224   5.407  1.00  0.00              
ATOM    715  C   LEU   236       3.138   9.250   6.522  1.00  0.00              
ATOM    716  O   LEU   236       2.178  10.011   6.584  1.00  0.00              
ATOM    717  N   SER   240       4.162   9.320   7.361  1.00  0.00              
ATOM    718  CA  SER   240       4.161  10.261   8.472  1.00  0.00              
ATOM    719  C   SER   240       4.111  11.713   8.017  1.00  0.00              
ATOM    720  O   SER   240       3.370  12.516   8.584  1.00  0.00              
ATOM    721  N   ASN   241       4.897  12.051   6.995  1.00  0.00              
ATOM    722  CA  ASN   241       4.929  13.420   6.507  1.00  0.00              
ATOM    723  C   ASN   241       3.551  13.832   6.013  1.00  0.00              
ATOM    724  O   ASN   241       3.049  14.896   6.378  1.00  0.00              
ATOM    725  N   ASN   242       2.899  12.941   5.264  1.00  0.00              
ATOM    726  CA  ASN   242       1.565  13.202   4.723  1.00  0.00              
ATOM    727  C   ASN   242       0.582  13.568   5.831  1.00  0.00              
ATOM    728  O   ASN   242      -0.188  14.526   5.696  1.00  0.00              
ATOM    729  N   PRO   243       0.639  12.837   6.941  1.00  0.00              
ATOM    730  CA  PRO   243      -0.243  13.114   8.059  1.00  0.00              
ATOM    731  C   PRO   243       0.099  14.467   8.650  1.00  0.00              
ATOM    732  O   PRO   243      -0.790  15.284   8.908  1.00  0.00              
ATOM    733  N   LEU   245       1.389  14.708   8.861  1.00  0.00              
ATOM    734  CA  LEU   245       1.831  15.973   9.433  1.00  0.00              
ATOM    735  C   LEU   245       1.343  17.172   8.591  1.00  0.00              
ATOM    736  O   LEU   245       0.854  18.170   9.147  1.00  0.00              
ATOM    737  N   HIS   246      -1.250  17.169   6.321  1.00  0.00              
ATOM    738  CA  HIS   246      -2.717  17.163   6.301  1.00  0.00              
ATOM    739  C   HIS   246      -3.234  17.947   7.510  1.00  0.00              
ATOM    740  O   HIS   246      -4.041  18.885   7.383  1.00  0.00              
ATOM    741  N   ILE   251      -2.704  17.590   8.674  1.00  0.00              
ATOM    742  CA  ILE   251      -3.080  18.224   9.917  1.00  0.00              
ATOM    743  C   ILE   251      -2.765  19.711   9.946  1.00  0.00              
ATOM    744  O   ILE   251      -3.584  20.509  10.401  1.00  0.00              
ATOM    745  N   GLY   256      -1.587  20.091   9.462  1.00  0.00              
ATOM    746  CA  GLY   256      -1.207  21.502   9.424  1.00  0.00              
ATOM    747  C   GLY   256      -2.212  22.287   8.601  1.00  0.00              
ATOM    748  O   GLY   256      -2.560  23.425   8.938  1.00  0.00              
ATOM    749  N   LYS   257      -2.656  21.692   7.501  1.00  0.00              
ATOM    750  CA  LYS   257      -3.611  22.359   6.628  1.00  0.00              
ATOM    751  C   LYS   257      -4.975  22.489   7.291  1.00  0.00              
ATOM    752  O   LYS   257      -5.524  23.582   7.365  1.00  0.00              
ATOM    753  N   ASP   258      -5.477  21.386   7.837  1.00  0.00              
ATOM    754  CA  ASP   258      -6.766  21.367   8.520  1.00  0.00              
ATOM    755  C   ASP   258      -6.779  22.413   9.621  1.00  0.00              
ATOM    756  O   ASP   258      -7.801  23.050   9.869  1.00  0.00              
ATOM    757  N   ALA   259      -5.633  22.561  10.280  1.00  0.00              
ATOM    758  CA  ALA   259      -5.467  23.487  11.387  1.00  0.00              
ATOM    759  C   ALA   259      -5.163  24.931  10.984  1.00  0.00              
ATOM    760  O   ALA   259      -4.917  25.774  11.845  1.00  0.00              
ATOM    761  N   GLU   260      -5.174  25.218   9.685  1.00  0.00              
ATOM    762  CA  GLU   260      -4.906  26.568   9.173  1.00  0.00              
ATOM    763  C   GLU   260      -3.524  27.040   9.646  1.00  0.00              
ATOM    764  O   GLU   260      -3.275  28.233   9.839  1.00  0.00              
ATOM    765  N   GLY   261      -2.618  26.080   9.818  1.00  0.00              
ATOM    766  CA  GLY   261      -1.266  26.364  10.273  1.00  0.00              
ATOM    767  C   GLY   261      -0.196  26.229   9.192  1.00  0.00              
ATOM    768  O   GLY   261       0.944  26.651   9.384  1.00  0.00              
ATOM    769  N   GLU   262      -0.566  25.682   8.041  1.00  0.00              
ATOM    770  CA  GLU   262       0.393  25.500   6.962  1.00  0.00              
ATOM    771  C   GLU   262       1.108  26.789   6.554  1.00  0.00              
ATOM    772  O   GLU   262       2.343  26.813   6.396  1.00  0.00              
ATOM    773  N   ARG   263       0.342  27.857   6.371  1.00  0.00              
ATOM    774  CA  ARG   263       0.927  29.130   5.979  1.00  0.00              
ATOM    775  C   ARG   263       1.433  29.916   7.188  1.00  0.00              
ATOM    776  O   ARG   263       1.888  31.053   7.064  1.00  0.00              
ATOM    777  N   SER   264       1.403  29.292   8.358  1.00  0.00              
ATOM    778  CA  SER   264       1.887  29.959   9.560  1.00  0.00              
ATOM    779  C   SER   264       3.362  29.633   9.798  1.00  0.00              
ATOM    780  O   SER   264       3.965  30.135  10.746  1.00  0.00              
ATOM    781  N   SER   265       3.932  28.783   8.943  1.00  0.00              
ATOM    782  CA  SER   265       5.336  28.378   9.040  1.00  0.00              
ATOM    783  C   SER   265       5.997  28.457   7.663  1.00  0.00              
ATOM    784  O   SER   265       5.323  28.286   6.641  1.00  0.00              
ATOM    785  N   ASN   268       7.304  28.731   7.647  1.00  0.00              
ATOM    786  CA  ASN   268       8.090  28.839   6.408  1.00  0.00              
ATOM    787  C   ASN   268       8.323  27.464   5.804  1.00  0.00              
ATOM    788  O   ASN   268       8.363  27.305   4.583  1.00  0.00              
ATOM    789  N   THR   269       8.272  19.678   7.775  1.00  0.00              
ATOM    790  CA  THR   269       8.516  18.358   7.222  1.00  0.00              
ATOM    791  C   THR   269       8.859  17.382   8.342  1.00  0.00              
ATOM    792  O   THR   269       8.950  17.758   9.516  1.00  0.00              
ATOM    793  N   VAL   274       9.055  16.129   7.961  1.00  0.00              
ATOM    794  CA  VAL   274       9.379  15.077   8.905  1.00  0.00              
ATOM    795  C   VAL   274      10.740  14.502   8.570  1.00  0.00              
ATOM    796  O   VAL   274      11.140  14.477   7.407  1.00  0.00              
ATOM    797  N   VAL   275      11.483  14.127   9.597  1.00  0.00              
ATOM    798  CA  VAL   275      12.797  13.527   9.422  1.00  0.00              
ATOM    799  C   VAL   275      12.733  12.116  10.009  1.00  0.00              
ATOM    800  O   VAL   275      12.157  11.909  11.068  1.00  0.00              
ATOM    801  N   ASP   276      13.295  11.139   9.319  1.00  0.00              
ATOM    802  CA  ASP   276      13.275   9.777   9.823  1.00  0.00              
ATOM    803  C   ASP   276      14.562   9.482  10.596  1.00  0.00              
ATOM    804  O   ASP   276      15.667   9.676  10.074  1.00  0.00              
ATOM    805  N   LYS   277      14.425   9.035  11.844  1.00  0.00              
ATOM    806  CA  LYS   277      15.603   8.706  12.652  1.00  0.00              
ATOM    807  C   LYS   277      15.704   7.196  12.759  1.00  0.00              
ATOM    808  O   LYS   277      14.757   6.532  13.182  1.00  0.00              
ATOM    809  N   PHE   280      16.862   6.632  12.383  1.00  0.00              
ATOM    810  CA  PHE   280      17.065   5.182  12.448  1.00  0.00              
ATOM    811  C   PHE   280      17.416   4.729  13.874  1.00  0.00              
ATOM    812  O   PHE   280      18.471   4.131  14.102  1.00  0.00              
ATOM    813  N   GLY   290      16.555   5.049  14.835  1.00  0.00              
ATOM    814  CA  GLY   290      16.785   4.667  16.225  1.00  0.00              
ATOM    815  C   GLY   290      15.582   3.887  16.727  1.00  0.00              
ATOM    816  O   GLY   290      14.450   4.152  16.324  1.00  0.00              
ATOM    817  N   TYR   292      15.835   2.935  17.618  1.00  0.00              
ATOM    818  CA  TYR   292      14.779   2.082  18.146  1.00  0.00              
ATOM    819  C   TYR   292      14.088   2.568  19.405  1.00  0.00              
ATOM    820  O   TYR   292      14.706   3.143  20.295  1.00  0.00              
ATOM    821  N   VAL   294      12.775   2.384  19.420  1.00  0.00              
ATOM    822  CA  VAL   294      11.923   2.769  20.533  1.00  0.00              
ATOM    823  C   VAL   294      10.938   1.619  20.700  1.00  0.00              
ATOM    824  O   VAL   294      10.417   1.108  19.704  1.00  0.00              
ATOM    825  N   THR   297      10.696   1.200  21.944  1.00  0.00              
ATOM    826  CA  THR   297       9.773   0.098  22.214  1.00  0.00              
ATOM    827  C   THR   297       8.536   0.165  21.324  1.00  0.00              
ATOM    828  O   THR   297       7.782   1.132  21.366  1.00  0.00              
ATOM    829  N   LEU   298       8.368  -0.876  20.513  1.00  0.00              
ATOM    830  CA  LEU   298       7.259  -0.983  19.583  1.00  0.00              
ATOM    831  C   LEU   298       5.856  -0.813  20.132  1.00  0.00              
ATOM    832  O   LEU   298       5.609  -0.913  21.340  1.00  0.00              
ATOM    833  N   GLU   299       4.923  -0.553  19.228  1.00  0.00              
ATOM    834  CA  GLU   299       3.537  -0.361  19.604  1.00  0.00              
ATOM    835  C   GLU   299       2.817  -1.706  19.663  1.00  0.00              
ATOM    836  O   GLU   299       2.934  -2.525  18.743  1.00  0.00              
ATOM    837  N   ARG   300       2.101  -1.945  20.763  1.00  0.00              
ATOM    838  CA  ARG   300       1.352  -3.188  20.934  1.00  0.00              
ATOM    839  C   ARG   300       0.321  -3.281  19.813  1.00  0.00              
ATOM    840  O   ARG   300      -0.698  -2.584  19.818  1.00  0.00              
ATOM    841  N   ALA   301       0.619  -4.135  18.844  1.00  0.00              
ATOM    842  CA  ALA   301      -0.247  -4.321  17.698  1.00  0.00              
ATOM    843  C   ALA   301       0.653  -4.585  16.511  1.00  0.00              
ATOM    844  O   ALA   301       0.510  -5.596  15.825  1.00  0.00              
ATOM    845  N   GLY   302       1.641  -3.713  16.329  1.00  0.00              
ATOM    846  CA  GLY   302       2.600  -3.838  15.236  1.00  0.00              
ATOM    847  C   GLY   302       3.344  -5.168  15.292  1.00  0.00              
ATOM    848  O   GLY   302       3.810  -5.685  14.273  1.00  0.00              
END
