
#######################################################
#                                                     #
#                        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   37 (  148),  selected   37 , name T0316AL044_4-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316AL044_4-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    T     224      -       -           -
LGA    D     226      -       -           -
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      G     220          2.859
LGA    Y     238      R     221          0.683
LGA    Y     239      -       -           -
LGA    T     240      -       -           -
LGA    I     241      M     222          2.620
LGA    G     242      M     223          2.068
LGA    Q     243      T     224          2.594
LGA    G     246      V     225          3.275
LGA    L     247      D     226          5.778
LGA    G     254      G     227           -
LGA    -       -      R     228           -
LGA    -       -      D     229           -
LGA    G     255      M     230           #
LGA    D     256      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     246           -
LGA    -       -      L     247           -
LGA    -       -      G     248           -
LGA    -       -      I     249           -
LGA    -       -      G     250           -
LGA    -       -      G     251           -
LGA    N     257      D     256          1.384
LGA    A     258      N     257          1.260
LGA    W     260      A     258          1.041
LGA    F     261      P     259          3.706
LGA    -       -      W     260           -
LGA    -       -      F     261           -
LGA    -       -      V     262           -
LGA    -       -      V     263           -
LGA    -       -      G     264           -
LGA    -       -      K     265           -
LGA    -       -      D     266           -
LGA    -       -      L     267           -
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    -       -      I     271           -
LGA    -       -      L     272           -
LGA    -       -      Y     273           -
LGA    -       -      V     274           -
LGA    -       -      G     275           -
LGA    -       -      Q     276           -
LGA    V     262      G     277          1.317
LGA    V     263      F     278          1.578
LGA    G     264      Y     279          1.062
LGA    K     265      H     280          0.983
LGA    D     266      D     281           #
LGA    L     267      S     282          5.870
LGA    S     268      L     283          1.254
LGA    L     272      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   37   60    5.0     17    2.78     0.00     19.905     0.590

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.846348 * X  +  -0.227348 * Y  +  -0.481672 * Z  + 105.135223
  Y_new =   0.026710 * X  +   0.921305 * Y  +  -0.387921 * Z  +  54.505768
  Z_new =   0.531960 * X  +   0.315451 * Y  +   0.785817 * Z  + -46.887421 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.381739   -2.759854  [ DEG:    21.8720   -158.1280 ]
  Theta =  -0.560914   -2.580679  [ DEG:   -32.1380   -147.8620 ]
  Phi   =   0.031549   -3.110044  [ DEG:     1.8076   -178.1924 ]
 
# 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_4-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL044_4-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   37   60   5.0   17   2.78    0.00  19.905
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL044_4-D2
REMARK Aligment from pdb entry: 1wy5_A
ATOM    641  N   GLY   220      65.164  24.906  -9.958  1.00  0.00              
ATOM    642  CA  GLY   220      64.863  25.065 -11.386  1.00  0.00              
ATOM    643  C   GLY   220      64.730  23.737 -12.131  1.00  0.00              
ATOM    644  O   GLY   220      63.800  23.557 -12.915  1.00  0.00              
ATOM    645  N   ARG   221      65.647  22.808 -11.890  1.00  0.00              
ATOM    646  CA  ARG   221      65.595  21.513 -12.560  1.00  0.00              
ATOM    647  C   ARG   221      64.336  20.768 -12.151  1.00  0.00              
ATOM    648  O   ARG   221      63.677  20.123 -12.967  1.00  0.00              
ATOM    649  N   MET   222      64.008  20.863 -10.875  1.00  0.00              
ATOM    650  CA  MET   222      62.827  20.217 -10.342  1.00  0.00              
ATOM    651  C   MET   222      61.539  20.845 -10.903  1.00  0.00              
ATOM    652  O   MET   222      60.610  20.144 -11.323  1.00  0.00              
ATOM    653  N   THR   224      61.504  22.171 -10.908  1.00  0.00              
ATOM    654  CA  THR   224      60.374  22.921 -11.415  1.00  0.00              
ATOM    655  C   THR   224      60.078  22.560 -12.880  1.00  0.00              
ATOM    656  O   THR   224      58.917  22.346 -13.249  1.00  0.00              
ATOM    657  N   ASP   226      61.122  22.493 -13.709  1.00  0.00              
ATOM    658  CA  ASP   226      60.946  22.151 -15.122  1.00  0.00              
ATOM    659  C   ASP   226      60.225  20.820 -15.298  1.00  0.00              
ATOM    660  O   ASP   226      59.411  20.667 -16.206  1.00  0.00              
ATOM    661  N   ASP   229      60.519  19.849 -14.438  1.00  0.00              
ATOM    662  CA  ASP   229      59.856  18.555 -14.546  1.00  0.00              
ATOM    663  C   ASP   229      58.364  18.694 -14.257  1.00  0.00              
ATOM    664  O   ASP   229      57.541  18.036 -14.897  1.00  0.00              
ATOM    665  N   MET   230      58.022  19.554 -13.300  1.00  0.00              
ATOM    666  CA  MET   230      56.625  19.795 -12.944  1.00  0.00              
ATOM    667  C   MET   230      55.932  20.380 -14.169  1.00  0.00              
ATOM    668  O   MET   230      54.868  19.915 -14.572  1.00  0.00              
ATOM    669  N   GLY   231      56.642  20.128 -17.308  1.00  0.00              
ATOM    670  CA  GLY   231      56.429  19.109 -18.324  1.00  0.00              
ATOM    671  C   GLY   231      55.296  18.156 -17.941  1.00  0.00              
ATOM    672  O   GLY   231      54.503  17.751 -18.792  1.00  0.00              
ATOM    673  N   GLU   232      55.207  17.790 -16.669  1.00  0.00              
ATOM    674  CA  GLU   232      54.119  16.915 -16.266  1.00  0.00              
ATOM    675  C   GLU   232      52.799  17.685 -16.445  1.00  0.00              
ATOM    676  O   GLU   232      51.849  17.183 -17.061  1.00  0.00              
ATOM    677  N   HIS   233      52.751  18.913 -15.927  1.00  0.00              
ATOM    678  CA  HIS   233      51.553  19.737 -16.030  1.00  0.00              
ATOM    679  C   HIS   233      51.104  19.952 -17.475  1.00  0.00              
ATOM    680  O   HIS   233      49.918  19.821 -17.777  1.00  0.00              
ATOM    681  N   ALA   234      52.037  20.260 -18.374  1.00  0.00              
ATOM    682  CA  ALA   234      51.673  20.478 -19.773  1.00  0.00              
ATOM    683  C   ALA   234      51.067  19.259 -20.469  1.00  0.00              
ATOM    684  O   ALA   234      50.201  19.416 -21.324  1.00  0.00              
ATOM    685  N   GLY   235      51.505  18.052 -20.117  1.00  0.00              
ATOM    686  CA  GLY   235      50.934  16.857 -20.736  1.00  0.00              
ATOM    687  C   GLY   235      49.537  16.648 -20.159  1.00  0.00              
ATOM    688  O   GLY   235      48.599  16.297 -20.874  1.00  0.00              
ATOM    689  N   LEU   236      49.396  16.886 -18.858  1.00  0.00              
ATOM    690  CA  LEU   236      48.101  16.732 -18.208  1.00  0.00              
ATOM    691  C   LEU   236      47.102  17.766 -18.742  1.00  0.00              
ATOM    692  O   LEU   236      45.922  17.463 -18.918  1.00  0.00              
ATOM    693  N   MET   237      47.572  18.982 -19.015  1.00  0.00              
ATOM    694  CA  MET   237      46.691  20.024 -19.540  1.00  0.00              
ATOM    695  C   MET   237      46.263  19.650 -20.954  1.00  0.00              
ATOM    696  O   MET   237      45.088  19.737 -21.309  1.00  0.00              
ATOM    697  N   TYR   238      42.481  19.245 -22.274  1.00  0.00              
ATOM    698  CA  TYR   238      41.972  20.024 -23.396  1.00  0.00              
ATOM    699  C   TYR   238      41.410  19.124 -24.511  1.00  0.00              
ATOM    700  O   TYR   238      40.324  19.389 -25.033  1.00  0.00              
ATOM    701  N   TYR   239      42.129  18.053 -24.853  1.00  0.00              
ATOM    702  CA  TYR   239      41.681  17.122 -25.898  1.00  0.00              
ATOM    703  C   TYR   239      40.357  16.471 -25.516  1.00  0.00              
ATOM    704  O   TYR   239      39.481  16.275 -26.359  1.00  0.00              
ATOM    705  N   THR   240      40.223  16.120 -24.241  1.00  0.00              
ATOM    706  CA  THR   240      39.005  15.484 -23.766  1.00  0.00              
ATOM    707  C   THR   240      37.856  16.480 -23.686  1.00  0.00              
ATOM    708  O   THR   240      36.729  16.163 -24.059  1.00  0.00              
ATOM    709  N   ILE   241      38.145  17.687 -23.214  1.00  0.00              
ATOM    710  CA  ILE   241      37.115  18.707 -23.099  1.00  0.00              
ATOM    711  C   ILE   241      36.588  19.087 -24.478  1.00  0.00              
ATOM    712  O   ILE   241      35.439  19.507 -24.619  1.00  0.00              
ATOM    713  N   GLY   242      37.433  18.927 -25.493  1.00  0.00              
ATOM    714  CA  GLY   242      37.057  19.258 -26.862  1.00  0.00              
ATOM    715  C   GLY   242      36.108  18.214 -27.447  1.00  0.00              
ATOM    716  O   GLY   242      35.134  18.559 -28.116  1.00  0.00              
ATOM    717  N   GLN   243      36.390  16.941 -27.193  1.00  0.00              
ATOM    718  CA  GLN   243      35.539  15.870 -27.696  1.00  0.00              
ATOM    719  C   GLN   243      34.141  16.028 -27.108  1.00  0.00              
ATOM    720  O   GLN   243      33.141  15.962 -27.827  1.00  0.00              
ATOM    721  N   GLY   246      34.085  16.233 -25.795  1.00  0.00              
ATOM    722  CA  GLY   246      32.822  16.390 -25.088  1.00  0.00              
ATOM    723  C   GLY   246      32.102  17.648 -25.566  1.00  0.00              
ATOM    724  O   GLY   246      30.875  17.676 -25.651  1.00  0.00              
ATOM    725  N   LEU   247      30.232  17.364 -28.698  1.00  0.00              
ATOM    726  CA  LEU   247      29.363  16.214 -28.502  1.00  0.00              
ATOM    727  C   LEU   247      28.118  16.649 -27.741  1.00  0.00              
ATOM    728  O   LEU   247      27.060  16.023 -27.831  1.00  0.00              
ATOM    729  N   GLY   254      28.261  17.737 -26.994  1.00  0.00              
ATOM    730  CA  GLY   254      27.176  18.281 -26.195  1.00  0.00              
ATOM    731  C   GLY   254      26.661  19.595 -26.783  1.00  0.00              
ATOM    732  O   GLY   254      25.616  20.108 -26.373  1.00  0.00              
ATOM    733  N   GLY   255      27.394  20.137 -27.750  1.00  0.00              
ATOM    734  CA  GLY   255      26.986  21.388 -28.371  1.00  0.00              
ATOM    735  C   GLY   255      26.180  21.167 -29.643  1.00  0.00              
ATOM    736  O   GLY   255      26.428  20.227 -30.402  1.00  0.00              
ATOM    737  N   ASP   256      25.205  22.046 -29.853  1.00  0.00              
ATOM    738  CA  ASP   256      24.333  22.011 -31.020  1.00  0.00              
ATOM    739  C   ASP   256      23.800  23.425 -31.230  1.00  0.00              
ATOM    740  O   ASP   256      22.935  23.901 -30.488  1.00  0.00              
ATOM    741  N   ASN   257      24.339  24.096 -32.243  1.00  0.00              
ATOM    742  CA  ASN   257      23.936  25.459 -32.515  1.00  0.00              
ATOM    743  C   ASN   257      24.678  26.351 -31.543  1.00  0.00              
ATOM    744  O   ASN   257      25.905  26.384 -31.541  1.00  0.00              
ATOM    745  N   ALA   258      23.933  27.070 -30.712  1.00  0.00              
ATOM    746  CA  ALA   258      24.517  27.956 -29.710  1.00  0.00              
ATOM    747  C   ALA   258      24.123  27.451 -28.333  1.00  0.00              
ATOM    748  O   ALA   258      24.138  28.205 -27.361  1.00  0.00              
ATOM    749  N   TRP   260      23.765  26.174 -28.248  1.00  0.00              
ATOM    750  CA  TRP   260      23.341  25.611 -26.976  1.00  0.00              
ATOM    751  C   TRP   260      24.115  24.369 -26.551  1.00  0.00              
ATOM    752  O   TRP   260      24.803  23.740 -27.358  1.00  0.00              
ATOM    753  N   PHE   261      23.991  24.031 -25.270  1.00  0.00              
ATOM    754  CA  PHE   261      24.669  22.880 -24.687  1.00  0.00              
ATOM    755  C   PHE   261      23.654  21.902 -24.110  1.00  0.00              
ATOM    756  O   PHE   261      22.735  22.303 -23.396  1.00  0.00              
ATOM    757  N   VAL   262      23.820  20.621 -24.425  1.00  0.00              
ATOM    758  CA  VAL   262      22.920  19.581 -23.931  1.00  0.00              
ATOM    759  C   VAL   262      23.197  19.352 -22.446  1.00  0.00              
ATOM    760  O   VAL   262      24.113  18.612 -22.083  1.00  0.00              
ATOM    761  N   VAL   263      22.397  19.986 -21.595  1.00  0.00              
ATOM    762  CA  VAL   263      22.555  19.883 -20.149  1.00  0.00              
ATOM    763  C   VAL   263      22.358  18.468 -19.604  1.00  0.00              
ATOM    764  O   VAL   263      23.004  18.075 -18.634  1.00  0.00              
ATOM    765  N   GLY   264      21.479  17.694 -20.224  1.00  0.00              
ATOM    766  CA  GLY   264      21.237  16.340 -19.746  1.00  0.00              
ATOM    767  C   GLY   264      22.383  15.394 -20.082  1.00  0.00              
ATOM    768  O   GLY   264      22.436  14.269 -19.583  1.00  0.00              
ATOM    769  N   LYS   265      23.304  15.859 -20.921  1.00  0.00              
ATOM    770  CA  LYS   265      24.470  15.066 -21.291  1.00  0.00              
ATOM    771  C   LYS   265      25.688  15.537 -20.501  1.00  0.00              
ATOM    772  O   LYS   265      26.446  14.724 -19.972  1.00  0.00              
ATOM    773  N   ASP   266      25.863  16.854 -20.420  1.00  0.00              
ATOM    774  CA  ASP   266      26.989  17.458 -19.710  1.00  0.00              
ATOM    775  C   ASP   266      27.026  17.110 -18.227  1.00  0.00              
ATOM    776  O   ASP   266      28.059  16.696 -17.698  1.00  0.00              
ATOM    777  N   LEU   267      25.889  17.298 -17.568  1.00  0.00              
ATOM    778  CA  LEU   267      25.730  17.042 -16.140  1.00  0.00              
ATOM    779  C   LEU   267      26.193  15.653 -15.685  1.00  0.00              
ATOM    780  O   LEU   267      26.568  15.462 -14.528  1.00  0.00              
ATOM    781  N   SER   268      26.181  14.692 -16.600  1.00  0.00              
ATOM    782  CA  SER   268      26.590  13.329 -16.280  1.00  0.00              
ATOM    783  C   SER   268      28.096  13.131 -16.438  1.00  0.00              
ATOM    784  O   SER   268      28.602  12.030 -16.223  1.00  0.00              
ATOM    785  N   LEU   272      28.807  14.190 -16.819  1.00  0.00              
ATOM    786  CA  LEU   272      30.248  14.110 -17.039  1.00  0.00              
ATOM    787  C   LEU   272      31.075  14.575 -15.836  1.00  0.00              
ATOM    788  O   LEU   272      30.553  15.211 -14.922  1.00  0.00              
END
