
#######################################################
#                                                     #
#                        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   48 (  192),  selected   48 , name T0316AL316_4-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316AL316_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      G     220           -
LGA    R     221      R     221           -
LGA    M     222      M     222           -
LGA    M     223      M     223           -
LGA    T     224      T     224           -
LGA    V     225      V     225           -
LGA    D     226      D     226           -
LGA    G     227      G     227           -
LGA    R     228      R     228           -
LGA    D     229      D     229           -
LGA    M     230      M     230           -
LGA    G     231      G     231           -
LGA    E     232      -       -           -
LGA    H     233      -       -           -
LGA    A     234      -       -           -
LGA    G     235      -       -           -
LGA    L     236      -       -           -
LGA    M     237      -       -           -
LGA    Y     238      E     232           #
LGA    Y     239      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    T     240      G     246           #
LGA    G     242      L     247           #
LGA    Q     243      G     248          1.758
LGA    R     244      I     249          2.842
LGA    G     245      G     250          2.807
LGA    G     246      G     251          3.310
LGA    L     247      -       -           -
LGA    G     248      -       -           -
LGA    I     249      -       -           -
LGA    G     250      -       -           -
LGA    G     251      D     256           #
LGA    D     256      N     257          5.515
LGA    N     257      A     258          2.183
LGA    A     258      P     259           #
LGA    P     259      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    W     260      Q     276          2.817
LGA    F     261      G     277          2.490
LGA    V     262      F     278          4.584
LGA    V     263      Y     279          3.702
LGA    G     264      H     280          3.224
LGA    K     265      D     281          2.381
LGA    D     266      S     282          3.781
LGA    L     267      -       -           -
LGA    S     268      -       -           -
LGA    K     269      -       -           -
LGA    N     270      -       -           -
LGA    I     271      L     283          2.514
LGA    L     272      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   48   60    5.0     14    3.28    14.29     15.534     0.414

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.220500 * X  +  -0.257391 * Y  +   0.940813 * Z  + -40.340942
  Y_new =   0.628409 * X  +  -0.775180 * Y  +  -0.064795 * Z  +  66.646011
  Z_new =   0.745977 * X  +   0.576928 * Y  +   0.332674 * Z  + -89.829926 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.047738   -2.093855  [ DEG:    60.0310   -119.9690 ]
  Theta =  -0.842000   -2.299592  [ DEG:   -48.2431   -131.7569 ]
  Phi   =   1.908261   -1.233332  [ DEG:   109.3353    -70.6647 ]
 
# 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: T0316AL316_4-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL316_4-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   48   60   5.0   14   3.28   14.29  15.534
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL316_4-D2
REMARK Aligment from pdb entry: 1ct9_A
ATOM    773  N   GLY   220      60.096  45.288  -1.817  1.00  0.00              
ATOM    774  CA  GLY   220      58.868  45.536  -1.077  1.00  0.00              
ATOM    775  C   GLY   220      57.579  45.524  -1.884  1.00  0.00              
ATOM    776  O   GLY   220      56.528  45.135  -1.396  1.00  0.00              
ATOM    777  N   ARG   221      57.679  45.991  -3.116  1.00  0.00              
ATOM    778  CA  ARG   221      56.563  46.058  -4.010  1.00  0.00              
ATOM    779  C   ARG   221      56.036  44.674  -4.099  1.00  0.00              
ATOM    780  O   ARG   221      54.840  44.480  -4.060  1.00  0.00              
ATOM    781  N   MET   222      56.981  43.734  -4.186  1.00  0.00              
ATOM    782  CA  MET   222      56.667  42.313  -4.271  1.00  0.00              
ATOM    783  C   MET   222      56.060  41.742  -2.982  1.00  0.00              
ATOM    784  O   MET   222      54.973  41.172  -2.965  1.00  0.00              
ATOM    785  N   MET   223      56.794  41.920  -1.900  1.00  0.00              
ATOM    786  CA  MET   223      56.415  41.408  -0.605  1.00  0.00              
ATOM    787  C   MET   223      55.041  41.818  -0.163  1.00  0.00              
ATOM    788  O   MET   223      54.345  41.062   0.533  1.00  0.00              
ATOM    789  N   THR   224      54.658  43.033  -0.497  1.00  0.00              
ATOM    790  CA  THR   224      53.349  43.463  -0.035  1.00  0.00              
ATOM    791  C   THR   224      52.334  43.574  -1.130  1.00  0.00              
ATOM    792  O   THR   224      51.340  44.279  -1.025  1.00  0.00              
ATOM    793  N   VAL   225      52.627  42.804  -2.165  1.00  0.00              
ATOM    794  CA  VAL   225      51.787  42.732  -3.310  1.00  0.00              
ATOM    795  C   VAL   225      50.583  41.835  -3.046  1.00  0.00              
ATOM    796  O   VAL   225      50.729  40.618  -2.863  1.00  0.00              
ATOM    797  N   ASP   226      49.402  42.488  -3.063  1.00  0.00              
ATOM    798  CA  ASP   226      48.106  41.831  -2.922  1.00  0.00              
ATOM    799  C   ASP   226      47.667  41.266  -4.267  1.00  0.00              
ATOM    800  O   ASP   226      48.178  41.629  -5.325  1.00  0.00              
ATOM    801  N   GLY   227      46.662  40.404  -4.210  1.00  0.00              
ATOM    802  CA  GLY   227      46.139  39.838  -5.426  1.00  0.00              
ATOM    803  C   GLY   227      44.858  40.549  -5.798  1.00  0.00              
ATOM    804  O   GLY   227      44.219  41.177  -4.955  1.00  0.00              
ATOM    805  N   ARG   228      44.555  40.502  -7.088  1.00  0.00              
ATOM    806  CA  ARG   228      43.378  41.157  -7.537  1.00  0.00              
ATOM    807  C   ARG   228      42.420  40.336  -8.298  1.00  0.00              
ATOM    808  O   ARG   228      42.829  39.653  -9.206  1.00  0.00              
ATOM    809  N   ASP   229      41.160  40.456  -7.925  1.00  0.00              
ATOM    810  CA  ASP   229      40.162  39.675  -8.606  1.00  0.00              
ATOM    811  C   ASP   229      40.128  39.792 -10.118  1.00  0.00              
ATOM    812  O   ASP   229      40.095  38.807 -10.856  1.00  0.00              
ATOM    813  N   MET   230      40.054  41.052 -10.518  1.00  0.00              
ATOM    814  CA  MET   230      39.859  41.493 -11.870  1.00  0.00              
ATOM    815  C   MET   230      41.059  41.606 -12.803  1.00  0.00              
ATOM    816  O   MET   230      41.044  42.342 -13.795  1.00  0.00              
ATOM    817  N   GLY   231      42.080  40.805 -12.475  1.00  0.00              
ATOM    818  CA  GLY   231      43.323  40.677 -13.239  1.00  0.00              
ATOM    819  C   GLY   231      43.745  39.195 -13.429  1.00  0.00              
ATOM    820  O   GLY   231      43.809  38.431 -12.459  1.00  0.00              
ATOM    821  N   GLU   232      44.010  38.782 -14.686  1.00  0.00              
ATOM    822  CA  GLU   232      44.421  37.402 -15.055  1.00  0.00              
ATOM    823  C   GLU   232      45.906  37.311 -15.396  1.00  0.00              
ATOM    824  O   GLU   232      46.360  37.777 -16.446  1.00  0.00              
ATOM    825  N   HIS   233      46.661  36.709 -14.485  1.00  0.00              
ATOM    826  CA  HIS   233      48.114  36.594 -14.575  1.00  0.00              
ATOM    827  C   HIS   233      48.715  36.282 -15.915  1.00  0.00              
ATOM    828  O   HIS   233      49.658  36.955 -16.375  1.00  0.00              
ATOM    829  N   ALA   234      48.151  35.236 -16.502  1.00  0.00              
ATOM    830  CA  ALA   234      48.574  34.714 -17.798  1.00  0.00              
ATOM    831  C   ALA   234      48.080  35.529 -18.995  1.00  0.00              
ATOM    832  O   ALA   234      48.587  35.456 -20.122  1.00  0.00              
ATOM    833  N   GLY   235      47.077  36.325 -18.717  1.00  0.00              
ATOM    834  CA  GLY   235      46.500  37.182 -19.723  1.00  0.00              
ATOM    835  C   GLY   235      45.014  36.921 -19.875  1.00  0.00              
ATOM    836  O   GLY   235      44.560  35.836 -20.198  1.00  0.00              
ATOM    837  N   LEU   236      44.256  37.968 -19.643  1.00  0.00              
ATOM    838  CA  LEU   236      42.823  37.912 -19.763  1.00  0.00              
ATOM    839  C   LEU   236      42.220  37.203 -20.983  1.00  0.00              
ATOM    840  O   LEU   236      41.124  36.641 -20.927  1.00  0.00              
ATOM    841  N   MET   237      42.891  37.278 -22.114  1.00  0.00              
ATOM    842  CA  MET   237      42.401  36.700 -23.353  1.00  0.00              
ATOM    843  C   MET   237      42.324  35.183 -23.317  1.00  0.00              
ATOM    844  O   MET   237      41.531  34.553 -24.015  1.00  0.00              
ATOM    845  N   TYR   238      43.178  34.581 -22.505  1.00  0.00              
ATOM    846  CA  TYR   238      43.177  33.136 -22.427  1.00  0.00              
ATOM    847  C   TYR   238      41.788  32.552 -22.093  1.00  0.00              
ATOM    848  O   TYR   238      41.126  31.907 -22.887  1.00  0.00              
ATOM    849  N   TYR   239      41.298  32.833 -20.913  1.00  0.00              
ATOM    850  CA  TYR   239      39.992  32.327 -20.587  1.00  0.00              
ATOM    851  C   TYR   239      38.888  32.820 -21.485  1.00  0.00              
ATOM    852  O   TYR   239      38.029  32.063 -21.911  1.00  0.00              
ATOM    853  N   THR   240      38.935  34.102 -21.730  1.00  0.00              
ATOM    854  CA  THR   240      37.978  34.781 -22.567  1.00  0.00              
ATOM    855  C   THR   240      37.773  34.025 -23.855  1.00  0.00              
ATOM    856  O   THR   240      36.661  33.879 -24.321  1.00  0.00              
ATOM    857  N   GLY   242      38.869  33.517 -24.395  1.00  0.00              
ATOM    858  CA  GLY   242      38.821  32.772 -25.615  1.00  0.00              
ATOM    859  C   GLY   242      38.366  31.361 -25.352  1.00  0.00              
ATOM    860  O   GLY   242      37.711  30.736 -26.180  1.00  0.00              
ATOM    861  N   GLN   243      38.735  30.858 -24.181  1.00  0.00              
ATOM    862  CA  GLN   243      38.323  29.518 -23.844  1.00  0.00              
ATOM    863  C   GLN   243      36.815  29.519 -23.756  1.00  0.00              
ATOM    864  O   GLN   243      36.177  28.606 -24.237  1.00  0.00              
ATOM    865  N   ARG   244      36.237  30.518 -23.091  1.00  0.00              
ATOM    866  CA  ARG   244      34.790  30.544 -22.951  1.00  0.00              
ATOM    867  C   ARG   244      34.077  30.662 -24.291  1.00  0.00              
ATOM    868  O   ARG   244      33.104  29.980 -24.605  1.00  0.00              
ATOM    869  N   GLY   245      34.616  31.567 -25.068  1.00  0.00              
ATOM    870  CA  GLY   245      34.149  31.907 -26.385  1.00  0.00              
ATOM    871  C   GLY   245      34.072  30.712 -27.310  1.00  0.00              
ATOM    872  O   GLY   245      33.137  30.507 -28.075  1.00  0.00              
ATOM    873  N   GLY   246      35.102  29.911 -27.240  1.00  0.00              
ATOM    874  CA  GLY   246      35.204  28.742 -28.064  1.00  0.00              
ATOM    875  C   GLY   246      34.174  27.685 -27.667  1.00  0.00              
ATOM    876  O   GLY   246      33.590  27.004 -28.506  1.00  0.00              
ATOM    877  N   LEU   247      33.954  27.565 -26.370  1.00  0.00              
ATOM    878  CA  LEU   247      33.027  26.597 -25.851  1.00  0.00              
ATOM    879  C   LEU   247      31.632  26.944 -26.252  1.00  0.00              
ATOM    880  O   LEU   247      30.846  26.069 -26.595  1.00  0.00              
ATOM    881  N   GLY   248      31.328  28.231 -26.156  1.00  0.00              
ATOM    882  CA  GLY   248      30.013  28.720 -26.502  1.00  0.00              
ATOM    883  C   GLY   248      29.703  28.400 -27.942  1.00  0.00              
ATOM    884  O   GLY   248      28.610  27.976 -28.313  1.00  0.00              
ATOM    885  N   ILE   249      30.710  28.572 -28.767  1.00  0.00              
ATOM    886  CA  ILE   249      30.519  28.341 -30.182  1.00  0.00              
ATOM    887  C   ILE   249      30.488  26.877 -30.569  1.00  0.00              
ATOM    888  O   ILE   249      30.034  26.474 -31.635  1.00  0.00              
ATOM    889  N   GLY   250      30.966  26.042 -29.691  1.00  0.00              
ATOM    890  CA  GLY   250      31.031  24.664 -30.089  1.00  0.00              
ATOM    891  C   GLY   250      30.016  23.761 -29.439  1.00  0.00              
ATOM    892  O   GLY   250      29.831  22.624 -29.863  1.00  0.00              
ATOM    893  N   GLY   251      29.354  24.273 -28.411  1.00  0.00              
ATOM    894  CA  GLY   251      28.401  23.443 -27.701  1.00  0.00              
ATOM    895  C   GLY   251      27.032  24.037 -27.797  1.00  0.00              
ATOM    896  O   GLY   251      26.859  25.194 -27.477  1.00  0.00              
ATOM    897  N   ASP   256      26.070  23.242 -28.230  1.00  0.00              
ATOM    898  CA  ASP   256      24.727  23.757 -28.363  1.00  0.00              
ATOM    899  C   ASP   256      24.017  23.863 -27.074  1.00  0.00              
ATOM    900  O   ASP   256      24.313  23.197 -26.091  1.00  0.00              
ATOM    901  N   ASN   257      23.044  24.738 -27.118  1.00  0.00              
ATOM    902  CA  ASN   257      22.245  24.972 -25.956  1.00  0.00              
ATOM    903  C   ASN   257      21.572  23.685 -25.510  1.00  0.00              
ATOM    904  O   ASN   257      21.475  23.351 -24.335  1.00  0.00              
ATOM    905  N   ALA   258      21.116  22.953 -26.496  1.00  0.00              
ATOM    906  CA  ALA   258      20.440  21.723 -26.243  1.00  0.00              
ATOM    907  C   ALA   258      21.355  20.665 -25.686  1.00  0.00              
ATOM    908  O   ALA   258      20.957  19.947 -24.763  1.00  0.00              
ATOM    909  N   PRO   259      22.560  20.573 -26.282  1.00  0.00              
ATOM    910  CA  PRO   259      23.521  19.555 -25.855  1.00  0.00              
ATOM    911  C   PRO   259      23.717  19.781 -24.393  1.00  0.00              
ATOM    912  O   PRO   259      23.850  18.875 -23.583  1.00  0.00              
ATOM    913  N   TRP   260      23.712  21.073 -24.069  1.00  0.00              
ATOM    914  CA  TRP   260      23.870  21.436 -22.689  1.00  0.00              
ATOM    915  C   TRP   260      22.653  21.044 -21.888  1.00  0.00              
ATOM    916  O   TRP   260      22.769  20.446 -20.806  1.00  0.00              
ATOM    917  N   PHE   261      21.492  21.379 -22.441  1.00  0.00              
ATOM    918  CA  PHE   261      20.266  21.055 -21.758  1.00  0.00              
ATOM    919  C   PHE   261      20.109  19.563 -21.556  1.00  0.00              
ATOM    920  O   PHE   261      19.635  19.082 -20.523  1.00  0.00              
ATOM    921  N   VAL   262      20.526  18.792 -22.539  1.00  0.00              
ATOM    922  CA  VAL   262      20.386  17.383 -22.340  1.00  0.00              
ATOM    923  C   VAL   262      21.605  16.651 -21.767  1.00  0.00              
ATOM    924  O   VAL   262      21.597  15.429 -21.749  1.00  0.00              
ATOM    925  N   VAL   263      22.648  17.373 -21.331  1.00  0.00              
ATOM    926  CA  VAL   263      23.910  16.803 -20.782  1.00  0.00              
ATOM    927  C   VAL   263      23.742  15.529 -19.953  1.00  0.00              
ATOM    928  O   VAL   263      24.511  14.571 -20.046  1.00  0.00              
ATOM    929  N   GLY   264      22.722  15.588 -19.091  1.00  0.00              
ATOM    930  CA  GLY   264      22.434  14.503 -18.194  1.00  0.00              
ATOM    931  C   GLY   264      22.219  13.163 -18.897  1.00  0.00              
ATOM    932  O   GLY   264      22.606  12.122 -18.405  1.00  0.00              
ATOM    933  N   LYS   265      21.663  13.149 -20.086  1.00  0.00              
ATOM    934  CA  LYS   265      21.487  11.869 -20.759  1.00  0.00              
ATOM    935  C   LYS   265      22.774  11.304 -21.265  1.00  0.00              
ATOM    936  O   LYS   265      22.836  10.128 -21.632  1.00  0.00              
ATOM    937  N   ASP   266      23.777  12.167 -21.345  1.00  0.00              
ATOM    938  CA  ASP   266      25.047  11.729 -21.903  1.00  0.00              
ATOM    939  C   ASP   266      26.109  11.549 -20.886  1.00  0.00              
ATOM    940  O   ASP   266      26.826  10.551 -21.017  1.00  0.00              
ATOM    941  N   LEU   267      26.135  12.478 -19.895  1.00  0.00              
ATOM    942  CA  LEU   267      27.073  12.537 -18.783  1.00  0.00              
ATOM    943  C   LEU   267      26.317  12.575 -17.509  1.00  0.00              
ATOM    944  O   LEU   267      26.229  13.630 -16.855  1.00  0.00              
ATOM    945  N   SER   268      25.782  11.408 -17.191  1.00  0.00              
ATOM    946  CA  SER   268      24.963  11.232 -16.010  1.00  0.00              
ATOM    947  C   SER   268      25.751  11.494 -14.710  1.00  0.00              
ATOM    948  O   SER   268      25.177  11.966 -13.732  1.00  0.00              
ATOM    949  N   LYS   269      27.065  11.194 -14.697  1.00  0.00              
ATOM    950  CA  LYS   269      27.921  11.448 -13.529  1.00  0.00              
ATOM    951  C   LYS   269      28.515  12.858 -13.601  1.00  0.00              
ATOM    952  O   LYS   269      29.128  13.225 -14.624  1.00  0.00              
ATOM    953  N   ASN   270      28.296  13.634 -12.519  1.00  0.00              
ATOM    954  CA  ASN   270      28.792  14.998 -12.420  1.00  0.00              
ATOM    955  C   ASN   270      28.509  15.747 -13.693  1.00  0.00              
ATOM    956  O   ASN   270      29.453  16.187 -14.328  1.00  0.00              
ATOM    957  N   ILE   271      27.262  15.828 -14.078  1.00  0.00              
ATOM    958  CA  ILE   271      26.911  16.468 -15.321  1.00  0.00              
ATOM    959  C   ILE   271      27.514  17.844 -15.469  1.00  0.00              
ATOM    960  O   ILE   271      27.416  18.645 -14.537  1.00  0.00              
ATOM    961  N   LEU   272      28.131  18.111 -16.639  1.00  0.00              
ATOM    962  CA  LEU   272      28.681  19.444 -16.919  1.00  0.00              
ATOM    963  C   LEU   272      27.530  20.441 -16.877  1.00  0.00              
ATOM    964  O   LEU   272      26.495  20.203 -17.509  1.00  0.00              
END
