
#######################################################
#                                                     #
#                        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   44 (  176),  selected   44 , name T0372AL333_4-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372AL333_4-D1.T0372_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    I       2      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    P       3      F      39           #
LGA    D       6      L      40           #
LGA    I       7      Y      41          5.362
LGA    T       8      D      42           #
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    L       9      F      45          3.040
LGA    A      10      A      46          4.161
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    D      11      V      53          4.265
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    R      12      P      67          4.979
LGA    D      13      V      68          4.158
LGA    T      14      G      69          2.976
LGA    G      71      N      70          3.423
LGA    D      72      G      71          3.937
LGA    -       -      D      72           -
LGA    L      73      L      73          2.865
LGA    K      74      K      74          2.917
LGA    A      75      A      75          4.156
LGA    V      76      V      76          3.439
LGA    L      77      L      77          0.894
LGA    R      78      R      78          1.787
LGA    -       -      K      79           -
LGA    K      79      L      80          2.378
LGA    L      80      I      81          1.670
LGA    I      81      E      82          2.606
LGA    E      82      D      83          3.574
LGA    D      83      A      84          2.568
LGA    A      84      D      85          1.995
LGA    D      85      K      86          5.183
LGA    K      86      E      87          4.957
LGA    E      87      K      88          1.380
LGA    K      88      H      89          1.468
LGA    H      89      N      90          2.593
LGA    N      90      F      91          2.434
LGA    F      91      C      92          1.793
LGA    C      92      M      93          2.191
LGA    M      93      L      94          3.765
LGA    -       -      G      95           -
LGA    L      94      V      96          2.128
LGA    G      95      C      97          1.243
LGA    V      96      S      98          1.793
LGA    C      97      N      99          3.691
LGA    T     115      M     100           -
LGA    E     116      R     101           #
LGA    D     117      A     102          4.908
LGA    D     297      D     103           -
LGA    H     298      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44  126    5.0     35    3.28    20.00     17.303     1.034

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.837895 * X  +   0.544013 * Y  +  -0.044504 * Z  +  39.470043
  Y_new =  -0.545704 * X  +  -0.836667 * Y  +   0.046850 * Z  +  40.719913
  Z_new =  -0.011748 * X  +   0.063541 * Y  +   0.997910 * Z  + -20.260153 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.063589   -3.078004  [ DEG:     3.6434   -176.3566 ]
  Theta =   0.011748    3.129844  [ DEG:     0.6731    179.3269 ]
  Phi   =  -2.564318    0.577274  [ DEG:  -146.9246     33.0754 ]
 
# 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: T0372AL333_4-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372AL333_4-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44  126   5.0   35   3.28   20.00  17.303
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL333_4-D1
REMARK Aligment from pdb entry: 1gm5_A
ATOM      1  N   MET     1      54.092  36.256  -0.293  1.00  0.00              
ATOM      2  CA  MET     1      53.759  36.834  -1.585  1.00  0.00              
ATOM      3  C   MET     1      52.552  37.693  -1.241  1.00  0.00              
ATOM      4  O   MET     1      51.931  38.417  -2.083  1.00  0.00              
ATOM      5  N   ILE     2      52.147  37.602   0.013  1.00  0.00              
ATOM      6  CA  ILE     2      50.900  38.213   0.149  1.00  0.00              
ATOM      7  C   ILE     2      51.027  39.557   0.665  1.00  0.00              
ATOM      8  O   ILE     2      51.463  39.850   1.829  1.00  0.00              
ATOM      9  N   PRO     3      50.546  40.309  -0.273  1.00  0.00              
ATOM     10  CA  PRO     3      50.474  41.706  -0.226  1.00  0.00              
ATOM     11  C   PRO     3      49.100  42.005   0.313  1.00  0.00              
ATOM     12  O   PRO     3      48.191  41.153   0.202  1.00  0.00              
ATOM     13  N   ASP     6      48.946  43.201   0.859  1.00  0.00              
ATOM     14  CA  ASP     6      47.683  43.533   1.476  1.00  0.00              
ATOM     15  C   ASP     6      47.048  44.858   1.157  1.00  0.00              
ATOM     16  O   ASP     6      47.723  45.828   0.808  1.00  0.00              
ATOM     17  N   ILE     7      45.762  44.887   1.366  1.00  0.00              
ATOM     18  CA  ILE     7      44.973  46.046   1.131  1.00  0.00              
ATOM     19  C   ILE     7      45.505  47.391   1.607  1.00  0.00              
ATOM     20  O   ILE     7      45.542  47.639   2.789  1.00  0.00              
ATOM     21  N   THR     8      45.849  48.277   0.682  1.00  0.00              
ATOM     22  CA  THR     8      46.132  49.671   1.037  1.00  0.00              
ATOM     23  C   THR     8      44.792  50.203   1.553  1.00  0.00              
ATOM     24  O   THR     8      43.848  50.425   0.818  1.00  0.00              
ATOM     25  N   LEU     9      44.630  50.194   2.871  1.00  0.00              
ATOM     26  CA  LEU     9      43.426  50.700   3.502  1.00  0.00              
ATOM     27  C   LEU     9      43.551  52.211   3.634  1.00  0.00              
ATOM     28  O   LEU     9      44.580  52.709   4.101  1.00  0.00              
ATOM     29  N   ALA    10      42.524  52.956   3.250  1.00  0.00              
ATOM     30  CA  ALA    10      42.567  54.395   3.444  1.00  0.00              
ATOM     31  C   ALA    10      41.311  54.847   4.135  1.00  0.00              
ATOM     32  O   ALA    10      40.278  54.182   4.057  1.00  0.00              
ATOM     33  N   ASP    11      41.398  55.979   4.825  1.00  0.00              
ATOM     34  CA  ASP    11      40.247  56.578   5.493  1.00  0.00              
ATOM     35  C   ASP    11      40.009  57.956   4.945  1.00  0.00              
ATOM     36  O   ASP    11      40.883  58.787   4.936  1.00  0.00              
ATOM     37  N   ARG    12      38.806  58.192   4.478  1.00  0.00              
ATOM     38  CA  ARG    12      38.501  59.408   3.757  1.00  0.00              
ATOM     39  C   ARG    12      37.352  60.159   4.413  1.00  0.00              
ATOM     40  O   ARG    12      36.327  59.578   4.756  1.00  0.00              
ATOM     41  N   ASP    13      37.527  61.466   4.568  1.00  0.00              
ATOM     42  CA  ASP    13      36.439  62.376   4.926  1.00  0.00              
ATOM     43  C   ASP    13      35.241  62.202   4.022  1.00  0.00              
ATOM     44  O   ASP    13      35.348  61.637   2.941  1.00  0.00              
ATOM     45  N   THR    14      34.099  62.708   4.451  1.00  0.00              
ATOM     46  CA  THR    14      32.985  62.738   3.550  1.00  0.00              
ATOM     47  C   THR    14      33.332  63.665   2.397  1.00  0.00              
ATOM     48  O   THR    14      34.354  63.489   1.736  1.00  0.00              
ATOM     49  N   GLY    71      32.477  64.652   2.166  1.00  0.00              
ATOM     50  CA  GLY    71      32.627  65.585   1.054  1.00  0.00              
ATOM     51  C   GLY    71      33.381  64.942  -0.073  1.00  0.00              
ATOM     52  O   GLY    71      32.823  64.685  -1.135  1.00  0.00              
ATOM     53  N   ASP    72      34.661  64.694   0.164  1.00  0.00              
ATOM     54  CA  ASP    72      35.518  64.005  -0.796  1.00  0.00              
ATOM     55  C   ASP    72      35.061  62.578  -1.108  1.00  0.00              
ATOM     56  O   ASP    72      35.863  61.728  -1.498  1.00  0.00              
ATOM     57  N   LEU    73      33.774  62.318  -0.917  1.00  0.00              
ATOM     58  CA  LEU    73      33.240  60.983  -1.096  1.00  0.00              
ATOM     59  C   LEU    73      33.113  60.722  -2.567  1.00  0.00              
ATOM     60  O   LEU    73      33.293  59.598  -3.009  1.00  0.00              
ATOM     61  N   LYS    74      32.777  61.771  -3.314  1.00  0.00              
ATOM     62  CA  LYS    74      32.612  61.643  -4.738  1.00  0.00              
ATOM     63  C   LYS    74      33.974  61.387  -5.269  1.00  0.00              
ATOM     64  O   LYS    74      34.177  61.157  -6.451  1.00  0.00              
ATOM     65  N   ALA    75      34.922  61.376  -4.362  1.00  0.00              
ATOM     66  CA  ALA    75      36.282  61.147  -4.769  1.00  0.00              
ATOM     67  C   ALA    75      36.409  59.674  -5.048  1.00  0.00              
ATOM     68  O   ALA    75      36.674  59.251  -6.166  1.00  0.00              
ATOM     69  N   VAL    76      36.205  58.886  -4.004  1.00  0.00              
ATOM     70  CA  VAL    76      36.209  57.446  -4.140  1.00  0.00              
ATOM     71  C   VAL    76      35.288  57.069  -5.299  1.00  0.00              
ATOM     72  O   VAL    76      35.748  56.568  -6.297  1.00  0.00              
ATOM     73  N   LEU    77      34.008  57.378  -5.205  1.00  0.00              
ATOM     74  CA  LEU    77      33.091  57.140  -6.328  1.00  0.00              
ATOM     75  C   LEU    77      33.830  57.099  -7.682  1.00  0.00              
ATOM     76  O   LEU    77      33.734  56.153  -8.457  1.00  0.00              
ATOM     77  N   ARG    78      34.575  58.136  -7.963  1.00  0.00              
ATOM     78  CA  ARG    78      35.348  58.159  -9.184  1.00  0.00              
ATOM     79  C   ARG    78      36.424  57.082  -9.292  1.00  0.00              
ATOM     80  O   ARG    78      36.505  56.392 -10.311  1.00  0.00              
ATOM     81  N   LYS    79      37.274  56.976  -8.270  1.00  0.00              
ATOM     82  CA  LYS    79      38.349  55.969  -8.230  1.00  0.00              
ATOM     83  C   LYS    79      37.933  54.582  -8.745  1.00  0.00              
ATOM     84  O   LYS    79      38.739  53.813  -9.299  1.00  0.00              
ATOM     85  N   LEU    80      36.657  54.282  -8.521  1.00  0.00              
ATOM     86  CA  LEU    80      36.037  53.073  -8.981  1.00  0.00              
ATOM     87  C   LEU    80      35.789  53.169 -10.452  1.00  0.00              
ATOM     88  O   LEU    80      36.107  52.267 -11.194  1.00  0.00              
ATOM     89  N   ILE    81      35.160  54.251 -10.866  1.00  0.00              
ATOM     90  CA  ILE    81      34.869  54.418 -12.260  1.00  0.00              
ATOM     91  C   ILE    81      36.057  53.891 -12.952  1.00  0.00              
ATOM     92  O   ILE    81      35.941  53.219 -13.969  1.00  0.00              
ATOM     93  N   GLU    82      37.222  54.232 -12.411  1.00  0.00              
ATOM     94  CA  GLU    82      38.486  53.717 -12.940  1.00  0.00              
ATOM     95  C   GLU    82      38.629  52.233 -12.671  1.00  0.00              
ATOM     96  O   GLU    82      38.153  51.380 -13.410  1.00  0.00              
ATOM     97  N   ASP    83      39.273  51.913 -11.582  1.00  0.00              
ATOM     98  CA  ASP    83      39.492  50.514 -11.333  1.00  0.00              
ATOM     99  C   ASP    83      38.407  49.652 -11.952  1.00  0.00              
ATOM    100  O   ASP    83      38.664  48.550 -12.400  1.00  0.00              
ATOM    101  N   ALA    84      37.184  50.134 -11.976  1.00  0.00              
ATOM    102  CA  ALA    84      36.098  49.277 -12.451  1.00  0.00              
ATOM    103  C   ALA    84      36.048  49.333 -13.942  1.00  0.00              
ATOM    104  O   ALA    84      35.539  48.449 -14.585  1.00  0.00              
ATOM    105  N   ASP    85      36.570  50.415 -14.481  1.00  0.00              
ATOM    106  CA  ASP    85      36.623  50.584 -15.902  1.00  0.00              
ATOM    107  C   ASP    85      37.758  49.742 -16.430  1.00  0.00              
ATOM    108  O   ASP    85      37.694  49.243 -17.527  1.00  0.00              
ATOM    109  N   LYS    86      38.806  49.593 -15.632  1.00  0.00              
ATOM    110  CA  LYS    86      39.947  48.755 -15.990  1.00  0.00              
ATOM    111  C   LYS    86      39.618  47.266 -15.709  1.00  0.00              
ATOM    112  O   LYS    86      40.522  46.406 -15.764  1.00  0.00              
ATOM    113  N   GLU    87      38.327  46.983 -15.431  1.00  0.00              
ATOM    114  CA  GLU    87      37.792  45.638 -15.180  1.00  0.00              
ATOM    115  C   GLU    87      37.819  45.075 -13.751  1.00  0.00              
ATOM    116  O   GLU    87      38.302  43.982 -13.488  1.00  0.00              
ATOM    117  N   LYS    88      37.317  45.816 -12.796  1.00  0.00              
ATOM    118  CA  LYS    88      37.354  45.311 -11.448  1.00  0.00              
ATOM    119  C   LYS    88      36.014  45.654 -10.859  1.00  0.00              
ATOM    120  O   LYS    88      35.215  46.292 -11.556  1.00  0.00              
ATOM    121  N   HIS    89      35.767  45.261  -9.604  1.00  0.00              
ATOM    122  CA  HIS    89      34.497  45.597  -8.946  1.00  0.00              
ATOM    123  C   HIS    89      34.531  46.172  -7.519  1.00  0.00              
ATOM    124  O   HIS    89      35.484  46.021  -6.775  1.00  0.00              
ATOM    125  N   ASN    90      33.444  46.820  -7.149  1.00  0.00              
ATOM    126  CA  ASN    90      33.464  47.644  -5.989  1.00  0.00              
ATOM    127  C   ASN    90      32.227  47.425  -5.162  1.00  0.00              
ATOM    128  O   ASN    90      31.138  47.648  -5.653  1.00  0.00              
ATOM    129  N   PHE    91      32.400  47.041  -3.898  1.00  0.00              
ATOM    130  CA  PHE    91      31.320  47.050  -2.911  1.00  0.00              
ATOM    131  C   PHE    91      30.901  48.450  -2.460  1.00  0.00              
ATOM    132  O   PHE    91      31.688  49.366  -2.525  1.00  0.00              
ATOM    133  N   CYS    92      29.684  48.630  -1.972  1.00  0.00              
ATOM    134  CA  CYS    92      29.385  49.884  -1.289  1.00  0.00              
ATOM    135  C   CYS    92      28.413  49.673  -0.131  1.00  0.00              
ATOM    136  O   CYS    92      27.255  49.361  -0.353  1.00  0.00              
ATOM    137  N   MET    93      28.875  49.851   1.100  1.00  0.00              
ATOM    138  CA  MET    93      28.064  49.524   2.259  1.00  0.00              
ATOM    139  C   MET    93      27.526  50.784   2.938  1.00  0.00              
ATOM    140  O   MET    93      28.251  51.741   3.163  1.00  0.00              
ATOM    141  N   LEU    94      26.240  50.767   3.257  1.00  0.00              
ATOM    142  CA  LEU    94      25.546  51.899   3.841  1.00  0.00              
ATOM    143  C   LEU    94      24.654  51.263   4.893  1.00  0.00              
ATOM    144  O   LEU    94      23.715  50.572   4.545  1.00  0.00              
ATOM    145  N   GLY    95      24.996  51.417   6.166  1.00  0.00              
ATOM    146  CA  GLY    95      24.203  50.923   7.299  1.00  0.00              
ATOM    147  C   GLY    95      22.729  51.285   7.307  1.00  0.00              
ATOM    148  O   GLY    95      22.120  51.392   6.265  1.00  0.00              
ATOM    149  N   VAL    96      22.147  51.458   8.483  1.00  0.00              
ATOM    150  CA  VAL    96      20.733  51.817   8.565  1.00  0.00              
ATOM    151  C   VAL    96      20.507  53.252   9.044  1.00  0.00              
ATOM    152  O   VAL    96      21.246  53.763   9.888  1.00  0.00              
ATOM    153  N   CYS    97      19.478  53.894   8.498  1.00  0.00              
ATOM    154  CA  CYS    97      19.086  55.235   8.922  1.00  0.00              
ATOM    155  C   CYS    97      17.610  55.273   9.299  1.00  0.00              
ATOM    156  O   CYS    97      17.263  55.511  10.455  1.00  0.00              
ATOM    157  N   THR   115      15.277  52.405   2.614  1.00  0.00              
ATOM    158  CA  THR   115      14.559  53.269   1.691  1.00  0.00              
ATOM    159  C   THR   115      15.498  54.303   1.108  1.00  0.00              
ATOM    160  O   THR   115      15.632  54.420  -0.111  1.00  0.00              
ATOM    161  N   GLU   116      16.139  55.066   1.987  1.00  0.00              
ATOM    162  CA  GLU   116      17.188  55.966   1.551  1.00  0.00              
ATOM    163  C   GLU   116      18.024  55.099   0.645  1.00  0.00              
ATOM    164  O   GLU   116      18.615  55.562  -0.322  1.00  0.00              
ATOM    165  N   ASP   117      18.045  53.816   0.971  1.00  0.00              
ATOM    166  CA  ASP   117      18.882  52.880   0.266  1.00  0.00              
ATOM    167  C   ASP   117      18.544  53.025  -1.191  1.00  0.00              
ATOM    168  O   ASP   117      19.423  53.182  -2.040  1.00  0.00              
ATOM    569  N   ASP   297      42.055  31.051  34.552  1.00  0.00              
ATOM    570  CA  ASP   297      42.762  29.849  34.944  1.00  0.00              
ATOM    571  C   ASP   297      42.230  29.406  36.285  1.00  0.00              
ATOM    572  O   ASP   297      41.983  28.225  36.496  1.00  0.00              
ATOM    573  N   HIS   298      42.023  30.360  37.187  1.00  0.00              
ATOM    574  CA  HIS   298      41.457  30.026  38.483  1.00  0.00              
ATOM    575  C   HIS   298      40.341  29.047  38.155  1.00  0.00              
ATOM    576  O   HIS   298      40.033  28.138  38.922  1.00  0.00              
END
