
#######################################################
#                                                     #
#                        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   40 (  160),  selected   40 , name T0350AL333_2-D1
# Molecule2: number of CA atoms   91 ( 1511),  selected   91 , name T0350_D1.pdb
# PARAMETERS: T0350AL333_2-D1.T0350_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    N       2      N       2           -
LGA    -       -      I       3           -
LGA    -       -      E       4           -
LGA    -       -      R       5           -
LGA    -       -      L       6           -
LGA    -       -      T       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      Q      10           -
LGA    -       -      P      11           -
LGA    -       -      V      12           -
LGA    -       -      W      13           -
LGA    -       -      D      14           -
LGA    -       -      R      15           -
LGA    D      17      Y      16           #
LGA    T      18      D      17          4.346
LGA    Q      19      T      18          3.388
LGA    I      20      Q      19          4.017
LGA    H      21      I      20           #
LGA    -       -      H      21           -
LGA    -       -      S      36           -
LGA    -       -      Y      37           -
LGA    -       -      T      38           -
LGA    -       -      N      39           -
LGA    -       -      L      40           -
LGA    -       -      A      41           -
LGA    -       -      E      42           -
LGA    -       -      M      43           -
LGA    -       -      V      44           -
LGA    -       -      G      45           -
LGA    -       -      E      46           -
LGA    -       -      M      47           -
LGA    -       -      N      48           -
LGA    -       -      K      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      E      52           -
LGA    -       -      P      53           -
LGA    -       -      S      54           -
LGA    S      36      Q      55          2.389
LGA    Y      37      V      56          1.699
LGA    T      38      H      57          3.395
LGA    N      39      L      58          2.587
LGA    -       -      K      59           -
LGA    L      40      F      60          2.538
LGA    A      41      E      61          2.866
LGA    -       -      L      62           -
LGA    -       -      H      63           -
LGA    -       -      D      64           -
LGA    -       -      K      65           -
LGA    -       -      L      66           -
LGA    -       -      N      67           -
LGA    -       -      E      68           -
LGA    -       -      Y      69           -
LGA    -       -      Y      70           -
LGA    -       -      V      71           -
LGA    -       -      K      72           -
LGA    -       -      V      73           -
LGA    E      42      I      74          1.650
LGA    M      43      E      75           #
LGA    -       -      D      76           -
LGA    -       -      S      77           -
LGA    -       -      T      78           -
LGA    -       -      N      79           -
LGA    V      44      E      80           #
LGA    G      45      V      81          3.364
LGA    E      46      I      82          1.469
LGA    M      47      R      83          1.911
LGA    N      48      E      84          2.414
LGA    I      85      I      85          2.261
LGA    P      86      P      86          1.921
LGA    P      87      P      87          3.996
LGA    K      88      K      88          4.210
LGA    R      89      R      89          2.058
LGA    W      90      W      90          3.178
LGA    L      91      -       -           -
LGA    D      92      L      91          1.510
LGA    F      93      D      92          2.838
LGA    Y      94      F      93          3.084
LGA    A      95      Y      94          2.220
LGA    A      96      A      95          1.422
LGA    M      97      A      96          2.049
LGA    T      98      M      97          4.597
LGA    E      99      T      98          5.001
LGA    L     101      -       -           -
LGA    G     102      E      99          2.476
LGA    L     103      F     100          0.703
LGA    F     104      L     101          1.669
LGA    V     105      G     102          3.639
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      V     105           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   40   91    5.0     32    2.91    21.88     21.753     1.064

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.452463 * X  +  -0.884340 * Y  +   0.114981 * Z  + -34.043346
  Y_new =  -0.890526 * X  +  -0.441209 * Y  +   0.110900 * Z  +  11.366999
  Z_new =  -0.047343 * X  +  -0.152572 * Y  +  -0.987158 * Z  +  -9.954546 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.988249    0.153344  [ DEG:  -171.2141      8.7859 ]
  Theta =   0.047361    3.094232  [ DEG:     2.7136    177.2864 ]
  Phi   =  -1.100701    2.040891  [ DEG:   -63.0655    116.9345 ]
 
# 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: T0350AL333_2-D1                               
REMARK     2: T0350_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350AL333_2-D1.T0350_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   40   91   5.0   32   2.91   21.88  21.753
REMARK  ---------------------------------------------------------- 
MOLECULE T0350AL333_2-D1
REMARK Aligment from pdb entry: 1lva_A
ATOM      1  N   MET     1      -3.251 -13.581 -20.229  1.00  0.00              
ATOM      2  CA  MET     1      -1.906 -13.384 -20.766  1.00  0.00              
ATOM      3  C   MET     1      -1.190 -14.696 -21.040  1.00  0.00              
ATOM      4  O   MET     1      -1.549 -15.737 -20.504  1.00  0.00              
ATOM      5  N   ASN     2      -0.164 -14.627 -21.877  1.00  0.00              
ATOM      6  CA  ASN     2       0.654 -15.783 -22.194  1.00  0.00              
ATOM      7  C   ASN     2       1.736 -15.767 -21.115  1.00  0.00              
ATOM      8  O   ASN     2       1.973 -14.728 -20.496  1.00  0.00              
ATOM      9  N   ASP    17       2.390 -16.902 -20.886  1.00  0.00              
ATOM     10  CA  ASP    17       3.435 -16.960 -19.872  1.00  0.00              
ATOM     11  C   ASP    17       4.540 -15.936 -20.120  1.00  0.00              
ATOM     12  O   ASP    17       5.159 -15.458 -19.174  1.00  0.00              
ATOM     13  N   THR    18       4.785 -15.599 -21.384  1.00  0.00              
ATOM     14  CA  THR    18       5.793 -14.603 -21.722  1.00  0.00              
ATOM     15  C   THR    18       5.301 -13.211 -21.320  1.00  0.00              
ATOM     16  O   THR    18       6.074 -12.384 -20.829  1.00  0.00              
ATOM     17  N   GLN    19       4.013 -12.957 -21.532  1.00  0.00              
ATOM     18  CA  GLN    19       3.426 -11.675 -21.167  1.00  0.00              
ATOM     19  C   GLN    19       3.461 -11.534 -19.646  1.00  0.00              
ATOM     20  O   GLN    19       3.778 -10.460 -19.117  1.00  0.00              
ATOM     21  N   ILE    20       3.147 -12.627 -18.951  1.00  0.00              
ATOM     22  CA  ILE    20       3.144 -12.620 -17.495  1.00  0.00              
ATOM     23  C   ILE    20       4.522 -12.288 -16.941  1.00  0.00              
ATOM     24  O   ILE    20       4.644 -11.504 -16.001  1.00  0.00              
ATOM     25  N   HIS    21       5.562 -12.875 -17.525  1.00  0.00              
ATOM     26  CA  HIS    21       6.908 -12.617 -17.042  1.00  0.00              
ATOM     27  C   HIS    21       7.296 -11.161 -17.244  1.00  0.00              
ATOM     28  O   HIS    21       7.847 -10.526 -16.345  1.00  0.00              
ATOM     85  N   SER    36      13.668   6.549  -7.531  1.00  0.00              
ATOM     86  CA  SER    36      14.501   6.960  -8.653  1.00  0.00              
ATOM     87  C   SER    36      14.080   6.055  -9.820  1.00  0.00              
ATOM     88  O   SER    36      14.885   5.303 -10.368  1.00  0.00              
ATOM     89  N   TYR    37      12.791   6.113 -10.201  1.00  0.00              
ATOM     90  CA  TYR    37      12.274   5.293 -11.296  1.00  0.00              
ATOM     91  C   TYR    37      12.992   5.516 -12.602  1.00  0.00              
ATOM     92  O   TYR    37      13.439   6.617 -12.909  1.00  0.00              
ATOM     93  N   THR    38      13.125   4.458 -13.393  1.00  0.00              
ATOM     94  CA  THR    38      13.799   4.611 -14.678  1.00  0.00              
ATOM     95  C   THR    38      12.808   5.375 -15.551  1.00  0.00              
ATOM     96  O   THR    38      11.594   5.330 -15.297  1.00  0.00              
ATOM     97  N   ASN    39      13.294   6.082 -16.563  1.00  0.00              
ATOM     98  CA  ASN    39      12.380   6.817 -17.443  1.00  0.00              
ATOM     99  C   ASN    39      11.769   5.857 -18.468  1.00  0.00              
ATOM    100  O   ASN    39      12.180   4.704 -18.568  1.00  0.00              
ATOM    101  N   LEU    40      10.781   6.338 -19.217  1.00  0.00              
ATOM    102  CA  LEU    40      10.117   5.539 -20.244  1.00  0.00              
ATOM    103  C   LEU    40      11.156   5.041 -21.257  1.00  0.00              
ATOM    104  O   LEU    40      11.213   3.851 -21.576  1.00  0.00              
ATOM    105  N   ALA    41      11.978   5.955 -21.765  1.00  0.00              
ATOM    106  CA  ALA    41      13.012   5.589 -22.733  1.00  0.00              
ATOM    107  C   ALA    41      13.979   4.561 -22.165  1.00  0.00              
ATOM    108  O   ALA    41      14.330   3.598 -22.845  1.00  0.00              
ATOM    109  N   GLU    42      14.411   4.763 -20.920  1.00  0.00              
ATOM    110  CA  GLU    42      15.333   3.834 -20.273  1.00  0.00              
ATOM    111  C   GLU    42      14.756   2.421 -20.256  1.00  0.00              
ATOM    112  O   GLU    42      15.405   1.467 -20.684  1.00  0.00              
ATOM    113  N   MET    43      13.536   2.291 -19.749  1.00  0.00              
ATOM    114  CA  MET    43      12.885   0.988 -19.686  1.00  0.00              
ATOM    115  C   MET    43      12.753   0.412 -21.092  1.00  0.00              
ATOM    116  O   MET    43      12.967  -0.778 -21.312  1.00  0.00              
ATOM    117  N   VAL    44      12.391   1.270 -22.039  1.00  0.00              
ATOM    118  CA  VAL    44      12.231   0.845 -23.422  1.00  0.00              
ATOM    119  C   VAL    44      13.497   0.151 -23.914  1.00  0.00              
ATOM    120  O   VAL    44      13.439  -0.933 -24.494  1.00  0.00              
ATOM    121  N   GLY    45      14.641   0.787 -23.680  1.00  0.00              
ATOM    122  CA  GLY    45      15.904   0.220 -24.115  1.00  0.00              
ATOM    123  C   GLY    45      16.269  -1.064 -23.390  1.00  0.00              
ATOM    124  O   GLY    45      16.578  -2.083 -24.014  1.00  0.00              
ATOM    125  N   GLU    46      16.228  -1.011 -22.064  1.00  0.00              
ATOM    126  CA  GLU    46      16.561  -2.153 -21.226  1.00  0.00              
ATOM    127  C   GLU    46      15.848  -3.425 -21.671  1.00  0.00              
ATOM    128  O   GLU    46      16.487  -4.439 -21.941  1.00  0.00              
ATOM    129  N   MET    47      14.524  -3.370 -21.748  1.00  0.00              
ATOM    130  CA  MET    47      13.730  -4.527 -22.156  1.00  0.00              
ATOM    131  C   MET    47      13.617  -4.596 -23.673  1.00  0.00              
ATOM    132  O   MET    47      12.957  -5.478 -24.221  1.00  0.00              
ATOM    133  N   ASN    48      14.256  -3.647 -24.342  1.00  0.00              
ATOM    134  CA  ASN    48      14.222  -3.567 -25.795  1.00  0.00              
ATOM    135  C   ASN    48      12.815  -3.762 -26.349  1.00  0.00              
ATOM    136  O   ASN    48      12.512  -4.776 -26.984  1.00  0.00              
ATOM    137  N   ILE    85      11.957  -2.778 -26.104  1.00  0.00              
ATOM    138  CA  ILE    85      10.583  -2.826 -26.582  1.00  0.00              
ATOM    139  C   ILE    85      10.311  -1.552 -27.360  1.00  0.00              
ATOM    140  O   ILE    85      10.973  -0.545 -27.146  1.00  0.00              
ATOM    141  N   PRO    86       9.347  -1.598 -28.270  1.00  0.00              
ATOM    142  CA  PRO    86       8.986  -0.410 -29.027  1.00  0.00              
ATOM    143  C   PRO    86       8.129   0.449 -28.114  1.00  0.00              
ATOM    144  O   PRO    86       7.492  -0.060 -27.186  1.00  0.00              
ATOM    145  N   PRO    87       8.094   1.765 -28.364  1.00  0.00              
ATOM    146  CA  PRO    87       7.299   2.678 -27.536  1.00  0.00              
ATOM    147  C   PRO    87       5.858   2.205 -27.339  1.00  0.00              
ATOM    148  O   PRO    87       5.337   2.209 -26.220  1.00  0.00              
ATOM    149  N   LYS    88       5.224   1.812 -28.440  1.00  0.00              
ATOM    150  CA  LYS    88       3.838   1.351 -28.442  1.00  0.00              
ATOM    151  C   LYS    88       3.589   0.209 -27.458  1.00  0.00              
ATOM    152  O   LYS    88       2.650   0.248 -26.656  1.00  0.00              
ATOM    153  N   ARG    89       4.441  -0.804 -27.534  1.00  0.00              
ATOM    154  CA  ARG    89       4.333  -1.973 -26.682  1.00  0.00              
ATOM    155  C   ARG    89       4.531  -1.630 -25.208  1.00  0.00              
ATOM    156  O   ARG    89       3.738  -2.049 -24.358  1.00  0.00              
ATOM    157  N   TRP    90       5.577  -0.867 -24.897  1.00  0.00              
ATOM    158  CA  TRP    90       5.834  -0.512 -23.503  1.00  0.00              
ATOM    159  C   TRP    90       4.676   0.293 -22.911  1.00  0.00              
ATOM    160  O   TRP    90       4.227   0.005 -21.807  1.00  0.00              
ATOM    161  N   LEU    91       4.184   1.290 -23.638  1.00  0.00              
ATOM    162  CA  LEU    91       3.085   2.101 -23.123  1.00  0.00              
ATOM    163  C   LEU    91       1.886   1.239 -22.760  1.00  0.00              
ATOM    164  O   LEU    91       1.216   1.470 -21.748  1.00  0.00              
ATOM    165  N   ASP    92       1.628   0.232 -23.587  1.00  0.00              
ATOM    166  CA  ASP    92       0.495  -0.656 -23.366  1.00  0.00              
ATOM    167  C   ASP    92       0.659  -1.460 -22.080  1.00  0.00              
ATOM    168  O   ASP    92      -0.300  -1.642 -21.328  1.00  0.00              
ATOM    169  N   PHE    93       1.875  -1.932 -21.834  1.00  0.00              
ATOM    170  CA  PHE    93       2.170  -2.711 -20.638  1.00  0.00              
ATOM    171  C   PHE    93       2.095  -1.823 -19.405  1.00  0.00              
ATOM    172  O   PHE    93       1.513  -2.201 -18.387  1.00  0.00              
ATOM    173  N   TYR    94       2.684  -0.638 -19.496  1.00  0.00              
ATOM    174  CA  TYR    94       2.676   0.301 -18.381  1.00  0.00              
ATOM    175  C   TYR    94       1.271   0.787 -18.060  1.00  0.00              
ATOM    176  O   TYR    94       0.911   0.926 -16.890  1.00  0.00              
ATOM    177  N   ALA    95       0.470   1.046 -19.089  1.00  0.00              
ATOM    178  CA  ALA    95      -0.881   1.513 -18.849  1.00  0.00              
ATOM    179  C   ALA    95      -1.699   0.409 -18.214  1.00  0.00              
ATOM    180  O   ALA    95      -2.559   0.672 -17.372  1.00  0.00              
ATOM    181  N   ALA    96      -1.430  -0.830 -18.609  1.00  0.00              
ATOM    182  CA  ALA    96      -2.134  -1.945 -18.006  1.00  0.00              
ATOM    183  C   ALA    96      -1.725  -2.019 -16.518  1.00  0.00              
ATOM    184  O   ALA    96      -2.554  -2.247 -15.654  1.00  0.00              
ATOM    185  N   MET    97      -0.440  -1.839 -16.228  1.00  0.00              
ATOM    186  CA  MET    97       0.034  -1.880 -14.837  1.00  0.00              
ATOM    187  C   MET    97      -0.548  -0.726 -14.029  1.00  0.00              
ATOM    188  O   MET    97      -0.753  -0.848 -12.825  1.00  0.00              
ATOM    189  N   THR    98      -0.821   0.396 -14.685  1.00  0.00              
ATOM    190  CA  THR    98      -1.422   1.523 -13.986  1.00  0.00              
ATOM    191  C   THR    98      -2.872   1.175 -13.611  1.00  0.00              
ATOM    192  O   THR    98      -3.311   1.455 -12.490  1.00  0.00              
ATOM    193  N   GLU    99      -3.609   0.555 -14.534  1.00  0.00              
ATOM    194  CA  GLU    99      -5.002   0.165 -14.271  1.00  0.00              
ATOM    195  C   GLU    99      -5.103  -0.874 -13.160  1.00  0.00              
ATOM    196  O   GLU    99      -6.058  -0.878 -12.389  1.00  0.00              
ATOM    197  N   LEU   101      -4.128  -1.767 -13.084  1.00  0.00              
ATOM    198  CA  LEU   101      -4.143  -2.778 -12.043  1.00  0.00              
ATOM    199  C   LEU   101      -3.684  -2.160 -10.732  1.00  0.00              
ATOM    200  O   LEU   101      -3.752  -2.794  -9.690  1.00  0.00              
ATOM    201  N   GLY   102      -3.204  -0.922 -10.793  1.00  0.00              
ATOM    202  CA  GLY   102      -2.755  -0.243  -9.589  1.00  0.00              
ATOM    203  C   GLY   102      -1.342  -0.581  -9.162  1.00  0.00              
ATOM    204  O   GLY   102      -0.933  -0.251  -8.059  1.00  0.00              
ATOM    205  N   LEU   103      -0.592  -1.239 -10.037  1.00  0.00              
ATOM    206  CA  LEU   103       0.783  -1.622  -9.737  1.00  0.00              
ATOM    207  C   LEU   103       1.718  -0.423  -9.851  1.00  0.00              
ATOM    208  O   LEU   103       2.683  -0.294  -9.097  1.00  0.00              
ATOM    209  N   PHE   104       1.424   0.449 -10.806  1.00  0.00              
ATOM    210  CA  PHE   104       2.217   1.648 -11.031  1.00  0.00              
ATOM    211  C   PHE   104       1.274   2.836 -11.065  1.00  0.00              
ATOM    212  O   PHE   104       0.077   2.673 -11.257  1.00  0.00              
ATOM    213  N   VAL   105       1.829   4.027 -10.872  1.00  0.00              
ATOM    214  CA  VAL   105       1.066   5.270 -10.915  1.00  0.00              
ATOM    215  C   VAL   105       1.884   6.165 -11.836  1.00  0.00              
ATOM    216  O   VAL   105       3.111   6.219 -11.715  1.00  0.00              
END
