
#######################################################
#                                                     #
#                        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 T0363AL316_5-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL316_5-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11           -
LGA    Q      12      Q      12           -
LGA    I      13      I      13           -
LGA    N      14      N      14           -
LGA    I      15      I      15           -
LGA    E      16      E      16           -
LGA    I      17      -       -           -
LGA    A      18      I      17           #
LGA    Y      19      A      18           #
LGA    A      20      -       -           -
LGA    F      21      Y      19           #
LGA    P      22      A      20          3.221
LGA    E      23      F      21          2.201
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    R      24      Y      25          2.631
LGA    Y      25      Y      26           #
LGA    Y      26      L      27           -
LGA    L      27      K      28          3.706
LGA    K      28      S      29          1.520
LGA    S      29      F      30          4.418
LGA    F      30      Q      31          2.314
LGA    Q      31      V      32          2.332
LGA    -       -      D      33           -
LGA    -       -      E      34           -
LGA    -       -      G      35           -
LGA    V      32      I      36          2.828
LGA    D      33      T      37          6.080
LGA    E      34      V      38           -
LGA    -       -      Q      39           -
LGA    -       -      T      40           -
LGA    G      35      A      41          2.286
LGA    I      36      I      42          3.672
LGA    T      37      T      43          4.383
LGA    V      38      Q      44          3.253
LGA    Q      39      S      45          3.923
LGA    T      40      -       -           -
LGA    A      41      G      46          2.225
LGA    I      42      I      47          1.618
LGA    T      43      L      48          1.148
LGA    Q      44      S      49          2.030
LGA    I      47      Q      50          2.222
LGA    L      48      F      51          1.742
LGA    S      49      P      52          2.389
LGA    Q      50      -       -           -
LGA    F      51      -       -           -
LGA    P      52      -       -           -
LGA    E      53      E      53          2.589
LGA    I      54      I      54          1.210
LGA    D      55      D      55          3.411
LGA    L      56      L      56          2.633

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44   46    5.0     26    2.98    26.92     37.245     0.844

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.725269 * X  +   0.682965 * Y  +  -0.086852 * Z  +  13.773244
  Y_new =   0.623280 * X  +   0.704935 * Y  +   0.338510 * Z  + -20.246958
  Z_new =   0.292416 * X  +   0.191377 * Y  +  -0.936946 * Z  +   1.054531 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.940108   -0.201485  [ DEG:   168.4558    -11.5442 ]
  Theta =  -0.296752   -2.844841  [ DEG:   -17.0026   -162.9974 ]
  Phi   =   2.431679   -0.709913  [ DEG:   139.3250    -40.6750 ]
 
# 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: T0363AL316_5-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL316_5-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44   46   5.0   26   2.98   26.92  37.245
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL316_5-D1
REMARK Aligment from pdb entry: 2cmx_A
ATOM      9  N   ASN    11      28.760   2.452  -2.861  1.00  0.00              
ATOM     10  CA  ASN    11      30.108   2.971  -2.989  1.00  0.00              
ATOM     11  C   ASN    11      30.228   4.330  -2.295  1.00  0.00              
ATOM     12  O   ASN    11      29.708   5.328  -2.789  1.00  0.00              
ATOM     13  N   GLN    12      30.908   4.359  -1.148  1.00  0.00              
ATOM     14  CA  GLN    12      31.058   5.586  -0.353  1.00  0.00              
ATOM     15  C   GLN    12      31.671   6.732  -1.146  1.00  0.00              
ATOM     16  O   GLN    12      31.304   7.898  -0.952  1.00  0.00              
ATOM     17  N   ILE    13      32.606   6.397  -2.033  1.00  0.00              
ATOM     18  CA  ILE    13      33.283   7.399  -2.844  1.00  0.00              
ATOM     19  C   ILE    13      32.343   8.050  -3.858  1.00  0.00              
ATOM     20  O   ILE    13      32.333   9.273  -3.987  1.00  0.00              
ATOM     21  N   ASN    14      31.565   7.237  -4.572  1.00  0.00              
ATOM     22  CA  ASN    14      30.568   7.758  -5.513  1.00  0.00              
ATOM     23  C   ASN    14      29.551   8.671  -4.820  1.00  0.00              
ATOM     24  O   ASN    14      29.126   9.680  -5.392  1.00  0.00              
ATOM     25  N   ILE    15      29.178   8.319  -3.589  1.00  0.00              
ATOM     26  CA  ILE    15      28.242   9.120  -2.798  1.00  0.00              
ATOM     27  C   ILE    15      28.875  10.443  -2.402  1.00  0.00              
ATOM     28  O   ILE    15      28.206  11.478  -2.372  1.00  0.00              
ATOM     29  N   GLU    16      31.231  12.044  -4.019  1.00  0.00              
ATOM     30  CA  GLU    16      31.292  12.889  -5.219  1.00  0.00              
ATOM     31  C   GLU    16      29.998  13.681  -5.382  1.00  0.00              
ATOM     32  O   GLU    16      30.022  14.841  -5.788  1.00  0.00              
ATOM     33  N   ILE    17      28.870  13.053  -5.058  1.00  0.00              
ATOM     34  CA  ILE    17      27.577  13.745  -5.101  1.00  0.00              
ATOM     35  C   ILE    17      27.592  14.888  -4.086  1.00  0.00              
ATOM     36  O   ILE    17      27.216  16.016  -4.409  1.00  0.00              
ATOM     37  N   ALA    18      28.059  14.598  -2.876  1.00  0.00              
ATOM     38  CA  ALA    18      28.120  15.610  -1.826  1.00  0.00              
ATOM     39  C   ALA    18      29.092  16.737  -2.174  1.00  0.00              
ATOM     40  O   ALA    18      28.855  17.881  -1.811  1.00  0.00              
ATOM     41  N   TYR    19      30.174  16.415  -2.877  1.00  0.00              
ATOM     42  CA  TYR    19      31.200  17.407  -3.196  1.00  0.00              
ATOM     43  C   TYR    19      30.649  18.519  -4.089  1.00  0.00              
ATOM     44  O   TYR    19      30.958  19.698  -3.882  1.00  0.00              
ATOM     45  N   ALA    20      29.832  18.159  -5.073  1.00  0.00              
ATOM     46  CA  ALA    20      29.211  19.183  -5.905  1.00  0.00              
ATOM     47  C   ALA    20      28.045  19.892  -5.211  1.00  0.00              
ATOM     48  O   ALA    20      27.738  21.035  -5.540  1.00  0.00              
ATOM     49  N   PHE    21      27.423  19.235  -4.234  1.00  0.00              
ATOM     50  CA  PHE    21      26.464  19.913  -3.358  1.00  0.00              
ATOM     51  C   PHE    21      27.182  20.941  -2.459  1.00  0.00              
ATOM     52  O   PHE    21      26.625  22.000  -2.147  1.00  0.00              
ATOM     53  N   PRO    22      28.420  20.631  -2.072  1.00  0.00              
ATOM     54  CA  PRO    22      29.258  21.540  -1.282  1.00  0.00              
ATOM     55  C   PRO    22      29.539  22.843  -2.039  1.00  0.00              
ATOM     56  O   PRO    22      29.516  23.934  -1.461  1.00  0.00              
ATOM     57  N   GLU    23      29.829  22.707  -3.331  1.00  0.00              
ATOM     58  CA  GLU    23      30.116  23.841  -4.210  1.00  0.00              
ATOM     59  C   GLU    23      28.907  24.766  -4.331  1.00  0.00              
ATOM     60  O   GLU    23      29.059  25.989  -4.369  1.00  0.00              
ATOM     61  N   ARG    24      27.714  24.175  -4.395  1.00  0.00              
ATOM     62  CA  ARG    24      26.465  24.933  -4.461  1.00  0.00              
ATOM     63  C   ARG    24      26.138  25.578  -3.118  1.00  0.00              
ATOM     64  O   ARG    24      25.779  26.756  -3.050  1.00  0.00              
ATOM     65  N   TYR    25      26.270  24.792  -2.057  1.00  0.00              
ATOM     66  CA  TYR    25      25.799  25.181  -0.736  1.00  0.00              
ATOM     67  C   TYR    25      26.818  26.016   0.038  1.00  0.00              
ATOM     68  O   TYR    25      26.438  26.834   0.877  1.00  0.00              
ATOM     69  N   TYR    26      20.551  14.077   5.566  1.00  0.00              
ATOM     70  CA  TYR    26      19.319  14.631   5.002  1.00  0.00              
ATOM     71  C   TYR    26      19.225  14.349   3.511  1.00  0.00              
ATOM     72  O   TYR    26      18.164  13.994   3.002  1.00  0.00              
ATOM     73  N   LEU    27      20.339  14.509   2.811  1.00  0.00              
ATOM     74  CA  LEU    27      20.371  14.269   1.370  1.00  0.00              
ATOM     75  C   LEU    27      20.005  12.825   1.008  1.00  0.00              
ATOM     76  O   LEU    27      19.176  12.597   0.127  1.00  0.00              
ATOM     77  N   LYS    28      20.616  11.866   1.697  1.00  0.00              
ATOM     78  CA  LYS    28      20.498  10.453   1.331  1.00  0.00              
ATOM     79  C   LYS    28      19.465   9.647   2.132  1.00  0.00              
ATOM     80  O   LYS    28      19.003   8.601   1.659  1.00  0.00              
ATOM     81  N   SER    29      19.096  10.143   3.316  1.00  0.00              
ATOM     82  CA  SER    29      18.151   9.467   4.225  1.00  0.00              
ATOM     83  C   SER    29      18.654   8.076   4.644  1.00  0.00              
ATOM     84  O   SER    29      17.955   7.061   4.513  1.00  0.00              
ATOM     85  N   PHE    30      19.868   8.083   5.188  1.00  0.00              
ATOM     86  CA  PHE    30      20.603   6.888   5.560  1.00  0.00              
ATOM     87  C   PHE    30      20.955   6.932   7.047  1.00  0.00              
ATOM     88  O   PHE    30      20.653   7.906   7.739  1.00  0.00              
ATOM     89  N   GLN    31      21.592   5.869   7.529  1.00  0.00              
ATOM     90  CA  GLN    31      22.012   5.780   8.925  1.00  0.00              
ATOM     91  C   GLN    31      23.261   6.630   9.213  1.00  0.00              
ATOM     92  O   GLN    31      23.965   7.063   8.300  1.00  0.00              
ATOM     93  N   VAL    32      23.528   6.852  10.497  1.00  0.00              
ATOM     94  CA  VAL    32      24.698   7.611  10.928  1.00  0.00              
ATOM     95  C   VAL    32      26.012   6.906  10.553  1.00  0.00              
ATOM     96  O   VAL    32      26.918   7.549  10.016  1.00  0.00              
ATOM     97  N   ASP    33      26.129   5.591  10.834  1.00  0.00              
ATOM     98  CA  ASP    33      27.341   4.883  10.406  1.00  0.00              
ATOM     99  C   ASP    33      27.616   4.986   8.895  1.00  0.00              
ATOM    100  O   ASP    33      28.764   5.189   8.496  1.00  0.00              
ATOM    101  N   GLU    34      26.571   4.854   8.076  1.00  0.00              
ATOM    102  CA  GLU    34      26.699   4.987   6.615  1.00  0.00              
ATOM    103  C   GLU    34      27.153   6.384   6.213  1.00  0.00              
ATOM    104  O   GLU    34      27.996   6.540   5.336  1.00  0.00              
ATOM    105  N   GLY    35      26.569   7.391   6.852  1.00  0.00              
ATOM    106  CA  GLY    35      26.913   8.783   6.587  1.00  0.00              
ATOM    107  C   GLY    35      28.372   9.078   6.940  1.00  0.00              
ATOM    108  O   GLY    35      29.029   9.848   6.235  1.00  0.00              
ATOM    109  N   ILE    36      28.869   8.476   8.022  1.00  0.00              
ATOM    110  CA  ILE    36      30.281   8.620   8.412  1.00  0.00              
ATOM    111  C   ILE    36      31.239   8.020   7.379  1.00  0.00              
ATOM    112  O   ILE    36      32.325   8.554   7.166  1.00  0.00              
ATOM    113  N   THR    37      30.846   6.913   6.750  1.00  0.00              
ATOM    114  CA  THR    37      31.658   6.316   5.680  1.00  0.00              
ATOM    115  C   THR    37      31.772   7.270   4.499  1.00  0.00              
ATOM    116  O   THR    37      32.838   7.407   3.903  1.00  0.00              
ATOM    117  N   VAL    38      30.663   7.926   4.172  1.00  0.00              
ATOM    118  CA  VAL    38      30.632   8.903   3.083  1.00  0.00              
ATOM    119  C   VAL    38      31.454  10.134   3.459  1.00  0.00              
ATOM    120  O   VAL    38      32.236  10.631   2.647  1.00  0.00              
ATOM    121  N   GLN    39      31.283  10.613   4.689  1.00  0.00              
ATOM    122  CA  GLN    39      32.060  11.744   5.189  1.00  0.00              
ATOM    123  C   GLN    39      33.562  11.479   5.109  1.00  0.00              
ATOM    124  O   GLN    39      34.341  12.370   4.772  1.00  0.00              
ATOM    125  N   THR    40      33.967  10.257   5.433  1.00  0.00              
ATOM    126  CA  THR    40      35.371   9.877   5.335  1.00  0.00              
ATOM    127  C   THR    40      35.877   9.957   3.887  1.00  0.00              
ATOM    128  O   THR    40      36.988  10.432   3.642  1.00  0.00              
ATOM    129  N   ALA    41      35.057   9.509   2.934  1.00  0.00              
ATOM    130  CA  ALA    41      35.416   9.587   1.512  1.00  0.00              
ATOM    131  C   ALA    41      35.377  11.036   1.001  1.00  0.00              
ATOM    132  O   ALA    41      36.192  11.427   0.161  1.00  0.00              
ATOM    133  N   ILE    42      34.439  11.827   1.515  1.00  0.00              
ATOM    134  CA  ILE    42      34.349  13.252   1.175  1.00  0.00              
ATOM    135  C   ILE    42      35.601  14.002   1.624  1.00  0.00              
ATOM    136  O   ILE    42      36.110  14.855   0.900  1.00  0.00              
ATOM    137  N   THR    43      36.089  13.676   2.818  1.00  0.00              
ATOM    138  CA  THR    43      37.335  14.242   3.332  1.00  0.00              
ATOM    139  C   THR    43      38.515  13.927   2.403  1.00  0.00              
ATOM    140  O   THR    43      39.366  14.790   2.158  1.00  0.00              
ATOM    141  N   GLN    44      38.558  12.701   1.880  1.00  0.00              
ATOM    142  CA  GLN    44      39.611  12.300   0.944  1.00  0.00              
ATOM    143  C   GLN    44      39.543  13.109  -0.358  1.00  0.00              
ATOM    144  O   GLN    44      40.575  13.541  -0.867  1.00  0.00              
ATOM    145  N   ILE    47      38.333  13.332  -0.874  1.00  0.00              
ATOM    146  CA  ILE    47      38.141  14.150  -2.085  1.00  0.00              
ATOM    147  C   ILE    47      38.576  15.603  -1.858  1.00  0.00              
ATOM    148  O   ILE    47      39.239  16.192  -2.712  1.00  0.00              
ATOM    149  N   LEU    48      38.203  16.171  -0.712  1.00  0.00              
ATOM    150  CA  LEU    48      38.596  17.544  -0.369  1.00  0.00              
ATOM    151  C   LEU    48      40.112  17.724  -0.278  1.00  0.00              
ATOM    152  O   LEU    48      40.651  18.744  -0.713  1.00  0.00              
ATOM    153  N   SER    49      40.789  16.732   0.288  1.00  0.00              
ATOM    154  CA  SER    49      42.245  16.755   0.418  1.00  0.00              
ATOM    155  C   SER    49      42.952  16.683  -0.939  1.00  0.00              
ATOM    156  O   SER    49      44.094  17.128  -1.061  1.00  0.00              
ATOM    157  N   GLN    50      42.275  16.149  -1.958  1.00  0.00              
ATOM    158  CA  GLN    50      42.802  16.172  -3.329  1.00  0.00              
ATOM    159  C   GLN    50      42.683  17.549  -3.988  1.00  0.00              
ATOM    160  O   GLN    50      43.341  17.810  -5.001  1.00  0.00              
ATOM    161  N   PHE    51      41.844  18.417  -3.423  1.00  0.00              
ATOM    162  CA  PHE    51      41.610  19.756  -3.968  1.00  0.00              
ATOM    163  C   PHE    51      41.643  20.807  -2.858  1.00  0.00              
ATOM    164  O   PHE    51      40.623  21.432  -2.554  1.00  0.00              
ATOM    165  N   PRO    52      42.823  21.017  -2.253  1.00  0.00              
ATOM    166  CA  PRO    52      42.919  21.934  -1.112  1.00  0.00              
ATOM    167  C   PRO    52      42.705  23.407  -1.485  1.00  0.00              
ATOM    168  O   PRO    52      42.451  24.234  -0.601  1.00  0.00              
ATOM    169  N   GLU    53      37.977  23.000   2.072  1.00  0.00              
ATOM    170  CA  GLU    53      38.653  23.108   3.351  1.00  0.00              
ATOM    171  C   GLU    53      37.882  22.298   4.384  1.00  0.00              
ATOM    172  O   GLU    53      36.686  22.523   4.595  1.00  0.00              
ATOM    173  N   ILE    54      38.563  21.347   5.010  1.00  0.00              
ATOM    174  CA  ILE    54      37.972  20.563   6.077  1.00  0.00              
ATOM    175  C   ILE    54      38.249  21.291   7.387  1.00  0.00              
ATOM    176  O   ILE    54      39.394  21.351   7.844  1.00  0.00              
ATOM    177  N   ASP    55      37.203  21.868   7.971  1.00  0.00              
ATOM    178  CA  ASP    55      37.318  22.555   9.250  1.00  0.00              
ATOM    179  C   ASP    55      36.983  21.580  10.373  1.00  0.00              
ATOM    180  O   ASP    55      35.847  21.518  10.843  1.00  0.00              
ATOM    181  N   LEU    56      37.980  20.795  10.772  1.00  0.00              
ATOM    182  CA  LEU    56      37.831  19.884  11.898  1.00  0.00              
ATOM    183  C   LEU    56      37.929  20.699  13.178  1.00  0.00              
ATOM    184  O   LEU    56      38.991  21.233  13.506  1.00  0.00              
END
