
#######################################################
#                                                     #
#                        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   50 (  200),  selected   50 , name T0356AL333_5-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356AL333_5-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    Y      58      N       7           -
LGA    S      59      D       8           -
LGA    M      60      L       9           -
LGA    P      61      R      10           -
LGA    V      62      D      11           -
LGA    L      63      F      12           -
LGA    C      64      L      13           -
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    -       -      L      16           -
LGA    -       -      E      17           -
LGA    N      65      Q      18          3.817
LGA    L      66      Q      19          0.697
LGA    F      67      G      20          3.370
LGA    V      73      E      21          2.173
LGA    A      74      L      22          2.923
LGA    M      75      K      23          3.505
LGA    -       -      R      24           -
LGA    G      76      I      25          4.902
LGA    M      77      T      26           -
LGA    -       -      L      27           -
LGA    -       -      P      28           -
LGA    -       -      V      29           -
LGA    -       -      D      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      I      35           -
LGA    G      78      T      36          4.115
LGA    -       -      E      37           -
LGA    -       -      I      38           -
LGA    Q      79      A      39          1.746
LGA    -       -      D      40           -
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    E      80      L      43          4.334
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      A      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      E      53           -
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    -       -      P      61           -
LGA    -       -      V      62           -
LGA    -       -      L      63           -
LGA    -       -      C      64           -
LGA    D      81      N      65          3.471
LGA    V      82      L      66          0.557
LGA    S      83      F      67          1.249
LGA    A      84      G      68          2.894
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    L      85      K      71           #
LGA    R      86      R      72          4.035
LGA    E      87      V      73          0.943
LGA    V      88      A      74          3.627
LGA    G      89      M      75          0.826
LGA    -       -      G      76           -
LGA    K      90      M      77          3.459
LGA    L      91      G      78           #
LGA    L      92      Q      79           -
LGA    -       -      E      80           -
LGA    A      93      D      81          4.266
LGA    F      94      V      82          3.051
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    -       -      L      85           -
LGA    -       -      R      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      G      89           -
LGA    -       -      K      90           -
LGA    -       -      L      91           -
LGA    -       -      L      92           -
LGA    -       -      A      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      K      96           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    -       -      I     316           -
LGA    -       -      Y     317           -
LGA    -       -      H     318           -
LGA    -       -      S     319           -
LGA    -       -      T     320           -
LGA    G     323      Y     321           #
LGA    R     324      T     322           -
LGA    P     325      G     323           -
LGA    P     326      R     324           -
LGA    D     327      P     325           -
LGA    E     328      P     326           -
LGA    P     329      D     327           -
LGA    A     330      E     328           -
LGA    V     331      P     329           -
LGA    V     339      A     330           -
LGA    F     340      V     331           -
LGA    V     341      L     332           -
LGA    P     342      G     333           -
LGA    I     343      V     334           -
LGA    L     344      A     335           -
LGA    Q     345      L     336           -
LGA    K     346      N     337           -
LGA    Q     347      E     338           -
LGA    -       -      V     339           -
LGA    -       -      F     340           -
LGA    -       -      V     341           -
LGA    -       -      P     342           -
LGA    -       -      I     343           -
LGA    -       -      L     344           -
LGA    -       -      Q     345           -
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   50  124    5.0     21    3.14     4.76     10.254     0.647

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.773307 * X  +  -0.041572 * Y  +   0.632668 * Z  +  57.731041
  Y_new =   0.574276 * X  +   0.376972 * Y  +   0.726704 * Z  +  19.877386
  Z_new =  -0.268709 * X  +   0.925291 * Y  +  -0.267641 * Z  +  97.923378 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.852363   -1.289230  [ DEG:   106.1326    -73.8674 ]
  Theta =   0.272052    2.869541  [ DEG:    15.5874    164.4126 ]
  Phi   =   2.502829   -0.638764  [ DEG:   143.4015    -36.5985 ]
 
# 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: T0356AL333_5-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL333_5-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   50  124   5.0   21   3.14    4.76  10.254
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL333_5-D1
REMARK Aligment from pdb entry: 1p6x_A
ATOM      1  N   TYR    58      74.996 101.158  76.594  1.00  0.00              
ATOM      2  CA  TYR    58      74.625 102.612  76.429  1.00  0.00              
ATOM      3  C   TYR    58      73.221 102.819  75.816  1.00  0.00              
ATOM      4  O   TYR    58      72.409 103.616  76.326  1.00  0.00              
ATOM      5  N   SER    59      72.950 102.107  74.720  1.00  0.00              
ATOM      6  CA  SER    59      71.632 102.050  74.081  1.00  0.00              
ATOM      7  C   SER    59      70.637 101.348  75.039  1.00  0.00              
ATOM      8  O   SER    59      70.999 100.341  75.640  1.00  0.00              
ATOM      9  N   MET    60      69.420 101.880  75.198  1.00  0.00              
ATOM     10  CA  MET    60      68.482 101.402  76.242  1.00  0.00              
ATOM     11  C   MET    60      67.854 100.049  75.905  1.00  0.00              
ATOM     12  O   MET    60      67.510  99.797  74.750  1.00  0.00              
ATOM     13  N   PRO    61      67.697  99.192  76.921  1.00  0.00              
ATOM     14  CA  PRO    61      67.097  97.867  76.730  1.00  0.00              
ATOM     15  C   PRO    61      66.022  97.614  77.808  1.00  0.00              
ATOM     16  O   PRO    61      66.258  97.842  78.998  1.00  0.00              
ATOM     17  N   VAL    62      64.851  97.169  77.376  1.00  0.00              
ATOM     18  CA  VAL    62      63.759  96.807  78.279  1.00  0.00              
ATOM     19  C   VAL    62      63.835  95.323  78.677  1.00  0.00              
ATOM     20  O   VAL    62      63.939  94.442  77.826  1.00  0.00              
ATOM     21  N   LEU    63      63.775  95.060  79.978  1.00  0.00              
ATOM     22  CA  LEU    63      63.955  93.712  80.490  1.00  0.00              
ATOM     23  C   LEU    63      62.766  93.353  81.351  1.00  0.00              
ATOM     24  O   LEU    63      62.341  94.160  82.190  1.00  0.00              
ATOM     25  N   CYS    64      62.221  92.161  81.124  1.00  0.00              
ATOM     26  CA  CYS    64      61.377  91.509  82.140  1.00  0.00              
ATOM     27  C   CYS    64      62.189  90.400  82.818  1.00  0.00              
ATOM     28  O   CYS    64      62.725  89.500  82.143  1.00  0.00              
ATOM     29  N   ASN    65      62.297  90.468  84.134  1.00  0.00              
ATOM     30  CA  ASN    65      62.842  89.327  84.864  1.00  0.00              
ATOM     31  C   ASN    65      61.771  88.586  85.653  1.00  0.00              
ATOM     32  O   ASN    65      60.867  89.186  86.301  1.00  0.00              
ATOM     33  N   LEU    66      61.860  87.268  85.534  1.00  0.00              
ATOM     34  CA  LEU    66      60.930  86.322  86.118  1.00  0.00              
ATOM     35  C   LEU    66      61.714  85.306  86.947  1.00  0.00              
ATOM     36  O   LEU    66      62.692  84.687  86.459  1.00  0.00              
ATOM     37  N   PHE    67      61.330  85.165  88.210  1.00  0.00              
ATOM     38  CA  PHE    67      61.851  84.067  89.038  1.00  0.00              
ATOM     39  C   PHE    67      60.765  83.016  89.086  1.00  0.00              
ATOM     40  O   PHE    67      59.660  83.264  89.593  1.00  0.00              
ATOM     41  N   VAL    73      61.042  81.864  88.485  1.00  0.00              
ATOM     42  CA  VAL    73      60.076  80.781  88.458  1.00  0.00              
ATOM     43  C   VAL    73      60.366  79.962  89.688  1.00  0.00              
ATOM     44  O   VAL    73      61.494  79.498  89.854  1.00  0.00              
ATOM     45  N   ALA    74      59.376  79.767  90.547  1.00  0.00              
ATOM     46  CA  ALA    74      59.641  79.089  91.808  1.00  0.00              
ATOM     47  C   ALA    74      58.567  78.063  92.133  1.00  0.00              
ATOM     48  O   ALA    74      57.495  78.034  91.501  1.00  0.00              
ATOM     49  N   MET    75      58.858  77.223  93.121  1.00  0.00              
ATOM     50  CA  MET    75      57.861  76.300  93.622  1.00  0.00              
ATOM     51  C   MET    75      58.481  75.026  94.128  1.00  0.00              
ATOM     52  O   MET    75      59.704  74.930  94.227  1.00  0.00              
ATOM     53  N   GLY    76      57.641  74.023  94.386  1.00  0.00              
ATOM     54  CA  GLY    76      58.124  72.775  94.992  1.00  0.00              
ATOM     55  C   GLY    76      58.919  71.978  93.981  1.00  0.00              
ATOM     56  O   GLY    76      58.589  71.977  92.797  1.00  0.00              
ATOM     57  N   MET    77      59.975  71.309  94.428  1.00  0.00              
ATOM     58  CA  MET    77      60.759  70.505  93.513  1.00  0.00              
ATOM     59  C   MET    77      59.911  69.409  92.881  1.00  0.00              
ATOM     60  O   MET    77      58.997  68.864  93.503  1.00  0.00              
ATOM     61  N   GLY    78      60.181  69.134  91.619  1.00  0.00              
ATOM     62  CA  GLY    78      59.494  68.064  90.934  1.00  0.00              
ATOM     63  C   GLY    78      58.280  68.437  90.114  1.00  0.00              
ATOM     64  O   GLY    78      57.733  67.552  89.470  1.00  0.00              
ATOM     65  N   GLN    79      57.816  69.689  90.174  1.00  0.00              
ATOM     66  CA  GLN    79      56.589  70.098  89.443  1.00  0.00              
ATOM     67  C   GLN    79      56.799  70.352  87.932  1.00  0.00              
ATOM     68  O   GLN    79      55.824  70.352  87.155  1.00  0.00              
ATOM     69  N   GLU    80      58.048  70.590  87.512  1.00  0.00              
ATOM     70  CA  GLU    80      58.350  70.826  86.099  1.00  0.00              
ATOM     71  C   GLU    80      58.842  72.232  85.787  1.00  0.00              
ATOM     72  O   GLU    80      58.858  72.650  84.642  1.00  0.00              
ATOM     73  N   ASP    81      59.261  72.955  86.825  1.00  0.00              
ATOM     74  CA  ASP    81      59.797  74.314  86.707  1.00  0.00              
ATOM     75  C   ASP    81      61.032  74.436  85.790  1.00  0.00              
ATOM     76  O   ASP    81      61.054  75.257  84.848  1.00  0.00              
ATOM     77  N   VAL    82      62.043  73.612  86.040  1.00  0.00              
ATOM     78  CA  VAL    82      63.301  73.689  85.295  1.00  0.00              
ATOM     79  C   VAL    82      63.107  73.409  83.810  1.00  0.00              
ATOM     80  O   VAL    82      63.664  74.118  82.955  1.00  0.00              
ATOM     81  N   SER    83      62.267  72.411  83.505  1.00  0.00              
ATOM     82  CA  SER    83      61.939  72.060  82.129  1.00  0.00              
ATOM     83  C   SER    83      61.164  73.217  81.447  1.00  0.00              
ATOM     84  O   SER    83      61.439  73.567  80.302  1.00  0.00              
ATOM     85  N   ALA    84      60.207  73.791  82.159  1.00  0.00              
ATOM     86  CA  ALA    84      59.482  74.972  81.661  1.00  0.00              
ATOM     87  C   ALA    84      60.440  76.126  81.334  1.00  0.00              
ATOM     88  O   ALA    84      60.410  76.681  80.232  1.00  0.00              
ATOM     89  N   LEU    85      61.314  76.458  82.290  1.00  0.00              
ATOM     90  CA  LEU    85      62.300  77.504  82.101  1.00  0.00              
ATOM     91  C   LEU    85      63.221  77.276  80.901  1.00  0.00              
ATOM     92  O   LEU    85      63.525  78.207  80.152  1.00  0.00              
ATOM     93  N   ARG    86      63.655  76.040  80.703  1.00  0.00              
ATOM     94  CA  ARG    86      64.518  75.709  79.575  1.00  0.00              
ATOM     95  C   ARG    86      63.793  75.921  78.242  1.00  0.00              
ATOM     96  O   ARG    86      64.386  76.454  77.294  1.00  0.00              
ATOM     97  N   GLU    87      62.511  75.552  78.182  1.00  0.00              
ATOM     98  CA  GLU    87      61.724  75.753  76.953  1.00  0.00              
ATOM     99  C   GLU    87      61.561  77.243  76.682  1.00  0.00              
ATOM    100  O   GLU    87      61.732  77.707  75.535  1.00  0.00              
ATOM    101  N   VAL    88      61.299  78.010  77.742  1.00  0.00              
ATOM    102  CA  VAL    88      61.213  79.466  77.603  1.00  0.00              
ATOM    103  C   VAL    88      62.461  80.051  76.944  1.00  0.00              
ATOM    104  O   VAL    88      62.377  80.898  76.042  1.00  0.00              
ATOM    105  N   GLY    89      63.620  79.594  77.386  1.00  0.00              
ATOM    106  CA  GLY    89      64.876  80.077  76.838  1.00  0.00              
ATOM    107  C   GLY    89      65.164  79.595  75.430  1.00  0.00              
ATOM    108  O   GLY    89      65.909  80.243  74.688  1.00  0.00              
ATOM    109  N   LYS    90      64.597  78.453  75.065  1.00  0.00              
ATOM    110  CA  LYS    90      64.796  77.884  73.731  1.00  0.00              
ATOM    111  C   LYS    90      64.180  78.791  72.689  1.00  0.00              
ATOM    112  O   LYS    90      63.078  79.246  72.863  1.00  0.00              
ATOM    113  N   LEU    91      64.881  79.004  71.574  1.00  0.00              
ATOM    114  CA  LEU    91      64.336  79.731  70.438  1.00  0.00              
ATOM    115  C   LEU    91      63.040  79.121  69.889  1.00  0.00              
ATOM    116  O   LEU    91      62.179  79.846  69.364  1.00  0.00              
ATOM    117  N   LEU    92      62.890  77.799  70.009  1.00  0.00              
ATOM    118  CA  LEU    92      61.699  77.118  69.504  1.00  0.00              
ATOM    119  C   LEU    92      60.398  77.634  70.148  1.00  0.00              
ATOM    120  O   LEU    92      59.320  77.534  69.544  1.00  0.00              
ATOM    121  N   ALA    93      60.491  78.196  71.355  1.00  0.00              
ATOM    122  CA  ALA    93      59.281  78.710  71.999  1.00  0.00              
ATOM    123  C   ALA    93      58.903  80.096  71.510  1.00  0.00              
ATOM    124  O   ALA    93      57.867  80.615  71.912  1.00  0.00              
ATOM    125  N   PHE    94      59.733  80.704  70.667  1.00  0.00              
ATOM    126  CA  PHE    94      59.402  82.011  70.108  1.00  0.00              
ATOM    127  C   PHE    94      59.333  83.090  71.179  1.00  0.00              
ATOM    128  O   PHE    94      60.088  83.051  72.147  1.00  0.00              
ATOM    685  N   GLY   323      62.434  59.368  89.571  1.00  0.00              
ATOM    686  CA  GLY   323      63.138  58.583  90.587  1.00  0.00              
ATOM    687  C   GLY   323      63.634  57.229  90.066  1.00  0.00              
ATOM    688  O   GLY   323      63.108  56.699  89.084  1.00  0.00              
ATOM    689  N   ARG   324      64.638  56.671  90.743  1.00  0.00              
ATOM    690  CA  ARG   324      65.203  55.367  90.383  1.00  0.00              
ATOM    691  C   ARG   324      64.237  54.214  90.682  1.00  0.00              
ATOM    692  O   ARG   324      63.078  54.439  91.051  1.00  0.00              
ATOM    693  N   PRO   325      64.744  52.989  90.544  1.00  0.00              
ATOM    694  CA  PRO   325      63.934  51.764  90.540  1.00  0.00              
ATOM    695  C   PRO   325      62.866  51.663  91.637  1.00  0.00              
ATOM    696  O   PRO   325      61.686  51.431  91.341  1.00  0.00              
ATOM    697  N   PRO   326      63.275  51.835  92.891  1.00  0.00              
ATOM    698  CA  PRO   326      62.353  51.700  94.004  1.00  0.00              
ATOM    699  C   PRO   326      62.424  52.845  94.992  1.00  0.00              
ATOM    700  O   PRO   326      61.974  52.711  96.137  1.00  0.00              
ATOM    701  N   ASP   327      62.985  53.963  94.534  1.00  0.00              
ATOM    702  CA  ASP   327      63.286  55.129  95.363  1.00  0.00              
ATOM    703  C   ASP   327      62.041  55.692  96.050  1.00  0.00              
ATOM    704  O   ASP   327      61.006  55.893  95.420  1.00  0.00              
ATOM    705  N   GLU   328      62.152  55.943  97.346  1.00  0.00              
ATOM    706  CA  GLU   328      61.073  56.573  98.097  1.00  0.00              
ATOM    707  C   GLU   328      60.971  58.068  97.793  1.00  0.00              
ATOM    708  O   GLU   328      61.935  58.698  97.338  1.00  0.00              
ATOM    709  N   PRO   329      59.794  58.625  98.037  1.00  0.00              
ATOM    710  CA  PRO   329      59.595  60.059  97.934  1.00  0.00              
ATOM    711  C   PRO   329      59.147  60.581  99.300  1.00  0.00              
ATOM    712  O   PRO   329      58.269  59.992  99.929  1.00  0.00              
ATOM    713  N   ALA   330      59.785  61.655  99.771  1.00  0.00              
ATOM    714  CA  ALA   330      59.399  62.280 101.031  1.00  0.00              
ATOM    715  C   ALA   330      58.060  63.007 100.864  1.00  0.00              
ATOM    716  O   ALA   330      58.021  64.233 100.694  1.00  0.00              
ATOM    717  N   VAL   331      56.969  62.243 100.919  1.00  0.00              
ATOM    718  CA  VAL   331      55.624  62.796 100.740  1.00  0.00              
ATOM    719  C   VAL   331      55.265  63.869 101.771  1.00  0.00              
ATOM    720  O   VAL   331      54.621  64.865 101.450  1.00  0.00              
ATOM    721  N   VAL   339      55.662  63.654 103.011  1.00  0.00              
ATOM    722  CA  VAL   339      55.386  64.615 104.076  1.00  0.00              
ATOM    723  C   VAL   339      56.052  65.990 103.845  1.00  0.00              
ATOM    724  O   VAL   339      55.454  67.063 104.081  1.00  0.00              
ATOM    725  N   PHE   340      57.302  65.950 103.419  1.00  0.00              
ATOM    726  CA  PHE   340      58.032  67.151 103.051  1.00  0.00              
ATOM    727  C   PHE   340      57.353  67.860 101.867  1.00  0.00              
ATOM    728  O   PHE   340      57.170  69.075 101.864  1.00  0.00              
ATOM    729  N   VAL   341      56.988  67.093 100.854  1.00  0.00              
ATOM    730  CA  VAL   341      56.336  67.684  99.670  1.00  0.00              
ATOM    731  C   VAL   341      54.996  68.338 100.032  1.00  0.00              
ATOM    732  O   VAL   341      54.726  69.477  99.630  1.00  0.00              
ATOM    733  N   PRO   342      54.184  67.648 100.832  1.00  0.00              
ATOM    734  CA  PRO   342      52.924  68.219 101.316  1.00  0.00              
ATOM    735  C   PRO   342      53.113  69.569 102.027  1.00  0.00              
ATOM    736  O   PRO   342      52.373  70.535 101.799  1.00  0.00              
ATOM    737  N   ILE   343      54.117  69.634 102.887  1.00  0.00              
ATOM    738  CA  ILE   343      54.423  70.849 103.643  1.00  0.00              
ATOM    739  C   ILE   343      54.923  71.964 102.705  1.00  0.00              
ATOM    740  O   ILE   343      54.479  73.093 102.803  1.00  0.00              
ATOM    741  N   LEU   344      55.838  71.629 101.795  1.00  0.00              
ATOM    742  CA  LEU   344      56.419  72.624 100.868  1.00  0.00              
ATOM    743  C   LEU   344      55.340  73.196  99.969  1.00  0.00              
ATOM    744  O   LEU   344      55.339  74.372  99.704  1.00  0.00              
ATOM    745  N   GLN   345      54.413  72.338  99.538  1.00  0.00              
ATOM    746  CA  GLN   345      53.283  72.774  98.750  1.00  0.00              
ATOM    747  C   GLN   345      52.469  73.825  99.499  1.00  0.00              
ATOM    748  O   GLN   345      52.088  74.848  98.913  1.00  0.00              
ATOM    749  N   LYS   346      52.186  73.593 100.787  1.00  0.00              
ATOM    750  CA  LYS   346      51.487  74.600 101.598  1.00  0.00              
ATOM    751  C   LYS   346      52.309  75.873 101.778  1.00  0.00              
ATOM    752  O   LYS   346      51.759  76.986 101.711  1.00  0.00              
ATOM    753  N   GLN   347      53.609  75.710 102.056  1.00  0.00              
ATOM    754  CA  GLN   347      54.522  76.857 102.214  1.00  0.00              
ATOM    755  C   GLN   347      54.537  77.751 100.961  1.00  0.00              
ATOM    756  O   GLN   347      54.513  78.988 101.070  1.00  0.00              
END
