
#######################################################
#                                                     #
#                        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   29 (  116),  selected   29 , name T0356AL044_1-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356AL044_1-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      -       -           -
LGA    A     315      N       7          3.387
LGA    I     316      D       8          2.897
LGA    Y     317      L       9          4.158
LGA    H     318      R      10          2.100
LGA    -       -      D      11           -
LGA    S     319      F      12          2.131
LGA    T     320      L      13          2.449
LGA    Y     321      T      14           -
LGA    T     322      L      15           -
LGA    G     323      L      16           -
LGA    -       -      E      17           -
LGA    -       -      Q      18           -
LGA    -       -      Q      19           -
LGA    -       -      G      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      K      23           -
LGA    -       -      R      24           -
LGA    -       -      I      25           -
LGA    -       -      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    -       -      T      36           -
LGA    -       -      E      37           -
LGA    -       -      I      38           -
LGA    -       -      A      39           -
LGA    -       -      D      40           -
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    -       -      L      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      A      49           -
LGA    -       -      L      50           -
LGA    R     324      L      51          1.593
LGA    P     325      F      52          4.121
LGA    P     326      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    D     327      L      63           #
LGA    E     328      C      64          2.544
LGA    P     329      N      65          2.516
LGA    A     330      L      66          0.930
LGA    V     331      F      67          2.994
LGA    L     332      G      68          0.473
LGA    G     333      T      69          3.521
LGA    A     335      P      70          1.479
LGA    L     336      K      71          3.639
LGA    N     337      R      72          2.930
LGA    E     338      V      73          2.750
LGA    P     342      A      74          3.315
LGA    I     343      M      75          1.193
LGA    L     344      G      76          2.906
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    Q     345      Q      79          1.324
LGA    K     346      E      80          3.335
LGA    -       -      D      81           -
LGA    -       -      V      82           -
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    -       -      Y     321           -
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    -       -      D     327           -
LGA    -       -      E     328           -
LGA    -       -      P     329           -
LGA    -       -      A     330           -
LGA    -       -      V     331           -
LGA    -       -      L     332           -
LGA    -       -      G     333           -
LGA    -       -      V     334           -
LGA    -       -      A     335           -
LGA    -       -      L     336           -
LGA    -       -      N     337           -
LGA    -       -      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)   29  124    5.0     23    2.74     4.35     11.966     0.811

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.609604 * X  +  -0.739618 * Y  +   0.285215 * Z  +  87.735535
  Y_new =   0.108027 * X  +   0.278931 * Y  +   0.954216 * Z  +  18.948936
  Z_new =  -0.785311 * X  +   0.612505 * Y  +  -0.090139 * Z  +  84.948425 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.716912   -1.424681  [ DEG:    98.3718    -81.6282 ]
  Theta =   0.903198    2.238394  [ DEG:    51.7494    128.2505 ]
  Phi   =   2.966204   -0.175388  [ DEG:   169.9510    -10.0490 ]
 
# 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: T0356AL044_1-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_1-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   29  124   5.0   23   2.74    4.35  11.966
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_1-D1
REMARK Aligment from pdb entry: 1jwq_A
ATOM     93  N   ASP   314      82.886  84.743  77.322  1.00  0.00              
ATOM     94  CA  ASP   314      82.299  83.508  77.815  1.00  0.00              
ATOM     95  C   ASP   314      81.525  83.697  79.099  1.00  0.00              
ATOM     96  O   ASP   314      82.011  84.307  80.050  1.00  0.00              
ATOM     97  N   ALA   315      80.317  83.159  79.130  1.00  0.00              
ATOM     98  CA  ALA   315      79.497  83.267  80.324  1.00  0.00              
ATOM     99  C   ALA   315      78.919  81.915  80.694  1.00  0.00              
ATOM    100  O   ALA   315      78.806  81.019  79.855  1.00  0.00              
ATOM    101  N   ILE   316      78.583  81.767  81.967  1.00  0.00              
ATOM    102  CA  ILE   316      77.988  80.534  82.454  1.00  0.00              
ATOM    103  C   ILE   316      76.653  80.936  83.053  1.00  0.00              
ATOM    104  O   ILE   316      76.576  81.836  83.891  1.00  0.00              
ATOM    105  N   TYR   317      75.596  80.283  82.598  1.00  0.00              
ATOM    106  CA  TYR   317      74.264  80.601  83.070  1.00  0.00              
ATOM    107  C   TYR   317      73.737  79.549  84.029  1.00  0.00              
ATOM    108  O   TYR   317      73.777  78.362  83.735  1.00  0.00              
ATOM    109  N   HIS   318      73.280  79.996  85.193  1.00  0.00              
ATOM    110  CA  HIS   318      72.675  79.100  86.172  1.00  0.00              
ATOM    111  C   HIS   318      71.218  79.526  86.042  1.00  0.00              
ATOM    112  O   HIS   318      70.787  80.505  86.647  1.00  0.00              
ATOM    113  N   SER   319      70.475  78.792  85.222  1.00  0.00              
ATOM    114  CA  SER   319      69.086  79.124  84.928  1.00  0.00              
ATOM    115  C   SER   319      68.144  79.231  86.115  1.00  0.00              
ATOM    116  O   SER   319      67.353  80.165  86.193  1.00  0.00              
ATOM    117  N   THR   320      68.227  78.271  87.026  1.00  0.00              
ATOM    118  CA  THR   320      67.370  78.275  88.196  1.00  0.00              
ATOM    119  C   THR   320      67.852  77.220  89.169  1.00  0.00              
ATOM    120  O   THR   320      68.809  76.502  88.873  1.00  0.00              
ATOM    121  N   TYR   321      67.194  77.113  90.320  1.00  0.00              
ATOM    122  CA  TYR   321      67.587  76.140  91.342  1.00  0.00              
ATOM    123  C   TYR   321      66.778  74.856  91.319  1.00  0.00              
ATOM    124  O   TYR   321      65.556  74.878  91.435  1.00  0.00              
ATOM    125  N   THR   322      67.479  73.734  91.179  1.00  0.00              
ATOM    126  CA  THR   322      66.844  72.426  91.153  1.00  0.00              
ATOM    127  C   THR   322      66.565  71.952  92.574  1.00  0.00              
ATOM    128  O   THR   322      65.911  70.932  92.777  1.00  0.00              
ATOM    129  N   GLY   323      67.081  72.699  93.546  1.00  0.00              
ATOM    130  CA  GLY   323      66.908  72.374  94.959  1.00  0.00              
ATOM    131  C   GLY   323      65.603  72.932  95.524  1.00  0.00              
ATOM    132  O   GLY   323      65.244  72.662  96.672  1.00  0.00              
ATOM    133  N   ARG   324      64.905  73.724  94.715  1.00  0.00              
ATOM    134  CA  ARG   324      63.626  74.304  95.104  1.00  0.00              
ATOM    135  C   ARG   324      62.556  73.518  94.350  1.00  0.00              
ATOM    136  O   ARG   324      62.614  73.397  93.132  1.00  0.00              
ATOM    137  N   PRO   325      61.592  72.973  95.084  1.00  0.00              
ATOM    138  CA  PRO   325      60.534  72.167  94.483  1.00  0.00              
ATOM    139  C   PRO   325      59.813  72.820  93.309  1.00  0.00              
ATOM    140  O   PRO   325      59.711  72.230  92.231  1.00  0.00              
ATOM    141  N   PRO   326      59.303  74.029  93.514  1.00  0.00              
ATOM    142  CA  PRO   326      58.583  74.726  92.451  1.00  0.00              
ATOM    143  C   PRO   326      59.486  75.074  91.273  1.00  0.00              
ATOM    144  O   PRO   326      59.118  74.872  90.116  1.00  0.00              
ATOM    145  N   ASP   327      60.674  75.590  91.572  1.00  0.00              
ATOM    146  CA  ASP   327      61.602  75.975  90.522  1.00  0.00              
ATOM    147  C   ASP   327      62.096  74.781  89.708  1.00  0.00              
ATOM    148  O   ASP   327      62.258  74.881  88.492  1.00  0.00              
ATOM    149  N   GLU   328      62.338  73.653  90.369  1.00  0.00              
ATOM    150  CA  GLU   328      62.781  72.460  89.651  1.00  0.00              
ATOM    151  C   GLU   328      61.716  72.069  88.627  1.00  0.00              
ATOM    152  O   GLU   328      62.026  71.779  87.473  1.00  0.00              
ATOM    153  N   PRO   329      60.459  72.048  89.060  1.00  0.00              
ATOM    154  CA  PRO   329      59.357  71.696  88.167  1.00  0.00              
ATOM    155  C   PRO   329      59.332  72.654  86.981  1.00  0.00              
ATOM    156  O   PRO   329      59.159  72.242  85.832  1.00  0.00              
ATOM    157  N   ALA   330      61.851  74.471  85.723  1.00  0.00              
ATOM    158  CA  ALA   330      62.980  74.271  84.822  1.00  0.00              
ATOM    159  C   ALA   330      62.766  73.088  83.885  1.00  0.00              
ATOM    160  O   ALA   330      63.302  73.066  82.777  1.00  0.00              
ATOM    161  N   VAL   331      61.984  72.104  84.321  1.00  0.00              
ATOM    162  CA  VAL   331      61.722  70.956  83.467  1.00  0.00              
ATOM    163  C   VAL   331      60.400  71.065  82.727  1.00  0.00              
ATOM    164  O   VAL   331      59.893  70.081  82.192  1.00  0.00              
ATOM    165  N   LEU   332      59.854  72.274  82.694  1.00  0.00              
ATOM    166  CA  LEU   332      58.612  72.535  81.978  1.00  0.00              
ATOM    167  C   LEU   332      59.002  72.911  80.551  1.00  0.00              
ATOM    168  O   LEU   332      59.832  73.797  80.338  1.00  0.00              
ATOM    169  N   GLY   333      58.408  72.232  79.576  1.00  0.00              
ATOM    170  CA  GLY   333      58.715  72.486  78.174  1.00  0.00              
ATOM    171  C   GLY   333      58.563  73.923  77.713  1.00  0.00              
ATOM    172  O   GLY   333      59.434  74.444  77.018  1.00  0.00              
ATOM    173  N   ALA   335      57.465  74.569  78.090  1.00  0.00              
ATOM    174  CA  ALA   335      57.241  75.946  77.674  1.00  0.00              
ATOM    175  C   ALA   335      58.302  76.869  78.260  1.00  0.00              
ATOM    176  O   ALA   335      58.791  77.772  77.585  1.00  0.00              
ATOM    177  N   LEU   336      58.653  76.634  79.519  1.00  0.00              
ATOM    178  CA  LEU   336      59.675  77.425  80.196  1.00  0.00              
ATOM    179  C   LEU   336      60.977  77.323  79.411  1.00  0.00              
ATOM    180  O   LEU   336      61.592  78.335  79.076  1.00  0.00              
ATOM    181  N   ASN   337      61.385  76.094  79.116  1.00  0.00              
ATOM    182  CA  ASN   337      62.622  75.858  78.377  1.00  0.00              
ATOM    183  C   ASN   337      62.635  76.561  77.028  1.00  0.00              
ATOM    184  O   ASN   337      63.623  77.190  76.659  1.00  0.00              
ATOM    185  N   GLU   338      61.538  76.459  76.289  1.00  0.00              
ATOM    186  CA  GLU   338      61.469  77.094  74.981  1.00  0.00              
ATOM    187  C   GLU   338      61.602  78.606  75.071  1.00  0.00              
ATOM    188  O   GLU   338      62.283  79.227  74.259  1.00  0.00              
ATOM    189  N   PRO   342      60.949  79.189  76.067  1.00  0.00              
ATOM    190  CA  PRO   342      60.983  80.628  76.276  1.00  0.00              
ATOM    191  C   PRO   342      62.396  81.082  76.649  1.00  0.00              
ATOM    192  O   PRO   342      62.911  82.071  76.122  1.00  0.00              
ATOM    193  N   ILE   343      63.015  80.341  77.560  1.00  0.00              
ATOM    194  CA  ILE   343      64.361  80.654  78.021  1.00  0.00              
ATOM    195  C   ILE   343      65.384  80.423  76.919  1.00  0.00              
ATOM    196  O   ILE   343      66.323  81.201  76.768  1.00  0.00              
ATOM    197  N   LEU   344      65.194  79.357  76.144  1.00  0.00              
ATOM    198  CA  LEU   344      66.103  79.052  75.048  1.00  0.00              
ATOM    199  C   LEU   344      66.092  80.209  74.058  1.00  0.00              
ATOM    200  O   LEU   344      67.126  80.571  73.494  1.00  0.00              
ATOM    201  N   GLN   345      64.917  80.789  73.841  1.00  0.00              
ATOM    202  CA  GLN   345      64.820  81.910  72.915  1.00  0.00              
ATOM    203  C   GLN   345      65.539  83.113  73.504  1.00  0.00              
ATOM    204  O   GLN   345      66.187  83.870  72.785  1.00  0.00              
ATOM    205  N   LYS   346      65.417  83.285  74.817  1.00  0.00              
ATOM    206  CA  LYS   346      66.075  84.396  75.479  1.00  0.00              
ATOM    207  C   LYS   346      67.583  84.270  75.362  1.00  0.00              
ATOM    208  O   LYS   346      68.281  85.249  75.092  1.00  0.00              
END
