
#######################################################
#                                                     #
#                        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  112 (  112),  selected  112 , name T0356TS677_1-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS677_1-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N       7           -
LGA    -       -      D       8           -
LGA    -       -      L       9           -
LGA    -       -      R      10           -
LGA    -       -      D      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    L       9      T      14          4.570
LGA    R      10      L      15          3.345
LGA    D      11      -       -           -
LGA    F      12      -       -           -
LGA    L      13      L      16          5.655
LGA    T      14      -       -           -
LGA    L      15      -       -           -
LGA    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      E      17          2.849
LGA    I      38      Q      18          3.076
LGA    A      39      -       -           -
LGA    D      40      Q      19          2.188
LGA    R      41      G      20          3.450
LGA    T      42      E      21           -
LGA    L      43      -       -           -
LGA    R      44      -       -           -
LGA    A      49      -       -           -
LGA    L      50      -       -           -
LGA    L      51      L      22          3.192
LGA    F      52      K      23          3.161
LGA    E      53      R      24          2.582
LGA    N      54      I      25          4.102
LGA    P      55      T      26           -
LGA    -       -      L      27           -
LGA    K      56      P      28          4.391
LGA    G      57      V      29          1.424
LGA    Y      58      D      30          1.190
LGA    S      59      P      31          2.669
LGA    -       -      H      32           -
LGA    M      60      L      33          1.509
LGA    P      61      E      34          1.462
LGA    V      62      I      35          0.768
LGA    L      63      T      36          0.621
LGA    C      64      E      37          0.925
LGA    N      65      I      38          0.689
LGA    L      66      A      39          0.771
LGA    F      67      D      40          0.594
LGA    G      68      R      41          1.335
LGA    T      69      T      42          1.435
LGA    P      70      L      43          1.530
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    K      71      N      65          3.694
LGA    R      72      L      66          4.010
LGA    V      73      F      67          3.599
LGA    A      74      G      68           -
LGA    M      75      T      69           -
LGA    G      76      P      70           -
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      M      75           -
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
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    M      77      D     314           #
LGA    -       -      A     315           -
LGA    V      82      I     316          2.547
LGA    S      83      -       -           -
LGA    A      84      -       -           -
LGA    L      85      Y     317          1.572
LGA    R      86      -       -           -
LGA    E      87      -       -           -
LGA    V      88      H     318          4.797
LGA    G      89      S     319          2.301
LGA    K      90      -       -           -
LGA    L      91      T     320          3.517
LGA    L      92      Y     321          2.494
LGA    A      93      T     322          3.483
LGA    F      94      G     323          4.105
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    L      95      D     327          4.435
LGA    K      96      E     328          2.894
LGA    D     314      P     329           -
LGA    A     315      A     330           -
LGA    I     316      V     331           -
LGA    Y     317      L     332           -
LGA    T     320      G     333           -
LGA    Y     321      V     334           -
LGA    T     322      A     335           -
LGA    G     323      L     336           -
LGA    R     324      N     337           -
LGA    P     325      E     338           -
LGA    P     326      V     339           -
LGA    D     327      F     340           -
LGA    E     328      V     341           -
LGA    P     329      P     342           -
LGA    A     330      I     343           -
LGA    V     331      L     344           -
LGA    L     332      Q     345           -
LGA    G     333      K     346           -
LGA    V     334      Q     347           -
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)  112  124    5.0     39    2.96    10.26     19.920     1.275

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.031352 * X  +  -0.725520 * Y  +   0.687487 * Z  +  62.983208
  Y_new =   0.057347 * X  +  -0.685386 * Y  +  -0.725918 * Z  + 104.249481
  Z_new =   0.997862 * X  +   0.062185 * Y  +   0.020118 * Z  +  88.604843 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.257901   -1.883692  [ DEG:    72.0724   -107.9276 ]
  Theta =  -1.505391   -1.636201  [ DEG:   -86.2526    -93.7474 ]
  Phi   =   1.070484   -2.071109  [ DEG:    61.3342   -118.6658 ]
 
# 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: T0356TS677_1-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS677_1-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  112  124   5.0   39   2.96   10.26  19.920
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS677_1-D1
PFRMAT TS
TARGET T0356
MODEL  1
PARENT 2D1Q_A
ATOM     65  CA  LEU     9      68.910  85.993  84.334  1.00 54.00
ATOM     66  CA  ARG    10      65.640  87.624  83.233  1.00 35.00
ATOM     67  CA  ASP    11      67.132  88.333  79.780  1.00 11.00
ATOM     68  CA  PHE    12      68.621  84.828  79.555  1.00 31.00
ATOM     69  CA  LEU    13      65.260  83.148  80.213  1.00 58.00
ATOM     70  CA  THR    14      63.608  85.203  77.477  1.00 82.00
ATOM     71  CA  LEU    15      66.376  84.344  75.024  1.00 99.00
ATOM     72  CA  LEU    16      65.982  80.709  76.086  1.00 99.00
ATOM     73  CA  GLU    17      62.390  80.922  74.843  1.00 99.00
ATOM     75  CA  GLN    18      57.156  83.470  77.329  1.00 76.00
ATOM     76  CA  GLN    19      54.833  85.197  79.783  1.00 72.00
ATOM     77  CA  GLY    20      53.067  82.528  81.903  1.00 71.00
ATOM     78  CA  GLU    21      55.875  79.999  81.500  1.00 99.00
ATOM     79  CA  LEU    22      57.097  78.034  84.535  1.00 99.00
ATOM     80  CA  LYS    23      60.396  77.534  86.312  1.00 99.00
ATOM     81  CA  ARG    24      61.184  75.881  89.623  1.00 99.00
ATOM     82  CA  ILE    25      63.773  75.841  92.367  1.00 99.00
ATOM     83  CA  THR    26      64.824  72.890  94.446  1.00 86.00
ATOM     84  CA  LEU    27      67.177  74.182  97.067  1.00 47.00
ATOM     85  CA  PRO    28      67.844  74.457 100.763  1.00 56.00
ATOM     86  CA  VAL    29      68.473  78.031 101.941  1.00 62.00
ATOM     87  CA  ASP    30      71.440  79.541 100.145  1.00 79.00
ATOM     88  CA  PRO    31      72.328  83.159  99.329  1.00 77.00
ATOM     89  CA  HIS    32      71.567  82.633  95.584  1.00 63.00
ATOM     90  CA  LEU    33      67.994  81.420  96.251  1.00 54.00
ATOM     91  CA  GLU    34      66.200  84.621  95.199  1.00 48.00
ATOM     92  CA  ILE    35      67.941  85.245  91.885  1.00 74.00
ATOM     93  CA  THR    36      65.595  82.852  89.967  1.00 99.00
ATOM     94  CA  GLU    37      62.646  84.124  92.027  1.00 99.00
ATOM     95  CA  ILE    38      63.307  87.790  91.237  1.00 99.00
ATOM     96  CA  ALA    39      64.096  87.147  87.575  1.00 99.00
ATOM     97  CA  ASP    40      60.870  85.146  87.177  1.00 99.00
ATOM     98  CA  ARG    41      58.959  88.103  88.677  1.00 99.00
ATOM     99  CA  THR    42      60.729  90.514  86.294  1.00 99.00
ATOM    100  CA  LEU    43      59.574  88.616  83.176  1.00 54.00
ATOM    101  CA  ARG    44      56.122  87.313  84.159  1.00 53.00
ATOM    102  CA  ALA    49      57.120  83.651  84.461  1.00 49.00
ATOM    103  CA  LEU    50      55.627  81.655  87.382  1.00 34.00
ATOM    104  CA  LEU    51      58.119  80.352  89.954  1.00 57.00
ATOM    105  CA  PHE    52      57.630  77.153  91.990  1.00 57.00
ATOM    106  CA  GLU    53      59.913  76.943  95.007  1.00 64.00
ATOM    108  CA  ASN    54      63.206  72.513  99.201  1.00 70.00
ATOM    109  CA  PRO    55      65.991  69.922  98.919  1.00 69.00
ATOM    110  CA  LYS    56      64.601  68.278 102.099  1.00 81.00
ATOM    111  CA  GLY    57      61.459  67.090 100.279  1.00 79.00
ATOM    112  CA  TYR    58      61.155  63.316 100.005  1.00 99.00
ATOM    113  CA  SER    59      61.303  62.170  96.360  1.00 99.00
ATOM    114  CA  MET    60      57.603  61.333  96.489  1.00 99.00
ATOM    115  CA  PRO    61      56.764  64.903  97.503  1.00 73.00
ATOM    116  CA  VAL    62      59.048  66.325  94.810  1.00 92.00
ATOM    117  CA  LEU    63      57.674  64.199  91.961  1.00 71.00
ATOM    118  CA  CYS    64      54.161  65.245  92.990  1.00 62.00
ATOM    119  CA  ASN    65      54.984  68.938  93.593  1.00 92.00
ATOM    120  CA  LEU    66      56.870  69.416  90.303  1.00 86.00
ATOM    121  CA  PHE    67      54.315  67.175  88.601  1.00 68.00
ATOM    122  CA  GLY    68      51.763  69.879  89.378  1.00 54.00
ATOM    123  CA  THR    69      53.735  73.009  88.460  1.00 99.00
ATOM    124  CA  PRO    70      55.393  71.540  85.351  1.00 86.00
ATOM    125  CA  LYS    71      58.587  73.649  85.173  1.00 99.00
ATOM    126  CA  ARG    72      60.631  73.871  81.987  1.00 99.00
ATOM    127  CA  VAL    73      63.839  74.604  83.949  1.00 99.00
ATOM    128  CA  ALA    74      64.823  73.596  87.479  1.00 38.00
ATOM    129  CA  MET    75      67.383  75.637  89.392  1.00 47.00
ATOM    130  CA  GLY    76      68.815  73.061  91.776  1.00 61.00
ATOM    131  CA  MET    77      71.429  73.331  94.516  1.00 64.00
ATOM    132  CA  VAL    82      74.432  70.909  94.409  1.00 73.00
ATOM    133  CA  SER    83      72.868  68.879  97.244  1.00 89.00
ATOM    134  CA  ALA    84      69.504  68.677  95.469  1.00 99.00
ATOM    135  CA  LEU    85      70.842  67.589  92.066  1.00 80.00
ATOM    136  CA  ARG    86      70.478  63.799  92.696  1.00 67.00
ATOM    137  CA  GLU    87      66.781  64.166  93.607  1.00 55.00
ATOM    138  CA  VAL    88      66.045  66.520  90.675  1.00 51.00
ATOM    139  CA  GLY    89      67.700  64.084  88.204  1.00 22.00
ATOM    140  CA  LYS    90      65.376  61.355  89.523  1.00 41.00
ATOM    141  CA  LEU    91      62.343  63.606  89.329  1.00 58.00
ATOM    142  CA  LEU    92      63.187  64.266  85.670  1.00 97.00
ATOM    143  CA  ALA    93      62.691  60.546  84.819  1.00 99.00
ATOM    144  CA  PHE    94      58.995  60.858  85.847  1.00 99.00
ATOM    145  CA  LEU    95      58.295  64.568  85.186  1.00 99.00
ATOM    146  CA  LYS    96      59.736  64.435  81.676  1.00 99.00
ATOM    431  CA  ASP   314      40.681  94.887 122.239  1.00 99.00
ATOM    432  CA  ALA   315      40.631  92.895 118.948  1.00 86.00
ATOM    433  CA  ILE   316      43.885  91.022 119.648  1.00 85.00
ATOM    434  CA  TYR   317      43.752  87.568 117.989  1.00 64.00
ATOM    435  CA  THR   320      44.832  84.369 119.733  1.00 66.00
ATOM    436  CA  TYR   321      45.491  81.293 117.618  1.00 25.00
ATOM    437  CA  THR   322      45.086  78.074 119.578  1.00 36.00
ATOM    438  CA  GLY   323      45.694  75.123 117.237  1.00 24.00
ATOM    439  CA  ARG   324      44.481  73.368 114.094  1.00 41.00
ATOM    440  CA  PRO   325      40.862  72.097 114.096  1.00 35.00
ATOM    441  CA  PRO   326      41.940  68.713 112.639  1.00 67.00
ATOM    442  CA  ASP   327      44.269  68.316 115.690  1.00 82.00
ATOM    443  CA  GLU   328      41.752  68.743 118.524  1.00 92.00
ATOM    444  CA  PRO   329      41.654  65.632 120.684  1.00 99.00
ATOM    445  CA  ALA   330      38.118  64.298 121.048  1.00 99.00
ATOM    446  CA  VAL   331      38.151  63.018 124.634  1.00 99.00
ATOM    447  CA  LEU   332      34.505  62.263 125.432  1.00 99.00
ATOM    448  CA  GLY   333      32.696  65.569 124.783  1.00 99.00
ATOM    449  CA  VAL   334      35.870  67.667 125.198  1.00 84.00
ATOM    450  CA  ALA   335      37.929  69.205 122.422  1.00 67.00
ATOM    451  CA  LEU   336      41.507  69.314 123.751  1.00 99.00
ATOM    452  CA  ASN   337      44.157  71.395 121.863  1.00 99.00
ATOM    453  CA  GLU   338      47.558  69.616 121.718  1.00 99.00
ATOM    454  CA  VAL   339      49.304  73.026 121.786  1.00 99.00
ATOM    455  CA  PHE   340      47.982  73.742 125.289  1.00 99.00
ATOM    456  CA  VAL   341      49.521  70.495 126.582  1.00 80.00
ATOM    457  CA  PRO   342      52.712  71.008 124.568  1.00 49.00
ATOM    458  CA  ILE   343      53.138  74.341 126.392  1.00 80.00
ATOM    459  CA  LEU   344      52.959  72.745 129.839  1.00 99.00
ATOM    460  CA  GLN   345      55.444  70.078 128.754  1.00 99.00
ATOM    461  CA  LYS   346      57.846  72.729 127.413  1.00 99.00
ATOM    462  CA  GLN   347      57.967  74.561 130.758  1.00 99.00
TER
END
