
#######################################################
#                                                     #
#                        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   38 (  188),  selected   38 , name T0321TS102_1-D1
# Molecule2: number of CA atoms   96 (  710),  selected   96 , name T0321_D1.pdb
# PARAMETERS: T0321TS102_1-D1.T0321_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      W       2           -
LGA    -       -      E       3           -
LGA    -       -      I       4           -
LGA    -       -      Y       5           -
LGA    -       -      D       6           -
LGA    -       -      A       7           -
LGA    -       -      M       8           -
LGA    -       -      I       9           -
LGA    -       -      N      10           -
LGA    -       -      G      11           -
LGA    -       -      I      12           -
LGA    -       -      P      13           -
LGA    -       -      E      14           -
LGA    -       -      D      15           -
LGA    -       -      F      16           -
LGA    -       -      L      17           -
LGA    -       -      V      18           -
LGA    -       -      D      19           -
LGA    -       -      E      20           -
LGA    -       -      L      21           -
LGA    -       -      V      22           -
LGA    -       -      C      23           -
LGA    -       -      G      24           -
LGA    -       -      T      25           -
LGA    -       -      T      26           -
LGA    -       -      H      27           -
LGA    -       -      S      28           -
LGA    -       -      V      29           -
LGA    -       -      I      30           -
LGA    -       -      R      31           -
LGA    -       -      S      32           -
LGA    -       -      G      33           -
LGA    -       -      N      34           -
LGA    -       -      G      35           -
LGA    -       -      V      36           -
LGA    -       -      G      37           -
LGA    -       -      L      38           -
LGA    -       -      G      39           -
LGA    M       1      P      40          0.763
LGA    W       2      N      41          2.104
LGA    E       3      R      42          1.860
LGA    I       4      P      43           -
LGA    Y       5      F      44           -
LGA    D       6      E      45          5.676
LGA    A       7      T      46           -
LGA    M       8      R      47           -
LGA    I       9      M      48           -
LGA    N      10      P      49           -
LGA    G      11      M      50           -
LGA    I      12      L      51           -
LGA    P      13      T      52           -
LGA    E      14      Q      53           -
LGA    -       -      N      54           -
LGA    -       -      L      55           -
LGA    -       -      L      56           -
LGA    -       -      G      57           -
LGA    -       -      L      58           -
LGA    -       -      P      59           -
LGA    -       -      L      60           -
LGA    -       -      R      61           -
LGA    -       -      V      62           -
LGA    -       -      A      63           -
LGA    -       -      A      64           -
LGA    -       -      G      65           -
LGA    -       -      C      66           -
LGA    -       -      V      67           -
LGA    -       -      K      68           -
LGA    D      15      S      69           #
LGA    F      16      W      70          2.761
LGA    L      55      -       -           -
LGA    L      56      N      71          1.992
LGA    G      57      Y      72          4.092
LGA    L      58      V      73          4.143
LGA    -       -      E      74           -
LGA    P      59      A      75          3.173
LGA    L      60      S      76          4.191
LGA    R      61      I      77          2.868
LGA    V      62      G      78          2.013
LGA    A      63      L      79          2.189
LGA    A      64      A      80          1.422
LGA    A      80      A      81          0.685
LGA    A      81      I      82          1.404
LGA    I      82      N      83          1.088
LGA    N      83      A      84          0.668
LGA    A      84      Y      85          0.570
LGA    Y      85      Y      86          0.688
LGA    Y      86      N      87          1.180
LGA    N      87      N      88          2.169
LGA    -       -      P      89           -
LGA    -       -      Q      90           -
LGA    N      88      V      91          1.201
LGA    -       -      A      92           -
LGA    P      89      R      93          2.007
LGA    Q      90      E      94          2.874
LGA    V      91      H      95          3.501
LGA    -       -      G      96           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   38   96    5.0     26    2.56    15.38     20.590     0.979

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.196572 * X  +   0.579594 * Y  +   0.790842 * Z  +  -4.663052
  Y_new =   0.157069 * X  +   0.814776 * Y  +  -0.558094 * Z  +  30.074789
  Z_new =  -0.967827 * X  +   0.014511 * Y  +  -0.251199 * Z  +  75.861404 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.083889   -0.057703  [ DEG:   176.6938     -3.3062 ]
  Theta =   1.316445    1.825148  [ DEG:    75.4267    104.5733 ]
  Phi   =   2.467437   -0.674155  [ DEG:   141.3737    -38.6263 ]
 
# 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: T0321TS102_1-D1                               
REMARK     2: T0321_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS102_1-D1.T0321_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   38   96   5.0   26   2.56   15.38  20.590
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS102_1-D1
PFRMAT TS
TARGET T0321
MODEL 1
PARENT 1wk4_A
ATOM      1  N   MET     1       2.490  55.525  62.992  1.00  1.00
ATOM      2  CA  MET     1       2.515  54.190  62.391  1.00  1.00
ATOM      3  C   MET     1       2.555  54.269  60.873  1.00  1.00
ATOM      4  O   MET     1       3.516  53.819  60.240  1.00  1.00
ATOM      5  CB  MET     1       1.290  53.373  62.823  1.00  1.00
ATOM      6  N   TRP     2       1.502  54.841  60.302  1.00  1.00
ATOM      7  CA  TRP     2       1.382  54.980  58.859  1.00  1.00
ATOM      8  C   TRP     2       2.536  55.777  58.254  1.00  1.00
ATOM      9  O   TRP     2       3.192  55.321  57.320  1.00  1.00
ATOM     10  CB  TRP     2       0.046  55.656  58.491  1.00  1.00
ATOM     11  N   GLU     3       2.791  56.964  58.788  1.00  1.00
ATOM     12  CA  GLU     3       3.868  57.789  58.266  1.00  1.00
ATOM     13  C   GLU     3       5.212  57.086  58.294  1.00  1.00
ATOM     14  O   GLU     3       5.961  57.149  57.320  1.00  1.00
ATOM     15  CB  GLU     3       3.948  59.103  59.035  1.00  1.00
ATOM     16  N   ILE     4       5.517  56.405  59.392  1.00  1.00
ATOM     17  CA  ILE     4       6.791  55.709  59.505  1.00  1.00
ATOM     18  C   ILE     4       6.781  54.432  58.673  1.00  1.00
ATOM     19  O   ILE     4       7.817  53.988  58.178  1.00  1.00
ATOM     20  CB  ILE     4       7.124  55.387  60.987  1.00  1.00
ATOM     21  N   TYR     5       5.611  53.832  58.515  1.00  1.00
ATOM     22  CA  TYR     5       5.524  52.627  57.703  1.00  1.00
ATOM     23  C   TYR     5       5.827  52.996  56.254  1.00  1.00
ATOM     24  O   TYR     5       6.745  52.453  55.637  1.00  1.00
ATOM     25  CB  TYR     5       4.128  52.010  57.783  1.00  1.00
ATOM     26  N   ASP     6       5.046  53.929  55.722  1.00  1.00
ATOM     27  CA  ASP     6       5.212  54.390  54.353  1.00  1.00
ATOM     28  C   ASP     6       6.664  54.758  54.055  1.00  1.00
ATOM     29  O   ASP     6       7.247  54.290  53.073  1.00  1.00
ATOM     30  CB  ASP     6       4.330  55.616  54.108  1.00  1.00
ATOM     31  N   ALA     7       7.236  55.599  54.913  1.00  1.00
ATOM     32  CA  ALA     7       8.610  56.073  54.760  1.00  1.00
ATOM     33  C   ALA     7       9.678  55.017  54.967  1.00  1.00
ATOM     34  O   ALA     7      10.858  55.267  54.726  1.00  1.00
ATOM     35  CB  ALA     7       8.863  57.230  55.718  1.00  1.00
ATOM     36  N   MET     8       9.011  51.089  54.538  1.00  1.00
ATOM     37  CA  MET     8       8.852  49.898  53.731  1.00  1.00
ATOM     38  C   MET     8       8.636  50.139  52.251  1.00  1.00
ATOM     39  O   MET     8       8.696  49.201  51.457  1.00  1.00
ATOM     40  CB  MET     8       7.732  49.041  54.330  1.00  1.00
ATOM     41  N   ILE     9       8.403  51.389  51.869  1.00  1.00
ATOM     42  CA  ILE     9       8.201  51.677  50.461  1.00  1.00
ATOM     43  C   ILE     9       9.373  51.034  49.730  1.00  1.00
ATOM     44  O   ILE     9      10.511  51.089  50.206  1.00  1.00
ATOM     45  CB  ILE     9       8.179  53.187  50.196  1.00  1.00
ATOM     46  N   ASN    10       9.086  50.400  48.595  1.00  1.00
ATOM     47  CA  ASN    10      10.129  49.751  47.818  1.00  1.00
ATOM     48  C   ASN    10      10.472  48.374  48.348  1.00  1.00
ATOM     49  O   ASN    10      11.267  47.652  47.746  1.00  1.00
ATOM     50  CB  ASN    10      11.395  50.622  47.902  1.00  1.00
ATOM     51  N   GLY    11       9.876  48.019  49.485  1.00  1.00
ATOM     52  CA  GLY    11      10.087  46.717  50.122  1.00  1.00
ATOM     53  C   GLY    11       8.740  46.015  50.224  1.00  1.00
ATOM     54  O   GLY    11       8.647  44.793  50.137  1.00  1.00
ATOM     55  N   ILE    12       7.702  46.818  50.413  1.00  1.00
ATOM     56  CA  ILE    12       6.339  46.329  50.517  1.00  1.00
ATOM     57  C   ILE    12       5.557  47.021  49.411  1.00  1.00
ATOM     58  O   ILE    12       5.651  48.235  49.246  1.00  1.00
ATOM     59  CB  ILE    12       5.718  46.689  51.883  1.00  1.00
ATOM     60  N   PRO    13       4.781  46.255  48.631  1.00  1.00
ATOM     61  CA  PRO    13       3.986  46.810  47.533  1.00  1.00
ATOM     62  C   PRO    13       3.238  48.097  47.882  1.00  1.00
ATOM     63  O   PRO    13       2.502  48.154  48.865  1.00  1.00
ATOM     64  CB  PRO    13       3.044  45.664  47.190  1.00  1.00
ATOM     65  N   GLU    14       3.438  49.120  47.056  1.00  1.00
ATOM     66  CA  GLU    14       2.801  50.420  47.233  1.00  1.00
ATOM     67  C   GLU    14       1.308  50.389  47.517  1.00  1.00
ATOM     68  O   GLU    14       0.795  51.237  48.249  1.00  1.00
ATOM     69  CB  GLU    14       3.041  51.294  46.002  1.00  1.00
ATOM     70  N   ASP    15       0.602  49.434  46.925  1.00  1.00
ATOM     71  CA  ASP    15      -0.833  49.333  47.144  1.00  1.00
ATOM     72  C   ASP    15      -1.098  49.188  48.635  1.00  1.00
ATOM     73  O   ASP    15      -1.995  49.833  49.186  1.00  1.00
ATOM     74  CB  ASP    15      -1.387  48.146  46.398  1.00  1.00
ATOM     75  N   PHE    16      -0.298  48.337  49.273  1.00  1.00
ATOM     76  CA  PHE    16      -0.400  48.083  50.706  1.00  1.00
ATOM     77  C   PHE    16      -0.250  49.386  51.489  1.00  1.00
ATOM     78  O   PHE    16      -1.163  49.804  52.196  1.00  1.00
ATOM     79  CB  PHE    16       0.693  47.107  51.131  1.00  1.00
ATOM     80  N   LEU    55       0.911  50.019  51.363  1.00  1.00
ATOM     81  CA  LEU    55       1.166  51.276  52.055  1.00  1.00
ATOM     82  C   LEU    55       0.047  52.279  51.793  1.00  1.00
ATOM     83  O   LEU    55      -0.564  52.795  52.729  1.00  1.00
ATOM     84  CB  LEU    55       2.506  51.877  51.608  1.00  1.00
ATOM     85  N   LEU    56      -0.223  52.558  50.522  1.00  1.00
ATOM     86  CA  LEU    56      -1.277  53.502  50.179  1.00  1.00
ATOM     87  C   LEU    56      -2.594  52.981  50.726  1.00  1.00
ATOM     88  O   LEU    56      -3.554  53.733  50.887  1.00  1.00
ATOM     89  CB  LEU    56      -1.358  53.691  48.664  1.00  1.00
ATOM     90  N   GLY    57      -2.615  51.685  51.026  1.00  1.00
ATOM     91  CA  GLY    57      -3.801  51.056  51.578  1.00  1.00
ATOM     92  C   GLY    57      -3.879  51.187  53.093  1.00  1.00
ATOM     93  O   GLY    57      -4.851  50.752  53.706  1.00  1.00
ATOM     94  N   LEU    58      -2.851  51.774  53.700  1.00  1.00
ATOM     95  CA  LEU    58      -2.831  51.975  55.146  1.00  1.00
ATOM     96  C   LEU    58      -3.777  53.127  55.464  1.00  1.00
ATOM     97  O   LEU    58      -3.942  54.034  54.646  1.00  1.00
ATOM     98  CB  LEU    58      -1.420  52.331  55.624  1.00  1.00
ATOM     99  N   PRO    59      -4.393  53.097  56.646  1.00  1.00
ATOM    100  CA  PRO    59      -5.329  54.149  57.042  1.00  1.00
ATOM    101  C   PRO    59      -5.078  54.748  58.417  1.00  1.00
ATOM    102  O   PRO    59      -4.774  54.037  59.370  1.00  1.00
ATOM    103  CB  PRO    59      -6.766  53.629  57.006  1.00  1.00
ATOM    104  N   LEU    60      -5.224  56.064  58.512  1.00  1.00
ATOM    105  CA  LEU    60      -5.037  56.759  59.775  1.00  1.00
ATOM    106  C   LEU    60      -6.131  56.359  60.763  1.00  1.00
ATOM    107  O   LEU    60      -5.854  55.959  61.894  1.00  1.00
ATOM    108  CB  LEU    60      -5.105  58.275  59.573  1.00  1.00
ATOM    109  N   ARG    61      -7.379  56.476  60.322  1.00  1.00
ATOM    110  CA  ARG    61      -8.519  56.165  61.167  1.00  1.00
ATOM    111  C   ARG    61      -8.634  54.700  61.554  1.00  1.00
ATOM    112  O   ARG    61      -8.694  54.360  62.740  1.00  1.00
ATOM    113  CB  ARG    61      -9.803  56.631  60.484  1.00  1.00
ATOM    114  N   VAL    62      -8.671  53.833  60.550  1.00  1.00
ATOM    115  CA  VAL    62      -8.790  52.412  60.817  1.00  1.00
ATOM    116  C   VAL    62      -7.683  51.915  61.717  1.00  1.00
ATOM    117  O   VAL    62      -7.904  51.060  62.572  1.00  1.00
ATOM    118  CB  VAL    62      -8.689  51.664  59.475  1.00  1.00
ATOM    119  N   ALA    63      -6.482  52.444  61.523  1.00  1.00
ATOM    120  CA  ALA    63      -5.355  52.037  62.340  1.00  1.00
ATOM    121  C   ALA    63      -5.636  52.453  63.782  1.00  1.00
ATOM    122  O   ALA    63      -5.401  51.686  64.717  1.00  1.00
ATOM    123  CB  ALA    63      -4.072  52.699  61.845  1.00  1.00
ATOM    124  N   ALA    64      -6.140  53.673  63.953  1.00  1.00
ATOM    125  CA  ALA    64      -6.468  54.183  65.278  1.00  1.00
ATOM    126  C   ALA    64      -7.476  53.223  65.902  1.00  1.00
ATOM    127  O   ALA    64      -7.390  52.907  67.088  1.00  1.00
ATOM    128  CB  ALA    64      -7.060  55.587  65.174  1.00  1.00
ATOM    129  N   ALA    80      -8.422  52.757  65.086  1.00  1.00
ATOM    130  CA  ALA    80      -9.442  51.809  65.537  1.00  1.00
ATOM    131  C   ALA    80      -8.759  50.541  66.045  1.00  1.00
ATOM    132  O   ALA    80      -8.992  50.105  67.169  1.00  1.00
ATOM    133  CB  ALA    80     -10.381  51.446  64.384  1.00  1.00
ATOM    134  N   ALA    81      -7.915  49.955  65.205  1.00  1.00
ATOM    135  CA  ALA    81      -7.185  48.745  65.563  1.00  1.00
ATOM    136  C   ALA    81      -6.688  48.815  67.010  1.00  1.00
ATOM    137  O   ALA    81      -7.013  47.960  67.837  1.00  1.00
ATOM    138  CB  ALA    81      -6.005  48.559  64.603  1.00  1.00
ATOM    139  N   ILE    82      -5.908  49.844  67.316  1.00  1.00
ATOM    140  CA  ILE    82      -5.383  50.009  68.661  1.00  1.00
ATOM    141  C   ILE    82      -6.445  50.526  69.618  1.00  1.00
ATOM    142  O   ILE    82      -6.242  50.537  70.833  1.00  1.00
ATOM    143  CB  ILE    82      -4.191  50.964  68.651  1.00  1.00
ATOM    144  N   ASN    83      -7.579  50.948  69.069  1.00  1.00
ATOM    145  CA  ASN    83      -8.674  51.471  69.881  1.00  1.00
ATOM    146  C   ASN    83      -9.388  50.367  70.649  1.00  1.00
ATOM    147  O   ASN    83      -9.433  50.380  71.880  1.00  1.00
ATOM    148  CB  ASN    83      -9.671  52.223  69.002  1.00  1.00
ATOM    149  N   ALA    84      -9.945  49.407  69.915  1.00  1.00
ATOM    150  CA  ALA    84     -10.667  48.309  70.535  1.00  1.00
ATOM    151  C   ALA    84      -9.803  47.544  71.518  1.00  1.00
ATOM    152  O   ALA    84     -10.271  47.166  72.590  1.00  1.00
ATOM    153  CB  ALA    84     -11.208  47.350  69.473  1.00  1.00
ATOM    154  N   TYR    85      -8.540  47.324  71.163  1.00  1.00
ATOM    155  CA  TYR    85      -7.631  46.581  72.030  1.00  1.00
ATOM    156  C   TYR    85      -7.334  47.279  73.362  1.00  1.00
ATOM    157  O   TYR    85      -7.177  46.615  74.388  1.00  1.00
ATOM    158  CB  TYR    85      -6.338  46.255  71.273  1.00  1.00
ATOM    159  N   TYR    86      -7.264  48.609  73.349  1.00  1.00
ATOM    160  CA  TYR    86      -7.024  49.368  74.577  1.00  1.00
ATOM    161  C   TYR    86      -8.205  49.105  75.499  1.00  1.00
ATOM    162  O   TYR    86      -8.049  48.920  76.709  1.00  1.00
ATOM    163  CB  TYR    86      -6.943  50.870  74.278  1.00  1.00
ATOM    164  N   ASN    87      -9.392  49.084  74.900  1.00  1.00
ATOM    165  CA  ASN    87     -10.636  48.845  75.618  1.00  1.00
ATOM    166  C   ASN    87     -10.914  47.346  75.708  1.00  1.00
ATOM    167  O   ASN    87     -11.806  46.829  75.036  1.00  1.00
ATOM    168  CB  ASN    87     -11.794  49.525  74.889  1.00  1.00
ATOM    169  N   ASN    88     -10.143  46.651  76.536  1.00  1.00
ATOM    170  CA  ASN    88     -10.309  45.215  76.721  1.00  1.00
ATOM    171  C   ASN    88      -9.530  44.794  77.955  1.00  1.00
ATOM    172  O   ASN    88      -8.341  44.486  77.878  1.00  1.00
ATOM    173  CB  ASN    88      -9.792  44.417  75.507  1.00  1.00
ATOM    174  N   PRO    89     -10.199  44.777  79.116  1.00  1.00
ATOM    175  CA  PRO    89      -9.610  44.403  80.406  1.00  1.00
ATOM    176  C   PRO    89      -8.762  43.133  80.359  1.00  1.00
ATOM    177  O   PRO    89      -7.789  43.001  81.103  1.00  1.00
ATOM    178  CB  PRO    89     -10.834  44.247  81.301  1.00  1.00
ATOM    179  N   GLN    90      -9.132  42.207  79.480  1.00  1.00
ATOM    180  CA  GLN    90      -8.413  40.943  79.340  1.00  1.00
ATOM    181  C   GLN    90      -7.179  41.032  78.442  1.00  1.00
ATOM    182  O   GLN    90      -6.489  40.032  78.229  1.00  1.00
ATOM    183  CB  GLN    90      -9.351  39.828  78.799  1.00  1.00
ATOM    184  N   VAL    91      -6.892  42.227  77.929  1.00  1.00
ATOM    185  CA  VAL    91      -5.739  42.418  77.053  1.00  1.00
ATOM    186  C   VAL    91      -4.492  42.900  77.804  1.00  1.00
ATOM    187  O   VAL    91      -4.443  44.031  78.288  1.00  1.00
ATOM    188  CB  VAL    91      -6.087  43.404  75.939  1.00  1.00
TER
END
