
#######################################################
#                                                     #
#                        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  146 (  146),  selected  146 , name T0312TS393_1
# Molecule2: number of CA atoms  140 ( 1114),  selected  140 , name T0312.pdb
# PARAMETERS: T0312TS393_1.T0312.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    -       -      K       2           -
LGA    -       -      V       3           -
LGA    -       -      F       4           -
LGA    -       -      E       5           -
LGA    -       -      F       6           -
LGA    -       -      E       7           -
LGA    -       -      V       8           -
LGA    -       -      G       9           -
LGA    -       -      K      10           -
LGA    -       -      G      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      L      14           -
LGA    -       -      R      15           -
LGA    -       -      L      16           -
LGA    K       2      D      17           #
LGA    V       3      Y      18           #
LGA    F       4      G      19           #
LGA    E       5      K      20          4.807
LGA    F       6      D      21          2.994
LGA    E       7      L      22           #
LGA    V       8      V      23           -
LGA    G       9      -       -           -
LGA    K      10      -       -           -
LGA    G      11      -       -           -
LGA    F      12      R      24          2.089
LGA    L      13      Q      25          2.941
LGA    L      14      I      26          3.474
LGA    R      15      E      27           -
LGA    L      16      -       -           -
LGA    D      17      -       -           -
LGA    Y      18      -       -           -
LGA    G      19      -       -           -
LGA    K      20      -       -           -
LGA    D      21      -       -           -
LGA    L      22      -       -           -
LGA    V      23      -       -           -
LGA    R      24      -       -           -
LGA    Q      25      -       -           -
LGA    I      26      -       -           -
LGA    E      27      -       -           -
LGA    E      28      -       -           -
LGA    F      29      -       -           -
LGA    L      30      -       -           -
LGA    E      31      -       -           -
LGA    E      32      -       -           -
LGA    K      33      -       -           -
LGA    G      34      -       -           -
LGA    I      35      -       -           -
LGA    H      36      -       -           -
LGA    A      37      E      28          3.574
LGA    A      38      -       -           -
LGA    H      39      -       -           -
LGA    I      40      -       -           -
LGA    S      41      F      29          4.055
LGA    A      42      L      30          2.703
LGA    I      43      E      31          2.028
LGA    -       -      E      32           -
LGA    -       -      K      33           -
LGA    G      44      G      34          1.370
LGA    A      45      I      35          3.847
LGA    V      46      H      36          3.472
LGA    R      47      A      37          1.243
LGA    S      48      A      38          4.365
LGA    A      49      H      39          3.200
LGA    V      50      I      40          1.932
LGA    I      51      S      41          2.482
LGA    G      52      A      42          1.658
LGA    Y      53      I      43          4.501
LGA    -       -      G      44           -
LGA    -       -      A      45           -
LGA    -       -      V      46           -
LGA    -       -      R      47           -
LGA    -       -      S      48           -
LGA    -       -      A      49           -
LGA    -       -      V      50           -
LGA    -       -      I      51           -
LGA    -       -      G      52           -
LGA    -       -      Y      53           -
LGA    -       -      Y      54           -
LGA    -       -      D      55           -
LGA    -       -      Q      56           -
LGA    -       -      E      57           -
LGA    -       -      K      58           -
LGA    -       -      K      59           -
LGA    -       -      E      60           -
LGA    -       -      Y      61           -
LGA    -       -      V      62           -
LGA    -       -      K      63           -
LGA    -       -      K      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      M      67           -
LGA    -       -      E      68           -
LGA    -       -      P      69           -
LGA    -       -      L      70           -
LGA    -       -      E      71           -
LGA    Y      54      I      72          5.031
LGA    D      55      L      73           #
LGA    Q      56      -       -           -
LGA    E      57      -       -           -
LGA    K      58      -       -           -
LGA    K      59      -       -           -
LGA    E      60      -       -           -
LGA    Y      61      -       -           -
LGA    V      62      S      74           #
LGA    K      63      L      75           #
LGA    K      64      S      76          4.919
LGA    E      65      G      77           #
LGA    L      66      N      78          3.696
LGA    M      67      V      79           #
LGA    E      68      S      80          3.670
LGA    P      69      M      81          3.133
LGA    L      70      K      82          3.658
LGA    E      71      D      83          4.559
LGA    -       -      S      84           -
LGA    I      72      K      85          2.641
LGA    L      73      P      86          3.445
LGA    S      74      F      87          2.542
LGA    L      75      C      88          2.117
LGA    S      76      H      89           #
LGA    G      77      I      90          1.431
LGA    N      78      H      91          1.764
LGA    V      79      V      92          2.917
LGA    S      80      L      93          2.315
LGA    M      81      L      94           #
LGA    K      82      G      95           -
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      G      98           -
LGA    D      83      E      99           #
LGA    S      84      V     100          3.626
LGA    K      85      Y     101          3.242
LGA    -       -      G     102           -
LGA    P      86      G     103           #
LGA    F      87      H     104          4.924
LGA    C      88      L     105          3.220
LGA    -       -      F     106           -
LGA    H      89      S     107           #
LGA    I      90      -       -           -
LGA    H      91      -       -           -
LGA    V      92      -       -           -
LGA    L      93      -       -           -
LGA    L      94      -       -           -
LGA    G      95      -       -           -
LGA    K      96      -       -           -
LGA    D      97      -       -           -
LGA    G      98      -       -           -
LGA    E      99      -       -           -
LGA    V     100      -       -           -
LGA    Y     101      -       -           -
LGA    G     102      -       -           -
LGA    G     103      -       -           -
LGA    H     104      -       -           -
LGA    L     105      -       -           -
LGA    F     106      -       -           -
LGA    S     107      A     108          2.881
LGA    A     108      E     109          1.481
LGA    E     109      V     110          4.464
LGA    V     110      F     111          4.060
LGA    F     111      A     112          4.481
LGA    A     112      C     113          3.157
LGA    C     113      E     114          1.878
LGA    E     114      V     115          1.360
LGA    V     115      F     116          4.563
LGA    F     116      V     117          3.296
LGA    V     117      L     118          2.569
LGA    L     118      P     119          2.000
LGA    P     119      L     120          2.276
LGA    L     120      S     121           #
LGA    S     121      G     122           -
LGA    G     122      E     123           -
LGA    E     123      A     124           -
LGA    A     124      P     125           -
LGA    P     125      E     126           -
LGA    E     126      R     127           -
LGA    R     127      A     128           -
LGA    A     128      F     129           -
LGA    F     129      D     130           -
LGA    D     130      E     131           -
LGA    E     131      Q     132           -
LGA    Q     132      T     133           -
LGA    T     133      G     134           -
LGA    G     134      L     135           -
LGA    L     135      F     136           -
LGA    F     136      L     137           -
LGA    L     137      W     138           -
LGA    W     138      L     139           -
LGA    L     139      E     140           -
LGA    E     140      -       -           -
LGA    H     141      -       -           -
LGA    H     142      -       -           -
LGA    H     143      -       -           -
LGA    H     144      -       -           -
LGA    H     145      -       -           -
LGA    H     146      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  146  140    5.0     51    3.28     3.92     20.478     1.510

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.427051 * X  +  -0.862481 * Y  +  -0.271577 * Z  +  56.394978
  Y_new =  -0.301051 * X  +   0.147589 * Y  +  -0.942118 * Z  +  12.611761
  Z_new =   0.852640 * X  +   0.484091 * Y  +  -0.196623 * Z  +  13.932662 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.956610   -1.184983  [ DEG:   112.1055    -67.8945 ]
  Theta =  -1.021018   -2.120575  [ DEG:   -58.5000   -121.5000 ]
  Phi   =  -0.614043    2.527550  [ DEG:   -35.1821    144.8179 ]
 
# 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: T0312TS393_1                                  
REMARK     2: T0312.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312TS393_1.T0312.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  146  140   5.0   51   3.28    3.92  20.478
REMARK  ---------------------------------------------------------- 
MOLECULE T0312TS393_1
PFRMAT TS
TARGET T0312
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      47.042  15.228   4.042  1.00 25.00           C
ATOM      2  CA  LYS     2      49.932  16.535   6.221  1.00 25.00           C
ATOM      3  CA  VAL     3      49.847  14.065   9.099  1.00 25.00           C
ATOM      4  CA  PHE     4      52.296  11.218   9.422  1.00 25.00           C
ATOM      5  CA  GLU     5      55.847  10.300   8.460  1.00 25.00           C
ATOM      6  CA  PHE     6      58.555   7.711   9.376  1.00 25.00           C
ATOM      7  CA  GLU     7      58.476   4.349   7.538  1.00 25.00           C
ATOM      8  CA  VAL     8      58.607   0.769   6.366  1.00 25.00           C
ATOM      9  CA  GLY     9      62.361   0.111   6.513  1.00 25.00           C
ATOM     10  CA  LYS    10      64.782   1.494   9.090  1.00 25.00           C
ATOM     11  CA  GLY    11      63.642   4.979  10.181  1.00 25.00           C
ATOM     12  CA  PHE    12      63.721   8.715  10.010  1.00 25.00           C
ATOM     13  CA  LEU    13      63.293  11.571  12.408  1.00 25.00           C
ATOM     14  CA  LEU    14      59.825  12.175  11.011  1.00 25.00           C
ATOM     15  CA  ARG    15      60.125  15.501  12.830  1.00 25.00           C
ATOM     16  CA  LEU    16      60.174  19.023  11.365  1.00 25.00           C
ATOM     17  CA  ASP    17      61.914  22.034   9.866  1.00 25.00           C
ATOM     18  CA  TYR    18      62.605  25.347   8.131  1.00 25.00           C
ATOM     19  CA  GLY    19      62.292  28.184   5.671  1.00 25.00           C
ATOM     20  CA  LYS    20      61.765  26.692   2.231  1.00 25.00           C
ATOM     21  CA  ASP    21      65.573  26.289   2.268  1.00 25.00           C
ATOM     22  CA  LEU    22      65.237  23.074   4.321  1.00 25.00           C
ATOM     23  CA  VAL    23      62.645  21.732   1.841  1.00 25.00           C
ATOM     24  CA  ARG    24      64.982  22.550  -1.081  1.00 25.00           C
ATOM     25  CA  GLN    25      67.862  20.745   0.684  1.00 25.00           C
ATOM     26  CA  ILE    26      65.626  17.691   1.263  1.00 25.00           C
ATOM     27  CA  GLU    27      64.622  17.694  -2.433  1.00 25.00           C
ATOM     28  CA  GLU    28      68.307  17.884  -3.459  1.00 25.00           C
ATOM     29  CA  PHE    29      69.131  14.952  -1.136  1.00 25.00           C
ATOM     30  CA  LEU    30      66.260  12.917  -2.647  1.00 25.00           C
ATOM     31  CA  GLU    31      67.534  13.694  -6.174  1.00 25.00           C
ATOM     32  CA  GLU    32      71.062  12.597  -5.168  1.00 25.00           C
ATOM     33  CA  LYS    33      74.062  14.066  -3.410  1.00 25.00           C
ATOM     34  CA  GLY    34      73.829  11.822  -0.303  1.00 25.00           C
ATOM     35  CA  ILE    35      71.874  12.881   2.852  1.00 25.00           C
ATOM     36  CA  HIS    36      70.709  13.769   6.405  1.00 25.00           C
ATOM     37  CA  ALA    37      67.366  13.012   8.120  1.00 25.00           C
ATOM     38  CA  ALA    38      63.674  13.812   7.929  1.00 25.00           C
ATOM     39  CA  HIS    39      63.481  17.613   7.753  1.00 25.00           C
ATOM     40  CA  ILE    40      65.163  17.458  11.188  1.00 25.00           C
ATOM     41  CA  SER    41      66.119  18.063  14.814  1.00 25.00           C
ATOM     42  CA  ALA    42      66.183  14.336  15.738  1.00 25.00           C
ATOM     43  CA  ILE    43      69.326  12.173  15.878  1.00 25.00           C
ATOM     44  CA  GLY    44      71.803  11.563  18.696  1.00 25.00           C
ATOM     45  CA  ALA    45      70.597   8.386  20.296  1.00 25.00           C
ATOM     46  CA  VAL    46      67.928   5.795  20.892  1.00 25.00           C
ATOM     47  CA  ARG    47      67.194   7.425  24.252  1.00 25.00           C
ATOM     48  CA  SER    48      63.682   5.984  24.516  1.00 25.00           C
ATOM     49  CA  ALA    49      60.782   8.055  23.331  1.00 25.00           C
ATOM     50  CA  VAL    50      57.197   9.443  23.198  1.00 25.00           C
ATOM     51  CA  ILE    51      53.995   9.854  21.137  1.00 25.00           C
ATOM     52  CA  GLY    52      52.823  13.320  19.947  1.00 25.00           C
ATOM     53  CA  TYR    53      49.229  13.095  21.081  1.00 25.00           C
ATOM     54  CA  TYR    54      46.209  13.142  18.677  1.00 25.00           C
ATOM     55  CA  ASP    55      43.465  14.194  21.142  1.00 25.00           C
ATOM     56  CA  GLN    56      40.028  15.365  22.068  1.00 25.00           C
ATOM     57  CA  GLU    57      37.687  15.415  25.121  1.00 25.00           C
ATOM     58  CA  LYS    58      40.226  14.933  27.911  1.00 25.00           C
ATOM     59  CA  LYS    59      40.836  11.473  26.451  1.00 25.00           C
ATOM     60  CA  GLU    60      41.987   8.081  25.352  1.00 25.00           C
ATOM     61  CA  TYR    61      45.319   6.827  24.068  1.00 25.00           C
ATOM     62  CA  VAL    62      47.760   4.620  26.029  1.00 25.00           C
ATOM     63  CA  LYS    63      51.438   4.031  25.176  1.00 25.00           C
ATOM     64  CA  LYS    64      55.177   4.969  25.380  1.00 25.00           C
ATOM     65  CA  GLU    65      56.976   1.617  25.626  1.00 25.00           C
ATOM     66  CA  LEU    66      59.975   2.697  23.547  1.00 25.00           C
ATOM     67  CA  MET    67      62.390   0.703  25.668  1.00 25.00           C
ATOM     68  CA  GLU    68      66.120   0.923  24.881  1.00 25.00           C
ATOM     69  CA  PRO    69      67.830  -0.350  21.749  1.00 25.00           C
ATOM     70  CA  LEU    70      70.974   1.784  21.356  1.00 25.00           C
ATOM     71  CA  GLU    71      69.740   2.125  17.724  1.00 25.00           C
ATOM     72  CA  ILE    72      69.847   5.600  16.095  1.00 25.00           C
ATOM     73  CA  LEU    73      66.041   5.637  15.841  1.00 25.00           C
ATOM     74  CA  SER    74      63.085   3.599  17.212  1.00 25.00           C
ATOM     75  CA  LEU    75      60.066   5.122  18.953  1.00 25.00           C
ATOM     76  CA  SER    76      57.337   7.534  17.830  1.00 25.00           C
ATOM     77  CA  GLY    77      55.072   5.018  19.501  1.00 25.00           C
ATOM     78  CA  ASN    78      51.428   4.348  18.840  1.00 25.00           C
ATOM     79  CA  VAL    79      49.804   7.602  17.771  1.00 25.00           C
ATOM     80  CA  SER    80      46.640   6.201  19.269  1.00 25.00           C
ATOM     81  CA  MET    81      43.293   4.442  19.961  1.00 25.00           C
ATOM     82  CA  LYS    82      40.501   1.813  20.126  1.00 25.00           C
ATOM     83  CA  ASP    83      39.457  -0.616  17.392  1.00 25.00           C
ATOM     84  CA  SER    84      42.102   0.935  15.094  1.00 25.00           C
ATOM     85  CA  LYS    85      45.600   2.371  14.621  1.00 25.00           C
ATOM     86  CA  PRO    86      48.924   4.072  14.063  1.00 25.00           C
ATOM     87  CA  PHE    87      52.581   2.860  14.166  1.00 25.00           C
ATOM     88  CA  CYS    88      56.301   3.168  14.868  1.00 25.00           C
ATOM     89  CA  HIS    89      59.255   3.840  12.562  1.00 25.00           C
ATOM     90  CA  ILE    90      60.833   6.981  14.145  1.00 25.00           C
ATOM     91  CA  HIS    91      62.439   9.100  16.875  1.00 25.00           C
ATOM     92  CA  VAL    92      65.657   9.756  18.759  1.00 25.00           C
ATOM     93  CA  LEU    93      64.970  13.005  20.587  1.00 25.00           C
ATOM     94  CA  LEU    94      68.405  14.584  20.876  1.00 25.00           C
ATOM     95  CA  GLY    95      70.117  16.683  18.236  1.00 25.00           C
ATOM     96  CA  LYS    96      70.702  19.269  20.977  1.00 25.00           C
ATOM     97  CA  ASP    97      69.514  19.191  24.561  1.00 25.00           C
ATOM     98  CA  GLY    98      65.744  19.370  25.330  1.00 25.00           C
ATOM     99  CA  GLU    99      64.632  20.485  21.882  1.00 25.00           C
ATOM    100  CA  VAL   100      63.607  17.705  19.436  1.00 25.00           C
ATOM    101  CA  TYR   101      61.468  15.067  17.632  1.00 25.00           C
ATOM    102  CA  GLY   102      59.439  12.327  19.245  1.00 25.00           C
ATOM    103  CA  GLY   103      57.999  11.967  15.712  1.00 25.00           C
ATOM    104  CA  HIS   104      54.267  11.816  15.191  1.00 25.00           C
ATOM    105  CA  LEU   105      54.892   8.652  13.206  1.00 25.00           C
ATOM    106  CA  PHE   106      53.193   6.377  10.651  1.00 25.00           C
ATOM    107  CA  SER   107      50.279   6.657   8.173  1.00 25.00           C
ATOM    108  CA  ALA   108      53.068   7.024   5.575  1.00 25.00           C
ATOM    109  CA  GLU   109      52.413   9.766   3.015  1.00 25.00           C
ATOM    110  CA  VAL   110      53.595  12.926   4.807  1.00 25.00           C
ATOM    111  CA  PHE   111      54.594  15.179   7.779  1.00 25.00           C
ATOM    112  CA  ALA   112      55.338  14.885  11.514  1.00 25.00           C
ATOM    113  CA  CYS   113      52.787  16.529  13.839  1.00 25.00           C
ATOM    114  CA  GLU   114      55.761  16.827  16.192  1.00 25.00           C
ATOM    115  CA  VAL   115      58.017  19.622  17.441  1.00 25.00           C
ATOM    116  CA  PHE   116      58.198  17.591  20.616  1.00 25.00           C
ATOM    117  CA  VAL   117      60.636  16.879  23.388  1.00 25.00           C
ATOM    118  CA  LEU   118      63.311  14.723  25.131  1.00 25.00           C
ATOM    119  CA  PRO   119      66.184  14.489  27.548  1.00 25.00           C
ATOM    120  CA  LEU   120      63.556  15.392  30.139  1.00 25.00           C
ATOM    121  CA  SER   121      63.398  14.677  33.886  1.00 25.00           C
ATOM    122  CA  GLY   122      61.130  11.783  34.549  1.00 25.00           C
ATOM    123  CA  GLU   123      59.430  12.399  31.231  1.00 25.00           C
ATOM    124  CA  ALA   124      57.885  13.724  28.044  1.00 25.00           C
ATOM    125  CA  PRO   125      55.904  14.714  24.912  1.00 25.00           C
ATOM    126  CA  GLU   126      54.771  18.281  24.301  1.00 25.00           C
ATOM    127  CA  ARG   127      51.669  18.835  22.171  1.00 25.00           C
ATOM    128  CA  ALA   128      50.756  17.805  18.683  1.00 25.00           C
ATOM    129  CA  PHE   129      47.888  17.735  16.259  1.00 25.00           C
ATOM    130  CA  ASP   130      45.867  19.993  18.554  1.00 25.00           C
ATOM    131  CA  GLU   131      45.905  23.744  19.167  1.00 25.00           C
ATOM    132  CA  GLN   132      45.389  26.504  16.585  1.00 25.00           C
ATOM    133  CA  THR   133      44.025  24.918  13.477  1.00 25.00           C
ATOM    134  CA  GLY   134      44.057  21.421  12.004  1.00 25.00           C
ATOM    135  CA  LEU   135      41.306  21.532   9.326  1.00 25.00           C
ATOM    136  CA  PHE   136      38.343  23.821   8.444  1.00 25.00           C
ATOM    137  CA  LEU   137      36.429  22.964   5.271  1.00 25.00           C
ATOM    138  CA  TRP   138      35.186  22.747   1.687  1.00 25.00           C
ATOM    139  CA  LEU   139      31.579  21.774   1.155  1.00 25.00           C
ATOM    140  CA  GLU   140      27.956  20.650   1.015  1.00 25.00           C
ATOM    141  CA  HIS   141      29.166  17.162   0.106  1.00 25.00           C
ATOM    142  CA  HIS   142      29.534  14.669  -2.726  1.00 25.00           C
ATOM    143  CA  HIS   143      30.168  17.439  -5.238  1.00 25.00           C
ATOM    144  CA  HIS   144      33.551  18.244  -6.886  1.00 25.00           C
ATOM    145  CA  HIS   145      33.636  14.618  -8.028  1.00 25.00           C
ATOM    146  CA  HIS   146      36.939  12.915  -7.198  1.00 25.00           C
TER
END
