
#######################################################
#                                                     #
#                        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  132 (  132),  selected  132 , name T0312TS393_1-D1
# Molecule2: number of CA atoms  132 ( 1043),  selected  132 , name T0312_D1.pdb
# PARAMETERS: T0312TS393_1-D1.T0312_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G       9      G       9           -
LGA    -       -      K      10           -
LGA    -       -      G      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      L      14           -
LGA    -       -      R      15           -
LGA    -       -      L      16           -
LGA    -       -      D      17           -
LGA    -       -      Y      18           -
LGA    -       -      G      19           -
LGA    -       -      K      20           -
LGA    -       -      D      21           -
LGA    K      10      L      22           #
LGA    G      11      V      23           #
LGA    F      12      R      24          1.563
LGA    L      13      Q      25          2.325
LGA    L      14      I      26          4.104
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          3.797
LGA    A      38      -       -           -
LGA    H      39      -       -           -
LGA    I      40      -       -           -
LGA    S      41      F      29          3.782
LGA    A      42      L      30          3.199
LGA    I      43      E      31          2.177
LGA    -       -      E      32           -
LGA    -       -      K      33           -
LGA    G      44      G      34          1.555
LGA    A      45      I      35          3.382
LGA    V      46      H      36          3.425
LGA    R      47      A      37          0.957
LGA    S      48      A      38          3.865
LGA    A      49      H      39          3.060
LGA    V      50      I      40          1.800
LGA    I      51      S      41          2.751
LGA    G      52      A      42          0.924
LGA    Y      53      I      43          3.822
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          4.122
LGA    D      55      L      73          4.768
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          4.457
LGA    E      65      G      77           #
LGA    L      66      N      78          3.381
LGA    M      67      V      79           #
LGA    E      68      S      80          3.344
LGA    P      69      M      81          2.908
LGA    L      70      K      82          4.099
LGA    E      71      D      83          4.905
LGA    -       -      S      84           -
LGA    I      72      K      85          2.899
LGA    L      73      P      86          3.681
LGA    S      74      F      87          2.763
LGA    L      75      C      88          2.368
LGA    S      76      H      89           #
LGA    G      77      I      90          1.505
LGA    N      78      H      91          1.773
LGA    V      79      V      92          2.505
LGA    S      80      L      93          1.718
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          4.183
LGA    K      85      Y     101          2.907
LGA    -       -      G     102           -
LGA    P      86      G     103           #
LGA    F      87      H     104          4.474
LGA    C      88      L     105          2.857
LGA    H      89      F     106          4.560
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      S     107           #
LGA    F     106      A     108          2.182
LGA    S     107      -       -           -
LGA    A     108      E     109          2.719
LGA    E     109      V     110           #
LGA    V     110      F     111          4.668
LGA    F     111      A     112          4.876
LGA    A     112      C     113          3.279
LGA    C     113      -       -           -
LGA    E     114      E     114          2.210
LGA    V     115      V     115          3.890
LGA    F     116      F     116          1.609
LGA    V     117      V     117          2.147
LGA    L     118      L     118          1.299
LGA    P     119      P     119          1.996
LGA    -       -      L     120           -
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      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  132  132    5.0     49    3.20    16.33     21.064     1.483

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.422630 * X  +  -0.874107 * Y  +  -0.239419 * Z  +  55.927567
  Y_new =  -0.222152 * X  +   0.156197 * Y  +  -0.962419 * Z  +  12.090433
  Z_new =   0.878654 * X  +   0.459935 * Y  +  -0.128171 * Z  +  13.251546 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.842574   -1.299019  [ DEG:   105.5717    -74.4283 ]
  Theta =  -1.073035   -2.068558  [ DEG:   -61.4804   -118.5196 ]
  Phi   =  -0.483951    2.657642  [ DEG:   -27.7283    152.2717 ]
 
# 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-D1                               
REMARK     2: T0312_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312TS393_1-D1.T0312_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  132  132   5.0   49   3.20   16.33  21.064
REMARK  ---------------------------------------------------------- 
MOLECULE T0312TS393_1-D1
PFRMAT TS
TARGET T0312
MODEL 1
PARENT N/A
ATOM      9  CA  GLY     9      62.390  -0.739   6.883  1.00 25.00           C
ATOM     10  CA  LYS    10      64.727   0.911   9.379  1.00 25.00           C
ATOM     11  CA  GLY    11      63.464   4.431  10.187  1.00 25.00           C
ATOM     12  CA  PHE    12      63.431   8.144   9.734  1.00 25.00           C
ATOM     13  CA  LEU    13      62.877  11.157  11.902  1.00 25.00           C
ATOM     14  CA  LEU    14      59.415  11.544  10.418  1.00 25.00           C
ATOM     15  CA  ARG    15      59.585  15.005  11.983  1.00 25.00           C
ATOM     16  CA  LEU    16      59.548  18.406  10.255  1.00 25.00           C
ATOM     17  CA  ASP    17      61.218  21.350   8.556  1.00 25.00           C
ATOM     18  CA  TYR    18      61.834  24.543   6.583  1.00 25.00           C
ATOM     19  CA  GLY    19      61.473  27.175   3.912  1.00 25.00           C
ATOM     20  CA  LYS    20      61.046  25.412   0.588  1.00 25.00           C
ATOM     21  CA  ASP    21      64.864  25.133   0.706  1.00 25.00           C
ATOM     22  CA  LEU    22      64.595  22.073   2.992  1.00 25.00           C
ATOM     23  CA  VAL    23      62.084  20.466   0.588  1.00 25.00           C
ATOM     24  CA  ARG    24      64.440  21.136  -2.357  1.00 25.00           C
ATOM     25  CA  GLN    25      67.346  19.562  -0.422  1.00 25.00           C
ATOM     26  CA  ILE    26      65.196  16.490   0.357  1.00 25.00           C
ATOM     27  CA  GLU    27      64.251  16.182  -3.342  1.00 25.00           C
ATOM     28  CA  GLU    28      67.944  16.412  -4.329  1.00 25.00           C
ATOM     29  CA  PHE    29      68.821  13.691  -1.780  1.00 25.00           C
ATOM     30  CA  LEU    30      66.038  11.458  -3.170  1.00 25.00           C
ATOM     31  CA  GLU    31      67.343  12.006  -6.729  1.00 25.00           C
ATOM     32  CA  GLU    32      70.887  11.101  -5.595  1.00 25.00           C
ATOM     33  CA  LYS    33      73.812  12.793  -3.914  1.00 25.00           C
ATOM     34  CA  GLY    34      73.599  10.784  -0.649  1.00 25.00           C
ATOM     35  CA  ILE    35      71.563  12.015   2.390  1.00 25.00           C
ATOM     36  CA  HIS    36      70.316  13.131   5.850  1.00 25.00           C
ATOM     37  CA  ALA    37      66.971  12.400   7.573  1.00 25.00           C
ATOM     38  CA  ALA    38      63.260  13.065   7.272  1.00 25.00           C
ATOM     39  CA  HIS    39      62.953  16.834   6.805  1.00 25.00           C
ATOM     40  CA  ILE    40      64.585  16.992  10.264  1.00 25.00           C
ATOM     41  CA  SER    41      65.464  17.899  13.847  1.00 25.00           C
ATOM     42  CA  ALA    42      65.629  14.257  15.051  1.00 25.00           C
ATOM     43  CA  ILE    43      68.834  12.211  15.397  1.00 25.00           C
ATOM     44  CA  GLY    44      71.284  11.894  18.286  1.00 25.00           C
ATOM     45  CA  ALA    45      70.151   8.810  20.107  1.00 25.00           C
ATOM     46  CA  VAL    46      67.553   6.188  20.861  1.00 25.00           C
ATOM     47  CA  ARG    47      66.717   8.042  24.078  1.00 25.00           C
ATOM     48  CA  SER    48      63.247   6.515  24.404  1.00 25.00           C
ATOM     49  CA  ALA    49      60.304   8.397  23.027  1.00 25.00           C
ATOM     50  CA  VAL    50      56.680   9.657  22.740  1.00 25.00           C
ATOM     51  CA  ILE    51      53.501   9.809  20.612  1.00 25.00           C
ATOM     52  CA  GLY    52      52.241  13.137  19.146  1.00 25.00           C
ATOM     53  CA  TYR    53      48.639  12.884  20.246  1.00 25.00           C
ATOM     54  CA  TYR    54      45.657  12.653  17.806  1.00 25.00           C
ATOM     55  CA  ASP    55      42.843  13.801  20.147  1.00 25.00           C
ATOM     56  CA  GLN    56      39.358  14.927  20.935  1.00 25.00           C
ATOM     57  CA  GLU    57      36.969  15.133  23.944  1.00 25.00           C
ATOM     58  CA  LYS    58      39.477  14.944  26.797  1.00 25.00           C
ATOM     59  CA  LYS    59      40.216  11.405  25.611  1.00 25.00           C
ATOM     60  CA  GLU    60      41.488   7.978  24.789  1.00 25.00           C
ATOM     61  CA  TYR    61      44.877   6.738  23.647  1.00 25.00           C
ATOM     62  CA  VAL    62      47.352   4.763  25.803  1.00 25.00           C
ATOM     63  CA  LYS    63      51.060   4.229  25.047  1.00 25.00           C
ATOM     64  CA  LYS    64      54.765   5.298  25.228  1.00 25.00           C
ATOM     65  CA  GLU    65      56.662   2.034  25.752  1.00 25.00           C
ATOM     66  CA  LEU    66      59.659   3.048  23.637  1.00 25.00           C
ATOM     67  CA  MET    67      62.100   1.297  25.936  1.00 25.00           C
ATOM     68  CA  GLU    68      65.834   1.576  25.184  1.00 25.00           C
ATOM     69  CA  PRO    69      67.631   0.125  22.181  1.00 25.00           C
ATOM     70  CA  LEU    70      70.714   2.322  21.669  1.00 25.00           C
ATOM     71  CA  GLU    71      69.526   2.349  18.005  1.00 25.00           C
ATOM     72  CA  ILE    72      69.552   5.692  16.119  1.00 25.00           C
ATOM     73  CA  LEU    73      65.752   5.590  15.812  1.00 25.00           C
ATOM     74  CA  SER    74      62.839   3.568  17.294  1.00 25.00           C
ATOM     75  CA  LEU    75      59.747   5.121  18.874  1.00 25.00           C
ATOM     76  CA  SER    76      56.963   7.353  17.535  1.00 25.00           C
ATOM     77  CA  GLY    77      54.751   4.900  19.362  1.00 25.00           C
ATOM     78  CA  ASN    78      51.140   4.067  18.705  1.00 25.00           C
ATOM     79  CA  VAL    79      49.434   7.178  17.370  1.00 25.00           C
ATOM     80  CA  SER    80      46.292   5.793  18.928  1.00 25.00           C
ATOM     81  CA  MET    81      42.989   3.986  19.707  1.00 25.00           C
ATOM     82  CA  LYS    82      40.277   1.290  20.034  1.00 25.00           C
ATOM     83  CA  ASP    83      39.351  -1.370  17.478  1.00 25.00           C
ATOM     84  CA  SER    84      41.983   0.086  15.105  1.00 25.00           C
ATOM     85  CA  LYS    85      45.443   1.593  14.571  1.00 25.00           C
ATOM     86  CA  PRO    86      48.721   3.351  13.930  1.00 25.00           C
ATOM     87  CA  PHE    87      52.412   2.268  14.173  1.00 25.00           C
ATOM     88  CA  CYS    88      56.108   2.746  14.899  1.00 25.00           C
ATOM     89  CA  HIS    89      59.077   3.335  12.589  1.00 25.00           C
ATOM     90  CA  ILE    90      60.532   6.636  13.949  1.00 25.00           C
ATOM     91  CA  HIS    91      62.030   9.004  16.532  1.00 25.00           C
ATOM     92  CA  VAL    92      65.195   9.903  18.404  1.00 25.00           C
ATOM     93  CA  LEU    93      64.381  13.257  19.970  1.00 25.00           C
ATOM     94  CA  LEU    94      67.761  14.962  20.185  1.00 25.00           C
ATOM     95  CA  GLY    95      69.449  16.908  17.417  1.00 25.00           C
ATOM     96  CA  LYS    96      69.911  19.711  19.961  1.00 25.00           C
ATOM     97  CA  ASP    97      68.670  19.866  23.524  1.00 25.00           C
ATOM     98  CA  GLY    98      64.885  19.983  24.227  1.00 25.00           C
ATOM     99  CA  GLU    99      63.793  20.798  20.689  1.00 25.00           C
ATOM    100  CA  VAL   100      62.892  17.811  18.449  1.00 25.00           C
ATOM    101  CA  TYR   101      60.864  14.977  16.822  1.00 25.00           C
ATOM    102  CA  GLY   102      58.895  12.304  18.610  1.00 25.00           C
ATOM    103  CA  GLY   103      57.522  11.633  15.096  1.00 25.00           C
ATOM    104  CA  HIS   104      53.806  11.325  14.538  1.00 25.00           C
ATOM    105  CA  LEU   105      54.559   8.042  12.808  1.00 25.00           C
ATOM    106  CA  PHE   106      52.970   5.527  10.410  1.00 25.00           C
ATOM    107  CA  SER   107      50.088   5.526   7.879  1.00 25.00           C
ATOM    108  CA  ALA   108      52.905   5.786   5.298  1.00 25.00           C
ATOM    109  CA  GLU   109      52.207   8.304   2.529  1.00 25.00           C
ATOM    110  CA  VAL   110      53.263  11.626   4.092  1.00 25.00           C
ATOM    111  CA  PHE   111      54.146  14.128   6.897  1.00 25.00           C
ATOM    112  CA  ALA   112      54.840  14.140  10.653  1.00 25.00           C
ATOM    113  CA  CYS   113      52.203  15.872  12.812  1.00 25.00           C
ATOM    114  CA  GLU   114      55.129  16.441  15.176  1.00 25.00           C
ATOM    115  CA  VAL   115      57.278  19.394  16.239  1.00 25.00           C
ATOM    116  CA  PHE   116      57.472  17.614  19.562  1.00 25.00           C
ATOM    117  CA  VAL   117      59.887  17.191  22.412  1.00 25.00           C
ATOM    118  CA  LEU   118      62.598  15.259  24.349  1.00 25.00           C
ATOM    119  CA  PRO   119      65.439  15.299  26.814  1.00 25.00           C
ATOM    120  CA  LEU   120      62.745  16.312  29.294  1.00 25.00           C
ATOM    121  CA  SER   121      62.550  15.877  33.082  1.00 25.00           C
ATOM    122  CA  GLY   122      60.361  12.970  33.933  1.00 25.00           C
ATOM    123  CA  GLU   123      58.695  13.280  30.555  1.00 25.00           C
ATOM    124  CA  ALA   124      57.161  14.311  27.256  1.00 25.00           C
ATOM    125  CA  PRO   125      55.200  14.998  24.032  1.00 25.00           C
ATOM    126  CA  GLU   126      53.968  18.471  23.137  1.00 25.00           C
ATOM    127  CA  ARG   127      50.884  18.764  20.930  1.00 25.00           C
ATOM    128  CA  ALA   128      50.058  17.445  17.519  1.00 25.00           C
ATOM    129  CA  PHE   129      47.232  17.102  15.068  1.00 25.00           C
ATOM    130  CA  ASP   130      45.106  19.460  17.158  1.00 25.00           C
ATOM    131  CA  GLU   131      45.020  23.246  17.485  1.00 25.00           C
ATOM    132  CA  GLN   132      44.460  25.787  14.695  1.00 25.00           C
ATOM    133  CA  THR   133      43.195  23.928  11.698  1.00 25.00           C
ATOM    134  CA  GLY   134      43.357  20.332  10.496  1.00 25.00           C
ATOM    135  CA  LEU   135      40.647  20.153   7.780  1.00 25.00           C
ATOM    136  CA  PHE   136      37.628  22.275   6.687  1.00 25.00           C
ATOM    137  CA  LEU   137      35.792  21.120   3.564  1.00 25.00           C
ATOM    138  CA  TRP   138      34.613  20.594  -0.010  1.00 25.00           C
ATOM    139  CA  LEU   139      31.046  19.469  -0.515  1.00 25.00           C
ATOM    140  CA  GLU   140      27.462  18.224  -0.618  1.00 25.00           C
TER
END
