
#######################################################
#                                                     #
#                        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  128 (  128),  selected  128 , name T0322TS393_3-D1
# Molecule2: number of CA atoms  128 (  980),  selected  128 , name T0322_D1.pdb
# PARAMETERS: T0322TS393_3-D1.T0322_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G      16      G      16           -
LGA    F      17      F      17           -
LGA    S      18      S      18           -
LGA    Q      19      Q      19           -
LGA    L      20      L      20           -
LGA    N      21      N      21           -
LGA    W      22      -       -           -
LGA    S      23      W      22          5.512
LGA    R      24      S      23          2.032
LGA    G      25      R      24          1.615
LGA    F      26      G      25          3.652
LGA    -       -      F      26           -
LGA    G      27      G      27          2.807
LGA    R      28      R      28          2.658
LGA    Q      29      Q      29          1.960
LGA    I      30      I      30          0.768
LGA    G      31      G      31          1.351
LGA    P      32      P      32           #
LGA    L      33      L      33          1.410
LGA    F      34      F      34          2.524
LGA    E      35      E      35          3.425
LGA    H      36      H      36          1.852
LGA    R      37      R      37           #
LGA    -       -      E      38           -
LGA    -       -      G      39           -
LGA    E      38      P      40          3.110
LGA    G      39      G      41          4.551
LGA    P      40      Q      42           #
LGA    G      41      -       -           -
LGA    Q      42      -       -           -
LGA    A      43      A      43          2.795
LGA    R      44      R      44          2.703
LGA    L      45      L      45          2.843
LGA    A      46      A      46          1.591
LGA    F      47      F      47          3.608
LGA    R      48      R      48          2.658
LGA    V      49      V      49          1.621
LGA    E      50      E      50          1.829
LGA    E      51      E      51          1.828
LGA    H      52      H      52          2.643
LGA    H      53      H      53          1.290
LGA    T      54      T      54          1.393
LGA    N      55      N      55          1.515
LGA    G      56      G      56           #
LGA    L      57      L      57          2.218
LGA    G      58      G      58          3.053
LGA    N      59      N      59          2.058
LGA    C      60      C      60          2.486
LGA    H      61      H      61          1.471
LGA    G      62      G      62          1.594
LGA    G      63      G      63          1.260
LGA    M      64      M      64          0.994
LGA    L      65      L      65          1.098
LGA    M      66      M      66          0.854
LGA    S      67      S      67          0.555
LGA    F      68      F      68          0.693
LGA    A      69      A      69          0.884
LGA    D      70      D      70          0.440
LGA    M      71      M      71          0.709
LGA    A      72      A      72          1.818
LGA    W      73      W      73          2.841
LGA    G      74      G      74          2.801
LGA    R      75      R      75          2.125
LGA    I      76      I      76          1.689
LGA    I      77      I      77          1.919
LGA    S      78      S      78          2.216
LGA    L      79      L      79          2.447
LGA    Q      80      Q      80          3.384
LGA    K      81      K      81          4.278
LGA    S      82      S      82           -
LGA    Y      83      Y      83          5.019
LGA    S      84      S      84          3.324
LGA    W      85      W      85          1.269
LGA    V      86      V      86          1.764
LGA    T      87      T      87          2.636
LGA    V      88      V      88          2.518
LGA    R      89      R      89          2.384
LGA    L      90      L      90          1.852
LGA    M      91      M      91          1.651
LGA    C      92      C      92          2.389
LGA    D      93      D      93          2.383
LGA    F      94      F      94          2.254
LGA    L      95      L      95          2.245
LGA    S      96      S      96          1.643
LGA    G      97      G      97          1.586
LGA    A      98      A      98          2.600
LGA    K      99      K      99          2.745
LGA    L     100      L     100          1.563
LGA    G     101      G     101          1.708
LGA    D     102      D     102          1.263
LGA    W     103      W     103          1.596
LGA    V     104      V     104          1.734
LGA    E     105      E     105          2.370
LGA    G     106      G     106          2.193
LGA    E     107      E     107          1.482
LGA    G     108      G     108          1.891
LGA    E     109      E     109          2.923
LGA    L     110      L     110          2.654
LGA    I     111      I     111          2.348
LGA    S     112      S     112          1.884
LGA    E     113      E     113          2.080
LGA    E     114      E     114          3.783
LGA    D     115      D     115          5.398
LGA    -       -      M     116           -
LGA    M     116      L     117          2.551
LGA    L     117      F     118          1.279
LGA    F     118      T     119          5.356
LGA    T     119      V     120          0.496
LGA    V     120      R     121          1.148
LGA    R     121      G     122          1.501
LGA    G     122      R     123          1.022
LGA    R     123      I     124          2.187
LGA    I     124      W     125          3.313
LGA    W     125      A     126          1.644
LGA    A     126      G     127          3.083
LGA    G     127      -       -           -
LGA    E     128      E     128          1.352
LGA    R     129      R     129          3.620
LGA    T     130      T     130          1.231
LGA    L     131      L     131          1.500
LGA    I     132      I     132          1.415
LGA    T     133      T     133          1.968
LGA    G     134      G     134          4.505
LGA    T     135      T     135          3.354
LGA    G     136      G     136          1.623
LGA    V     137      V     137          3.781
LGA    F     138      F     138          0.449
LGA    K     139      K     139          0.478
LGA    A     140      A     140          2.864
LGA    L     141      L     141          4.380
LGA    S     142      S     142           #
LGA    A     143      A     143           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  128  128    5.0    111    2.47    85.59     56.285     4.312

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.954016 * X  +  -0.178442 * Y  +   0.240855 * Z  +  10.327045
  Y_new =  -0.275265 * X  +  -0.839617 * Y  +   0.468265 * Z  +  -5.755910
  Z_new =   0.118668 * X  +  -0.513032 * Y  +  -0.850127 * Z  + -14.486823 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.598621    0.542972  [ DEG:  -148.8900     31.1100 ]
  Theta =  -0.118948   -3.022645  [ DEG:    -6.8152   -173.1848 ]
  Phi   =  -0.280903    2.860689  [ DEG:   -16.0946    163.9054 ]
 
# 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: T0322TS393_3-D1                               
REMARK     2: T0322_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0322TS393_3-D1.T0322_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  128  128   5.0  111   2.47   85.59  56.285
REMARK  ---------------------------------------------------------- 
MOLECULE T0322TS393_3-D1
PFRMAT TS
TARGET T0322
MODEL 3
PARENT N/A
ATOM     16  CA  GLY    16      22.094  -4.765   9.865  1.00 25.00           C
ATOM     17  CA  PHE    17      20.301  -7.071   7.485  1.00 25.00           C
ATOM     18  CA  SER    18      17.325  -7.420   9.799  1.00 25.00           C
ATOM     19  CA  GLN    19      13.670  -6.592   9.345  1.00 25.00           C
ATOM     20  CA  LEU    20      13.316  -4.012   6.525  1.00 25.00           C
ATOM     21  CA  ASN    21      11.169  -0.856   7.096  1.00 25.00           C
ATOM     22  CA  TRP    22      10.639   0.966   3.754  1.00 25.00           C
ATOM     23  CA  SER    23      12.799  -1.724   2.082  1.00 25.00           C
ATOM     24  CA  ARG    24      11.176  -2.750  -1.177  1.00 25.00           C
ATOM     25  CA  GLY    25       9.047   0.340  -1.834  1.00 25.00           C
ATOM     26  CA  PHE    26       8.982  -0.578  -5.549  1.00 25.00           C
ATOM     27  CA  GLY    27       8.592  -4.240  -6.599  1.00 25.00           C
ATOM     28  CA  ARG    28       6.714  -4.997  -3.347  1.00 25.00           C
ATOM     29  CA  GLN    29       4.402  -2.006  -3.958  1.00 25.00           C
ATOM     30  CA  ILE    30       2.814  -3.172  -7.205  1.00 25.00           C
ATOM     31  CA  GLY    31       3.450  -6.940  -6.815  1.00 25.00           C
ATOM     32  CA  PRO    32       5.162  -7.142 -10.221  1.00 25.00           C
ATOM     33  CA  LEU    33       7.172 -10.088  -8.907  1.00 25.00           C
ATOM     34  CA  PHE    34       9.745 -12.192 -10.658  1.00 25.00           C
ATOM     35  CA  GLU    35       9.496 -15.942 -10.900  1.00 25.00           C
ATOM     36  CA  HIS    36      11.756 -16.825 -13.833  1.00 25.00           C
ATOM     37  CA  ARG    37      12.016 -16.793 -17.629  1.00 25.00           C
ATOM     38  CA  GLU    38      14.067 -19.238 -19.611  1.00 25.00           C
ATOM     39  CA  GLY    39      17.770 -18.334 -19.101  1.00 25.00           C
ATOM     40  CA  PRO    40      20.439 -16.298 -20.945  1.00 25.00           C
ATOM     41  CA  GLY    41      18.129 -13.225 -21.071  1.00 25.00           C
ATOM     42  CA  GLN    42      15.012 -11.535 -19.772  1.00 25.00           C
ATOM     43  CA  ALA    43      13.831 -11.928 -16.119  1.00 25.00           C
ATOM     44  CA  ARG    44      10.001 -11.704 -16.119  1.00 25.00           C
ATOM     45  CA  LEU    45       7.164  -9.968 -14.394  1.00 25.00           C
ATOM     46  CA  ALA    46       4.795 -12.109 -12.249  1.00 25.00           C
ATOM     47  CA  PHE    47       1.421 -10.355 -12.266  1.00 25.00           C
ATOM     48  CA  ARG    48       0.406 -11.465  -8.771  1.00 25.00           C
ATOM     49  CA  VAL    49      -3.230 -10.975  -9.528  1.00 25.00           C
ATOM     50  CA  GLU    50      -5.107 -10.366  -6.296  1.00 25.00           C
ATOM     51  CA  GLU    51      -5.285  -8.538  -2.934  1.00 25.00           C
ATOM     52  CA  HIS    52      -7.551  -5.810  -4.379  1.00 25.00           C
ATOM     53  CA  HIS    53      -5.057  -5.207  -7.221  1.00 25.00           C
ATOM     54  CA  THR    54      -7.350  -7.028  -9.675  1.00 25.00           C
ATOM     55  CA  ASN    55     -10.916  -5.820  -8.818  1.00 25.00           C
ATOM     56  CA  GLY    56     -13.754  -3.670 -10.179  1.00 25.00           C
ATOM     57  CA  LEU    57     -15.835  -6.780  -9.475  1.00 25.00           C
ATOM     58  CA  GLY    58     -13.628  -9.692 -10.451  1.00 25.00           C
ATOM     59  CA  ASN    59     -10.921  -9.067 -13.071  1.00 25.00           C
ATOM     60  CA  CYS    60      -7.393  -9.124 -14.453  1.00 25.00           C
ATOM     61  CA  HIS    61      -7.646  -5.313 -14.572  1.00 25.00           C
ATOM     62  CA  GLY    62      -5.657  -5.570 -17.860  1.00 25.00           C
ATOM     63  CA  GLY    63      -3.927  -2.487 -16.390  1.00 25.00           C
ATOM     64  CA  MET    64      -1.981  -4.709 -13.953  1.00 25.00           C
ATOM     65  CA  LEU    65      -0.914  -6.985 -16.843  1.00 25.00           C
ATOM     66  CA  MET    66       0.244  -3.936 -18.849  1.00 25.00           C
ATOM     67  CA  SER    67       2.248  -2.683 -15.836  1.00 25.00           C
ATOM     68  CA  PHE    68       3.868  -6.132 -15.450  1.00 25.00           C
ATOM     69  CA  ALA    69       4.775  -6.151 -19.170  1.00 25.00           C
ATOM     70  CA  ASP    70       6.314  -2.660 -18.838  1.00 25.00           C
ATOM     71  CA  MET    71       8.346  -3.817 -15.806  1.00 25.00           C
ATOM     72  CA  ALA    72       9.576  -6.870 -17.764  1.00 25.00           C
ATOM     73  CA  TRP    73      10.590  -4.617 -20.690  1.00 25.00           C
ATOM     74  CA  GLY    74      12.482  -2.310 -18.289  1.00 25.00           C
ATOM     75  CA  ARG    75      14.284  -5.329 -16.770  1.00 25.00           C
ATOM     76  CA  ILE    76      15.240  -6.551 -20.272  1.00 25.00           C
ATOM     77  CA  ILE    77      16.580  -3.071 -21.147  1.00 25.00           C
ATOM     78  CA  SER    78      18.632  -3.022 -17.915  1.00 25.00           C
ATOM     79  CA  LEU    79      20.053  -6.483 -18.735  1.00 25.00           C
ATOM     80  CA  GLN    80      22.986  -5.207 -20.860  1.00 25.00           C
ATOM     81  CA  LYS    81      25.081  -4.175 -23.875  1.00 25.00           C
ATOM     82  CA  SER    82      24.633  -0.548 -25.061  1.00 25.00           C
ATOM     83  CA  TYR    83      22.687   1.512 -22.524  1.00 25.00           C
ATOM     84  CA  SER    84      20.475   2.164 -19.490  1.00 25.00           C
ATOM     85  CA  TRP    85      16.879   3.048 -18.754  1.00 25.00           C
ATOM     86  CA  VAL    86      13.528   4.740 -18.508  1.00 25.00           C
ATOM     87  CA  THR    87      10.080   3.383 -19.307  1.00 25.00           C
ATOM     88  CA  VAL    88       8.865   4.537 -22.685  1.00 25.00           C
ATOM     89  CA  ARG    89       5.694   4.386 -24.851  1.00 25.00           C
ATOM     90  CA  LEU    90       3.832   1.256 -23.638  1.00 25.00           C
ATOM     91  CA  MET    91       1.578  -0.222 -26.323  1.00 25.00           C
ATOM     92  CA  CYS    92      -1.614  -2.163 -25.473  1.00 25.00           C
ATOM     93  CA  ASP    93      -4.592  -4.542 -25.477  1.00 25.00           C
ATOM     94  CA  PHE    94      -6.566  -7.708 -26.057  1.00 25.00           C
ATOM     95  CA  LEU    95      -8.629 -10.165 -23.921  1.00 25.00           C
ATOM     96  CA  SER    96      -9.986 -13.088 -21.913  1.00 25.00           C
ATOM     97  CA  GLY    97      -9.973 -12.773 -18.117  1.00 25.00           C
ATOM     98  CA  ALA    98      -8.372 -15.209 -15.596  1.00 25.00           C
ATOM     99  CA  LYS    99      -9.030 -16.531 -12.082  1.00 25.00           C
ATOM    100  CA  LEU   100      -8.386 -14.707  -8.827  1.00 25.00           C
ATOM    101  CA  GLY   101      -6.170 -17.524  -7.595  1.00 25.00           C
ATOM    102  CA  ASP   102      -4.122 -18.127 -10.727  1.00 25.00           C
ATOM    103  CA  TRP   103      -1.088 -15.872 -10.843  1.00 25.00           C
ATOM    104  CA  VAL   104       1.625 -16.048 -13.517  1.00 25.00           C
ATOM    105  CA  GLU   105       4.029 -17.191 -16.197  1.00 25.00           C
ATOM    106  CA  GLY   106       6.076 -14.469 -17.997  1.00 25.00           C
ATOM    107  CA  GLU   107       7.999 -13.893 -21.212  1.00 25.00           C
ATOM    108  CA  GLY   108       9.918 -10.611 -21.764  1.00 25.00           C
ATOM    109  CA  GLU   109      12.135 -12.888 -23.927  1.00 25.00           C
ATOM    110  CA  LEU   110      14.750 -11.114 -25.986  1.00 25.00           C
ATOM    111  CA  ILE   111      13.614  -9.908 -29.441  1.00 25.00           C
ATOM    112  CA  SER   112      15.356  -7.257 -31.478  1.00 25.00           C
ATOM    113  CA  GLU   113      18.107  -4.705 -31.995  1.00 25.00           C
ATOM    114  CA  GLU   114      18.773  -2.623 -35.128  1.00 25.00           C
ATOM    115  CA  ASP   115      16.828   0.211 -33.424  1.00 25.00           C
ATOM    116  CA  MET   116      15.947  -0.731 -29.818  1.00 25.00           C
ATOM    117  CA  LEU   117      15.151  -2.916 -26.803  1.00 25.00           C
ATOM    118  CA  PHE   118      14.182  -6.153 -25.021  1.00 25.00           C
ATOM    119  CA  THR   119      10.772  -6.559 -26.787  1.00 25.00           C
ATOM    120  CA  VAL   120       7.758  -8.862 -27.238  1.00 25.00           C
ATOM    121  CA  ARG   121       5.937 -11.398 -25.031  1.00 25.00           C
ATOM    122  CA  GLY   122       3.026 -12.403 -22.800  1.00 25.00           C
ATOM    123  CA  ARG   123       2.745 -10.849 -19.339  1.00 25.00           C
ATOM    124  CA  ILE   124       0.394 -13.122 -17.455  1.00 25.00           C
ATOM    125  CA  TRP   125      -1.102 -16.562 -17.716  1.00 25.00           C
ATOM    126  CA  ALA   126      -1.949 -19.291 -15.135  1.00 25.00           C
ATOM    127  CA  GLY   127      -4.148 -22.241 -15.913  1.00 25.00           C
ATOM    128  CA  GLU   128      -3.251 -22.186 -19.605  1.00 25.00           C
ATOM    129  CA  ARG   129      -0.964 -19.946 -21.686  1.00 25.00           C
ATOM    130  CA  THR   130      -2.385 -17.048 -23.569  1.00 25.00           C
ATOM    131  CA  LEU   131      -3.119 -13.559 -22.317  1.00 25.00           C
ATOM    132  CA  ILE   132      -3.181  -9.830 -22.940  1.00 25.00           C
ATOM    133  CA  THR   133      -0.889  -8.638 -25.776  1.00 25.00           C
ATOM    134  CA  GLY   134       1.347  -7.531 -22.921  1.00 25.00           C
ATOM    135  CA  THR   135       4.112  -5.991 -25.033  1.00 25.00           C
ATOM    136  CA  GLY   136       6.451  -3.084 -24.665  1.00 25.00           C
ATOM    137  CA  VAL   137       8.917  -0.517 -23.465  1.00 25.00           C
ATOM    138  CA  PHE   138      12.575   0.385 -23.972  1.00 25.00           C
ATOM    139  CA  LYS   139      15.151   3.180 -23.972  1.00 25.00           C
ATOM    140  CA  ALA   140      18.291   1.526 -25.370  1.00 25.00           C
ATOM    141  CA  LEU   141      19.962   4.875 -25.182  1.00 25.00           C
ATOM    142  CA  SER   142      22.818   7.372 -25.093  1.00 25.00           C
ATOM    143  CA  ALA   143      24.934  10.544 -24.639  1.00 25.00           C
TER
END
