
#######################################################
#                                                     #
#                        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  153 (  153),  selected  153 , name T0332TS393_1-D1
# Molecule2: number of CA atoms  153 ( 1194),  selected  153 , name T0332_D1.pdb
# PARAMETERS: T0332TS393_1-D1.T0332_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R       7      R       7          2.034
LGA    L       8      L       8          0.876
LGA    I       9      I       9          1.209
LGA    V      10      V      10          1.621
LGA    V      11      V      11          2.001
LGA    A      12      A      12          1.718
LGA    S      13      S      13          3.703
LGA    L      14      L      14          1.811
LGA    I      15      I      15          1.851
LGA    D      16      D      16          3.208
LGA    K      17      K      17          2.426
LGA    P      18      P      18          1.208
LGA    T      19      T      19          1.128
LGA    N      20      N      20          1.000
LGA    L      21      L      21          0.996
LGA    G      22      G      22          1.042
LGA    G      23      G      23          1.427
LGA    L      24      L      24          1.293
LGA    C      25      C      25          1.136
LGA    R      26      R      26          1.419
LGA    T      27      T      27          1.463
LGA    C      28      C      28          1.000
LGA    E      29      E      29          1.755
LGA    V      30      V      30          2.250
LGA    F      31      F      31          0.521
LGA    G      32      G      32          2.793
LGA    A      33      A      33          2.308
LGA    S      34      S      34          2.534
LGA    V      35      V      35          1.141
LGA    L      36      L      36          0.980
LGA    V      37      V      37          1.835
LGA    V      38      V      38          1.962
LGA    G      39      G      39          2.417
LGA    S      40      S      40          4.561
LGA    L      41      L      41           -
LGA    Q      42      -       -           -
LGA    C      43      Q      42          5.113
LGA    I      44      C      43          3.071
LGA    S      45      I      44          5.919
LGA    D      46      S      45          1.866
LGA    K      47      D      46          1.910
LGA    Q      48      K      47          3.806
LGA    -       -      Q      48           -
LGA    F      49      F      49          3.541
LGA    Q      50      Q      50          4.435
LGA    -       -      H      51           -
LGA    H      51      L      52           #
LGA    L      52      S      53          2.959
LGA    S      53      V      54           #
LGA    V      54      -       -           -
LGA    S      55      S      55          0.798
LGA    A      56      A      56          1.164
LGA    E      57      E      57          2.631
LGA    Q      58      Q      58          1.938
LGA    W      59      W      59          2.732
LGA    L      60      L      60          2.129
LGA    P      61      P      61          0.989
LGA    L      62      L      62          0.574
LGA    V      63      V      63          2.845
LGA    E      64      E      64          2.411
LGA    V      65      V      65          1.064
LGA    K      66      K      66          1.294
LGA    P      67      P      67          3.987
LGA    P      68      P      68          3.726
LGA    Q      69      Q      69          4.250
LGA    L      70      L      70          1.608
LGA    I      71      I      71          0.515
LGA    D      72      D      72          1.288
LGA    Y      73      Y      73          2.047
LGA    L      74      L      74          1.539
LGA    Q      75      Q      75          1.820
LGA    Q      76      Q      76          2.941
LGA    K      77      K      77          3.433
LGA    K      78      K      78          3.535
LGA    T      79      T      79          3.886
LGA    E      80      E      80          2.548
LGA    G      81      G      81          2.425
LGA    Y      82      Y      82          1.444
LGA    T      83      T      83          5.876
LGA    I      84      I      84          3.495
LGA    I      85      I      85           #
LGA    G      86      G      86          5.325
LGA    V      87      V      87          1.853
LGA    E      88      E      88          2.313
LGA    Q      89      Q      89          5.163
LGA    T      90      T      90           #
LGA    A      91      A      91           -
LGA    K      92      K      92           -
LGA    S      93      S      93          3.512
LGA    L      94      L      94          1.429
LGA    D      95      D      95          1.588
LGA    L      96      L      96          0.510
LGA    T      97      T      97          2.842
LGA    Q      98      Q      98          1.971
LGA    Y      99      Y      99          1.186
LGA    C     100      C     100          1.154
LGA    F     101      F     101          1.156
LGA    P     102      P     102          2.832
LGA    E     103      E     103          3.733
LGA    K     104      K     104          0.990
LGA    S     105      S     105          0.374
LGA    L     106      L     106          3.644
LGA    L     107      L     107           #
LGA    L     108      L     108          2.781
LGA    L     109      L     109          2.178
LGA    G     110      G     110          1.574
LGA    N     111      N     111          1.926
LGA    E     112      E     112          1.060
LGA    R     113      R     113          0.177
LGA    E     114      E     114          2.211
LGA    G     115      G     115          0.683
LGA    I     116      I     116          0.878
LGA    P     117      P     117          1.088
LGA    A     118      A     118          2.484
LGA    N     119      N     119          1.820
LGA    L     120      L     120          1.241
LGA    I     121      I     121          2.001
LGA    Q     122      Q     122          1.721
LGA    Q     123      Q     123          0.657
LGA    L     124      L     124          1.563
LGA    D     125      D     125          0.513
LGA    V     126      V     126          0.437
LGA    C     127      C     127          1.030
LGA    V     128      V     128          1.072
LGA    E     129      E     129          3.428
LGA    I     130      I     130           #
LGA    P     131      P     131           #
LGA    Q     132      Q     132          3.119
LGA    Q     133      Q     133          2.248
LGA    G     134      G     134          2.378
LGA    I     135      I     135          2.078
LGA    I     136      I     136          1.895
LGA    R     137      R     137          3.134
LGA    S     138      S     138          2.341
LGA    L     139      L     139          1.892
LGA    N     140      N     140          1.682
LGA    V     141      V     141          0.532
LGA    H     142      H     142          0.688
LGA    V     143      V     143          0.521
LGA    S     144      S     144          0.469
LGA    G     145      G     145          0.911
LGA    A     146      A     146          1.008
LGA    L     147      L     147          0.744
LGA    L     148      L     148          0.739
LGA    I     149      I     149          1.538
LGA    W     150      W     150          1.609
LGA    E     151      E     151          0.876
LGA    Y     152      Y     152          1.276
LGA    T     153      T     153          2.138
LGA    R     154      R     154          1.932
LGA    Q     155      Q     155          0.903
LGA    Q     156      Q     156          1.871
LGA    L     157      L     157          2.418
LGA    L     158      L     158          1.797
LGA    S     159      S     159           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  153  153    5.0    140    2.33    95.00     60.860     5.765

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.800295 * X  +   0.175520 * Y  +   0.573342 * Z  +  27.352871
  Y_new =  -0.089590 * X  +   0.980466 * Y  +  -0.175102 * Z  +  42.856716
  Z_new =  -0.592876 * X  +   0.088767 * Y  +   0.800386 * Z  +  30.910507 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.110454   -3.031138  [ DEG:     6.3286   -173.6714 ]
  Theta =   0.634626    2.506967  [ DEG:    36.3614    143.6386 ]
  Phi   =  -0.111482    3.030111  [ DEG:    -6.3874    173.6126 ]
 
# 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: T0332TS393_1-D1                               
REMARK     2: T0332_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0332TS393_1-D1.T0332_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  153  153   5.0  140   2.33   95.00  60.860
REMARK  ---------------------------------------------------------- 
MOLECULE T0332TS393_1-D1
PFRMAT TS
TARGET T0332
MODEL 1
PARENT N/A
ATOM      7  CA  ARG     7      23.233  38.850  41.874  1.00 25.00           C
ATOM      8  CA  LEU     8      23.590  38.637  38.092  1.00 25.00           C
ATOM      9  CA  ILE     9      24.844  41.470  35.985  1.00 25.00           C
ATOM     10  CA  VAL    10      25.237  42.460  32.352  1.00 25.00           C
ATOM     11  CA  VAL    11      27.959  45.095  31.782  1.00 25.00           C
ATOM     12  CA  ALA    12      29.524  48.039  29.916  1.00 25.00           C
ATOM     13  CA  SER    13      32.953  49.738  30.433  1.00 25.00           C
ATOM     14  CA  LEU    14      31.893  52.249  27.768  1.00 25.00           C
ATOM     15  CA  ILE    15      29.105  52.264  25.177  1.00 25.00           C
ATOM     16  CA  ASP    16      28.169  52.898  21.567  1.00 25.00           C
ATOM     17  CA  LYS    17      25.975  55.979  21.039  1.00 25.00           C
ATOM     18  CA  PRO    18      23.699  54.462  23.661  1.00 25.00           C
ATOM     19  CA  THR    19      22.482  51.898  21.092  1.00 25.00           C
ATOM     20  CA  ASN    20      24.763  49.235  22.630  1.00 25.00           C
ATOM     21  CA  LEU    21      23.409  50.055  26.119  1.00 25.00           C
ATOM     22  CA  GLY    22      19.818  49.764  24.819  1.00 25.00           C
ATOM     23  CA  GLY    23      20.640  46.375  23.234  1.00 25.00           C
ATOM     24  CA  LEU    24      22.167  45.175  26.535  1.00 25.00           C
ATOM     25  CA  CYS    25      19.035  46.311  28.425  1.00 25.00           C
ATOM     26  CA  ARG    26      16.817  44.448  25.919  1.00 25.00           C
ATOM     27  CA  THR    27      18.939  41.290  26.351  1.00 25.00           C
ATOM     28  CA  CYS    28      18.640  41.580  30.158  1.00 25.00           C
ATOM     29  CA  GLU    29      14.843  41.969  29.856  1.00 25.00           C
ATOM     30  CA  VAL    30      14.681  38.875  27.605  1.00 25.00           C
ATOM     31  CA  PHE    31      15.778  37.554  31.019  1.00 25.00           C
ATOM     32  CA  GLY    32      16.994  37.149  34.651  1.00 25.00           C
ATOM     33  CA  ALA    33      20.230  39.147  34.125  1.00 25.00           C
ATOM     34  CA  SER    34      18.459  41.870  36.125  1.00 25.00           C
ATOM     35  CA  VAL    35      21.049  44.583  36.958  1.00 25.00           C
ATOM     36  CA  LEU    36      22.930  46.506  34.268  1.00 25.00           C
ATOM     37  CA  VAL    37      26.229  48.015  35.439  1.00 25.00           C
ATOM     38  CA  VAL    38      25.669  50.355  32.529  1.00 25.00           C
ATOM     39  CA  GLY    39      28.640  52.586  31.933  1.00 25.00           C
ATOM     40  CA  SER    40      30.145  56.048  31.591  1.00 25.00           C
ATOM     41  CA  LEU    41      32.939  57.091  29.283  1.00 25.00           C
ATOM     42  CA  GLN    42      30.074  58.610  27.219  1.00 25.00           C
ATOM     43  CA  CYS    43      26.238  58.739  27.266  1.00 25.00           C
ATOM     44  CA  ILE    44      23.354  59.388  29.660  1.00 25.00           C
ATOM     45  CA  SER    45      21.883  61.224  26.636  1.00 25.00           C
ATOM     46  CA  ASP    46      18.146  61.442  25.918  1.00 25.00           C
ATOM     47  CA  LYS    47      17.077  59.544  22.833  1.00 25.00           C
ATOM     48  CA  GLN    48      17.930  55.821  22.562  1.00 25.00           C
ATOM     49  CA  PHE    49      18.517  55.655  26.343  1.00 25.00           C
ATOM     50  CA  GLN    50      15.148  57.367  26.967  1.00 25.00           C
ATOM     51  CA  HIS    51      13.419  54.870  24.634  1.00 25.00           C
ATOM     52  CA  LEU    52      15.077  51.956  26.486  1.00 25.00           C
ATOM     53  CA  SER    53      13.919  53.396  29.841  1.00 25.00           C
ATOM     54  CA  VAL    54      10.107  53.429  30.401  1.00 25.00           C
ATOM     55  CA  SER    55      10.079  51.680  27.030  1.00 25.00           C
ATOM     56  CA  ALA    56      11.728  48.523  28.376  1.00 25.00           C
ATOM     57  CA  GLU    57      14.388  48.595  31.130  1.00 25.00           C
ATOM     58  CA  GLN    58      11.818  49.979  33.610  1.00 25.00           C
ATOM     59  CA  TRP    59      13.234  47.395  36.097  1.00 25.00           C
ATOM     60  CA  LEU    60      16.928  46.977  35.262  1.00 25.00           C
ATOM     61  CA  PRO    61      17.343  49.441  38.107  1.00 25.00           C
ATOM     62  CA  LEU    62      20.190  50.779  35.992  1.00 25.00           C
ATOM     63  CA  VAL    63      22.622  49.690  38.689  1.00 25.00           C
ATOM     64  CA  GLU    64      24.586  52.736  37.608  1.00 25.00           C
ATOM     65  CA  VAL    65      28.295  53.290  36.915  1.00 25.00           C
ATOM     66  CA  LYS    66      30.818  56.095  36.747  1.00 25.00           C
ATOM     67  CA  PRO    67      34.469  57.290  37.037  1.00 25.00           C
ATOM     68  CA  PRO    68      36.147  56.645  40.374  1.00 25.00           C
ATOM     69  CA  GLN    69      38.632  54.541  38.336  1.00 25.00           C
ATOM     70  CA  LEU    70      35.882  51.942  37.652  1.00 25.00           C
ATOM     71  CA  ILE    71      37.933  49.687  39.971  1.00 25.00           C
ATOM     72  CA  ASP    72      36.693  51.651  43.017  1.00 25.00           C
ATOM     73  CA  TYR    73      33.077  51.294  41.805  1.00 25.00           C
ATOM     74  CA  LEU    74      33.577  47.525  41.347  1.00 25.00           C
ATOM     75  CA  GLN    75      35.022  47.261  44.884  1.00 25.00           C
ATOM     76  CA  GLN    76      32.024  49.192  46.279  1.00 25.00           C
ATOM     77  CA  LYS    77      29.624  46.856  44.423  1.00 25.00           C
ATOM     78  CA  LYS    78      31.460  43.806  45.838  1.00 25.00           C
ATOM     79  CA  THR    79      31.227  45.273  49.368  1.00 25.00           C
ATOM     80  CA  GLU    80      28.936  42.382  50.153  1.00 25.00           C
ATOM     81  CA  GLY    81      29.306  39.469  47.690  1.00 25.00           C
ATOM     82  CA  TYR    82      29.926  39.379  43.972  1.00 25.00           C
ATOM     83  CA  THR    83      28.580  41.098  40.879  1.00 25.00           C
ATOM     84  CA  ILE    84      31.806  42.186  39.145  1.00 25.00           C
ATOM     85  CA  ILE    85      30.131  42.834  35.756  1.00 25.00           C
ATOM     86  CA  GLY    86      30.099  40.602  32.643  1.00 25.00           C
ATOM     87  CA  VAL    87      32.330  39.423  29.792  1.00 25.00           C
ATOM     88  CA  GLU    88      35.341  40.530  27.718  1.00 25.00           C
ATOM     89  CA  GLN    89      33.898  39.273  24.365  1.00 25.00           C
ATOM     90  CA  THR    90      33.440  35.622  23.337  1.00 25.00           C
ATOM     91  CA  ALA    91      33.555  32.603  20.995  1.00 25.00           C
ATOM     92  CA  LYS    92      36.859  31.549  22.558  1.00 25.00           C
ATOM     93  CA  SER    93      39.415  31.711  25.370  1.00 25.00           C
ATOM     94  CA  LEU    94      37.639  29.688  28.016  1.00 25.00           C
ATOM     95  CA  ASP    95      34.945  27.810  26.186  1.00 25.00           C
ATOM     96  CA  LEU    96      32.132  30.207  27.271  1.00 25.00           C
ATOM     97  CA  THR    97      29.381  27.583  27.734  1.00 25.00           C
ATOM     98  CA  GLN    98      31.655  25.576  30.073  1.00 25.00           C
ATOM     99  CA  TYR    99      32.133  28.530  32.352  1.00 25.00           C
ATOM    100  CA  CYS   100      29.896  27.867  35.351  1.00 25.00           C
ATOM    101  CA  PHE   101      27.565  30.761  36.235  1.00 25.00           C
ATOM    102  CA  PRO   102      25.692  30.544  39.460  1.00 25.00           C
ATOM    103  CA  GLU   103      28.786  31.952  41.112  1.00 25.00           C
ATOM    104  CA  LYS   104      27.230  35.293  41.959  1.00 25.00           C
ATOM    105  CA  SER   105      28.102  36.503  38.426  1.00 25.00           C
ATOM    106  CA  LEU   106      31.156  37.396  36.361  1.00 25.00           C
ATOM    107  CA  LEU   107      34.026  39.607  35.206  1.00 25.00           C
ATOM    108  CA  LEU   108      34.476  42.717  33.160  1.00 25.00           C
ATOM    109  CA  LEU   109      33.030  44.387  30.122  1.00 25.00           C
ATOM    110  CA  GLY   110      32.653  45.859  26.638  1.00 25.00           C
ATOM    111  CA  ASN   111      32.470  48.653  24.067  1.00 25.00           C
ATOM    112  CA  GLU   112      33.686  48.103  20.494  1.00 25.00           C
ATOM    113  CA  ARG   113      36.690  50.184  19.664  1.00 25.00           C
ATOM    114  CA  GLU   114      39.559  48.202  21.161  1.00 25.00           C
ATOM    115  CA  GLY   115      37.308  46.717  23.896  1.00 25.00           C
ATOM    116  CA  ILE   116      37.679  46.467  27.717  1.00 25.00           C
ATOM    117  CA  PRO   117      40.208  48.851  29.260  1.00 25.00           C
ATOM    118  CA  ALA   118      42.336  45.783  29.969  1.00 25.00           C
ATOM    119  CA  ASN   119      42.719  47.220  33.498  1.00 25.00           C
ATOM    120  CA  LEU   120      39.124  46.196  34.331  1.00 25.00           C
ATOM    121  CA  ILE   121      39.803  42.659  33.030  1.00 25.00           C
ATOM    122  CA  GLN   122      42.976  42.456  35.166  1.00 25.00           C
ATOM    123  CA  GLN   123      41.008  43.609  38.242  1.00 25.00           C
ATOM    124  CA  LEU   124      38.084  41.265  37.784  1.00 25.00           C
ATOM    125  CA  ASP   125      38.593  37.523  38.155  1.00 25.00           C
ATOM    126  CA  VAL   126      38.484  35.274  35.091  1.00 25.00           C
ATOM    127  CA  CYS   127      37.170  36.893  31.926  1.00 25.00           C
ATOM    128  CA  VAL   128      35.434  35.485  28.860  1.00 25.00           C
ATOM    129  CA  GLU   129      37.787  36.504  25.992  1.00 25.00           C
ATOM    130  CA  ILE   130      38.281  36.697  22.226  1.00 25.00           C
ATOM    131  CA  PRO   131      37.678  35.399  18.691  1.00 25.00           C
ATOM    132  CA  GLN   132      35.273  34.889  15.813  1.00 25.00           C
ATOM    133  CA  GLN   133      35.749  32.086  13.244  1.00 25.00           C
ATOM    134  CA  GLY   134      36.685  32.876   9.644  1.00 25.00           C
ATOM    135  CA  ILE   135      37.887  36.222  10.968  1.00 25.00           C
ATOM    136  CA  ILE   136      34.522  37.412   9.846  1.00 25.00           C
ATOM    137  CA  ARG   137      34.713  40.048  12.562  1.00 25.00           C
ATOM    138  CA  SER   138      32.615  39.361  15.614  1.00 25.00           C
ATOM    139  CA  LEU   139      30.706  41.918  17.797  1.00 25.00           C
ATOM    140  CA  ASN   140      28.359  44.796  18.459  1.00 25.00           C
ATOM    141  CA  VAL   141      28.629  43.985  22.108  1.00 25.00           C
ATOM    142  CA  HIS   142      24.819  43.646  22.297  1.00 25.00           C
ATOM    143  CA  VAL   143      24.996  40.323  20.402  1.00 25.00           C
ATOM    144  CA  SER   144      27.698  39.066  22.806  1.00 25.00           C
ATOM    145  CA  GLY   145      25.538  40.078  25.802  1.00 25.00           C
ATOM    146  CA  ALA   146      22.539  38.234  24.293  1.00 25.00           C
ATOM    147  CA  LEU   147      24.695  35.115  23.757  1.00 25.00           C
ATOM    148  CA  LEU   148      25.899  35.293  27.389  1.00 25.00           C
ATOM    149  CA  ILE   149      22.279  35.601  28.599  1.00 25.00           C
ATOM    150  CA  TRP   150      21.287  32.567  26.483  1.00 25.00           C
ATOM    151  CA  GLU   151      24.206  30.563  27.943  1.00 25.00           C
ATOM    152  CA  TYR   152      23.138  31.544  31.488  1.00 25.00           C
ATOM    153  CA  THR   153      19.544  30.458  30.732  1.00 25.00           C
ATOM    154  CA  ARG   154      20.814  27.106  29.385  1.00 25.00           C
ATOM    155  CA  GLN   155      22.922  26.607  32.544  1.00 25.00           C
ATOM    156  CA  GLN   156      19.873  27.384  34.730  1.00 25.00           C
ATOM    157  CA  LEU   157      17.129  25.316  32.996  1.00 25.00           C
ATOM    158  CA  LEU   158      18.527  21.884  33.911  1.00 25.00           C
ATOM    159  CA  SER   159      21.719  21.434  35.845  1.00 25.00           C
TER
END
