
#######################################################
#                                                     #
#                        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 T0332TS168_5-D1
# Molecule2: number of CA atoms  153 ( 1194),  selected  153 , name T0332_D1.pdb
# PARAMETERS: T0332TS168_5-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          0.671
LGA    L       8      L       8          4.039
LGA    I       9      I       9          4.872
LGA    V      10      V      10          4.198
LGA    V      11      V      11          3.680
LGA    A      12      A      12          1.809
LGA    S      13      S      13          3.121
LGA    L      14      L      14          1.510
LGA    I      15      I      15          2.515
LGA    D      16      D      16          2.593
LGA    K      17      K      17          3.282
LGA    P      18      P      18          2.794
LGA    T      19      T      19          2.469
LGA    N      20      N      20          1.527
LGA    L      21      L      21          1.996
LGA    G      22      G      22          2.223
LGA    G      23      G      23          1.755
LGA    L      24      L      24          1.769
LGA    C      25      C      25          2.123
LGA    R      26      R      26          1.880
LGA    T      27      T      27          1.648
LGA    C      28      C      28          1.539
LGA    E      29      E      29          1.512
LGA    V      30      V      30          1.871
LGA    F      31      F      31          1.160
LGA    G      32      G      32          1.535
LGA    A      33      A      33          1.132
LGA    S      34      S      34           #
LGA    V      35      V      35           #
LGA    L      36      L      36          4.559
LGA    V      37      V      37          1.243
LGA    V      38      V      38          1.312
LGA    G      39      G      39          2.065
LGA    S      40      -       -           -
LGA    L      41      -       -           -
LGA    Q      42      S      40           #
LGA    C      43      L      41          5.013
LGA    I      44      Q      42          2.691
LGA    S      45      C      43           #
LGA    D      46      I      44          5.010
LGA    K      47      S      45          1.202
LGA    Q      48      D      46          1.024
LGA    F      49      K      47           #
LGA    Q      50      Q      48           -
LGA    -       -      F      49           -
LGA    H      51      Q      50          1.465
LGA    -       -      H      51           -
LGA    L      52      L      52          3.732
LGA    S      53      S      53          1.216
LGA    V      54      V      54          2.623
LGA    S      55      S      55          4.339
LGA    A      56      A      56          2.213
LGA    E      57      E      57          1.779
LGA    Q      58      Q      58          1.196
LGA    W      59      W      59          1.779
LGA    L      60      L      60          1.622
LGA    P      61      P      61          0.731
LGA    L      62      L      62          2.466
LGA    V      63      V      63          2.404
LGA    E      64      E      64          0.953
LGA    V      65      V      65          1.407
LGA    K      66      K      66          2.367
LGA    P      67      P      67           #
LGA    P      68      P      68          4.019
LGA    Q      69      Q      69          3.822
LGA    L      70      L      70          1.536
LGA    I      71      I      71          2.611
LGA    D      72      D      72          2.186
LGA    Y      73      Y      73          0.825
LGA    L      74      L      74          2.250
LGA    Q      75      Q      75          3.063
LGA    Q      76      Q      76          1.951
LGA    K      77      K      77          0.945
LGA    K      78      K      78          2.763
LGA    T      79      T      79          2.800
LGA    E      80      E      80          1.508
LGA    G      81      G      81          0.726
LGA    Y      82      Y      82          0.809
LGA    T      83      T      83           #
LGA    I      84      -       -           -
LGA    I      85      I      84           #
LGA    G      86      I      85          3.279
LGA    V      87      G      86          1.820
LGA    E      88      V      87          3.661
LGA    Q      89      E      88          3.360
LGA    T      90      Q      89          5.178
LGA    A      91      T      90           -
LGA    K      92      -       -           -
LGA    S      93      A      91           #
LGA    -       -      K      92           -
LGA    -       -      S      93           -
LGA    L      94      L      94          2.184
LGA    D      95      D      95          1.247
LGA    L      96      L      96          0.582
LGA    T      97      T      97          1.866
LGA    Q      98      Q      98          2.192
LGA    Y      99      Y      99          1.686
LGA    C     100      C     100          1.981
LGA    F     101      F     101          2.073
LGA    P     102      P     102          3.186
LGA    E     103      E     103          2.537
LGA    K     104      K     104          0.675
LGA    S     105      S     105          1.498
LGA    L     106      L     106          2.399
LGA    L     107      L     107          2.036
LGA    L     108      L     108          4.027
LGA    L     109      L     109          1.047
LGA    G     110      G     110          2.025
LGA    N     111      N     111          1.980
LGA    E     112      E     112          1.704
LGA    R     113      R     113          1.294
LGA    E     114      E     114          1.585
LGA    G     115      G     115          0.737
LGA    I     116      I     116          1.194
LGA    P     117      P     117          1.858
LGA    A     118      A     118          2.242
LGA    N     119      N     119          2.154
LGA    L     120      L     120          2.147
LGA    I     121      I     121          2.313
LGA    Q     122      Q     122          2.395
LGA    Q     123      Q     123          1.984
LGA    L     124      L     124          1.892
LGA    D     125      D     125          1.530
LGA    V     126      V     126          1.211
LGA    C     127      C     127          0.942
LGA    V     128      V     128          1.727
LGA    E     129      E     129          4.115
LGA    I     130      I     130           #
LGA    P     131      P     131           #
LGA    Q     132      Q     132          2.489
LGA    Q     133      Q     133          2.259
LGA    G     134      G     134          1.935
LGA    I     135      I     135          1.678
LGA    I     136      I     136          2.393
LGA    R     137      R     137          2.527
LGA    S     138      S     138          1.238
LGA    L     139      L     139          1.021
LGA    N     140      N     140          1.185
LGA    V     141      V     141          1.558
LGA    H     142      H     142          1.687
LGA    V     143      V     143          1.607
LGA    S     144      S     144          1.377
LGA    G     145      G     145          1.245
LGA    A     146      A     146          1.423
LGA    L     147      L     147          1.141
LGA    L     148      L     148          0.565
LGA    I     149      I     149          1.256
LGA    W     150      W     150          1.509
LGA    E     151      E     151          1.026
LGA    Y     152      Y     152          0.665
LGA    T     153      T     153          1.461
LGA    R     154      R     154          2.087
LGA    Q     155      Q     155          1.750
LGA    Q     156      Q     156          0.922
LGA    L     157      L     157          3.070
LGA    L     158      L     158          3.557
LGA    S     159      S     159          4.265

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  153  153    5.0    136    2.33    91.91     58.389     5.597

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.786454 * X  +   0.195212 * Y  +   0.585989 * Z  +  27.354431
  Y_new =   0.510887 * X  +   0.327579 * Y  +  -0.794787 * Z  +  42.919155
  Z_new =  -0.347109 * X  +   0.924437 * Y  +   0.157894 * Z  +  30.962488 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.401628   -1.739964  [ DEG:    80.3074    -99.6926 ]
  Theta =   0.354487    2.787106  [ DEG:    20.3106    159.6894 ]
  Phi   =   0.576100   -2.565493  [ DEG:    33.0081   -146.9919 ]
 
# 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: T0332TS168_5-D1                               
REMARK     2: T0332_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0332TS168_5-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  136   2.33   91.91  58.389
REMARK  ---------------------------------------------------------- 
MOLECULE T0332TS168_5-D1
PFRMAT TS
TARGET T0332
MODEL 5
PARENT N/A
ATOM      7  CA  ARG     7      22.127  38.294  40.831  1.00 25.00           C
ATOM      8  CA  LEU     8      21.050  41.577  39.379  1.00 25.00           C
ATOM      9  CA  ILE     9      20.624  44.715  37.195  1.00 25.00           C
ATOM     10  CA  VAL    10      21.820  45.383  33.648  1.00 25.00           C
ATOM     11  CA  VAL    11      25.089  44.829  31.784  1.00 25.00           C
ATOM     12  CA  ALA    12      28.208  46.715  30.915  1.00 25.00           C
ATOM     13  CA  SER    13      30.861  49.137  29.721  1.00 25.00           C
ATOM     14  CA  LEU    14      32.690  51.751  27.601  1.00 25.00           C
ATOM     15  CA  ILE    15      30.195  53.238  25.117  1.00 25.00           C
ATOM     16  CA  ASP    16      29.900  54.676  21.546  1.00 25.00           C
ATOM     17  CA  LYS    17      26.940  57.040  21.113  1.00 25.00           C
ATOM     18  CA  PRO    18      25.473  55.184  24.095  1.00 25.00           C
ATOM     19  CA  THR    19      23.220  53.395  21.566  1.00 25.00           C
ATOM     20  CA  ASN    20      25.284  50.193  21.955  1.00 25.00           C
ATOM     21  CA  LEU    21      24.991  50.439  25.766  1.00 25.00           C
ATOM     22  CA  GLY    22      21.201  50.901  25.471  1.00 25.00           C
ATOM     23  CA  GLY    23      20.982  47.840  23.179  1.00 25.00           C
ATOM     24  CA  LEU    24      23.020  45.786  25.688  1.00 25.00           C
ATOM     25  CA  CYS    25      20.705  46.906  28.525  1.00 25.00           C
ATOM     26  CA  ARG    26      17.642  45.916  26.448  1.00 25.00           C
ATOM     27  CA  THR    27      19.194  42.485  25.750  1.00 25.00           C
ATOM     28  CA  CYS    28      19.889  42.011  29.486  1.00 25.00           C
ATOM     29  CA  GLU    29      16.268  42.953  30.304  1.00 25.00           C
ATOM     30  CA  VAL    30      15.003  40.444  27.701  1.00 25.00           C
ATOM     31  CA  PHE    31      16.772  37.943  29.921  1.00 25.00           C
ATOM     32  CA  GLY    32      15.226  38.232  33.400  1.00 25.00           C
ATOM     33  CA  ALA    33      17.964  40.591  34.540  1.00 25.00           C
ATOM     34  CA  SER    34      21.775  40.309  34.554  1.00 25.00           C
ATOM     35  CA  VAL    35      24.844  42.007  36.147  1.00 25.00           C
ATOM     36  CA  LEU    36      25.700  45.707  36.704  1.00 25.00           C
ATOM     37  CA  VAL    37      26.276  49.283  35.511  1.00 25.00           C
ATOM     38  CA  VAL    38      26.129  51.121  32.139  1.00 25.00           C
ATOM     39  CA  GLY    39      29.222  53.166  32.992  1.00 25.00           C
ATOM     40  CA  SER    40      30.598  56.415  31.553  1.00 25.00           C
ATOM     41  CA  LEU    41      31.275  57.651  28.050  1.00 25.00           C
ATOM     42  CA  GLN    42      27.929  58.769  26.742  1.00 25.00           C
ATOM     43  CA  CYS    43      25.032  59.656  29.021  1.00 25.00           C
ATOM     44  CA  ILE    44      23.090  59.148  32.212  1.00 25.00           C
ATOM     45  CA  SER    45      21.701  62.628  31.357  1.00 25.00           C
ATOM     46  CA  ASP    46      19.746  61.636  28.206  1.00 25.00           C
ATOM     47  CA  LYS    47      16.595  60.268  26.572  1.00 25.00           C
ATOM     48  CA  GLN    48      19.056  58.699  24.092  1.00 25.00           C
ATOM     49  CA  PHE    49      19.262  55.545  26.256  1.00 25.00           C
ATOM     50  CA  GLN    50      15.440  55.352  26.383  1.00 25.00           C
ATOM     51  CA  HIS    51      15.271  55.714  22.574  1.00 25.00           C
ATOM     52  CA  LEU    52      17.862  52.923  22.169  1.00 25.00           C
ATOM     53  CA  SER    53      15.841  50.672  24.517  1.00 25.00           C
ATOM     54  CA  VAL    54      13.095  48.007  24.321  1.00 25.00           C
ATOM     55  CA  SER    55      12.052  47.099  27.872  1.00 25.00           C
ATOM     56  CA  ALA    56      14.177  50.015  28.984  1.00 25.00           C
ATOM     57  CA  GLU    57      15.152  52.754  31.476  1.00 25.00           C
ATOM     58  CA  GLN    58      11.999  52.044  33.530  1.00 25.00           C
ATOM     59  CA  TRP    59      12.946  48.335  33.975  1.00 25.00           C
ATOM     60  CA  LEU    60      15.854  45.930  34.393  1.00 25.00           C
ATOM     61  CA  PRO    61      17.166  48.638  36.727  1.00 25.00           C
ATOM     62  CA  LEU    62      19.366  49.819  33.789  1.00 25.00           C
ATOM     63  CA  VAL    63      21.940  51.908  35.669  1.00 25.00           C
ATOM     64  CA  GLU    64      24.425  54.532  36.796  1.00 25.00           C
ATOM     65  CA  VAL    65      27.796  53.405  38.112  1.00 25.00           C
ATOM     66  CA  LYS    66      29.741  56.571  37.359  1.00 25.00           C
ATOM     67  CA  PRO    67      32.793  57.060  39.538  1.00 25.00           C
ATOM     68  CA  PRO    68      36.227  55.864  40.685  1.00 25.00           C
ATOM     69  CA  GLN    69      37.974  53.457  38.357  1.00 25.00           C
ATOM     70  CA  LEU    70      35.159  51.024  39.353  1.00 25.00           C
ATOM     71  CA  ILE    71      37.255  50.408  42.499  1.00 25.00           C
ATOM     72  CA  ASP    72      34.275  51.376  44.703  1.00 25.00           C
ATOM     73  CA  TYR    73      32.018  48.981  42.744  1.00 25.00           C
ATOM     74  CA  LEU    74      34.584  46.171  43.173  1.00 25.00           C
ATOM     75  CA  GLN    75      34.754  46.867  46.936  1.00 25.00           C
ATOM     76  CA  GLN    76      30.931  46.761  47.152  1.00 25.00           C
ATOM     77  CA  LYS    77      30.893  43.428  45.268  1.00 25.00           C
ATOM     78  CA  LYS    78      33.532  42.017  47.659  1.00 25.00           C
ATOM     79  CA  THR    79      31.457  43.166  50.665  1.00 25.00           C
ATOM     80  CA  GLU    80      29.141  40.396  49.515  1.00 25.00           C
ATOM     81  CA  GLY    81      30.695  37.646  47.327  1.00 25.00           C
ATOM     82  CA  TYR    82      29.922  38.550  43.672  1.00 25.00           C
ATOM     83  CA  THR    83      28.203  40.827  41.205  1.00 25.00           C
ATOM     84  CA  ILE    84      29.566  42.871  38.265  1.00 25.00           C
ATOM     85  CA  ILE    85      31.040  43.667  34.886  1.00 25.00           C
ATOM     86  CA  GLY    86      33.675  41.222  33.696  1.00 25.00           C
ATOM     87  CA  VAL    87      35.140  40.903  30.182  1.00 25.00           C
ATOM     88  CA  GLU    88      35.754  41.502  26.442  1.00 25.00           C
ATOM     89  CA  GLN    89      33.756  39.200  24.123  1.00 25.00           C
ATOM     90  CA  THR    90      34.011  35.499  23.267  1.00 25.00           C
ATOM     91  CA  ALA    91      34.544  32.241  21.346  1.00 25.00           C
ATOM     92  CA  LYS    92      37.387  29.629  21.331  1.00 25.00           C
ATOM     93  CA  SER    93      39.324  31.568  23.992  1.00 25.00           C
ATOM     94  CA  LEU    94      39.102  29.959  27.452  1.00 25.00           C
ATOM     95  CA  ASP    95      35.565  28.560  27.369  1.00 25.00           C
ATOM     96  CA  LEU    96      31.970  29.799  27.463  1.00 25.00           C
ATOM     97  CA  THR    97      29.665  26.785  26.941  1.00 25.00           C
ATOM     98  CA  GLN    98      31.239  25.028  29.958  1.00 25.00           C
ATOM     99  CA  TYR    99      30.814  27.998  32.247  1.00 25.00           C
ATOM    100  CA  CYS   100      29.335  28.592  35.653  1.00 25.00           C
ATOM    101  CA  PHE   101      27.008  31.504  36.625  1.00 25.00           C
ATOM    102  CA  PRO   102      25.836  29.355  39.481  1.00 25.00           C
ATOM    103  CA  GLU   103      27.458  32.072  41.585  1.00 25.00           C
ATOM    104  CA  LYS   104      26.594  35.719  40.855  1.00 25.00           C
ATOM    105  CA  SER   105      26.814  37.447  37.549  1.00 25.00           C
ATOM    106  CA  LEU   106      29.535  38.710  35.251  1.00 25.00           C
ATOM    107  CA  LEU   107      27.736  40.392  32.381  1.00 25.00           C
ATOM    108  CA  LEU   108      30.078  41.156  29.442  1.00 25.00           C
ATOM    109  CA  LEU   109      31.444  44.123  27.514  1.00 25.00           C
ATOM    110  CA  GLY   110      32.865  46.942  25.393  1.00 25.00           C
ATOM    111  CA  ASN   111      33.242  49.809  23.006  1.00 25.00           C
ATOM    112  CA  GLU   112      33.173  47.524  20.026  1.00 25.00           C
ATOM    113  CA  ARG   113      36.018  49.734  18.813  1.00 25.00           C
ATOM    114  CA  GLU   114      38.429  48.717  21.570  1.00 25.00           C
ATOM    115  CA  GLY   115      38.250  46.605  24.741  1.00 25.00           C
ATOM    116  CA  ILE   116      37.275  46.616  28.359  1.00 25.00           C
ATOM    117  CA  PRO   117      39.782  49.453  28.605  1.00 25.00           C
ATOM    118  CA  ALA   118      42.342  48.069  31.111  1.00 25.00           C
ATOM    119  CA  ASN   119      41.591  47.820  34.858  1.00 25.00           C
ATOM    120  CA  LEU   120      38.177  46.262  34.097  1.00 25.00           C
ATOM    121  CA  ILE   121      39.829  43.730  31.746  1.00 25.00           C
ATOM    122  CA  GLN   122      42.386  42.845  34.456  1.00 25.00           C
ATOM    123  CA  GLN   123      39.562  42.362  36.997  1.00 25.00           C
ATOM    124  CA  LEU   124      37.563  39.078  36.838  1.00 25.00           C
ATOM    125  CA  ASP   125      39.457  36.060  38.167  1.00 25.00           C
ATOM    126  CA  VAL   126      39.032  34.724  34.635  1.00 25.00           C
ATOM    127  CA  CYS   127      37.756  36.990  31.899  1.00 25.00           C
ATOM    128  CA  VAL   128      36.023  35.928  28.694  1.00 25.00           C
ATOM    129  CA  GLU   129      38.469  36.785  25.913  1.00 25.00           C
ATOM    130  CA  ILE   130      38.468  37.800  22.261  1.00 25.00           C
ATOM    131  CA  PRO   131      37.729  36.004  19.001  1.00 25.00           C
ATOM    132  CA  GLN   132      35.667  34.074  16.387  1.00 25.00           C
ATOM    133  CA  GLN   133      34.299  32.444  13.236  1.00 25.00           C
ATOM    134  CA  GLY   134      36.274  32.369   9.973  1.00 25.00           C
ATOM    135  CA  ILE   135      35.124  35.917   9.334  1.00 25.00           C
ATOM    136  CA  ILE   136      32.896  38.708  10.721  1.00 25.00           C
ATOM    137  CA  ARG   137      35.687  40.481  12.601  1.00 25.00           C
ATOM    138  CA  SER   138      33.841  40.468  15.916  1.00 25.00           C
ATOM    139  CA  LEU   139      30.336  40.860  17.159  1.00 25.00           C
ATOM    140  CA  ASN   140      27.837  43.634  17.817  1.00 25.00           C
ATOM    141  CA  VAL   141      28.153  42.921  21.502  1.00 25.00           C
ATOM    142  CA  HIS   142      24.381  42.604  22.089  1.00 25.00           C
ATOM    143  CA  VAL   143      24.418  39.081  20.588  1.00 25.00           C
ATOM    144  CA  SER   144      27.350  38.119  22.856  1.00 25.00           C
ATOM    145  CA  GLY   145      25.468  39.474  25.904  1.00 25.00           C
ATOM    146  CA  ALA   146      22.363  37.463  24.912  1.00 25.00           C
ATOM    147  CA  LEU   147      24.496  34.304  24.544  1.00 25.00           C
ATOM    148  CA  LEU   148      26.034  34.909  27.998  1.00 25.00           C
ATOM    149  CA  ILE   149      22.539  35.356  29.502  1.00 25.00           C
ATOM    150  CA  TRP   150      21.389  32.093  27.859  1.00 25.00           C
ATOM    151  CA  GLU   151      24.456  30.277  29.261  1.00 25.00           C
ATOM    152  CA  TYR   152      23.714  31.668  32.752  1.00 25.00           C
ATOM    153  CA  THR   153      20.078  30.498  32.472  1.00 25.00           C
ATOM    154  CA  ARG   154      21.256  27.011  31.413  1.00 25.00           C
ATOM    155  CA  GLN   155      23.656  26.889  34.395  1.00 25.00           C
ATOM    156  CA  GLN   156      20.817  27.916  36.753  1.00 25.00           C
ATOM    157  CA  LEU   157      18.860  24.714  35.829  1.00 25.00           C
ATOM    158  CA  LEU   158      21.399  21.940  36.135  1.00 25.00           C
ATOM    159  CA  SER   159      23.783  23.010  38.918  1.00 25.00           C
TER
END
