
#######################################################
#                                                     #
#                        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  145 (  145),  selected  145 , name T0380TS393_1
# Molecule2: number of CA atoms  142 ( 1146),  selected  142 , name T0380.pdb
# PARAMETERS: T0380TS393_1.T0380.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      I       2           -
LGA    -       -      D       3           -
LGA    -       -      E       4           -
LGA    -       -      K       5           -
LGA    M       1      F       6          5.216
LGA    I       2      L       7          3.322
LGA    D       3      -       -           -
LGA    E       4      I       8          1.429
LGA    K       5      E       9          1.453
LGA    F       6      S      10          1.461
LGA    L       7      N      11          1.461
LGA    I       8      E      12          1.586
LGA    E       9      L      13          2.396
LGA    S      10      V      14          2.802
LGA    N      11      E      15          3.194
LGA    E      12      S      16          3.537
LGA    L      13      -       -           -
LGA    V      14      -       -           -
LGA    E      15      S      17          3.839
LGA    S      16      K      18           -
LGA    S      17      -       -           -
LGA    K      18      I      19           #
LGA    I      19      V      20          1.055
LGA    V      20      M      21          2.884
LGA    M      21      V      22          2.204
LGA    V      22      G      23          3.443
LGA    G      23      T      24          3.709
LGA    T      24      N      25          5.254
LGA    N      25      G      26          3.769
LGA    G      26      -       -           -
LGA    E      27      -       -           -
LGA    N      28      -       -           -
LGA    G      29      -       -           -
LGA    Y      30      -       -           -
LGA    P      31      E      27          1.248
LGA    N      32      N      28           -
LGA    I      33      G      29           -
LGA    -       -      Y      30           -
LGA    -       -      P      31           -
LGA    -       -      N      32           -
LGA    K      34      I      33           #
LGA    A      35      K      34          2.480
LGA    M      36      A      35          2.195
LGA    M      37      M      36          1.857
LGA    R      38      M      37          1.300
LGA    L      39      R      38          1.763
LGA    K      40      L      39          3.480
LGA    H      41      K      40          2.932
LGA    D      42      H      41          4.207
LGA    G      43      D      42          3.558
LGA    -       -      G      43           -
LGA    L      44      L      44           #
LGA    K      45      K      45          3.959
LGA    K      46      K      46          1.636
LGA    F      47      F      47          2.151
LGA    -       -      W      48           -
LGA    W      48      L      49          3.945
LGA    L      49      S      50           #
LGA    S      50      T      51          4.311
LGA    T      51      N      52           #
LGA    N      52      T      53          3.743
LGA    T      53      S      54          5.328
LGA    S      54      T      55          2.431
LGA    T      55      -       -           -
LGA    R      56      R      56          1.676
LGA    M      57      M      57          1.841
LGA    V      58      V      58          0.991
LGA    E      59      E      59          1.321
LGA    R      60      R      60          2.106
LGA    L      61      L      61          1.996
LGA    K      62      K      62          1.675
LGA    K      63      K      63          2.663
LGA    N      64      N      64          3.202
LGA    N      65      N      65          3.075
LGA    K      66      K      66          3.834
LGA    I      67      I      67          3.731
LGA    C      68      -       -           -
LGA    L      69      C      68          3.539
LGA    Y      70      L      69          2.779
LGA    F      71      Y      70          1.026
LGA    V      72      F      71          3.729
LGA    D      73      V      72          2.156
LGA    -       -      D      73           -
LGA    D      74      D      74          3.421
LGA    N      75      N      75          1.863
LGA    K      76      K      76          2.205
LGA    -       -      F      77           -
LGA    F      77      A      78          3.020
LGA    A      78      G      79          3.458
LGA    G      79      L      80          1.309
LGA    L      80      M      81          4.714
LGA    M      81      L      82          3.514
LGA    L      82      V      83          4.980
LGA    V      83      G      84          2.278
LGA    G      84      T      85          1.450
LGA    T      85      -       -           -
LGA    I      86      I      86          2.508
LGA    E      87      E      87          1.230
LGA    I      88      I      88          2.344
LGA    L      89      L      89          3.341
LGA    H      90      H      90          4.620
LGA    D      91      D      91           #
LGA    R      92      R      92          4.916
LGA    A      93      A      93          2.409
LGA    S      94      S      94          1.187
LGA    K      95      K      95          3.599
LGA    E      96      -       -           -
LGA    M      97      -       -           -
LGA    L      98      E      96           #
LGA    W      99      M      97           -
LGA    T     100      L      98           -
LGA    D     101      W      99          2.560
LGA    G     102      T     100          2.777
LGA    C     103      D     101           -
LGA    -       -      G     102           -
LGA    -       -      C     103           -
LGA    -       -      E     104           -
LGA    -       -      I     105           -
LGA    -       -      Y     106           -
LGA    -       -      Y     107           -
LGA    -       -      P     108           -
LGA    -       -      L     109           -
LGA    -       -      G     110           -
LGA    -       -      I     111           -
LGA    -       -      D     112           -
LGA    -       -      D     113           -
LGA    -       -      P     114           -
LGA    -       -      D     115           -
LGA    -       -      Y     116           -
LGA    -       -      T     117           -
LGA    E     104      A     118           #
LGA    I     105      L     119          4.442
LGA    -       -      C     120           -
LGA    Y     106      F     121          0.870
LGA    Y     107      T     122          0.797
LGA    P     108      A     123          4.388
LGA    L     109      E     124          4.771
LGA    G     110      -       -           -
LGA    I     111      -       -           -
LGA    D     112      -       -           -
LGA    D     113      -       -           -
LGA    P     114      W     125          5.671
LGA    D     115      G     126           -
LGA    Y     116      -       -           -
LGA    T     117      -       -           -
LGA    A     118      -       -           -
LGA    L     119      -       -           -
LGA    C     120      -       -           -
LGA    F     121      -       -           -
LGA    T     122      -       -           -
LGA    A     123      -       -           -
LGA    E     124      -       -           -
LGA    W     125      -       -           -
LGA    G     126      -       -           -
LGA    N     127      -       -           -
LGA    Y     128      -       -           -
LGA    Y     129      -       -           -
LGA    R     130      -       -           -
LGA    H     131      -       -           -
LGA    L     132      -       -           -
LGA    K     133      -       -           -
LGA    N     134      -       -           -
LGA    I     135      -       -           -
LGA    T     136      -       -           -
LGA    F     137      -       -           -
LGA    K     138      -       -           -
LGA    I     139      -       -           -
LGA    D     140      N     127           #
LGA    E     141      Y     128           -
LGA    I     142      Y     129           -
LGA    Y     143      R     130           -
LGA    N     144      H     131           -
LGA    -       -      L     132           -
LGA    Y     145      K     133           #
LGA    -       -      N     134           -
LGA    -       -      I     135           -
LGA    -       -      T     136           -
LGA    -       -      F     137           -
LGA    -       -      K     138           -
LGA    -       -      I     139           -
LGA    -       -      D     140           -
LGA    -       -      E     141           -
LGA    -       -      I     142           -
LGA    -       -      Y     143           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  145  142    5.0     82    3.09    34.15     32.110     2.569

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.544232 * X  +  -0.565301 * Y  +   0.619876 * Z  +  -7.974158
  Y_new =  -0.462492 * X  +  -0.414296 * Y  +  -0.783875 * Z  +  -6.516992
  Z_new =   0.699937 * X  +  -0.713298 * Y  +  -0.035974 * Z  +  15.966906 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.621187    1.520406  [ DEG:   -92.8872     87.1128 ]
  Theta =  -0.775310   -2.366283  [ DEG:   -44.4220   -135.5780 ]
  Phi   =  -2.437211    0.704382  [ DEG:  -139.6419     40.3581 ]
 
# 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: T0380TS393_1                                  
REMARK     2: T0380.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0380TS393_1.T0380.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  145  142   5.0   82   3.09   34.15  32.110
REMARK  ---------------------------------------------------------- 
MOLECULE T0380TS393_1
PFRMAT TS
TARGET T0380
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1     -20.012   1.099   2.565  1.00 25.00           C
ATOM      2  CA  ILE     2     -21.672   4.261   3.883  1.00 25.00           C
ATOM      3  CA  ASP     3     -19.895   6.758   1.661  1.00 25.00           C
ATOM      4  CA  GLU     4     -16.182   6.314   2.499  1.00 25.00           C
ATOM      5  CA  LYS     5     -16.974   8.363   5.636  1.00 25.00           C
ATOM      6  CA  PHE     6     -16.408   5.274   7.827  1.00 25.00           C
ATOM      7  CA  LEU     7     -13.055   4.627   6.093  1.00 25.00           C
ATOM      8  CA  ILE     8     -12.027   8.271   6.667  1.00 25.00           C
ATOM      9  CA  GLU     9     -12.978   7.982  10.366  1.00 25.00           C
ATOM     10  CA  SER    10     -10.918   4.769  10.670  1.00 25.00           C
ATOM     11  CA  ASN    11      -7.924   6.504   9.029  1.00 25.00           C
ATOM     12  CA  GLU    12      -8.266   9.445  11.458  1.00 25.00           C
ATOM     13  CA  LEU    13      -8.383   7.019  14.418  1.00 25.00           C
ATOM     14  CA  VAL    14      -5.241   5.251  13.125  1.00 25.00           C
ATOM     15  CA  GLU    15      -3.458   8.621  12.777  1.00 25.00           C
ATOM     16  CA  SER    16      -3.870   8.891  16.566  1.00 25.00           C
ATOM     17  CA  SER    17      -4.100   5.386  18.169  1.00 25.00           C
ATOM     18  CA  LYS    18      -6.795   2.745  17.627  1.00 25.00           C
ATOM     19  CA  ILE    19      -6.645   0.004  14.990  1.00 25.00           C
ATOM     20  CA  VAL    20      -8.288  -3.104  16.386  1.00 25.00           C
ATOM     21  CA  MET    21      -6.909  -3.763  19.885  1.00 25.00           C
ATOM     22  CA  VAL    22      -7.061  -6.165  22.811  1.00 25.00           C
ATOM     23  CA  GLY    23      -6.181  -9.595  21.376  1.00 25.00           C
ATOM     24  CA  THR    24      -5.779 -12.828  23.432  1.00 25.00           C
ATOM     25  CA  ASN    25      -8.189 -15.433  24.895  1.00 25.00           C
ATOM     26  CA  GLY    26      -9.689 -18.540  26.521  1.00 25.00           C
ATOM     27  CA  GLU    27      -9.302 -22.298  27.224  1.00 25.00           C
ATOM     28  CA  ASN    28     -11.324 -22.198  30.446  1.00 25.00           C
ATOM     29  CA  GLY    29      -8.574 -20.319  32.300  1.00 25.00           C
ATOM     30  CA  TYR    30      -6.313 -17.298  32.388  1.00 25.00           C
ATOM     31  CA  PRO    31      -7.898 -14.251  30.852  1.00 25.00           C
ATOM     32  CA  ASN    32      -4.528 -12.951  29.705  1.00 25.00           C
ATOM     33  CA  ILE    33      -4.597  -9.762  27.694  1.00 25.00           C
ATOM     34  CA  LYS    34      -1.676  -8.299  25.668  1.00 25.00           C
ATOM     35  CA  ALA    35      -1.961  -5.843  22.732  1.00 25.00           C
ATOM     36  CA  MET    36      -1.765  -3.944  19.442  1.00 25.00           C
ATOM     37  CA  MET    37      -0.808  -2.378  16.079  1.00 25.00           C
ATOM     38  CA  ARG    38      -1.517  -1.988  12.355  1.00 25.00           C
ATOM     39  CA  LEU    39      -4.478  -2.025  10.012  1.00 25.00           C
ATOM     40  CA  LYS    40      -3.576  -2.347   6.281  1.00 25.00           C
ATOM     41  CA  HIS    41      -3.568  -2.465   2.485  1.00 25.00           C
ATOM     42  CA  ASP    42      -6.878  -2.698   0.618  1.00 25.00           C
ATOM     43  CA  GLY    43      -7.846  -6.287  -0.402  1.00 25.00           C
ATOM     44  CA  LEU    44     -11.552  -6.246   0.489  1.00 25.00           C
ATOM     45  CA  LYS    45     -11.207  -8.810   3.253  1.00 25.00           C
ATOM     46  CA  LYS    46      -9.710  -7.311   6.395  1.00 25.00           C
ATOM     47  CA  PHE    47      -8.088  -5.510   9.310  1.00 25.00           C
ATOM     48  CA  TRP    48      -6.076  -6.112  12.455  1.00 25.00           C
ATOM     49  CA  LEU    49      -3.952  -6.315  15.616  1.00 25.00           C
ATOM     50  CA  SER    50      -2.033  -8.808  17.706  1.00 25.00           C
ATOM     51  CA  THR    51      -1.496 -12.573  18.319  1.00 25.00           C
ATOM     52  CA  ASN    52       1.857 -13.934  17.196  1.00 25.00           C
ATOM     53  CA  THR    53       3.693 -17.138  18.260  1.00 25.00           C
ATOM     54  CA  SER    54       4.985 -18.494  21.617  1.00 25.00           C
ATOM     55  CA  THR    55       3.990 -15.472  23.643  1.00 25.00           C
ATOM     56  CA  ARG    56       1.640 -17.261  26.082  1.00 25.00           C
ATOM     57  CA  MET    57      -0.996 -15.263  24.154  1.00 25.00           C
ATOM     58  CA  VAL    58      -0.462 -17.481  21.078  1.00 25.00           C
ATOM     59  CA  GLU    59      -0.851 -20.617  23.241  1.00 25.00           C
ATOM     60  CA  ARG    60      -4.088 -19.217  24.732  1.00 25.00           C
ATOM     61  CA  LEU    61      -5.416 -18.475  21.217  1.00 25.00           C
ATOM     62  CA  LYS    62      -4.556 -22.040  20.113  1.00 25.00           C
ATOM     63  CA  LYS    63      -6.367 -23.453  23.177  1.00 25.00           C
ATOM     64  CA  ASN    64      -9.469 -21.922  21.673  1.00 25.00           C
ATOM     65  CA  ASN    65     -10.210 -19.717  18.686  1.00 25.00           C
ATOM     66  CA  LYS    66     -10.339 -16.328  20.444  1.00 25.00           C
ATOM     67  CA  ILE    67     -11.224 -12.791  21.637  1.00 25.00           C
ATOM     68  CA  CYS    68     -11.291  -9.129  22.756  1.00 25.00           C
ATOM     69  CA  LEU    69     -11.711  -6.076  20.521  1.00 25.00           C
ATOM     70  CA  TYR    70     -13.292  -3.744  17.941  1.00 25.00           C
ATOM     71  CA  PHE    71     -12.415  -0.067  17.150  1.00 25.00           C
ATOM     72  CA  VAL    72     -11.873   3.380  18.705  1.00 25.00           C
ATOM     73  CA  ASP    73     -13.311   6.768  17.674  1.00 25.00           C
ATOM     74  CA  ASP    74     -15.180   9.876  18.821  1.00 25.00           C
ATOM     75  CA  ASN    75     -13.223  12.802  17.382  1.00 25.00           C
ATOM     76  CA  LYS    76     -15.505  12.465  14.396  1.00 25.00           C
ATOM     77  CA  PHE    77     -18.105   9.767  14.075  1.00 25.00           C
ATOM     78  CA  ALA    78     -16.669   6.266  13.353  1.00 25.00           C
ATOM     79  CA  GLY    79     -15.721   2.637  13.639  1.00 25.00           C
ATOM     80  CA  LEU    80     -13.618  -0.207  12.251  1.00 25.00           C
ATOM     81  CA  MET    81     -12.848  -3.936  12.540  1.00 25.00           C
ATOM     82  CA  LEU    82     -11.892  -7.153  14.182  1.00 25.00           C
ATOM     83  CA  VAL    83     -14.484  -9.597  12.922  1.00 25.00           C
ATOM     84  CA  GLY    84     -12.809 -12.859  13.845  1.00 25.00           C
ATOM     85  CA  THR    85     -12.308 -16.547  14.770  1.00 25.00           C
ATOM     86  CA  ILE    86      -8.731 -15.488  15.450  1.00 25.00           C
ATOM     87  CA  GLU    87      -7.053 -17.276  12.541  1.00 25.00           C
ATOM     88  CA  ILE    88      -3.906 -15.823  13.969  1.00 25.00           C
ATOM     89  CA  LEU    89      -2.894 -14.804  10.498  1.00 25.00           C
ATOM     90  CA  HIS    90      -1.821 -17.845   8.484  1.00 25.00           C
ATOM     91  CA  ASP    91       0.067 -21.138   8.296  1.00 25.00           C
ATOM     92  CA  ARG    92       2.805 -19.591   6.138  1.00 25.00           C
ATOM     93  CA  ALA    93       4.130 -17.433   3.265  1.00 25.00           C
ATOM     94  CA  SER    94       1.548 -14.723   4.077  1.00 25.00           C
ATOM     95  CA  LYS    95       2.578 -14.811   7.764  1.00 25.00           C
ATOM     96  CA  GLU    96       6.261 -14.480   6.768  1.00 25.00           C
ATOM     97  CA  MET    97       5.410 -11.496   4.524  1.00 25.00           C
ATOM     98  CA  LEU    98       3.482  -9.853   7.396  1.00 25.00           C
ATOM     99  CA  TRP    99       6.461 -10.396   9.739  1.00 25.00           C
ATOM    100  CA  THR   100       8.814  -8.839   7.150  1.00 25.00           C
ATOM    101  CA  ASP   101       6.476  -5.825   6.802  1.00 25.00           C
ATOM    102  CA  GLY   102       3.225  -4.656   5.350  1.00 25.00           C
ATOM    103  CA  CYS   103       0.113  -6.092   6.977  1.00 25.00           C
ATOM    104  CA  GLU   104      -3.186  -8.060   6.982  1.00 25.00           C
ATOM    105  CA  ILE   105      -5.831 -10.178   8.805  1.00 25.00           C
ATOM    106  CA  TYR   106      -8.796 -10.414  11.174  1.00 25.00           C
ATOM    107  CA  TYR   107     -11.815 -11.214   9.010  1.00 25.00           C
ATOM    108  CA  PRO   108     -14.571 -12.294   6.667  1.00 25.00           C
ATOM    109  CA  LEU   109     -18.169 -13.485   6.480  1.00 25.00           C
ATOM    110  CA  GLY   110     -21.656 -14.596   5.446  1.00 25.00           C
ATOM    111  CA  ILE   111     -21.056 -17.294   8.039  1.00 25.00           C
ATOM    112  CA  ASP   112     -21.790 -14.882  10.874  1.00 25.00           C
ATOM    113  CA  ASP   113     -21.447 -14.703  14.702  1.00 25.00           C
ATOM    114  CA  PRO   114     -18.557 -12.333  14.000  1.00 25.00           C
ATOM    115  CA  ASP   115     -16.495 -12.122  17.202  1.00 25.00           C
ATOM    116  CA  TYR   116     -13.423 -10.077  18.045  1.00 25.00           C
ATOM    117  CA  THR   117      -9.611  -9.912  17.704  1.00 25.00           C
ATOM    118  CA  ALA   118      -6.258 -11.253  16.508  1.00 25.00           C
ATOM    119  CA  LEU   119      -3.944 -10.841  13.529  1.00 25.00           C
ATOM    120  CA  CYS   120      -1.503  -8.701  11.670  1.00 25.00           C
ATOM    121  CA  PHE   121       1.048  -7.141  13.998  1.00 25.00           C
ATOM    122  CA  THR   122       3.331  -5.980  16.760  1.00 25.00           C
ATOM    123  CA  ALA   123       5.040  -3.018  18.562  1.00 25.00           C
ATOM    124  CA  GLU   124       7.388  -2.926  21.513  1.00 25.00           C
ATOM    125  CA  TRP   125       5.599  -0.949  24.148  1.00 25.00           C
ATOM    126  CA  GLY   126       2.807   0.262  21.790  1.00 25.00           C
ATOM    127  CA  ASN   127       0.468   3.051  22.940  1.00 25.00           C
ATOM    128  CA  TYR   128      -3.351   2.821  23.109  1.00 25.00           C
ATOM    129  CA  TYR   129      -3.096  -0.690  24.617  1.00 25.00           C
ATOM    130  CA  ARG   130      -0.593   0.582  27.220  1.00 25.00           C
ATOM    131  CA  HIS   131      -3.555   0.768  29.665  1.00 25.00           C
ATOM    132  CA  LEU   132      -5.943   2.720  27.513  1.00 25.00           C
ATOM    133  CA  LYS   133      -8.676   1.599  29.834  1.00 25.00           C
ATOM    134  CA  ASN   134     -11.188  -0.404  31.945  1.00 25.00           C
ATOM    135  CA  ILE   135     -13.698  -0.080  29.093  1.00 25.00           C
ATOM    136  CA  THR   136     -13.037  -3.442  27.442  1.00 25.00           C
ATOM    137  CA  PHE   137     -12.901  -2.349  23.817  1.00 25.00           C
ATOM    138  CA  LYS   138     -15.960  -4.464  22.996  1.00 25.00           C
ATOM    139  CA  ILE   139     -18.674  -5.885  20.815  1.00 25.00           C
ATOM    140  CA  ASP   140     -22.413  -5.620  20.787  1.00 25.00           C
ATOM    141  CA  GLU   141     -25.963  -4.514  21.557  1.00 25.00           C
ATOM    142  CA  ILE   142     -29.717  -3.885  22.117  1.00 25.00           C
ATOM    143  CA  TYR   143     -31.675  -1.270  20.201  1.00 25.00           C
ATOM    144  CA  ASN   144     -31.831   2.386  21.274  1.00 25.00           C
ATOM    145  CA  TYR   145     -31.647   6.072  20.274  1.00 25.00           C
TER
END
