
#######################################################
#                                                     #
#                        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  149 (  149),  selected  149 , name T0341TS393_4-D1
# Molecule2: number of CA atoms  148 ( 1158),  selected  148 , name T0341_D1.pdb
# PARAMETERS: T0341TS393_4-D1.T0341_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L       7      L       7          4.284
LGA    K       8      K       8          3.498
LGA    A       9      A       9          2.488
LGA    V      10      V      10          4.949
LGA    L      11      L      11          5.113
LGA    V      12      V      12           #
LGA    D      13      -       -           -
LGA    L      14      D      13          4.072
LGA    N      15      L      14          4.032
LGA    G      16      N      15          3.273
LGA    T      17      G      16           #
LGA    L      18      T      17          4.133
LGA    H      19      L      18          4.570
LGA    I      20      H      19           #
LGA    E      21      I      20          3.117
LGA    D      22      E      21          4.657
LGA    A      23      D      22          5.050
LGA    A      24      A      23          2.288
LGA    V      25      A      24          1.893
LGA    P      26      V      25          2.796
LGA    -       -      P      26           -
LGA    G      27      G      27           #
LGA    A      28      -       -           -
LGA    Q      29      A      28          4.809
LGA    E      30      Q      29          2.912
LGA    A      31      E      30           -
LGA    -       -      A      31           -
LGA    L      32      L      32          2.801
LGA    K      33      K      33          3.308
LGA    R      34      R      34          5.135
LGA    L      35      L      35          3.284
LGA    R      36      R      36          2.720
LGA    A      37      A      37           #
LGA    T      38      T      38          3.702
LGA    S      39      S      39          3.652
LGA    V      40      V      40          3.280
LGA    M      41      M      41          1.646
LGA    V      42      V      42          2.175
LGA    R      43      R      43          0.714
LGA    F      44      F      44          1.800
LGA    V      45      V      45          2.421
LGA    T      46      T      46          3.237
LGA    N      47      N      47          0.833
LGA    T      48      T      48          2.694
LGA    T      49      T      49          3.100
LGA    K      50      K      50          2.974
LGA    E      51      E      51          0.697
LGA    T      52      T      52          1.228
LGA    K      53      K      53          2.342
LGA    K      54      K      54          2.849
LGA    D      55      D      55          2.682
LGA    L      56      L      56          1.818
LGA    L      57      L      57          1.848
LGA    E      58      E      58          1.428
LGA    R      59      R      59          2.936
LGA    L      60      L      60          3.758
LGA    K      61      K      61          2.622
LGA    K      62      K      62          2.811
LGA    L      63      L      63          3.515
LGA    E      64      E      64          3.626
LGA    -       -      F      65           -
LGA    F      65      E      66          1.331
LGA    E      66      I      67          4.300
LGA    I      67      S      68          1.365
LGA    S      68      E      69          4.169
LGA    E      69      D      70          3.164
LGA    D      70      -       -           -
LGA    E      71      E      71          1.801
LGA    I      72      I      72          3.447
LGA    F      73      F      73          2.849
LGA    T      74      T      74          1.664
LGA    K     179      K     179          3.615
LGA    P     180      P     180          3.350
LGA    E     181      E     181          3.821
LGA    K     182      K     182          2.423
LGA    T     183      T     183          3.065
LGA    F     184      F     184          3.563
LGA    F     185      F     185          2.221
LGA    L     186      L     186          2.282
LGA    E     187      E     187          2.787
LGA    A     188      A     188          2.294
LGA    L     189      L     189          1.366
LGA    R     190      R     190          2.221
LGA    D     191      D     191          1.535
LGA    A     192      A     192          3.050
LGA    D     193      -       -           -
LGA    C     194      D     193          4.389
LGA    A     195      C     194          0.449
LGA    P     196      A     195          0.406
LGA    E     197      P     196          3.619
LGA    E     198      E     198          4.367
LGA    A     199      A     199          4.182
LGA    V     200      V     200          4.461
LGA    M     201      M     201          2.483
LGA    I     202      I     202          2.159
LGA    G     203      G     203          1.909
LGA    D     204      D     204          2.047
LGA    D     205      D     205          2.814
LGA    C     206      -       -           -
LGA    R     207      C     206          1.972
LGA    D     208      R     207          4.138
LGA    D     209      D     208           #
LGA    V     210      D     209          4.781
LGA    D     211      V     210          2.594
LGA    G     212      D     211          2.657
LGA    A     213      G     212          4.208
LGA    Q     214      A     213          3.712
LGA    N     215      Q     214          3.194
LGA    I     216      N     215          3.683
LGA    -       -      I     216           -
LGA    G     217      G     217          0.586
LGA    M     218      M     218          3.290
LGA    L     219      L     219          3.441
LGA    G     220      G     220          2.474
LGA    -       -      I     221           -
LGA    I     221      L     222           #
LGA    L     222      -       -           -
LGA    V     223      -       -           -
LGA    K     224      V     223           #
LGA    T     225      K     224          3.694
LGA    G     226      T     225          1.111
LGA    -       -      G     226           -
LGA    K     227      K     227          4.423
LGA    Y     228      Y     228          2.975
LGA    K     229      K     229           #
LGA    A     230      A     230          4.133
LGA    A     231      -       -           -
LGA    D     232      A     231          2.304
LGA    E     233      D     232          3.006
LGA    E     234      E     233          4.714
LGA    K     235      E     234          2.153
LGA    I     236      K     235          4.236
LGA    -       -      I     236           -
LGA    N     237      N     237           #
LGA    P     238      P     238           #
LGA    P     239      P     239          4.365
LGA    P     240      P     240          1.121
LGA    Y     241      Y     241          1.602
LGA    L     242      L     242          2.082
LGA    T     243      T     243          2.580
LGA    C     244      C     244          3.831
LGA    E     245      E     245          3.244
LGA    S     246      S     246          2.896
LGA    F     247      F     247          2.997
LGA    -       -      P     248           -
LGA    -       -      H     249           -
LGA    -       -      A     250           -
LGA    P     248      V     251          3.605
LGA    H     249      D     252          2.588
LGA    A     250      H     253          4.364
LGA    V     251      I     254          3.911
LGA    D     252      L     255          2.365
LGA    H     253      -       -           -
LGA    I     254      -       -           -
LGA    L     255      -       -           -
LGA    Q     256      Q     256          3.147
LGA    H     257      H     257          3.124
LGA    L     258      L     258          3.010
LGA    L     259      L     259           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  149  148    5.0    125    3.16    67.20     44.548     3.832

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.979340 * X  +   0.072875 * Y  +  -0.188633 * Z  +  28.499578
  Y_new =   0.200430 * X  +  -0.473679 * Y  +   0.857588 * Z  +  33.774918
  Z_new =  -0.026855 * X  +  -0.877677 * Y  +  -0.478499 * Z  +  91.257324 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.069937    1.071655  [ DEG:  -118.5987     61.4013 ]
  Theta =   0.026858    3.114735  [ DEG:     1.5389    178.4612 ]
  Phi   =   0.201870   -2.939722  [ DEG:    11.5663   -168.4337 ]
 
# 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: T0341TS393_4-D1                               
REMARK     2: T0341_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0341TS393_4-D1.T0341_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  149  148   5.0  125   3.16   67.20  44.548
REMARK  ---------------------------------------------------------- 
MOLECULE T0341TS393_4-D1
PFRMAT TS
TARGET T0341
MODEL 4
PARENT N/A
ATOM      7  CA  LEU     7      28.042  44.580 102.659  1.00 25.00           C
ATOM      8  CA  LYS     8      25.504  42.324 104.391  1.00 25.00           C
ATOM      9  CA  ALA     9      25.388  40.585 101.007  1.00 25.00           C
ATOM     10  CA  VAL    10      24.133  38.073  98.473  1.00 25.00           C
ATOM     11  CA  LEU    11      24.230  35.985  95.277  1.00 25.00           C
ATOM     12  CA  VAL    12      23.915  32.221  94.981  1.00 25.00           C
ATOM     13  CA  ASP    13      25.955  28.995  94.788  1.00 25.00           C
ATOM     14  CA  LEU    14      29.637  28.492  95.797  1.00 25.00           C
ATOM     15  CA  ASN    15      31.168  25.314  94.283  1.00 25.00           C
ATOM     16  CA  GLY    16      33.158  26.963  91.477  1.00 25.00           C
ATOM     17  CA  THR    17      31.899  30.549  92.042  1.00 25.00           C
ATOM     18  CA  LEU    18      34.361  30.408  94.937  1.00 25.00           C
ATOM     19  CA  HIS    19      37.122  29.578  97.431  1.00 25.00           C
ATOM     20  CA  ILE    20      39.678  28.965 100.141  1.00 25.00           C
ATOM     21  CA  GLU    21      40.393  25.654  98.502  1.00 25.00           C
ATOM     22  CA  ASP    22      41.030  22.239  96.987  1.00 25.00           C
ATOM     23  CA  ALA    23      40.648  20.081 100.055  1.00 25.00           C
ATOM     24  CA  ALA    24      36.910  20.976 100.027  1.00 25.00           C
ATOM     25  CA  VAL    25      37.137  21.089 103.857  1.00 25.00           C
ATOM     26  CA  PRO    26      38.782  24.197 105.308  1.00 25.00           C
ATOM     27  CA  GLY    27      36.665  25.913 102.615  1.00 25.00           C
ATOM     28  CA  ALA    28      33.058  26.930 101.824  1.00 25.00           C
ATOM     29  CA  GLN    29      31.962  25.861 105.334  1.00 25.00           C
ATOM     30  CA  GLU    30      34.812  27.904 106.874  1.00 25.00           C
ATOM     31  CA  ALA    31      33.781  30.952 104.798  1.00 25.00           C
ATOM     32  CA  LEU    32      30.152  30.539 105.947  1.00 25.00           C
ATOM     33  CA  LYS    33      31.306  30.323 109.593  1.00 25.00           C
ATOM     34  CA  ARG    34      33.397  33.500 109.145  1.00 25.00           C
ATOM     35  CA  LEU    35      30.379  35.301 107.623  1.00 25.00           C
ATOM     36  CA  ARG    36      28.198  34.187 110.568  1.00 25.00           C
ATOM     37  CA  ALA    37      30.836  35.461 113.035  1.00 25.00           C
ATOM     38  CA  THR    38      28.670  38.597 113.061  1.00 25.00           C
ATOM     39  CA  SER    39      25.170  38.101 111.736  1.00 25.00           C
ATOM     40  CA  VAL    40      23.934  36.514 108.449  1.00 25.00           C
ATOM     41  CA  MET    41      23.167  37.023 104.765  1.00 25.00           C
ATOM     42  CA  VAL    42      25.811  35.468 102.508  1.00 25.00           C
ATOM     43  CA  ARG    43      23.794  33.196 100.135  1.00 25.00           C
ATOM     44  CA  PHE    44      27.097  32.884  98.258  1.00 25.00           C
ATOM     45  CA  VAL    45      28.806  33.344  94.911  1.00 25.00           C
ATOM     46  CA  THR    46      27.743  32.845  91.308  1.00 25.00           C
ATOM     47  CA  ASN    47      27.814  30.153  88.639  1.00 25.00           C
ATOM     48  CA  THR    48      28.373  26.682  90.031  1.00 25.00           C
ATOM     49  CA  THR    49      25.685  25.671  87.522  1.00 25.00           C
ATOM     50  CA  LYS    50      27.464  22.350  87.255  1.00 25.00           C
ATOM     51  CA  GLU    51      24.382  21.058  89.173  1.00 25.00           C
ATOM     52  CA  THR    52      21.291  22.466  90.855  1.00 25.00           C
ATOM     53  CA  LYS    53      21.892  21.502  94.526  1.00 25.00           C
ATOM     54  CA  LYS    54      22.058  18.000  96.068  1.00 25.00           C
ATOM     55  CA  ASP    55      25.873  18.254  96.291  1.00 25.00           C
ATOM     56  CA  LEU    56      25.571  21.675  97.986  1.00 25.00           C
ATOM     57  CA  LEU    57      23.051  20.240 100.487  1.00 25.00           C
ATOM     58  CA  GLU    58      25.417  17.324 101.238  1.00 25.00           C
ATOM     59  CA  ARG    59      28.306  19.779 101.790  1.00 25.00           C
ATOM     60  CA  LEU    60      26.125  21.849 104.162  1.00 25.00           C
ATOM     61  CA  LYS    61      25.183  18.683 106.100  1.00 25.00           C
ATOM     62  CA  LYS    62      28.880  17.720 106.368  1.00 25.00           C
ATOM     63  CA  LEU    63      30.567  21.157 106.720  1.00 25.00           C
ATOM     64  CA  GLU    64      27.997  21.723 109.421  1.00 25.00           C
ATOM     65  CA  PHE    65      24.822  23.796 108.862  1.00 25.00           C
ATOM     66  CA  GLU    66      21.517  22.944 107.259  1.00 25.00           C
ATOM     67  CA  ILE    67      20.010  25.806 105.289  1.00 25.00           C
ATOM     68  CA  SER    68      16.595  24.772 103.923  1.00 25.00           C
ATOM     69  CA  GLU    69      15.142  26.690 100.936  1.00 25.00           C
ATOM     70  CA  ASP    70      16.369  30.038 102.334  1.00 25.00           C
ATOM     71  CA  GLU    71      19.976  29.121 101.430  1.00 25.00           C
ATOM     72  CA  ILE    72      18.937  27.912  97.948  1.00 25.00           C
ATOM     73  CA  PHE    73      19.458  29.580  94.565  1.00 25.00           C
ATOM     74  CA  THR    74      21.845  29.139  91.615  1.00 25.00           C
ATOM    179  CA  LYS   179      29.991  37.361  89.554  1.00 25.00           C
ATOM    180  CA  PRO   180      28.709  40.410  87.715  1.00 25.00           C
ATOM    181  CA  GLU   181      26.855  43.101  85.774  1.00 25.00           C
ATOM    182  CA  LYS   182      23.706  43.192  87.863  1.00 25.00           C
ATOM    183  CA  THR   183      19.928  42.592  87.681  1.00 25.00           C
ATOM    184  CA  PHE   184      20.414  38.998  88.912  1.00 25.00           C
ATOM    185  CA  PHE   185      22.567  40.259  91.818  1.00 25.00           C
ATOM    186  CA  LEU   186      19.877  42.828  92.729  1.00 25.00           C
ATOM    187  CA  GLU   187      17.201  40.088  92.658  1.00 25.00           C
ATOM    188  CA  ALA   188      19.364  37.884  94.923  1.00 25.00           C
ATOM    189  CA  LEU   189      19.831  40.802  97.358  1.00 25.00           C
ATOM    190  CA  ARG   190      16.050  41.406  97.399  1.00 25.00           C
ATOM    191  CA  ASP   191      15.439  37.690  98.100  1.00 25.00           C
ATOM    192  CA  ALA   192      17.690  38.038 101.059  1.00 25.00           C
ATOM    193  CA  ASP   193      16.533  41.118 102.909  1.00 25.00           C
ATOM    194  CA  CYS   194      19.515  43.417 102.375  1.00 25.00           C
ATOM    195  CA  ALA   195      18.977  45.616  99.290  1.00 25.00           C
ATOM    196  CA  PRO   196      21.451  47.767  97.280  1.00 25.00           C
ATOM    197  CA  GLU   197      24.701  49.587  98.167  1.00 25.00           C
ATOM    198  CA  GLU   198      26.626  46.280  98.011  1.00 25.00           C
ATOM    199  CA  ALA   199      24.465  43.371  96.856  1.00 25.00           C
ATOM    200  CA  VAL   200      27.553  41.179  96.478  1.00 25.00           C
ATOM    201  CA  MET   201      29.329  37.865  97.022  1.00 25.00           C
ATOM    202  CA  ILE   202      32.477  35.785  97.645  1.00 25.00           C
ATOM    203  CA  GLY   203      36.166  34.989  97.654  1.00 25.00           C
ATOM    204  CA  ASP   204      38.917  35.839  95.184  1.00 25.00           C
ATOM    205  CA  ASP   205      40.205  33.726  92.289  1.00 25.00           C
ATOM    206  CA  CYS   206      41.202  36.433  89.754  1.00 25.00           C
ATOM    207  CA  ARG   207      37.719  37.674  90.472  1.00 25.00           C
ATOM    208  CA  ASP   208      39.230  41.191  90.572  1.00 25.00           C
ATOM    209  CA  ASP   209      38.019  41.840  86.997  1.00 25.00           C
ATOM    210  CA  VAL   210      34.506  40.645  87.944  1.00 25.00           C
ATOM    211  CA  ASP   211      34.515  42.959  90.995  1.00 25.00           C
ATOM    212  CA  GLY   212      35.602  45.898  88.793  1.00 25.00           C
ATOM    213  CA  ALA   213      32.794  45.110  86.312  1.00 25.00           C
ATOM    214  CA  GLN   214      30.260  44.993  89.181  1.00 25.00           C
ATOM    215  CA  ASN   215      31.527  48.369  90.471  1.00 25.00           C
ATOM    216  CA  ILE   216      27.967  49.490  89.765  1.00 25.00           C
ATOM    217  CA  GLY   217      27.548  48.642  93.488  1.00 25.00           C
ATOM    218  CA  MET   218      28.025  44.887  93.112  1.00 25.00           C
ATOM    219  CA  LEU   219      31.465  44.504  94.746  1.00 25.00           C
ATOM    220  CA  GLY   220      33.087  41.159  95.554  1.00 25.00           C
ATOM    221  CA  ILE   221      33.547  38.113  93.301  1.00 25.00           C
ATOM    222  CA  LEU   222      34.393  34.505  92.653  1.00 25.00           C
ATOM    223  CA  VAL   223      35.574  31.316  94.309  1.00 25.00           C
ATOM    224  CA  LYS   224      38.869  30.733  96.179  1.00 25.00           C
ATOM    225  CA  THR   225      40.638  32.679  98.837  1.00 25.00           C
ATOM    226  CA  GLY   226      43.758  30.657  98.067  1.00 25.00           C
ATOM    227  CA  LYS   227      45.150  31.384  94.616  1.00 25.00           C
ATOM    228  CA  TYR   228      45.442  35.188  94.688  1.00 25.00           C
ATOM    229  CA  LYS   229      48.679  35.001  96.653  1.00 25.00           C
ATOM    230  CA  ALA   230      50.672  38.228  96.865  1.00 25.00           C
ATOM    231  CA  ALA   231      52.741  39.903  94.112  1.00 25.00           C
ATOM    232  CA  ASP   232      50.410  38.452  91.442  1.00 25.00           C
ATOM    233  CA  GLU   233      47.361  39.750  93.362  1.00 25.00           C
ATOM    234  CA  GLU   234      48.961  43.220  93.606  1.00 25.00           C
ATOM    235  CA  LYS   235      48.342  44.908  90.283  1.00 25.00           C
ATOM    236  CA  ILE   236      44.914  46.496  90.237  1.00 25.00           C
ATOM    237  CA  ASN   237      46.686  49.351  91.952  1.00 25.00           C
ATOM    238  CA  PRO   238      43.492  49.454  94.045  1.00 25.00           C
ATOM    239  CA  PRO   239      43.632  46.228  96.079  1.00 25.00           C
ATOM    240  CA  PRO   240      39.963  45.701  95.159  1.00 25.00           C
ATOM    241  CA  TYR   241      39.344  46.799  98.772  1.00 25.00           C
ATOM    242  CA  LEU   242      38.522  43.132  99.437  1.00 25.00           C
ATOM    243  CA  THR   243      40.753  40.723 101.406  1.00 25.00           C
ATOM    244  CA  CYS   244      39.405  37.240 102.311  1.00 25.00           C
ATOM    245  CA  GLU   245      41.619  35.089 104.542  1.00 25.00           C
ATOM    246  CA  SER   246      40.279  31.581 105.107  1.00 25.00           C
ATOM    247  CA  PHE   247      37.087  32.873 106.773  1.00 25.00           C
ATOM    248  CA  PRO   248      34.970  33.940 109.782  1.00 25.00           C
ATOM    249  CA  HIS   249      37.726  36.351 110.899  1.00 25.00           C
ATOM    250  CA  ALA   250      37.903  37.824 107.368  1.00 25.00           C
ATOM    251  CA  VAL   251      34.100  38.280 107.342  1.00 25.00           C
ATOM    252  CA  ASP   252      34.261  40.026 110.747  1.00 25.00           C
ATOM    253  CA  HIS   253      37.023  42.342 109.457  1.00 25.00           C
ATOM    254  CA  ILE   254      34.919  43.170 106.365  1.00 25.00           C
ATOM    255  CA  LEU   255      31.904  43.943 108.595  1.00 25.00           C
ATOM    256  CA  GLN   256      34.071  46.226 110.776  1.00 25.00           C
ATOM    257  CA  HIS   257      35.350  48.037 107.654  1.00 25.00           C
ATOM    258  CA  LEU   258      31.754  48.504 106.422  1.00 25.00           C
ATOM    259  CA  LEU   259      30.955  50.320 109.626  1.00 25.00           C
TER
END
