
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms  148 ( 1158),  selected  148 , name T0341_D1.pdb
# PARAMETERS: T0341TS393_2-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           #
LGA    K       8      K       8           #
LGA    A       9      A       9          3.556
LGA    V      10      V      10          3.791
LGA    L      11      L      11          3.739
LGA    V      12      V      12           #
LGA    D      13      D      13          3.412
LGA    L      14      L      14          1.937
LGA    N      15      N      15          3.850
LGA    G      16      G      16          3.700
LGA    -       -      T      17           -
LGA    T      17      L      18           #
LGA    L      18      -       -           -
LGA    H      19      H      19           #
LGA    I      20      I      20           #
LGA    E      21      E      21          1.700
LGA    D      22      D      22          1.761
LGA    A      23      A      23          1.485
LGA    A      24      A      24          2.484
LGA    V      25      V      25          2.589
LGA    P      26      P      26          2.826
LGA    G      27      G      27           #
LGA    A      28      A      28          5.325
LGA    Q      29      Q      29          3.545
LGA    E      30      E      30           #
LGA    A      31      A      31           #
LGA    L      32      L      32          2.628
LGA    K      33      K      33          3.823
LGA    R      34      R      34          4.942
LGA    L      35      L      35          2.711
LGA    R      36      R      36          1.819
LGA    A      37      A      37          4.099
LGA    T      38      T      38          2.258
LGA    S      39      S      39          2.098
LGA    V      40      V      40          2.838
LGA    M      41      M      41          1.160
LGA    V      42      V      42          1.167
LGA    R      43      R      43          1.664
LGA    F      44      F      44          2.332
LGA    V      45      V      45          2.939
LGA    T      46      T      46          4.041
LGA    N      47      N      47          1.929
LGA    T      48      T      48          2.505
LGA    T      49      T      49          2.858
LGA    K      50      K      50          2.396
LGA    E      51      E      51          0.993
LGA    T      52      T      52          1.441
LGA    K      53      K      53          2.090
LGA    K      54      K      54          2.790
LGA    D      55      D      55          2.793
LGA    L      56      L      56          2.352
LGA    L      57      L      57          2.195
LGA    E      58      E      58          1.666
LGA    R      59      R      59          3.429
LGA    L      60      L      60          4.270
LGA    K      61      K      61          2.779
LGA    K      62      K      62          3.025
LGA    -       -      L      63           -
LGA    L      63      E      64          1.769
LGA    E      64      F      65          4.570
LGA    F      65      E      66          1.676
LGA    E      66      I      67          4.063
LGA    I      67      S      68          0.883
LGA    S      68      -       -           -
LGA    E      69      E      69          2.891
LGA    D      70      D      70          1.700
LGA    E      71      E      71          2.442
LGA    I      72      I      72          3.395
LGA    F      73      F      73          3.102
LGA    T      74      T      74          2.281
LGA    K     179      K     179          4.332
LGA    P     180      P     180          4.209
LGA    E     181      E     181           #
LGA    K     182      K     182          4.219
LGA    T     183      T     183          2.127
LGA    F     184      F     184          1.781
LGA    F     185      F     185          3.444
LGA    L     186      L     186          3.060
LGA    E     187      E     187          1.321
LGA    A     188      A     188          1.904
LGA    L     189      L     189          1.944
LGA    R     190      R     190          1.868
LGA    D     191      D     191          4.138
LGA    A     192      A     192          2.378
LGA    D     193      D     193          2.348
LGA    C     194      C     194          2.150
LGA    A     195      A     195          3.097
LGA    P     196      P     196          2.729
LGA    E     197      E     198          1.648
LGA    E     198      A     199          1.103
LGA    A     199      V     200           #
LGA    V     200      M     201          3.609
LGA    M     201      -       -           -
LGA    I     202      I     202          3.434
LGA    G     203      G     203          3.702
LGA    D     204      D     204          4.732
LGA    D     205      D     205          1.957
LGA    C     206      C     206          1.124
LGA    R     207      R     207          1.767
LGA    D     208      D     208          2.653
LGA    D     209      D     209          2.340
LGA    V     210      V     210          2.983
LGA    D     211      D     211          2.184
LGA    G     212      G     212          2.226
LGA    A     213      A     213          3.576
LGA    Q     214      Q     214          3.443
LGA    N     215      N     215          1.620
LGA    I     216      I     216          1.485
LGA    G     217      G     217          1.312
LGA    M     218      M     218          1.259
LGA    L     219      L     219          1.538
LGA    G     220      G     220          2.661
LGA    I     221      I     221          3.481
LGA    L     222      L     222          2.794
LGA    V     223      V     223          4.158
LGA    K     224      K     224           #
LGA    T     225      T     225          3.336
LGA    G     226      G     226          3.884
LGA    K     227      K     227          4.713
LGA    Y     228      Y     228          3.109
LGA    K     229      K     229          4.078
LGA    A     230      A     230          4.181
LGA    A     231      A     231          4.435
LGA    D     232      D     232          4.417
LGA    E     233      E     233          4.756
LGA    E     234      -       -           -
LGA    K     235      E     234          4.027
LGA    I     236      K     235           #
LGA    -       -      I     236           -
LGA    -       -      N     237           -
LGA    N     237      P     238           #
LGA    P     238      P     239          2.576
LGA    P     239      -       -           -
LGA    P     240      P     240          1.350
LGA    Y     241      Y     241          1.728
LGA    L     242      L     242          3.018
LGA    T     243      T     243          3.684
LGA    C     244      C     244          5.154
LGA    -       -      E     245           -
LGA    E     245      S     246          3.404
LGA    S     246      F     247          4.054
LGA    F     247      P     248          3.653
LGA    P     248      H     249          4.519
LGA    H     249      -       -           -
LGA    A     250      A     250           #
LGA    V     251      V     251          3.240
LGA    D     252      D     252          0.504
LGA    H     253      H     253          3.293
LGA    I     254      I     254           #
LGA    L     255      L     255          4.110
LGA    Q     256      Q     256          1.251
LGA    H     257      H     257          3.455
LGA    L     258      L     258          4.298
LGA    L     259      L     259           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  149  148    5.0    126    3.05    90.48     46.281     4.005

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.871893 * X  +  -0.031867 * Y  +   0.488658 * Z  +  29.534306
  Y_new =  -0.227451 * X  +  -0.910063 * Y  +   0.346485 * Z  +  33.470764
  Z_new =   0.433668 * X  +  -0.413244 * Y  +  -0.800726 * Z  +  90.869476 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.665159    0.476434  [ DEG:  -152.7024     27.2976 ]
  Theta =  -0.448559   -2.693033  [ DEG:   -25.7005   -154.2995 ]
  Phi   =  -0.255183    2.886409  [ DEG:   -14.6209    165.3791 ]
 
# 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_2-D1                               
REMARK     2: T0341_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0341TS393_2-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  126   3.05   90.48  46.281
REMARK  ---------------------------------------------------------- 
MOLECULE T0341TS393_2-D1
PFRMAT TS
TARGET T0341
MODEL 2
PARENT N/A
ATOM      7  CA  LEU     7      31.187  43.950 101.169  1.00 25.00           C
ATOM      8  CA  LYS     8      29.006  42.459 103.840  1.00 25.00           C
ATOM      9  CA  ALA     9      27.157  39.792 101.929  1.00 25.00           C
ATOM     10  CA  VAL    10      27.265  37.704  98.747  1.00 25.00           C
ATOM     11  CA  LEU    11      26.573  35.439  95.770  1.00 25.00           C
ATOM     12  CA  VAL    12      28.845  33.898  93.206  1.00 25.00           C
ATOM     13  CA  ASP    13      29.332  30.276  94.400  1.00 25.00           C
ATOM     14  CA  LEU    14      30.654  27.025  95.936  1.00 25.00           C
ATOM     15  CA  ASN    15      33.233  29.720  96.876  1.00 25.00           C
ATOM     16  CA  GLY    16      36.604  31.417  96.954  1.00 25.00           C
ATOM     17  CA  THR    17      37.332  30.756  93.222  1.00 25.00           C
ATOM     18  CA  LEU    18      35.185  27.617  92.721  1.00 25.00           C
ATOM     19  CA  HIS    19      34.048  24.159  93.614  1.00 25.00           C
ATOM     20  CA  ILE    20      33.862  20.404  92.805  1.00 25.00           C
ATOM     21  CA  GLU    21      36.306  18.873  95.283  1.00 25.00           C
ATOM     22  CA  ASP    22      38.095  17.844  98.480  1.00 25.00           C
ATOM     23  CA  ALA    23      38.117  19.113 102.006  1.00 25.00           C
ATOM     24  CA  ALA    24      38.233  22.655 100.676  1.00 25.00           C
ATOM     25  CA  VAL    25      37.340  24.476 103.926  1.00 25.00           C
ATOM     26  CA  PRO    26      39.022  27.436 105.662  1.00 25.00           C
ATOM     27  CA  GLY    27      37.910  29.671 102.718  1.00 25.00           C
ATOM     28  CA  ALA    28      34.157  29.458 101.980  1.00 25.00           C
ATOM     29  CA  GLN    29      33.536  27.961 105.450  1.00 25.00           C
ATOM     30  CA  GLU    30      35.570  30.780 107.057  1.00 25.00           C
ATOM     31  CA  ALA    31      33.552  33.384 105.105  1.00 25.00           C
ATOM     32  CA  LEU    32      30.285  31.747 106.251  1.00 25.00           C
ATOM     33  CA  LYS    33      31.504  31.798 109.882  1.00 25.00           C
ATOM     34  CA  ARG    34      32.414  35.503 109.550  1.00 25.00           C
ATOM     35  CA  LEU    35      28.944  36.251 108.110  1.00 25.00           C
ATOM     36  CA  ARG    36      27.307  34.372 111.017  1.00 25.00           C
ATOM     37  CA  ALA    37      29.411  36.363 113.523  1.00 25.00           C
ATOM     38  CA  THR    38      27.027  39.329 113.303  1.00 25.00           C
ATOM     39  CA  SER    39      23.935  39.282 111.084  1.00 25.00           C
ATOM     40  CA  VAL    40      23.865  36.928 108.125  1.00 25.00           C
ATOM     41  CA  MET    41      22.410  36.978 104.595  1.00 25.00           C
ATOM     42  CA  VAL    42      25.043  34.584 103.294  1.00 25.00           C
ATOM     43  CA  ARG    43      25.109  32.773  99.930  1.00 25.00           C
ATOM     44  CA  PHE    44      24.841  30.751  96.663  1.00 25.00           C
ATOM     45  CA  VAL    45      24.527  31.661  92.947  1.00 25.00           C
ATOM     46  CA  THR    46      26.327  32.454  89.678  1.00 25.00           C
ATOM     47  CA  ASN    47      28.372  29.207  89.885  1.00 25.00           C
ATOM     48  CA  THR    48      29.466  25.690  88.933  1.00 25.00           C
ATOM     49  CA  THR    49      26.284  24.273  87.387  1.00 25.00           C
ATOM     50  CA  LYS    50      26.474  20.549  87.971  1.00 25.00           C
ATOM     51  CA  GLU    51      23.857  20.977  90.640  1.00 25.00           C
ATOM     52  CA  THR    52      20.758  22.938  91.599  1.00 25.00           C
ATOM     53  CA  LYS    53      21.528  21.589  95.036  1.00 25.00           C
ATOM     54  CA  LYS    54      22.091  18.046  96.376  1.00 25.00           C
ATOM     55  CA  ASP    55      25.861  18.694  96.573  1.00 25.00           C
ATOM     56  CA  LEU    56      25.226  21.966  98.459  1.00 25.00           C
ATOM     57  CA  LEU    57      22.914  20.136 100.903  1.00 25.00           C
ATOM     58  CA  GLU    58      25.589  17.453 101.465  1.00 25.00           C
ATOM     59  CA  ARG    59      28.209  20.169 102.121  1.00 25.00           C
ATOM     60  CA  LEU    60      25.860  21.863 104.629  1.00 25.00           C
ATOM     61  CA  LYS    61      25.294  18.514 106.397  1.00 25.00           C
ATOM     62  CA  LYS    62      29.076  17.937 106.572  1.00 25.00           C
ATOM     63  CA  LEU    63      29.561  21.353 108.266  1.00 25.00           C
ATOM     64  CA  GLU    64      26.179  22.294 109.820  1.00 25.00           C
ATOM     65  CA  PHE    65      24.385  25.226 108.190  1.00 25.00           C
ATOM     66  CA  GLU    66      21.475  23.090 106.905  1.00 25.00           C
ATOM     67  CA  ILE    67      21.221  25.808 104.247  1.00 25.00           C
ATOM     68  CA  SER    68      17.496  25.381 104.691  1.00 25.00           C
ATOM     69  CA  GLU    69      16.113  25.490 101.096  1.00 25.00           C
ATOM     70  CA  ASP    70      15.637  29.173 100.162  1.00 25.00           C
ATOM     71  CA  GLU    71      19.311  29.404  99.105  1.00 25.00           C
ATOM     72  CA  ILE    72      20.040  26.525  96.738  1.00 25.00           C
ATOM     73  CA  PHE    73      20.697  28.329  93.449  1.00 25.00           C
ATOM     74  CA  THR    74      22.834  27.490  90.353  1.00 25.00           C
ATOM    179  CA  LYS   179      29.163  38.831  89.545  1.00 25.00           C
ATOM    180  CA  PRO   180      27.569  41.123  86.902  1.00 25.00           C
ATOM    181  CA  GLU   181      25.086  43.920  87.298  1.00 25.00           C
ATOM    182  CA  LYS   182      21.439  43.857  86.400  1.00 25.00           C
ATOM    183  CA  THR   183      19.980  40.319  86.550  1.00 25.00           C
ATOM    184  CA  PHE   184      22.869  39.199  88.802  1.00 25.00           C
ATOM    185  CA  PHE   185      22.274  42.203  91.100  1.00 25.00           C
ATOM    186  CA  LEU   186      18.543  41.358  91.283  1.00 25.00           C
ATOM    187  CA  GLU   187      19.384  37.724  92.152  1.00 25.00           C
ATOM    188  CA  ALA   188      21.774  38.908  94.901  1.00 25.00           C
ATOM    189  CA  LEU   189      19.054  41.208  96.308  1.00 25.00           C
ATOM    190  CA  ARG   190      16.560  38.301  96.303  1.00 25.00           C
ATOM    191  CA  ASP   191      19.097  36.089  98.129  1.00 25.00           C
ATOM    192  CA  ALA   192      19.009  38.884 100.766  1.00 25.00           C
ATOM    193  CA  ASP   193      16.510  41.759 100.593  1.00 25.00           C
ATOM    194  CA  CYS   194      18.427  44.889 101.594  1.00 25.00           C
ATOM    195  CA  ALA   195      18.558  46.595  98.215  1.00 25.00           C
ATOM    196  CA  PRO   196      22.222  47.225  97.386  1.00 25.00           C
ATOM    197  CA  GLU   197      23.569  46.531 100.904  1.00 25.00           C
ATOM    198  CA  GLU   198      26.192  44.145  99.455  1.00 25.00           C
ATOM    199  CA  ALA   199      25.473  43.683  95.792  1.00 25.00           C
ATOM    200  CA  VAL   200      28.603  41.621  95.791  1.00 25.00           C
ATOM    201  CA  MET   201      30.368  38.486  94.577  1.00 25.00           C
ATOM    202  CA  ILE   202      32.829  35.771  95.745  1.00 25.00           C
ATOM    203  CA  GLY   203      33.998  33.301  93.123  1.00 25.00           C
ATOM    204  CA  ASP   204      36.258  35.261  90.757  1.00 25.00           C
ATOM    205  CA  ASP   205      40.033  35.280  90.318  1.00 25.00           C
ATOM    206  CA  CYS   206      40.182  39.000  91.100  1.00 25.00           C
ATOM    207  CA  ARG   207      38.699  40.037  87.816  1.00 25.00           C
ATOM    208  CA  ASP   208      34.963  39.461  87.204  1.00 25.00           C
ATOM    209  CA  ASP   209      34.256  39.911  90.941  1.00 25.00           C
ATOM    210  CA  VAL   210      36.272  43.168  90.955  1.00 25.00           C
ATOM    211  CA  ASP   211      34.313  44.422  87.913  1.00 25.00           C
ATOM    212  CA  GLY   212      31.011  43.566  89.655  1.00 25.00           C
ATOM    213  CA  ALA   213      32.151  45.445  92.792  1.00 25.00           C
ATOM    214  CA  GLN   214      33.090  48.484  90.660  1.00 25.00           C
ATOM    215  CA  ASN   215      29.658  48.386  88.964  1.00 25.00           C
ATOM    216  CA  ILE   216      26.911  47.920  91.559  1.00 25.00           C
ATOM    217  CA  GLY   217      28.259  49.384  94.855  1.00 25.00           C
ATOM    218  CA  MET   218      29.722  46.481  96.746  1.00 25.00           C
ATOM    219  CA  LEU   219      32.825  44.566  97.763  1.00 25.00           C
ATOM    220  CA  GLY   220      32.920  40.800  98.258  1.00 25.00           C
ATOM    221  CA  ILE   221      35.705  40.143  95.790  1.00 25.00           C
ATOM    222  CA  LEU   222      37.829  37.075  95.635  1.00 25.00           C
ATOM    223  CA  VAL   223      37.711  33.517  96.884  1.00 25.00           C
ATOM    224  CA  LYS   224      39.549  31.708  94.088  1.00 25.00           C
ATOM    225  CA  THR   225      40.089  29.016  96.752  1.00 25.00           C
ATOM    226  CA  GLY   226      43.433  30.680  97.668  1.00 25.00           C
ATOM    227  CA  LYS   227      45.489  31.600  94.604  1.00 25.00           C
ATOM    228  CA  TYR   228      45.707  35.393  94.386  1.00 25.00           C
ATOM    229  CA  LYS   229      49.403  35.404  95.261  1.00 25.00           C
ATOM    230  CA  ALA   230      52.042  37.861  96.536  1.00 25.00           C
ATOM    231  CA  ALA   231      53.334  40.261  93.846  1.00 25.00           C
ATOM    232  CA  ASP   232      49.969  40.072  92.026  1.00 25.00           C
ATOM    233  CA  GLU   233      48.128  40.810  95.303  1.00 25.00           C
ATOM    234  CA  GLU   234      50.415  43.816  95.939  1.00 25.00           C
ATOM    235  CA  LYS   235      48.648  45.949  93.376  1.00 25.00           C
ATOM    236  CA  ILE   236      45.517  47.141  91.596  1.00 25.00           C
ATOM    237  CA  ASN   237      45.294  50.037  94.059  1.00 25.00           C
ATOM    238  CA  PRO   238      41.631  49.076  94.692  1.00 25.00           C
ATOM    239  CA  PRO   239      43.201  45.929  96.041  1.00 25.00           C
ATOM    240  CA  PRO   240      39.719  44.534  96.641  1.00 25.00           C
ATOM    241  CA  TYR   241      38.519  45.980  99.991  1.00 25.00           C
ATOM    242  CA  LEU   242      37.529  42.384 100.733  1.00 25.00           C
ATOM    243  CA  THR   243      40.073  39.738 101.823  1.00 25.00           C
ATOM    244  CA  CYS   244      38.543  36.289 101.335  1.00 25.00           C
ATOM    245  CA  GLU   245      37.786  33.592 103.926  1.00 25.00           C
ATOM    246  CA  SER   246      41.366  32.539 103.457  1.00 25.00           C
ATOM    247  CA  PHE   247      41.304  32.241 107.227  1.00 25.00           C
ATOM    248  CA  PRO   248      37.995  32.613 109.121  1.00 25.00           C
ATOM    249  CA  HIS   249      39.721  34.786 111.759  1.00 25.00           C
ATOM    250  CA  ALA   250      41.237  36.972 109.004  1.00 25.00           C
ATOM    251  CA  VAL   251      37.791  37.351 107.376  1.00 25.00           C
ATOM    252  CA  ASP   252      36.279  38.346 110.752  1.00 25.00           C
ATOM    253  CA  HIS   253      39.057  40.933 111.261  1.00 25.00           C
ATOM    254  CA  ILE   254      38.411  42.353 107.763  1.00 25.00           C
ATOM    255  CA  LEU   255      34.664  42.584 108.522  1.00 25.00           C
ATOM    256  CA  GLN   256      35.417  44.397 111.811  1.00 25.00           C
ATOM    257  CA  HIS   257      37.709  46.847 109.964  1.00 25.00           C
ATOM    258  CA  LEU   258      34.966  47.496 107.371  1.00 25.00           C
ATOM    259  CA  LEU   259      32.571  49.087 109.919  1.00 25.00           C
TER
END
