
#######################################################
#                                                     #
#                        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  124 (  124),  selected  124 , name T0356TS168_1-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS168_1-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N       7      -       -           -
LGA    D       8      -       -           -
LGA    L       9      -       -           -
LGA    R      10      -       -           -
LGA    D      11      -       -           -
LGA    F      12      -       -           -
LGA    L      13      -       -           -
LGA    T      14      -       -           -
LGA    L      15      -       -           -
LGA    L      16      -       -           -
LGA    E      17      -       -           -
LGA    Q      18      -       -           -
LGA    Q      19      -       -           -
LGA    G      20      -       -           -
LGA    E      21      -       -           -
LGA    L      22      -       -           -
LGA    K      23      -       -           -
LGA    R      24      N       7           #
LGA    -       -      D       8           -
LGA    -       -      L       9           -
LGA    -       -      R      10           -
LGA    I      25      D      11           #
LGA    T      26      F      12           -
LGA    L      27      L      13           -
LGA    P      28      -       -           -
LGA    V      29      -       -           -
LGA    D      30      -       -           -
LGA    P      31      -       -           -
LGA    H      32      -       -           -
LGA    L      33      -       -           -
LGA    E      34      -       -           -
LGA    I      35      -       -           -
LGA    T      36      T      14          3.277
LGA    E      37      L      15          4.713
LGA    I      38      L      16          5.670
LGA    A      39      E      17          1.968
LGA    D      40      Q      18           #
LGA    R      41      -       -           -
LGA    T      42      -       -           -
LGA    L      43      -       -           -
LGA    R      44      -       -           -
LGA    A      45      -       -           -
LGA    G      46      -       -           -
LGA    G      47      -       -           -
LGA    P      48      -       -           -
LGA    A      49      -       -           -
LGA    L      50      -       -           -
LGA    L      51      -       -           -
LGA    F      52      -       -           -
LGA    E      53      -       -           -
LGA    N      54      -       -           -
LGA    P      55      -       -           -
LGA    K      56      -       -           -
LGA    G      57      -       -           -
LGA    Y      58      -       -           -
LGA    S      59      -       -           -
LGA    M      60      Q      19           #
LGA    P      61      -       -           -
LGA    V      62      -       -           -
LGA    L      63      -       -           -
LGA    C      64      -       -           -
LGA    N      65      G      20           #
LGA    L      66      E      21          1.849
LGA    F      67      L      22          4.388
LGA    G      68      K      23           #
LGA    T      69      R      24           -
LGA    P      70      I      25           -
LGA    K      71      T      26           -
LGA    R      72      L      27           -
LGA    V      73      P      28           -
LGA    A      74      V      29           -
LGA    M      75      D      30           -
LGA    G      76      -       -           -
LGA    M      77      -       -           -
LGA    G      78      -       -           -
LGA    Q      79      -       -           -
LGA    E      80      P      31          3.462
LGA    D      81      H      32          1.335
LGA    V      82      L      33          2.708
LGA    S      83      -       -           -
LGA    A      84      E      34          1.198
LGA    L      85      I      35          2.023
LGA    R      86      T      36          3.424
LGA    E      87      E      37          3.140
LGA    V      88      I      38          1.779
LGA    G      89      A      39          2.645
LGA    K      90      D      40          5.440
LGA    L      91      R      41          5.785
LGA    L      92      T      42          3.490
LGA    A      93      L      43           #
LGA    F      94      R      44           -
LGA    L      95      A      45           -
LGA    K      96      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      A      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      E      53           -
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    -       -      P      61           -
LGA    -       -      V      62           -
LGA    -       -      L      63           -
LGA    -       -      C      64           -
LGA    -       -      N      65           -
LGA    -       -      L      66           -
LGA    -       -      F      67           -
LGA    -       -      G      68           -
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      M      75           -
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      V      82           -
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    -       -      L      85           -
LGA    D     314      R      86          1.342
LGA    -       -      E      87           -
LGA    A     315      V      88          2.785
LGA    I     316      G      89          3.082
LGA    -       -      K      90           -
LGA    -       -      L      91           -
LGA    Y     317      L      92           #
LGA    H     318      A      93           -
LGA    S     319      F      94           -
LGA    T     320      L      95           -
LGA    Y     321      K      96           -
LGA    T     322      D     314           -
LGA    G     323      A     315           -
LGA    -       -      I     316           -
LGA    R     324      Y     317           #
LGA    P     325      H     318          3.301
LGA    P     326      S     319          2.877
LGA    D     327      T     320          1.714
LGA    E     328      Y     321           #
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    P     329      P     326           #
LGA    A     330      D     327          5.080
LGA    V     331      E     328          4.163
LGA    L     332      P     329          1.689
LGA    G     333      A     330          2.580
LGA    V     334      V     331          3.185
LGA    A     335      L     332          2.273
LGA    L     336      G     333          0.688
LGA    N     337      V     334          1.568
LGA    E     338      A     335          2.858
LGA    V     339      L     336          2.630
LGA    F     340      N     337          1.604
LGA    V     341      E     338          1.990
LGA    P     342      V     339          2.270
LGA    I     343      F     340          2.095
LGA    L     344      V     341          1.777
LGA    Q     345      P     342          1.097
LGA    K     346      I     343          0.977
LGA    Q     347      L     344          1.579
LGA    -       -      Q     345           -
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  124  124    5.0     42    2.99     7.14     22.183     1.358

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.813395 * X  +   0.290673 * Y  +   0.503883 * Z  +  65.921486
  Y_new =   0.355966 * X  +  -0.933807 * Y  +  -0.035939 * Z  +  72.587425
  Z_new =   0.460083 * X  +   0.208598 * Y  +  -0.863024 * Z  +  72.318321 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.904435   -0.237157  [ DEG:   166.4119    -13.5881 ]
  Theta =  -0.478088   -2.663504  [ DEG:   -27.3924   -152.6076 ]
  Phi   =   0.412520   -2.729073  [ DEG:    23.6356   -156.3643 ]
 
# 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: T0356TS168_1-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS168_1-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  124  124   5.0   42   2.99    7.14  22.183
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS168_1-D1
PFRMAT TS
TARGET T0356
MODEL 1
PARENT N/A
ATOM      7  CA  ASN     7      68.888  89.157  66.720  1.00 25.00           C
ATOM      8  CA  ASP     8      67.256  92.125  68.508  1.00 25.00           C
ATOM      9  CA  LEU     9      67.899  90.465  71.900  1.00 25.00           C
ATOM     10  CA  ARG    10      71.562  89.881  70.947  1.00 25.00           C
ATOM     11  CA  ASP    11      71.900  93.549  69.899  1.00 25.00           C
ATOM     12  CA  PHE    12      70.374  94.666  73.229  1.00 25.00           C
ATOM     13  CA  LEU    13      72.819  92.416  75.134  1.00 25.00           C
ATOM     14  CA  THR    14      75.750  93.887  73.156  1.00 25.00           C
ATOM     15  CA  LEU    15      74.541  97.432  73.953  1.00 25.00           C
ATOM     16  CA  LEU    16      74.283  96.537  77.666  1.00 25.00           C
ATOM     17  CA  GLU    17      77.836  95.109  77.594  1.00 25.00           C
ATOM     18  CA  GLN    18      79.114  98.306  75.918  1.00 25.00           C
ATOM     19  CA  GLN    19      79.250  99.501  72.265  1.00 25.00           C
ATOM     20  CA  GLY    20      80.871  97.353  69.538  1.00 25.00           C
ATOM     21  CA  GLU    21      80.948  93.662  70.622  1.00 25.00           C
ATOM     22  CA  LEU    22      79.703  90.821  72.774  1.00 25.00           C
ATOM     23  CA  LYS    23      78.400  89.669  76.219  1.00 25.00           C
ATOM     24  CA  ARG    24      75.165  88.436  77.871  1.00 25.00           C
ATOM     25  CA  ILE    25      72.203  89.796  79.720  1.00 25.00           C
ATOM     26  CA  THR    26      74.439  92.064  81.877  1.00 25.00           C
ATOM     27  CA  LEU    27      73.969  92.612  85.610  1.00 25.00           C
ATOM     28  CA  PRO    28      71.078  95.073  85.375  1.00 25.00           C
ATOM     29  CA  VAL    29      67.457  95.571  84.552  1.00 25.00           C
ATOM     30  CA  ASP    30      63.738  96.122  84.106  1.00 25.00           C
ATOM     31  CA  PRO    31      63.228  92.653  82.561  1.00 25.00           C
ATOM     32  CA  HIS    32      65.183  89.532  81.514  1.00 25.00           C
ATOM     33  CA  LEU    33      67.816  90.249  84.202  1.00 25.00           C
ATOM     34  CA  GLU    34      65.058  90.658  86.827  1.00 25.00           C
ATOM     35  CA  ILE    35      63.496  87.336  85.742  1.00 25.00           C
ATOM     36  CA  THR    36      66.908  85.617  86.006  1.00 25.00           C
ATOM     37  CA  GLU    37      67.398  87.073  89.513  1.00 25.00           C
ATOM     38  CA  ILE    38      63.928  85.823  90.544  1.00 25.00           C
ATOM     39  CA  ALA    39      64.755  82.337  89.192  1.00 25.00           C
ATOM     40  CA  ASP    40      68.051  82.335  91.144  1.00 25.00           C
ATOM     41  CA  ARG    41      66.191  83.359  94.331  1.00 25.00           C
ATOM     42  CA  THR    42      63.654  80.541  93.786  1.00 25.00           C
ATOM     43  CA  LEU    43      66.508  78.033  93.301  1.00 25.00           C
ATOM     44  CA  ARG    44      68.165  79.257  96.528  1.00 25.00           C
ATOM     45  CA  ALA    45      71.392  79.182  94.482  1.00 25.00           C
ATOM     46  CA  GLY    46      73.006  81.939  92.312  1.00 25.00           C
ATOM     47  CA  GLY    47      72.711  82.704  88.588  1.00 25.00           C
ATOM     48  CA  PRO    48      70.077  80.537  86.900  1.00 25.00           C
ATOM     49  CA  ALA    49      68.406  81.400  83.618  1.00 25.00           C
ATOM     50  CA  LEU    50      65.863  79.305  81.689  1.00 25.00           C
ATOM     51  CA  LEU    51      65.531  82.190  79.255  1.00 25.00           C
ATOM     52  CA  PHE    52      63.460  85.249  78.283  1.00 25.00           C
ATOM     53  CA  GLU    53      60.819  87.372  76.451  1.00 25.00           C
ATOM     54  CA  ASN    54      60.802  90.465  78.726  1.00 25.00           C
ATOM     55  CA  PRO    55      59.341  93.891  79.547  1.00 25.00           C
ATOM     56  CA  LYS    56      57.957  93.732  83.128  1.00 25.00           C
ATOM     57  CA  GLY    57      54.259  93.407  82.297  1.00 25.00           C
ATOM     58  CA  TYR    58      55.453  89.968  81.168  1.00 25.00           C
ATOM     59  CA  SER    59      53.082  87.117  81.875  1.00 25.00           C
ATOM     60  CA  MET    60      55.882  84.606  81.724  1.00 25.00           C
ATOM     61  CA  PRO    61      55.585  84.428  77.950  1.00 25.00           C
ATOM     62  CA  VAL    62      54.646  82.396  74.915  1.00 25.00           C
ATOM     63  CA  LEU    63      56.037  79.390  76.866  1.00 25.00           C
ATOM     64  CA  CYS    64      58.166  76.778  78.701  1.00 25.00           C
ATOM     65  CA  ASN    65      59.061  78.862  81.755  1.00 25.00           C
ATOM     66  CA  LEU    66      58.810  81.243  84.747  1.00 25.00           C
ATOM     67  CA  PHE    67      57.145  80.451  88.083  1.00 25.00           C
ATOM     68  CA  GLY    68      53.960  78.720  87.028  1.00 25.00           C
ATOM     69  CA  THR    69      54.324  74.912  86.569  1.00 25.00           C
ATOM     70  CA  PRO    70      57.185  73.757  84.354  1.00 25.00           C
ATOM     71  CA  LYS    71      60.529  75.110  85.639  1.00 25.00           C
ATOM     72  CA  ARG    72      59.373  74.599  89.254  1.00 25.00           C
ATOM     73  CA  VAL    73      58.324  71.008  88.439  1.00 25.00           C
ATOM     74  CA  ALA    74      61.737  70.349  86.831  1.00 25.00           C
ATOM     75  CA  MET    75      63.495  71.754  89.931  1.00 25.00           C
ATOM     76  CA  GLY    76      61.365  69.509  92.187  1.00 25.00           C
ATOM     77  CA  MET    77      62.240  66.468  90.029  1.00 25.00           C
ATOM     78  CA  GLY    78      62.304  62.884  91.313  1.00 25.00           C
ATOM     79  CA  GLN    79      64.444  63.904  94.353  1.00 25.00           C
ATOM     80  CA  GLU    80      66.228  61.383  96.586  1.00 25.00           C
ATOM     81  CA  ASP    81      62.844  59.683  96.602  1.00 25.00           C
ATOM     82  CA  VAL    82      60.076  59.282  94.045  1.00 25.00           C
ATOM     83  CA  SER    83      56.933  59.494  96.224  1.00 25.00           C
ATOM     84  CA  ALA    84      58.175  62.785  97.737  1.00 25.00           C
ATOM     85  CA  LEU    85      58.833  64.177  94.230  1.00 25.00           C
ATOM     86  CA  ARG    86      55.312  63.148  93.134  1.00 25.00           C
ATOM     87  CA  GLU    87      53.824  64.860  96.219  1.00 25.00           C
ATOM     88  CA  VAL    88      55.811  68.041  95.443  1.00 25.00           C
ATOM     89  CA  GLY    89      54.556  67.970  91.824  1.00 25.00           C
ATOM     90  CA  LYS    90      50.953  67.560  93.056  1.00 25.00           C
ATOM     91  CA  LEU    91      51.407  70.521  95.445  1.00 25.00           C
ATOM     92  CA  LEU    92      52.801  72.648  92.581  1.00 25.00           C
ATOM     93  CA  ALA    93      49.811  71.696  90.385  1.00 25.00           C
ATOM     94  CA  PHE    94      47.403  72.645  93.209  1.00 25.00           C
ATOM     95  CA  LEU    95      49.178  76.014  93.622  1.00 25.00           C
ATOM     96  CA  LYS    96      48.983  77.570  97.074  1.00 25.00           C
ATOM    314  CA  ASP   314      61.977  76.567  64.413  1.00 25.00           C
ATOM    315  CA  ALA   315      64.747  78.122  66.557  1.00 25.00           C
ATOM    316  CA  ILE   316      66.190  74.682  65.821  1.00 25.00           C
ATOM    317  CA  TYR   317      65.977  71.977  68.477  1.00 25.00           C
ATOM    318  CA  HIS   318      65.676  69.262  71.167  1.00 25.00           C
ATOM    319  CA  SER   319      66.567  68.014  74.594  1.00 25.00           C
ATOM    320  CA  THR   320      66.206  70.054  77.752  1.00 25.00           C
ATOM    321  CA  TYR   321      67.058  68.230  81.009  1.00 25.00           C
ATOM    322  CA  THR   322      70.400  69.943  81.737  1.00 25.00           C
ATOM    323  CA  GLY   323      73.839  68.438  82.277  1.00 25.00           C
ATOM    324  CA  ARG   324      72.766  67.119  85.630  1.00 25.00           C
ATOM    325  CA  PRO   325      68.954  67.411  86.013  1.00 25.00           C
ATOM    326  CA  PRO   326      66.404  64.560  86.212  1.00 25.00           C
ATOM    327  CA  ASP   327      62.630  64.556  85.843  1.00 25.00           C
ATOM    328  CA  GLU   328      61.415  67.984  84.719  1.00 25.00           C
ATOM    329  CA  PRO   329      58.450  66.484  82.814  1.00 25.00           C
ATOM    330  CA  ALA   330      57.458  69.966  81.567  1.00 25.00           C
ATOM    331  CA  VAL   331      61.053  70.606  80.413  1.00 25.00           C
ATOM    332  CA  LEU   332      61.084  67.249  78.569  1.00 25.00           C
ATOM    333  CA  GLY   333      57.764  68.123  76.871  1.00 25.00           C
ATOM    334  CA  VAL   334      59.172  71.524  75.814  1.00 25.00           C
ATOM    335  CA  ALA   335      62.289  69.816  74.386  1.00 25.00           C
ATOM    336  CA  LEU   336      60.084  67.357  72.447  1.00 25.00           C
ATOM    337  CA  ASN   337      58.019  70.268  71.056  1.00 25.00           C
ATOM    338  CA  GLU   338      61.227  72.064  69.985  1.00 25.00           C
ATOM    339  CA  VAL   339      62.464  68.879  68.257  1.00 25.00           C
ATOM    340  CA  PHE   340      59.113  68.536  66.435  1.00 25.00           C
ATOM    341  CA  VAL   341      59.326  72.189  65.305  1.00 25.00           C
ATOM    342  CA  PRO   342      62.889  71.611  64.027  1.00 25.00           C
ATOM    343  CA  ILE   343      61.725  68.507  62.110  1.00 25.00           C
ATOM    344  CA  LEU   344      58.852  70.511  60.561  1.00 25.00           C
ATOM    345  CA  GLN   345      61.301  73.267  59.524  1.00 25.00           C
ATOM    346  CA  LYS   346      63.609  70.654  57.940  1.00 25.00           C
ATOM    347  CA  GLN   347      60.645  69.154  56.035  1.00 25.00           C
TER
END
