
#######################################################
#                                                     #
#                        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  122 (  122),  selected  122 , name T0356AL316_4-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356AL316_4-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N       7      N       7           -
LGA    D       8      D       8           -
LGA    L       9      L       9           -
LGA    R      10      R      10           -
LGA    D      11      D      11           -
LGA    F      12      F      12           -
LGA    -       -      L      13           -
LGA    -       -      T      14           -
LGA    L      13      L      15          4.613
LGA    T      14      L      16           -
LGA    L      15      -       -           -
LGA    L      16      E      17          2.738
LGA    E      17      Q      18          5.072
LGA    Q      18      Q      19           -
LGA    Q      19      -       -           -
LGA    L      22      G      20           #
LGA    K      23      E      21           -
LGA    R      24      L      22           -
LGA    I      25      K      23          3.855
LGA    T      26      R      24          2.200
LGA    L      27      I      25          3.633
LGA    P      28      T      26          3.062
LGA    V      29      L      27          4.978
LGA    D      30      -       -           -
LGA    P      31      P      28          1.425
LGA    H      32      V      29          2.009
LGA    L      33      D      30          2.668
LGA    E      34      P      31           #
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      I      35           -
LGA    -       -      T      36           -
LGA    -       -      E      37           -
LGA    -       -      I      38           -
LGA    -       -      A      39           -
LGA    -       -      D      40           -
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    I      35      P      55          2.894
LGA    -       -      K      56           -
LGA    T      36      G      57          2.870
LGA    E      37      Y      58          5.241
LGA    I      38      S      59           -
LGA    -       -      M      60           -
LGA    -       -      P      61           -
LGA    A      39      V      62           #
LGA    D      40      L      63           -
LGA    R      41      -       -           -
LGA    T      42      -       -           -
LGA    L      43      C      64           #
LGA    R      44      N      65           -
LGA    A      45      L      66           -
LGA    G      46      F      67           -
LGA    G      47      G      68           -
LGA    P      48      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    A      49      E      80           #
LGA    L      50      D      81          4.667
LGA    -       -      V      82           -
LGA    L      51      S      83          4.031
LGA    F      52      A      84           -
LGA    E      53      L      85           -
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      R      86          2.672
LGA    T      69      -       -           -
LGA    P      70      E      87          4.002
LGA    K      71      V      88          2.705
LGA    R      72      G      89          2.059
LGA    V      73      K      90          2.367
LGA    A      74      L      91          1.207
LGA    M      75      L      92          0.791
LGA    G      76      A      93          1.856
LGA    M      77      F      94          1.946
LGA    G      78      L      95          2.312
LGA    Q      79      K      96          3.616
LGA    E      80      D     314           -
LGA    D      81      A     315           -
LGA    V      82      I     316           -
LGA    S      83      Y     317           -
LGA    A      84      H     318           -
LGA    L      85      S     319           -
LGA    R      86      T     320           -
LGA    -       -      Y     321           -
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    -       -      D     327           -
LGA    -       -      E     328           -
LGA    -       -      P     329           -
LGA    -       -      A     330           -
LGA    -       -      V     331           -
LGA    -       -      L     332           -
LGA    E      87      G     333           #
LGA    V      88      V     334           -
LGA    -       -      A     335           -
LGA    -       -      L     336           -
LGA    -       -      N     337           -
LGA    -       -      E     338           -
LGA    G      89      V     339           #
LGA    K      90      F     340          1.938
LGA    L      91      -       -           -
LGA    L      92      V     341          3.425
LGA    A      93      P     342           -
LGA    F      94      I     343           -
LGA    L      95      L     344           -
LGA    K      96      Q     345           -
LGA    D     314      K     346           -
LGA    A     315      Q     347           -
LGA    I     316      -       -           -
LGA    Y     317      -       -           -
LGA    H     318      -       -           -
LGA    S     319      -       -           -
LGA    T     320      -       -           -
LGA    Y     321      -       -           -
LGA    T     322      -       -           -
LGA    G     323      -       -           -
LGA    R     324      -       -           -
LGA    P     325      -       -           -
LGA    P     326      -       -           -
LGA    D     327      -       -           -
LGA    E     328      -       -           -
LGA    P     329      -       -           -
LGA    A     330      -       -           -
LGA    V     331      -       -           -
LGA    L     332      -       -           -
LGA    G     333      -       -           -
LGA    V     334      -       -           -
LGA    A     335      -       -           -
LGA    L     336      -       -           -
LGA    N     337      -       -           -
LGA    E     338      -       -           -
LGA    V     339      -       -           -
LGA    F     340      -       -           -
LGA    V     341      -       -           -
LGA    P     342      -       -           -
LGA    I     343      -       -           -
LGA    L     344      -       -           -
LGA    Q     345      -       -           -
LGA    K     346      -       -           -
LGA    Q     347      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  122  124    5.0     29    3.22     6.90     14.534     0.874

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.684517 * X  +   0.147708 * Y  +   0.713876 * Z  + -208.858185
  Y_new =   0.644993 * X  +  -0.579078 * Y  +  -0.498650 * Z  + 143.199692
  Z_new =   0.339735 * X  +   0.801780 * Y  +  -0.491660 * Z  + 158.997620 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.120873   -1.020720  [ DEG:   121.5171    -58.4829 ]
  Theta =  -0.346635   -2.794957  [ DEG:   -19.8607   -160.1393 ]
  Phi   =   0.755679   -2.385914  [ DEG:    43.2972   -136.7028 ]
 
# 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: T0356AL316_4-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL316_4-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  122  124   5.0   29   3.22    6.90  14.534
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL316_4-D1
REMARK Aligment from pdb entry: 2cse_U
ATOM      7  CA  ASN     7      69.730  94.147  66.970  1.00  0.00              
ATOM      8  CA  ASP     8      63.425  96.467  83.355  1.00  0.00              
ATOM      9  CA  LEU     9      65.455  93.341  82.734  1.00  0.00              
ATOM     10  CA  ARG    10      68.067  93.824  85.462  1.00  0.00              
ATOM     11  CA  ASP    11      65.240  94.464  87.939  1.00  0.00              
ATOM     12  CA  PHE    12      63.392  91.426  86.673  1.00  0.00              
ATOM     13  CA  LEU    13      66.403  89.230  87.453  1.00  0.00              
ATOM     14  CA  THR    14      66.364  90.306  91.099  1.00  0.00              
ATOM     15  CA  LEU    15      62.586  89.959  91.377  1.00  0.00              
ATOM     16  CA  LEU    16      62.773  86.412  90.009  1.00  0.00              
ATOM     17  CA  GLU    17      65.835  85.348  91.969  1.00  0.00              
ATOM     18  CA  GLN    18      64.196  86.320  95.271  1.00  0.00              
ATOM     19  CA  GLN    19      60.831  84.661  94.770  1.00  0.00              
ATOM     20  CA  LEU    22      62.421  81.533  93.355  1.00  0.00              
ATOM     21  CA  LYS    23      64.562  81.302  96.459  1.00  0.00              
ATOM     22  CA  ARG    24      61.607  81.361  98.811  1.00  0.00              
ATOM     23  CA  ILE    25      59.995  78.568  96.830  1.00  0.00              
ATOM     24  CA  THR    26      63.174  76.497  96.878  1.00  0.00              
ATOM     25  CA  LEU    27      63.176  76.210 100.658  1.00  0.00              
ATOM     26  CA  PRO    28      59.469  75.421 100.589  1.00  0.00              
ATOM     27  CA  VAL    29      60.411  72.423  98.473  1.00  0.00              
ATOM     28  CA  ASP    30      63.362  71.384 100.610  1.00  0.00              
ATOM     29  CA  PRO    31      61.175  71.447 103.692  1.00  0.00              
ATOM     30  CA  HIS    32      59.121  68.558 102.306  1.00  0.00              
ATOM     31  CA  LEU    33      61.941  66.869 100.409  1.00  0.00              
ATOM     32  CA  GLU    34      65.222  67.196 102.329  1.00  0.00              
ATOM     33  CA  ILE    35      68.165  67.157  99.959  1.00  0.00              
ATOM     34  CA  THR    36      69.877  64.677 102.244  1.00  0.00              
ATOM     35  CA  GLU    37      67.441  62.013 101.054  1.00  0.00              
ATOM     36  CA  ILE    38      65.836  63.114  97.801  1.00  0.00              
ATOM     37  CA  ALA    39      68.781  64.612  95.895  1.00  0.00              
ATOM     38  CA  ASP    40      68.811  61.848  93.276  1.00  0.00              
ATOM     39  CA  ARG    41      65.065  61.226  92.989  1.00  0.00              
ATOM     40  CA  THR    42      63.230  61.975  89.743  1.00  0.00              
ATOM     41  CA  LEU    43      60.964  65.022  89.591  1.00  0.00              
ATOM     42  CA  ARG    44      60.584  97.491  66.058  1.00  0.00              
ATOM     43  CA  ALA    45      62.023  96.208  62.780  1.00  0.00              
ATOM     44  CA  GLY    46      65.067  95.102  64.745  1.00  0.00              
ATOM     45  CA  GLY    47      63.135  93.543  67.637  1.00  0.00              
ATOM     46  CA  PRO    48      63.132  89.737  67.830  1.00  0.00              
ATOM     47  CA  ALA    49      60.077  87.764  66.658  1.00  0.00              
ATOM     48  CA  LEU    50      58.253  85.971  69.471  1.00  0.00              
ATOM     49  CA  LEU    51      55.988  83.814  67.317  1.00  0.00              
ATOM     50  CA  PHE    52      53.003  84.477  69.543  1.00  0.00              
ATOM     51  CA  GLU    53      54.673  82.249  72.111  1.00  0.00              
ATOM     52  CA  ASN    54      54.678  85.343  74.356  1.00  0.00              
ATOM     53  CA  PRO    55      50.929  85.399  74.991  1.00  0.00              
ATOM     54  CA  LYS    56      48.417  83.684  77.301  1.00  0.00              
ATOM     55  CA  GLY    57      47.452  80.385  75.730  1.00  0.00              
ATOM     56  CA  TYR    58      48.938  79.855  72.290  1.00  0.00              
ATOM     57  CA  SER    59      50.674  55.997  72.496  1.00  0.00              
ATOM     58  CA  MET    60      49.680  57.712  69.255  1.00  0.00              
ATOM     59  CA  PRO    61      46.876  55.293  68.366  1.00  0.00              
ATOM     60  CA  VAL    62      45.089  56.810  71.360  1.00  0.00              
ATOM     61  CA  LEU    63      45.804  60.460  70.618  1.00  0.00              
ATOM     62  CA  CYS    64      44.554  59.878  67.109  1.00  0.00              
ATOM     63  CA  ASN    65      41.295  58.340  68.317  1.00  0.00              
ATOM     64  CA  LEU    66      41.073  61.152  70.809  1.00  0.00              
ATOM     65  CA  PHE    67      40.705  63.644  67.979  1.00  0.00              
ATOM     66  CA  GLY    68      60.589  75.551  64.003  1.00  0.00              
ATOM     67  CA  THR    69      60.943  75.324  60.246  1.00  0.00              
ATOM     68  CA  PRO    70      63.524  78.119  60.352  1.00  0.00              
ATOM     69  CA  LYS    71      65.296  76.553  63.295  1.00  0.00              
ATOM     70  CA  ARG    72      66.015  73.423  61.221  1.00  0.00              
ATOM     71  CA  VAL    73      66.892  75.272  58.053  1.00  0.00              
ATOM     72  CA  ALA    74      69.505  76.781  60.315  1.00  0.00              
ATOM     73  CA  MET    75      70.763  73.583  61.902  1.00  0.00              
ATOM     74  CA  GLY    76      71.041  71.988  58.461  1.00  0.00              
ATOM     75  CA  MET    77      73.826  74.452  57.748  1.00  0.00              
ATOM     76  CA  GLY    78      75.802  74.202  60.969  1.00  0.00              
ATOM     77  CA  GLN    79      75.620  70.440  60.657  1.00  0.00              
ATOM     78  CA  GLU    80      78.880  68.738  61.690  1.00  0.00              
ATOM     79  CA  ASP    81      79.096  64.898  61.735  1.00  0.00              
ATOM     80  CA  VAL    82      80.634  64.720  65.211  1.00  0.00              
ATOM     81  CA  SER    83      78.585  67.513  66.830  1.00  0.00              
ATOM     82  CA  ALA    84      75.259  66.339  68.364  1.00  0.00              
ATOM     83  CA  LEU    85      72.021  68.315  68.358  1.00  0.00              
ATOM     84  CA  ARG    86      68.974  68.185  70.609  1.00  0.00              
ATOM     85  CA  GLU    87      66.683  66.736  67.924  1.00  0.00              
ATOM     86  CA  VAL    88      67.401  65.503  64.429  1.00  0.00              
ATOM     87  CA  GLY    89      64.211  66.944  62.943  1.00  0.00              
ATOM     88  CA  LYS    90      63.044  70.170  64.582  1.00  0.00              
ATOM     89  CA  LEU    91      60.101  70.730  62.226  1.00  0.00              
ATOM     90  CA  LEU    92      56.571  70.378  63.525  1.00  0.00              
ATOM     91  CA  ALA    93      56.395  58.841  62.110  1.00  0.00              
ATOM     92  CA  PHE    94      58.771  58.777  59.169  1.00  0.00              
ATOM     93  CA  LEU    95      58.726  56.807  55.936  1.00  0.00              
ATOM     94  CA  LYS    96      61.460  56.673  53.294  1.00  0.00              
ATOM    297  CA  ASP   314      75.437  85.450  51.003  1.00  0.00              
ATOM    298  CA  ALA   315      74.774  89.165  51.164  1.00  0.00              
ATOM    299  CA  ILE   316      76.542  91.863  49.162  1.00  0.00              
ATOM    300  CA  TYR   317      98.067 100.601  20.616  1.00  0.00              
ATOM    301  CA  HIS   318      94.407  99.571  20.564  1.00  0.00              
ATOM    302  CA  SER   319      93.462 102.934  19.130  1.00  0.00              
ATOM    303  CA  THR   320      95.775 102.541  16.160  1.00  0.00              
ATOM    304  CA  TYR   321      94.328  99.122  15.410  1.00  0.00              
ATOM    305  CA  THR   322      90.754 100.404  15.254  1.00  0.00              
ATOM    306  CA  GLY   323      91.719 103.275  12.937  1.00  0.00              
ATOM    307  CA  ARG   324      93.955 101.202  10.650  1.00  0.00              
ATOM    308  CA  PRO   325      91.099  98.839   9.783  1.00  0.00              
ATOM    309  CA  PRO   326      88.128  99.789   7.576  1.00  0.00              
ATOM    310  CA  ASP   327      84.863  98.104   6.603  1.00  0.00              
ATOM    311  CA  GLU   328      85.358  94.716   5.001  1.00  0.00              
ATOM    312  CA  PRO   329      89.088  94.423   5.666  1.00  0.00              
ATOM    313  CA  ALA   330      90.003  90.944   6.867  1.00  0.00              
ATOM    314  CA  VAL   331      92.041  90.743  10.047  1.00  0.00              
ATOM    315  CA  LEU   332      94.618  88.409  11.536  1.00  0.00              
ATOM    316  CA  GLY   333      95.469  89.237  15.138  1.00  0.00              
ATOM    317  CA  VAL   334      98.259  87.264  16.789  1.00  0.00              
ATOM    318  CA  ALA   335      98.511  87.022  20.565  1.00  0.00              
ATOM    319  CA  LEU   336      94.877  87.921  21.158  1.00  0.00              
ATOM    320  CA  ASN   337      93.815  87.670  24.779  1.00  0.00              
ATOM    321  CA  GLU   338      90.988  85.388  25.951  1.00  0.00              
ATOM    322  CA  VAL   339      88.672  88.394  26.314  1.00  0.00              
ATOM    323  CA  PHE   340      89.978  93.319  19.405  1.00  0.00              
ATOM    324  CA  VAL   341      86.323  92.557  18.776  1.00  0.00              
ATOM    325  CA  PRO   342      85.433  96.005  20.157  1.00  0.00              
ATOM    326  CA  ILE   343      88.025  97.761  17.987  1.00  0.00              
ATOM    327  CA  LEU   344      87.661  96.533  14.417  1.00  0.00              
ATOM    328  CA  GLN   345      84.396  97.119  12.464  1.00  0.00              
ATOM    329  CA  LYS   346      81.541  94.645  12.874  1.00  0.00              
ATOM    330  CA  GLN   347      81.699  94.055   9.109  1.00  0.00              
END
