
#######################################################
#                                                     #
#                        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  119 (  119),  selected  119 , name T0356TS677_2-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS677_2-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    N       7      T      14          2.821
LGA    D       8      L      15          1.111
LGA    L       9      L      16          1.964
LGA    R      10      E      17          3.416
LGA    -       -      Q      18           -
LGA    D      11      Q      19          1.662
LGA    F      12      G      20           -
LGA    L      13      -       -           -
LGA    T      14      E      21          4.847
LGA    L      15      L      22           -
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      -       -           -
LGA    I      25      K      23           #
LGA    T      26      R      24           #
LGA    L      27      I      25          2.939
LGA    P      28      T      26           #
LGA    V      29      L      27           #
LGA    D      30      P      28          3.664
LGA    P      31      V      29          4.627
LGA    H      32      D      30          4.973
LGA    L      33      P      31          2.734
LGA    I      35      H      32          2.489
LGA    T      36      L      33           #
LGA    E      37      E      34          4.517
LGA    I      38      I      35          1.858
LGA    A      39      T      36          3.862
LGA    D      40      E      37          3.749
LGA    R      41      I      38          0.838
LGA    T      42      A      39          5.046
LGA    L      43      D      40           #
LGA    R      44      -       -           -
LGA    A      45      R      41          2.809
LGA    G      46      T      42           -
LGA    G      47      L      43           -
LGA    P      48      R      44           -
LGA    A      49      A      45           -
LGA    L      50      G      46           -
LGA    L      51      G      47           -
LGA    F      52      P      48           -
LGA    E      53      A      49           -
LGA    N      54      L      50           -
LGA    P      55      L      51           -
LGA    K      56      F      52           -
LGA    G      57      E      53           -
LGA    Y      58      N      54           -
LGA    S      59      P      55           -
LGA    P      61      K      56           -
LGA    V      62      G      57           #
LGA    L      63      -       -           -
LGA    C      64      -       -           -
LGA    N      65      -       -           -
LGA    L      66      -       -           -
LGA    F      67      Y      58          3.596
LGA    G      68      S      59          3.610
LGA    T      69      M      60          0.649
LGA    P      70      P      61          2.499
LGA    K      71      -       -           -
LGA    R      72      V      62          3.711
LGA    V      73      L      63          3.373
LGA    A      74      C      64          3.018
LGA    M      75      N      65          2.950
LGA    -       -      L      66           -
LGA    G      76      F      67           #
LGA    M      77      G      68          2.339
LGA    G      78      T      69          4.947
LGA    Q      79      -       -           -
LGA    E      80      -       -           -
LGA    D      81      -       -           -
LGA    V      82      P      70          3.846
LGA    S      83      K      71           -
LGA    A      84      R      72          4.722
LGA    L      85      V      73          1.663
LGA    R      86      -       -           -
LGA    E      87      A      74          3.532
LGA    V      88      M      75          1.931
LGA    G      89      G      76          3.054
LGA    K      90      M      77          4.699
LGA    L      91      G      78          4.245
LGA    L      92      Q      79           -
LGA    A      93      E      80           -
LGA    D     314      D      81           -
LGA    A     315      V      82           -
LGA    I     316      S      83           -
LGA    Y     317      A      84           -
LGA    H     318      L      85           -
LGA    S     319      R      86           -
LGA    T     320      E      87           -
LGA    Y     321      V      88           -
LGA    T     322      G      89           -
LGA    G     323      K      90           -
LGA    R     324      L      91           -
LGA    P     325      L      92           -
LGA    P     326      A      93           -
LGA    D     327      F      94           -
LGA    E     328      L      95           -
LGA    P     329      K      96           -
LGA    A     330      D     314           -
LGA    V     331      A     315           -
LGA    L     332      I     316           -
LGA    G     333      Y     317           -
LGA    V     334      H     318           -
LGA    A     335      S     319           -
LGA    L     336      T     320           -
LGA    N     337      Y     321           -
LGA    E     338      T     322           -
LGA    V     339      G     323           -
LGA    F     340      R     324           -
LGA    V     341      P     325           -
LGA    P     342      P     326           -
LGA    I     343      D     327           -
LGA    L     344      E     328           -
LGA    Q     345      P     329           -
LGA    K     346      A     330           -
LGA    Q     347      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)  119  124    5.0     37    3.41    13.51     16.882     1.054

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.452648 * X  +  -0.490601 * Y  +   0.744594 * Z  + 188.779800
  Y_new =  -0.670607 * X  +   0.737662 * Y  +   0.078363 * Z  + 100.057327
  Z_new =  -0.587704 * X  +  -0.463859 * Y  +  -0.662902 * Z  + 177.880508 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.531041    0.610552  [ DEG:  -145.0180     34.9820 ]
  Theta =   0.628218    2.513374  [ DEG:    35.9943    144.0057 ]
  Phi   =  -2.164534    0.977059  [ DEG:  -124.0187     55.9813 ]
 
# 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: T0356TS677_2-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS677_2-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  119  124   5.0   37   3.41   13.51  16.882
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS677_2-D1
PFRMAT TS
TARGET T0356
MODEL  2
PARENT 1T3T_A
ATOM    482  CA  ASN     7      66.077  83.087  89.536  1.00 53.00
ATOM    483  CA  ASP     8      66.854  84.721  86.191  1.00 37.00
ATOM    484  CA  LEU     9      65.100  81.808  84.478  1.00 49.00
ATOM    485  CA  ARG    10      62.100  82.077  86.797  1.00 76.00
ATOM    486  CA  ASP    11      62.025  85.831  86.077  1.00 65.00
ATOM    487  CA  PHE    12      62.054  85.251  82.304  1.00 70.00
ATOM    488  CA  LEU    13      59.138  82.870  82.857  1.00 97.00
ATOM    489  CA  THR    14      56.819  85.119  84.906  1.00 99.00
ATOM    490  CA  LEU    15      57.809  88.007  82.621  1.00 79.00
ATOM    491  CA  LEU    16      56.150  86.140  79.745  1.00 99.00
ATOM    492  CA  GLU    17      52.836  86.721  81.539  1.00 99.00
ATOM    493  CA  GLN    18      50.132  84.470  80.104  1.00 68.00
ATOM    494  CA  GLN    19      52.869  82.710  78.121  1.00 99.00
ATOM    495  CA  GLY    20      54.668  81.746  81.363  1.00 98.00
ATOM    496  CA  GLU    21      55.767  78.111  80.626  1.00 88.00
ATOM    497  CA  LEU    22      55.730  77.228  84.334  1.00 73.00
ATOM    498  CA  LYS    23      52.661  75.134  85.157  1.00 99.00
ATOM    499  CA  ARG    24      53.865  74.285  88.645  1.00 63.00
ATOM    500  CA  ILE    25      57.032  74.980  90.637  1.00 98.00
ATOM    501  CA  THR    26      58.304  73.980  94.061  1.00 99.00
ATOM    502  CA  LEU    27      61.588  74.383  95.908  1.00 99.00
ATOM    503  CA  PRO    28      63.814  71.408  96.694  1.00 99.00
ATOM    504  CA  VAL    29      64.651  71.279 100.388  1.00 99.00
ATOM    505  CA  ASP    30      64.359  68.638 103.110  1.00 80.00
ATOM    506  CA  PRO    31      64.289  65.111 101.704  1.00 84.00
ATOM    507  CA  HIS    32      65.579  66.464  98.412  1.00 52.00
ATOM    508  CA  LEU    33      63.942  65.123  95.277  1.00 55.00
ATOM    509  CA  ILE    35      62.353  62.287  97.301  1.00 91.00
ATOM    510  CA  THR    36      60.054  64.842  98.906  1.00 99.00
ATOM    511  CA  GLU    37      59.888  67.578  96.256  1.00 99.00
ATOM    512  CA  ILE    38      58.844  65.502  93.237  1.00 99.00
ATOM    513  CA  ALA    39      56.211  63.305  94.923  1.00 99.00
ATOM    514  CA  ASP    40      54.812  66.501  96.449  1.00 71.00
ATOM    515  CA  ARG    41      54.750  68.274  93.074  1.00 50.00
ATOM    516  CA  THR    42      52.833  65.535  91.228  1.00 48.00
ATOM    517  CA  LEU    43      50.601  64.843  94.242  1.00 60.00
ATOM    518  CA  ARG    44      49.534  68.494  94.494  1.00 52.00
ATOM    519  CA  ALA    45      48.557  68.273  90.833  1.00 41.00
ATOM    520  CA  GLY    46      46.600  65.057  91.346  1.00 51.00
ATOM    521  CA  GLY    47      49.027  63.181  89.102  1.00 53.00
ATOM    522  CA  PRO    48      51.603  60.423  89.337  1.00 71.00
ATOM    523  CA  ALA    49      55.076  60.371  87.836  1.00 99.00
ATOM    524  CA  LEU    50      57.616  58.210  86.038  1.00 99.00
ATOM    525  CA  LEU    51      61.229  59.275  86.470  1.00 99.00
ATOM    527  CA  PHE    52      67.443  58.274  87.698  1.00 99.00
ATOM    528  CA  GLU    53      70.190  58.789  85.108  1.00 73.00
ATOM    529  CA  ASN    54      68.589  61.961  83.754  1.00 50.00
ATOM    530  CA  PRO    55      69.244  63.821  87.028  1.00 42.00
ATOM    531  CA  LYS    56      72.396  65.990  86.904  1.00 68.00
ATOM    532  CA  GLY    57      75.099  64.641  89.224  1.00 70.00
ATOM    533  CA  TYR    58      78.561  65.789  90.300  1.00 70.00
ATOM    534  CA  SER    59      79.507  62.483  91.947  1.00 95.00
ATOM    539  CA  PRO    61      70.023  55.695  94.006  1.00 99.00
ATOM    540  CA  VAL    62      69.143  56.587  97.618  1.00 84.00
ATOM    541  CA  LEU    63      71.802  59.312  97.710  1.00 96.00
ATOM    542  CA  CYS    64      70.865  60.739  94.301  1.00 99.00
ATOM    543  CA  ASN    65      67.166  60.826  95.164  1.00 99.00
ATOM    544  CA  LEU    66      67.370  61.876  98.832  1.00 81.00
ATOM    545  CA  PHE    67      70.448  64.138  99.105  1.00 99.00
ATOM    546  CA  GLY    68      69.807  67.718 100.201  1.00 91.00
ATOM    547  CA  THR    69      71.998  69.498  97.650  1.00 75.00
ATOM    548  CA  PRO    70      71.138  73.170  97.339  1.00 44.00
ATOM    549  CA  LYS    71      69.964  75.593  94.656  1.00 53.00
ATOM    550  CA  ARG    72      67.440  73.207  93.079  1.00 45.00
ATOM    551  CA  VAL    73      63.837  73.659  91.970  1.00 33.00
ATOM    552  CA  ALA    74      61.369  71.159  90.516  1.00 21.00
ATOM    553  CA  MET    75      58.791  72.226  87.962  1.00 17.00
ATOM    554  CA  GLY    76      56.247  71.049  85.415  1.00  8.00
ATOM    555  CA  MET    77      56.280  72.305  81.822  1.00 18.00
ATOM    556  CA  GLY    78      54.063  71.374  78.864  1.00 38.00
ATOM    557  CA  GLN    79      55.984  69.306  76.299  1.00 49.00
ATOM    558  CA  GLU    80      55.441  71.894  73.543  1.00 82.00
ATOM    559  CA  ASP    81      56.985  74.561  75.796  1.00 98.00
ATOM    560  CA  VAL    82      60.261  72.685  76.290  1.00 94.00
ATOM    561  CA  SER    83      62.097  74.411  73.388  1.00 74.00
ATOM    562  CA  ALA    84      61.209  77.829  74.836  1.00 79.00
ATOM    563  CA  LEU    85      62.300  76.719  78.315  1.00 59.00
ATOM    564  CA  ARG    86      65.601  75.400  76.910  1.00 46.00
ATOM    565  CA  GLU    87      66.219  78.766  75.226  1.00 26.00
ATOM    566  CA  VAL    88      65.615  80.640  78.483  1.00 38.00
ATOM    567  CA  GLY    89      67.923  78.395  80.526  1.00 57.00
ATOM    568  CA  LYS    90      70.771  78.367  77.976  1.00 76.00
ATOM    569  CA  LEU    91      70.795  82.178  77.807  1.00 86.00
ATOM    570  CA  LEU    92      71.092  82.414  81.606  1.00 99.00
ATOM    571  CA  ALA    93      73.520  79.469  81.816  1.00 99.00
ATOM    836  CA  ASP   314      56.320  98.715 135.090  1.00 69.00
ATOM    837  CA  ALA   315      57.093  94.973 135.103  1.00 61.00
ATOM    842  CA  ILE   316      67.380  93.025 129.979  1.00 55.00
ATOM    843  CA  TYR   317      67.852  94.535 133.447  1.00 55.00
ATOM    844  CA  HIS   318      67.062  91.233 135.167  1.00 64.00
ATOM    845  CA  SER   319      69.255  89.176 132.793  1.00 67.00
ATOM    846  CA  THR   320      72.173  91.562 133.257  1.00 88.00
ATOM    847  CA  TYR   321      72.041  90.825 137.002  1.00 77.00
ATOM    848  CA  THR   322      71.686  87.059 136.480  1.00 79.00
ATOM    849  CA  GLY   323      68.039  87.002 137.525  1.00 67.00
ATOM    850  CA  ARG   324      64.645  86.226 136.036  1.00 50.00
ATOM    851  CA  PRO   325      62.461  88.399 138.239  1.00 47.00
ATOM    852  CA  PRO   326      58.830  88.139 139.323  1.00 99.00
ATOM    853  CA  ASP   327      56.279  89.241 136.707  1.00 99.00
ATOM    854  CA  GLU   328      57.031  90.116 133.062  1.00 99.00
ATOM    855  CA  PRO   329      55.387  92.598 130.716  1.00 99.00
ATOM    856  CA  ALA   330      52.279  91.618 128.742  1.00 99.00
ATOM    857  CA  VAL   331      49.628  93.175 126.506  1.00 67.00
ATOM    858  CA  LEU   332      47.696  95.034 129.220  1.00 94.00
ATOM    859  CA  GLY   333      44.771  96.254 127.109  1.00 86.00
ATOM    860  CA  VAL   334      44.001  94.911 123.624  1.00 78.00
ATOM    861  CA  ALA   335      41.785  97.880 122.739  1.00 89.00
ATOM    862  CA  LEU   336      44.540 100.347 123.696  1.00 99.00
ATOM    863  CA  ASN   337      47.160  98.461 121.656  1.00 93.00
ATOM    864  CA  GLU   338      44.788  98.666 118.701  1.00 68.00
ATOM    865  CA  VAL   339      44.046 102.307 119.542  1.00 75.00
ATOM    866  CA  PHE   340      47.780 103.020 119.755  1.00 61.00
ATOM    867  CA  VAL   341      48.405 101.623 116.267  1.00 51.00
ATOM    868  CA  PRO   342      45.464 103.597 114.853  1.00 28.00
ATOM    869  CA  ILE   343      46.590 106.807 116.563  1.00 54.00
ATOM    870  CA  LEU   344      50.110 106.400 115.202  1.00 42.00
ATOM    871  CA  GLN   345      48.737 105.847 111.694  1.00 68.00
ATOM    872  CA  LYS   346      46.764 109.080 111.998  1.00 63.00
ATOM    873  CA  GLN   347      49.824 111.017 113.185  1.00 76.00
TER
END
