
#######################################################
#                                                     #
#                        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   36 (  144),  selected   36 , name T0286AL044_2_2
# Molecule2: number of CA atoms  202 ( 1582),  selected  202 , name T0286.pdb
# PARAMETERS: T0286AL044_2_2.T0286.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      S       3           -
LGA    -       -      K       4           -
LGA    -       -      T       5           -
LGA    -       -      I       6           -
LGA    K       7      K       7          2.142
LGA    I       8      I       8          1.301
LGA    M       9      M       9          1.044
LGA    P      10      P      10          0.577
LGA    V      11      V      11          0.880
LGA    G      12      G      12          1.686
LGA    D      13      D      13          1.173
LGA    S      14      S      14          0.856
LGA    C      15      C      15          1.506
LGA    T      16      T      16          1.125
LGA    E      17      E      17          0.761
LGA    G      18      G      18          0.784
LGA    -       -      M      19           -
LGA    -       -      G      20           -
LGA    -       -      G      21           -
LGA    -       -      G      22           -
LGA    -       -      E      23           -
LGA    -       -      M      24           -
LGA    M      19      G      25          5.178
LGA    G      20      S      26          2.628
LGA    Y      27      -       -           -
LGA    R      28      -       -           -
LGA    T      29      -       -           -
LGA    E      30      Y      27          5.010
LGA    L      31      R      28          3.038
LGA    Y      32      T      29          2.170
LGA    R      33      E      30          2.335
LGA    L      34      L      31          1.630
LGA    L      35      Y      32          2.622
LGA    T      36      R      33          4.927
LGA    L      55      L      34          6.124
LGA    P      56      L      35          4.305
LGA    -       -      T      36           -
LGA    -       -      Q      37           -
LGA    -       -      A      38           -
LGA    -       -      G      39           -
LGA    -       -      L      40           -
LGA    -       -      S      41           -
LGA    -       -      I      42           -
LGA    D      57      D      43          2.753
LGA    K      58      F      44          2.198
LGA    D      59      V      45          3.401
LGA    -       -      G      46           -
LGA    -       -      S      47           -
LGA    -       -      Q      48           -
LGA    -       -      R      49           -
LGA    -       -      S      50           -
LGA    -       -      G      51           -
LGA    -       -      P      52           -
LGA    -       -      S      53           -
LGA    -       -      S      54           -
LGA    -       -      L      55           -
LGA    -       -      P      56           -
LGA    -       -      D      57           -
LGA    -       -      K      58           -
LGA    -       -      D      59           -
LGA    H      60      H      60          1.617
LGA    E      61      E      61          0.834
LGA    G      62      G      62          0.742
LGA    H      63      H      63          1.202
LGA    S      64      S      64          0.784
LGA    G      65      G      65          0.551
LGA    W      66      W      66          1.521
LGA    -       -      T      67           -
LGA    -       -      I      68           -
LGA    -       -      P      69           -
LGA    -       -      Q      70           -
LGA    -       -      I      71           -
LGA    -       -      A      72           -
LGA    -       -      S      73           -
LGA    -       -      N      74           -
LGA    -       -      I      75           -
LGA    -       -      N      76           -
LGA    -       -      N      77           -
LGA    -       -      W      78           -
LGA    -       -      L      79           -
LGA    -       -      N      80           -
LGA    -       -      T      81           -
LGA    -       -      H      82           -
LGA    -       -      N      83           -
LGA    -       -      P      84           -
LGA    -       -      D      85           -
LGA    -       -      V      86           -
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      L      89           -
LGA    -       -      W      90           -
LGA    -       -      I      91           -
LGA    -       -      G      92           -
LGA    -       -      G      93           -
LGA    -       -      N      94           -
LGA    -       -      D      95           -
LGA    -       -      L      96           -
LGA    -       -      L      97           -
LGA    -       -      L      98           -
LGA    -       -      N      99           -
LGA    -       -      G     100           -
LGA    -       -      N     101           -
LGA    -       -      L     102           -
LGA    -       -      N     103           -
LGA    -       -      A     104           -
LGA    -       -      T     105           -
LGA    -       -      G     106           -
LGA    -       -      L     107           -
LGA    -       -      S     108           -
LGA    -       -      N     109           -
LGA    -       -      L     110           -
LGA    -       -      I     111           -
LGA    -       -      D     112           -
LGA    -       -      Q     113           -
LGA    -       -      I     114           -
LGA    -       -      F     115           -
LGA    -       -      T     116           -
LGA    -       -      V     117           -
LGA    -       -      K     118           -
LGA    -       -      P     119           -
LGA    -       -      N     120           -
LGA    -       -      V     121           -
LGA    -       -      T     122           -
LGA    -       -      L     123           -
LGA    -       -      F     124           -
LGA    -       -      V     125           -
LGA    -       -      A     126           -
LGA    -       -      D     127           -
LGA    -       -      Y     128           -
LGA    -       -      Y     129           -
LGA    -       -      P     130           -
LGA    -       -      W     131           -
LGA    -       -      P     132           -
LGA    -       -      E     133           -
LGA    -       -      A     134           -
LGA    -       -      I     135           -
LGA    -       -      K     136           -
LGA    -       -      Q     137           -
LGA    -       -      Y     138           -
LGA    -       -      N     139           -
LGA    -       -      A     140           -
LGA    -       -      V     141           -
LGA    -       -      I     142           -
LGA    -       -      P     143           -
LGA    -       -      G     144           -
LGA    -       -      I     145           -
LGA    -       -      V     146           -
LGA    -       -      Q     147           -
LGA    -       -      Q     148           -
LGA    -       -      K     149           -
LGA    -       -      A     150           -
LGA    -       -      N     151           -
LGA    -       -      A     152           -
LGA    -       -      G     153           -
LGA    -       -      K     154           -
LGA    -       -      K     155           -
LGA    -       -      V     156           -
LGA    -       -      Y     157           -
LGA    -       -      F     158           -
LGA    -       -      V     159           -
LGA    -       -      K     160           -
LGA    -       -      L     161           -
LGA    -       -      S     162           -
LGA    -       -      E     163           -
LGA    -       -      I     164           -
LGA    -       -      Q     165           -
LGA    -       -      F     166           -
LGA    -       -      D     167           -
LGA    -       -      R     168           -
LGA    -       -      N     169           -
LGA    -       -      T     170           -
LGA    -       -      D     171           -
LGA    -       -      I     172           -
LGA    -       -      S     173           -
LGA    -       -      W     174           -
LGA    -       -      D     175           -
LGA    -       -      G     176           -
LGA    -       -      L     177           -
LGA    -       -      H     178           -
LGA    -       -      L     179           -
LGA    -       -      S     180           -
LGA    -       -      E     181           -
LGA    -       -      I     182           -
LGA    -       -      G     183           -
LGA    -       -      Y     184           -
LGA    -       -      K     185           -
LGA    -       -      K     186           -
LGA    -       -      I     187           -
LGA    -       -      A     188           -
LGA    -       -      N     189           -
LGA    -       -      I     190           -
LGA    -       -      W     191           -
LGA    -       -      Y     192           -
LGA    -       -      K     193           -
LGA    -       -      Y     194           -
LGA    -       -      T     195           -
LGA    -       -      I     196           -
LGA    -       -      D     197           -
LGA    -       -      I     198           -
LGA    -       -      L     199           -
LGA    -       -      R     200           -
LGA    -       -      A     201           -
LGA    -       -      L     202           -
LGA    -       -      A     203           -
LGA    -       -      G     204           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36  202    5.0     33    2.57    66.67     11.825     1.234

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.461316 * X  +  -0.072152 * Y  +   0.884297 * Z  + -132.949387
  Y_new =  -0.540490 * X  +  -0.813256 * Y  +   0.215605 * Z  +  52.883961
  Z_new =   0.703604 * X  +  -0.577416 * Y  +  -0.414165 * Z  +  17.845705 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.193022    0.948571  [ DEG:  -125.6509     54.3491 ]
  Theta =  -0.780456   -2.361136  [ DEG:   -44.7168   -135.2832 ]
  Phi   =  -0.864266    2.277327  [ DEG:   -49.5188    130.4812 ]
 
# 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: T0286AL044_2_2                                
REMARK     2: T0286.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0286AL044_2_2.T0286.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36  202   5.0   33   2.57   66.67  11.825
REMARK  ---------------------------------------------------------- 
MOLECULE T0286AL044_2_2
REMARK PARENT number 2
PARENT 1vyh_A
REMARK Aligment from pdb entry: 1vyh_A
ATOM    345  N   LYS     7      24.786  -0.564   4.807  1.00  0.00              
ATOM    346  CA  LYS     7      24.959  -0.138   6.165  1.00  0.00              
ATOM    347  C   LYS     7      26.174   0.760   6.169  1.00  0.00              
ATOM    348  O   LYS     7      26.275   1.688   6.957  1.00  0.00              
ATOM    349  N   ILE     8      27.111   0.469   5.278  1.00  0.00              
ATOM    350  CA  ILE     8      28.428   1.087   5.302  1.00  0.00              
ATOM    351  C   ILE     8      28.740   1.624   3.930  1.00  0.00              
ATOM    352  O   ILE     8      28.453   0.959   2.942  1.00  0.00              
ATOM    353  N   MET     9      29.356   2.802   3.872  1.00  0.00              
ATOM    354  CA  MET     9      29.634   3.457   2.601  1.00  0.00              
ATOM    355  C   MET     9      31.011   4.072   2.566  1.00  0.00              
ATOM    356  O   MET     9      31.339   4.939   3.386  1.00  0.00              
ATOM    357  N   PRO    10      31.802   3.615   1.605  1.00  0.00              
ATOM    358  CA  PRO    10      33.175   4.046   1.457  1.00  0.00              
ATOM    359  C   PRO    10      33.202   5.074   0.337  1.00  0.00              
ATOM    360  O   PRO    10      32.782   4.770  -0.765  1.00  0.00              
ATOM    361  N   VAL    11      33.676   6.284   0.580  1.00  0.00              
ATOM    362  CA  VAL    11      33.839   7.226  -0.520  1.00  0.00              
ATOM    363  C   VAL    11      35.238   7.745  -0.542  1.00  0.00              
ATOM    364  O   VAL    11      35.881   7.818   0.505  1.00  0.00              
ATOM    365  N   GLY    12      35.727   8.102  -1.725  1.00  0.00              
ATOM    366  CA  GLY    12      37.069   8.644  -1.828  1.00  0.00              
ATOM    367  C   GLY    12      37.804   8.328  -3.105  1.00  0.00              
ATOM    368  O   GLY    12      37.189   8.138  -4.140  1.00  0.00              
ATOM    369  N   ASP    13      39.125   8.273  -3.009  1.00  0.00              
ATOM    370  CA  ASP    13      39.997   8.163  -4.158  1.00  0.00              
ATOM    371  C   ASP    13      40.475   6.736  -4.372  1.00  0.00              
ATOM    372  O   ASP    13      39.875   5.789  -3.872  1.00  0.00              
ATOM    373  N   SER    14      41.574   6.585  -5.101  1.00  0.00              
ATOM    374  CA  SER    14      42.110   5.255  -5.404  1.00  0.00              
ATOM    375  C   SER    14      42.341   4.383  -4.170  1.00  0.00              
ATOM    376  O   SER    14      42.133   3.174  -4.241  1.00  0.00              
ATOM    377  N   CYS    15      42.742   4.978  -3.050  1.00  0.00              
ATOM    378  CA  CYS    15      42.926   4.210  -1.830  1.00  0.00              
ATOM    379  C   CYS    15      41.675   3.425  -1.515  1.00  0.00              
ATOM    380  O   CYS    15      41.750   2.274  -1.095  1.00  0.00              
ATOM    381  N   THR    16      40.524   4.058  -1.718  1.00  0.00              
ATOM    382  CA  THR    16      39.227   3.448  -1.435  1.00  0.00              
ATOM    383  C   THR    16      38.918   2.464  -2.508  1.00  0.00              
ATOM    384  O   THR    16      38.511   1.355  -2.244  1.00  0.00              
ATOM    385  N   GLU    17      39.085   2.889  -3.740  1.00  0.00              
ATOM    386  CA  GLU    17      38.629   2.072  -4.835  1.00  0.00              
ATOM    387  C   GLU    17      39.413   0.788  -4.964  1.00  0.00              
ATOM    388  O   GLU    17      38.822  -0.230  -5.289  1.00  0.00              
ATOM    389  N   GLY    18      40.719   0.834  -4.709  1.00  0.00              
ATOM    390  CA  GLY    18      41.576  -0.323  -4.851  1.00  0.00              
ATOM    391  C   GLY    18      41.345  -1.352  -3.764  1.00  0.00              
ATOM    392  O   GLY    18      41.529  -2.540  -3.970  1.00  0.00              
ATOM    393  N   MET    19      40.908  -0.889  -2.609  1.00  0.00              
ATOM    394  CA  MET    19      40.639  -1.771  -1.497  1.00  0.00              
ATOM    395  C   MET    19      39.698  -2.922  -1.876  1.00  0.00              
ATOM    396  O   MET    19      39.833  -4.037  -1.407  1.00  0.00              
ATOM    397  N   GLY    20      38.762  -2.648  -2.749  1.00  0.00              
ATOM    398  CA  GLY    20      37.785  -3.621  -3.119  1.00  0.00              
ATOM    399  C   GLY    20      38.380  -4.774  -3.905  1.00  0.00              
ATOM    400  O   GLY    20      37.830  -5.880  -3.943  1.00  0.00              
ATOM    401  N   TYR    27      39.508  -4.512  -4.537  1.00  0.00              
ATOM    402  CA  TYR    27      40.106  -5.474  -5.454  1.00  0.00              
ATOM    403  C   TYR    27      40.852  -6.608  -4.754  1.00  0.00              
ATOM    404  O   TYR    27      41.192  -7.621  -5.370  1.00  0.00              
ATOM    405  N   ARG    28      41.098  -6.435  -3.464  1.00  0.00              
ATOM    406  CA  ARG    28      41.856  -7.405  -2.708  1.00  0.00              
ATOM    407  C   ARG    28      40.987  -8.345  -1.866  1.00  0.00              
ATOM    408  O   ARG    28      39.888  -8.003  -1.443  1.00  0.00              
ATOM    409  N   THR    29      41.480  -9.553  -1.629  1.00  0.00              
ATOM    410  CA  THR    29      40.649 -10.568  -0.987  1.00  0.00              
ATOM    411  C   THR    29      40.083 -10.110   0.348  1.00  0.00              
ATOM    412  O   THR    29      39.019 -10.558   0.763  1.00  0.00              
ATOM    413  N   GLU    30      40.781  -9.181   0.992  1.00  0.00              
ATOM    414  CA  GLU    30      40.424  -8.705   2.318  1.00  0.00              
ATOM    415  C   GLU    30      39.119  -7.967   2.282  1.00  0.00              
ATOM    416  O   GLU    30      38.473  -7.819   3.282  1.00  0.00              
ATOM    417  N   LEU    31      38.709  -7.519   1.120  1.00  0.00              
ATOM    418  CA  LEU    31      37.452  -6.787   1.040  1.00  0.00              
ATOM    419  C   LEU    31      36.277  -7.741   1.211  1.00  0.00              
ATOM    420  O   LEU    31      35.327  -7.448   1.955  1.00  0.00              
ATOM    421  N   TYR    32      36.335  -8.873   0.521  1.00  0.00              
ATOM    422  CA  TYR    32      35.224  -9.805   0.566  1.00  0.00              
ATOM    423  C   TYR    32      35.229 -10.524   1.904  1.00  0.00              
ATOM    424  O   TYR    32      34.266 -11.220   2.233  1.00  0.00              
ATOM    425  N   ARG    33      36.303 -10.355   2.677  1.00  0.00              
ATOM    426  CA  ARG    33      36.409 -11.064   3.952  1.00  0.00              
ATOM    427  C   ARG    33      35.960 -10.235   5.133  1.00  0.00              
ATOM    428  O   ARG    33      35.518 -10.769   6.129  1.00  0.00              
ATOM    429  N   LEU    34      36.020  -8.927   4.984  1.00  0.00              
ATOM    430  CA  LEU    34      35.801  -7.998   6.074  1.00  0.00              
ATOM    431  C   LEU    34      34.535  -7.156   5.930  1.00  0.00              
ATOM    432  O   LEU    34      33.696  -7.094   6.836  1.00  0.00              
ATOM    433  N   LEU    35      34.421  -6.498   4.777  1.00  0.00              
ATOM    434  CA  LEU    35      33.413  -5.478   4.552  1.00  0.00              
ATOM    435  C   LEU    35      32.286  -5.936   3.681  1.00  0.00              
ATOM    436  O   LEU    35      31.185  -5.402   3.790  1.00  0.00              
ATOM    437  N   THR    36      32.540  -6.911   2.819  1.00  0.00              
ATOM    438  CA  THR    36      31.445  -7.456   2.036  1.00  0.00              
ATOM    439  C   THR    36      30.236  -7.860   2.888  1.00  0.00              
ATOM    440  O   THR    36      29.134  -7.461   2.572  1.00  0.00              
ATOM    441  N   LEU    55      30.421  -8.598   3.977  1.00  0.00              
ATOM    442  CA  LEU    55      29.283  -9.045   4.766  1.00  0.00              
ATOM    443  C   LEU    55      28.694  -7.937   5.612  1.00  0.00              
ATOM    444  O   LEU    55      27.705  -8.151   6.304  1.00  0.00              
ATOM    445  N   PRO    56      29.281  -6.752   5.546  1.00  0.00              
ATOM    446  CA  PRO    56      28.813  -5.639   6.349  1.00  0.00              
ATOM    447  C   PRO    56      27.753  -4.888   5.586  1.00  0.00              
ATOM    448  O   PRO    56      27.111  -3.987   6.132  1.00  0.00              
ATOM    449  N   ASP    57      27.549  -5.295   4.333  1.00  0.00              
ATOM    450  CA  ASP    57      26.660  -4.610   3.387  1.00  0.00              
ATOM    451  C   ASP    57      27.233  -3.256   3.107  1.00  0.00              
ATOM    452  O   ASP    57      26.703  -2.252   3.553  1.00  0.00              
ATOM    453  N   LYS    58      28.346  -3.244   2.387  1.00  0.00              
ATOM    454  CA  LYS    58      29.105  -2.026   2.174  1.00  0.00              
ATOM    455  C   LYS    58      29.204  -1.722   0.720  1.00  0.00              
ATOM    456  O   LYS    58      29.333  -2.619  -0.109  1.00  0.00              
ATOM    457  N   ASP    59      29.156  -0.435   0.418  1.00  0.00              
ATOM    458  CA  ASP    59      29.308   0.066  -0.942  1.00  0.00              
ATOM    459  C   ASP    59      30.579   0.884  -1.066  1.00  0.00              
ATOM    460  O   ASP    59      31.019   1.555  -0.113  1.00  0.00              
ATOM    461  N   HIS    60      31.170   0.823  -2.246  1.00  0.00              
ATOM    462  CA  HIS    60      32.453   1.454  -2.486  1.00  0.00              
ATOM    463  C   HIS    60      32.337   2.490  -3.589  1.00  0.00              
ATOM    464  O   HIS    60      32.214   2.134  -4.762  1.00  0.00              
ATOM    465  N   GLU    61      32.369   3.769  -3.236  1.00  0.00              
ATOM    466  CA  GLU    61      32.198   4.825  -4.230  1.00  0.00              
ATOM    467  C   GLU    61      33.523   5.470  -4.605  1.00  0.00              
ATOM    468  O   GLU    61      33.618   6.675  -4.811  1.00  0.00              
ATOM    469  N   GLY    62      34.554   4.660  -4.719  1.00  0.00              
ATOM    470  CA  GLY    62      35.858   5.219  -4.957  1.00  0.00              
ATOM    471  C   GLY    62      36.158   5.372  -6.414  1.00  0.00              
ATOM    472  O   GLY    62      35.814   4.506  -7.200  1.00  0.00              
ATOM    473  N   HIS    63      36.797   6.486  -6.757  1.00  0.00              
ATOM    474  CA  HIS    63      37.380   6.690  -8.078  1.00  0.00              
ATOM    475  C   HIS    63      38.855   7.060  -8.002  1.00  0.00              
ATOM    476  O   HIS    63      39.236   7.955  -7.246  1.00  0.00              
ATOM    477  N   SER    64      39.678   6.424  -8.824  1.00  0.00              
ATOM    478  CA  SER    64      41.099   6.720  -8.842  1.00  0.00              
ATOM    479  C   SER    64      41.430   8.141  -9.251  1.00  0.00              
ATOM    480  O   SER    64      40.826   8.699 -10.160  1.00  0.00              
ATOM    481  N   GLY    65      42.395   8.730  -8.560  1.00  0.00              
ATOM    482  CA  GLY    65      42.899  10.027  -8.941  1.00  0.00              
ATOM    483  C   GLY    65      41.982  11.180  -8.599  1.00  0.00              
ATOM    484  O   GLY    65      42.327  12.323  -8.900  1.00  0.00              
ATOM    485  N   TRP    66      40.831  10.888  -7.989  1.00  0.00              
ATOM    486  CA  TRP    66      39.874  11.907  -7.542  1.00  0.00              
ATOM    487  C   TRP    66      40.467  12.813  -6.486  1.00  0.00              
ATOM    488  O   TRP    66      41.288  12.392  -5.687  1.00  0.00              
TER
END
