
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0329AL242_4-D2
# Molecule2: number of CA atoms   92 (  716),  selected   92 , name T0329_D2.pdb
# PARAMETERS: T0329AL242_4-D2.T0329_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    T      17      T      17           -
LGA    S      18      S      18           -
LGA    -       -      A      19           -
LGA    -       -      D      20           -
LGA    -       -      L      21           -
LGA    -       -      T      22           -
LGA    -       -      S      23           -
LGA    A      19      A      24           #
LGA    D      20      L      25           -
LGA    -       -      N      26           -
LGA    -       -      Y      27           -
LGA    -       -      A      28           -
LGA    Q      86      F      29           #
LGA    T      87      E      30          3.149
LGA    -       -      Q      31           -
LGA    -       -      T      32           -
LGA    -       -      G      33           -
LGA    -       -      H      34           -
LGA    E      88      R      35          4.543
LGA    V      89      H      36          3.048
LGA    N      90      D      37          2.950
LGA    R      91      F      38          0.726
LGA    V      92      T      39           #
LGA    -       -      V      40           -
LGA    -       -      E      41           -
LGA    -       -      D      42           -
LGA    L      93      I      43          1.746
LGA    -       -      K      44           -
LGA    -       -      N      45           -
LGA    E      94      F      46          3.785
LGA    V      95      F      47          2.717
LGA    F      96      G      48          3.308
LGA    K      97      S      49          1.724
LGA    P      98      G      50          2.039
LGA    Y      99      V      51          1.503
LGA    -       -      V      52           -
LGA    -       -      V      53           -
LGA    Y     100      A      54          4.313
LGA    -       -      V      55           -
LGA    A     101      T      56           #
LGA    D     102      R      57           #
LGA    H     103      A      58          3.558
LGA    C     104      L      59          1.804
LGA    -       -      A      60           -
LGA    -       -      Y      61           -
LGA    -       -      E      62           -
LGA    -       -      A      63           -
LGA    -       -      G      64           -
LGA    -       -      S      65           -
LGA    -       -      S      66           -
LGA    -       -      R      67           -
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      L      70           -
LGA    -       -      V      71           -
LGA    -       -      A      72           -
LGA    -       -      F      73           -
LGA    -       -      G      74           -
LGA    -       -      T      75           -
LGA    -       -      K      76           -
LGA    -       -      D      77           -
LGA    -       -      E      78           -
LGA    -       -      Q      79           -
LGA    -       -      I      80           -
LGA    -       -      P      81           -
LGA    -       -      E      82           -
LGA    -       -      A      83           -
LGA    Q     105      V      84           #
LGA    -       -      T      85           -
LGA    -       -      Q      86           -
LGA    -       -      T      87           -
LGA    -       -      E      88           -
LGA    I     106      V      89          4.532
LGA    K     107      N      90           #
LGA    -       -      R      91           -
LGA    -       -      V      92           -
LGA    T     108      L      93          4.210
LGA    -       -      E      94           -
LGA    -       -      V      95           -
LGA    -       -      F      96           -
LGA    -       -      K      97           -
LGA    -       -      P      98           -
LGA    -       -      Y      99           -
LGA    -       -      Y     100           -
LGA    -       -      A     101           -
LGA    -       -      D     102           -
LGA    -       -      H     103           -
LGA    -       -      C     104           -
LGA    -       -      Q     105           -
LGA    -       -      I     106           -
LGA    -       -      K     107           -
LGA    -       -      T     108           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   27   92    5.0     17    3.13     0.00     12.470     0.526

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.533169 * X  +  -0.558941 * Y  +  -0.635071 * Z  +  -3.340812
  Y_new =   0.628060 * X  +   0.764438 * Y  +  -0.145517 * Z  +  25.709568
  Z_new =   0.566808 * X  +  -0.321278 * Y  +   0.758623 * Z  +  44.634888 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.400600    2.740993  [ DEG:   -22.9527    157.0473 ]
  Theta =  -0.602626   -2.538966  [ DEG:   -34.5279   -145.4721 ]
  Phi   =   0.866933   -2.274660  [ DEG:    49.6716   -130.3284 ]
 
# 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: T0329AL242_4-D2                               
REMARK     2: T0329_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0329AL242_4-D2.T0329_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27   92   5.0   17   3.13    0.00  12.470
REMARK  ---------------------------------------------------------- 
MOLECULE T0329AL242_4-D2
REMARK Aligment from pdb entry: 1u7p_A
ATOM     65  N   THR    17     -15.129  28.494  44.201  1.00  0.00              
ATOM     66  CA  THR    17     -16.532  28.118  44.069  1.00  0.00              
ATOM     67  C   THR    17     -17.015  27.459  45.346  1.00  0.00              
ATOM     68  O   THR    17     -16.212  27.154  46.229  1.00  0.00              
ATOM     69  N   SER    18     -18.329  27.257  45.441  1.00  0.00              
ATOM     70  CA  SER    18     -18.921  26.563  46.583  1.00  0.00              
ATOM     71  C   SER    18     -19.070  25.114  46.128  1.00  0.00              
ATOM     72  O   SER    18     -19.696  24.847  45.100  1.00  0.00              
ATOM     73  N   ALA    19     -18.497  24.185  46.883  1.00  0.00              
ATOM     74  CA  ALA    19     -18.574  22.778  46.518  1.00  0.00              
ATOM     75  C   ALA    19     -20.001  22.214  46.572  1.00  0.00              
ATOM     76  O   ALA    19     -20.294  21.205  45.934  1.00  0.00              
ATOM     77  N   ASP    20     -20.893  22.872  47.312  1.00  0.00              
ATOM     78  CA  ASP    20     -22.273  22.398  47.417  1.00  0.00              
ATOM     79  C   ASP    20     -23.205  23.083  46.416  1.00  0.00              
ATOM     80  O   ASP    20     -24.415  22.861  46.439  1.00  0.00              
ATOM     81  N   GLN    86     -22.640  23.892  45.525  1.00  0.00              
ATOM     82  CA  GLN    86     -23.452  24.625  44.564  1.00  0.00              
ATOM     83  C   GLN    86     -23.008  24.620  43.102  1.00  0.00              
ATOM     84  O   GLN    86     -23.788  24.280  42.213  1.00  0.00              
ATOM     85  N   THR    87     -21.762  25.006  42.857  1.00  0.00              
ATOM     86  CA  THR    87     -21.248  25.118  41.497  1.00  0.00              
ATOM     87  C   THR    87     -20.783  23.853  40.791  1.00  0.00              
ATOM     88  O   THR    87     -20.540  23.871  39.587  1.00  0.00              
ATOM     89  N   GLU    88     -20.651  22.762  41.529  1.00  0.00              
ATOM     90  CA  GLU    88     -20.193  21.515  40.941  1.00  0.00              
ATOM     91  C   GLU    88     -21.141  20.368  41.233  1.00  0.00              
ATOM     92  O   GLU    88     -22.044  20.487  42.057  1.00  0.00              
ATOM     93  N   VAL    89     -20.929  19.248  40.554  1.00  0.00              
ATOM     94  CA  VAL    89     -21.776  18.078  40.734  1.00  0.00              
ATOM     95  C   VAL    89     -20.896  16.850  40.993  1.00  0.00              
ATOM     96  O   VAL    89     -20.393  16.224  40.060  1.00  0.00              
ATOM     97  N   ASN    90     -20.681  16.518  42.280  1.00  0.00              
ATOM     98  CA  ASN    90     -19.869  15.384  42.744  1.00  0.00              
ATOM     99  C   ASN    90     -20.523  14.049  42.379  1.00  0.00              
ATOM    100  O   ASN    90     -21.718  13.995  42.120  1.00  0.00              
ATOM    101  N   ARG    91     -19.748  12.956  42.371  1.00  0.00              
ATOM    102  CA  ARG    91     -18.315  12.880  42.679  1.00  0.00              
ATOM    103  C   ARG    91     -17.434  13.444  41.569  1.00  0.00              
ATOM    104  O   ARG    91     -17.913  13.781  40.480  1.00  0.00              
ATOM    105  N   VAL    92     -16.138  13.529  41.851  1.00  0.00              
ATOM    106  CA  VAL    92     -15.172  14.039  40.892  1.00  0.00              
ATOM    107  C   VAL    92     -14.247  12.911  40.445  1.00  0.00              
ATOM    108  O   VAL    92     -14.285  11.815  40.996  1.00  0.00              
ATOM    109  N   LEU    93     -13.413  13.192  39.448  1.00  0.00              
ATOM    110  CA  LEU    93     -12.470  12.202  38.935  1.00  0.00              
ATOM    111  C   LEU    93     -11.420  12.880  38.063  1.00  0.00              
ATOM    112  O   LEU    93     -11.687  13.917  37.455  1.00  0.00              
ATOM    113  N   GLU    94     -10.228  12.294  38.003  1.00  0.00              
ATOM    114  CA  GLU    94      -9.170  12.845  37.168  1.00  0.00              
ATOM    115  C   GLU    94      -9.400  12.399  35.733  1.00  0.00              
ATOM    116  O   GLU    94      -9.660  11.226  35.473  1.00  0.00              
ATOM    117  N   VAL    95      -9.309  13.343  34.808  1.00  0.00              
ATOM    118  CA  VAL    95      -9.508  13.053  33.397  1.00  0.00              
ATOM    119  C   VAL    95      -8.200  12.540  32.799  1.00  0.00              
ATOM    120  O   VAL    95      -7.159  12.553  33.458  1.00  0.00              
ATOM    121  N   PHE    96      -8.257  12.085  31.552  1.00  0.00              
ATOM    122  CA  PHE    96      -7.074  11.564  30.878  1.00  0.00              
ATOM    123  C   PHE    96      -6.017  12.647  30.680  1.00  0.00              
ATOM    124  O   PHE    96      -4.826  12.350  30.598  1.00  0.00              
ATOM    125  N   LYS    97      -6.457  13.900  30.604  1.00  0.00              
ATOM    126  CA  LYS    97      -5.539  15.019  30.410  1.00  0.00              
ATOM    127  C   LYS    97      -4.995  15.564  31.729  1.00  0.00              
ATOM    128  O   LYS    97      -4.419  16.650  31.771  1.00  0.00              
ATOM    129  N   PRO    98      -5.187  14.807  32.805  1.00  0.00              
ATOM    130  CA  PRO    98      -4.689  15.221  34.110  1.00  0.00              
ATOM    131  C   PRO    98      -5.575  16.153  34.923  1.00  0.00              
ATOM    132  O   PRO    98      -5.312  16.384  36.101  1.00  0.00              
ATOM    133  N   TYR    99      -6.622  16.690  34.307  1.00  0.00              
ATOM    134  CA  TYR    99      -7.511  17.602  35.009  1.00  0.00              
ATOM    135  C   TYR    99      -8.471  16.885  35.958  1.00  0.00              
ATOM    136  O   TYR    99      -8.660  15.671  35.877  1.00  0.00              
ATOM    137  N   TYR   100      -9.060  17.643  36.875  1.00  0.00              
ATOM    138  CA  TYR   100     -10.044  17.096  37.797  1.00  0.00              
ATOM    139  C   TYR   100     -11.381  17.512  37.201  1.00  0.00              
ATOM    140  O   TYR   100     -11.555  18.660  36.785  1.00  0.00              
ATOM    141  N   ALA   101     -12.320  16.580  37.143  1.00  0.00              
ATOM    142  CA  ALA   101     -13.617  16.884  36.558  1.00  0.00              
ATOM    143  C   ALA   101     -14.766  16.405  37.429  1.00  0.00              
ATOM    144  O   ALA   101     -14.598  15.505  38.250  1.00  0.00              
ATOM    145  N   ASP   102     -15.933  17.011  37.239  1.00  0.00              
ATOM    146  CA  ASP   102     -17.121  16.621  37.982  1.00  0.00              
ATOM    147  C   ASP   102     -18.071  15.966  36.981  1.00  0.00              
ATOM    148  O   ASP   102     -17.771  15.909  35.785  1.00  0.00              
ATOM    149  N   HIS   103     -19.205  15.473  37.463  1.00  0.00              
ATOM    150  CA  HIS   103     -20.183  14.794  36.613  1.00  0.00              
ATOM    151  C   HIS   103     -20.633  15.556  35.365  1.00  0.00              
ATOM    152  O   HIS   103     -21.078  14.945  34.393  1.00  0.00              
ATOM    153  N   CYS   104     -20.530  16.880  35.387  1.00  0.00              
ATOM    154  CA  CYS   104     -20.953  17.679  34.241  1.00  0.00              
ATOM    155  C   CYS   104     -19.799  18.122  33.351  1.00  0.00              
ATOM    156  O   CYS   104     -19.929  19.071  32.575  1.00  0.00              
ATOM    157  N   GLN   105     -18.674  17.424  33.468  1.00  0.00              
ATOM    158  CA  GLN   105     -17.514  17.733  32.653  1.00  0.00              
ATOM    159  C   GLN   105     -16.826  19.056  32.938  1.00  0.00              
ATOM    160  O   GLN   105     -16.060  19.549  32.107  1.00  0.00              
ATOM    161  N   ILE   106     -17.086  19.638  34.104  1.00  0.00              
ATOM    162  CA  ILE   106     -16.459  20.906  34.460  1.00  0.00              
ATOM    163  C   ILE   106     -15.004  20.718  34.869  1.00  0.00              
ATOM    164  O   ILE   106     -14.652  19.755  35.544  1.00  0.00              
ATOM    165  N   LYS   107     -14.165  21.654  34.456  1.00  0.00              
ATOM    166  CA  LYS   107     -12.760  21.607  34.814  1.00  0.00              
ATOM    167  C   LYS   107     -12.696  22.202  36.219  1.00  0.00              
ATOM    168  O   LYS   107     -13.024  23.368  36.407  1.00  0.00              
ATOM    169  N   THR   108     -12.291  21.401  37.200  1.00  0.00              
ATOM    170  CA  THR   108     -12.209  21.878  38.580  1.00  0.00              
ATOM    171  C   THR   108     -10.773  22.286  38.892  1.00  0.00              
ATOM    172  O   THR   108      -9.862  21.479  38.761  1.00  0.00              
END
