
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0360AL381_5-D1
# Molecule2: number of CA atoms   97 (  785),  selected   97 , name T0360_D1.pdb
# PARAMETERS: T0360AL381_5-D1.T0360_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      K      20           -
LGA    -       -      K      21           -
LGA    -       -      K      22           -
LGA    -       -      Q      23           -
LGA    -       -      T      24           -
LGA    -       -      E      25           -
LGA    -       -      M      26           -
LGA    -       -      I      27           -
LGA    -       -      A      28           -
LGA    -       -      D      29           -
LGA    -       -      H      30           -
LGA    -       -      I      31           -
LGA    -       -      Y      32           -
LGA    -       -      G      33           -
LGA    -       -      K      34           -
LGA    -       -      Y      35           -
LGA    -       -      D      36           -
LGA    -       -      V      37           -
LGA    -       -      F      38           -
LGA    -       -      K      39           -
LGA    -       -      R      40           -
LGA    -       -      F      41           -
LGA    -       -      K      42           -
LGA    -       -      P      43           -
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      L      46           -
LGA    -       -      G      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      Q      50           -
LGA    -       -      D      51           -
LGA    -       -      L      52           -
LGA    -       -      I      53           -
LGA    Y      35      A      54          3.355
LGA    D      36      A      55           -
LGA    V      37      L      56           -
LGA    -       -      P      57           -
LGA    -       -      Q      58           -
LGA    F      38      Y      59          5.654
LGA    K      39      D      60          2.703
LGA    R      40      A      61          2.203
LGA    F      41      A      62          1.483
LGA    K      42      L      63          1.616
LGA    P      43      I      64          1.146
LGA    L      44      A      65          1.324
LGA    A      45      R      66          1.375
LGA    L      46      V      67          2.076
LGA    G      47      L      68          2.631
LGA    I      48      A      69          1.231
LGA    D      49      N      70          1.543
LGA    Q      50      H      71          1.626
LGA    D      51      C      72          1.992
LGA    L      52      R      73          2.107
LGA    I      53      R      74          1.730
LGA    -       -      P      75           -
LGA    A      54      R      76          3.187
LGA    A      55      Y      77          2.911
LGA    L      56      L      78          1.737
LGA    P      57      K      79          1.518
LGA    -       -      A      80           -
LGA    -       -      L      81           -
LGA    Q      58      A      82          1.864
LGA    -       -      R      83           -
LGA    -       -      G      84           -
LGA    -       -      G      85           -
LGA    -       -      K      86           -
LGA    -       -      R      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -
LGA    -       -      L      90           -
LGA    -       -      N      91           -
LGA    -       -      N      92           -
LGA    -       -      R      93           -
LGA    -       -      F      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      E      97           -
LGA    -       -      V      98           -
LGA    -       -      T      99           -
LGA    -       -      P     100           -
LGA    -       -      E     101           -
LGA    -       -      E     102           -
LGA    -       -      Q     103           -
LGA    -       -      A     104           -
LGA    -       -      I     105           -
LGA    -       -      A     106           -
LGA    -       -      Q     107           -
LGA    -       -      N     108           -
LGA    -       -      H     109           -
LGA    -       -      P     110           -
LGA    -       -      F     111           -
LGA    Y      59      V     112          1.307
LGA    D      60      Q     113          2.432
LGA    A      61      Q     114          1.757
LGA    A      62      A     115           -
LGA    L      63      L     116           -
LGA    I      64      -       -           -
LGA    A      65      -       -           -
LGA    R      66      -       -           -
LGA    V      67      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   33   97    5.0     25    2.30     4.00     21.718     1.041

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.337706 * X  +   0.293723 * Y  +   0.894249 * Z  + -107.726311
  Y_new =  -0.065545 * X  +   0.955096 * Y  +  -0.288956 * Z  +  19.619602
  Z_new =  -0.938967 * X  +   0.038968 * Y  +   0.341793 * Z  + -26.028496 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.113521   -3.028072  [ DEG:     6.5042   -173.4958 ]
  Theta =   1.219615    1.921978  [ DEG:    69.8788    110.1212 ]
  Phi   =  -0.191706    2.949886  [ DEG:   -10.9840    169.0160 ]
 
# 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: T0360AL381_5-D1                               
REMARK     2: T0360_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0360AL381_5-D1.T0360_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   33   97   5.0   25   2.30    4.00  21.718
REMARK  ---------------------------------------------------------- 
MOLECULE T0360AL381_5-D1
REMARK Aligment from pdb entry: 2awhA
ATOM      1  N   TYR    35     -85.880  -1.792 -25.824  1.00  0.00              
ATOM      2  CA  TYR    35     -86.616  -1.730 -24.564  1.00  0.00              
ATOM      3  C   TYR    35     -87.579  -0.556 -24.658  1.00  0.00              
ATOM      4  O   TYR    35     -87.345   0.391 -25.412  1.00  0.00              
ATOM      5  N   ASP    36     -88.680  -0.626 -23.938  1.00  0.00              
ATOM      6  CA  ASP    36     -89.576   0.508 -23.896  1.00  0.00              
ATOM      7  C   ASP    36     -88.777   1.689 -23.330  1.00  0.00              
ATOM      8  O   ASP    36     -87.889   1.508 -22.483  1.00  0.00              
ATOM      9  N   VAL    37     -89.105   2.883 -23.813  1.00  0.00              
ATOM     10  CA  VAL    37     -88.412   4.104 -23.460  1.00  0.00              
ATOM     11  C   VAL    37     -88.413   4.335 -21.948  1.00  0.00              
ATOM     12  O   VAL    37     -87.448   4.872 -21.409  1.00  0.00              
ATOM     13  N   PHE    38     -89.482   3.933 -21.259  1.00  0.00              
ATOM     14  CA  PHE    38     -89.507   4.087 -19.799  1.00  0.00              
ATOM     15  C   PHE    38     -88.473   3.192 -19.114  1.00  0.00              
ATOM     16  O   PHE    38     -87.869   3.597 -18.118  1.00  0.00              
ATOM     17  N   LYS    39     -88.274   1.980 -19.630  1.00  0.00              
ATOM     18  CA  LYS    39     -87.196   1.126 -19.090  1.00  0.00              
ATOM     19  C   LYS    39     -85.803   1.669 -19.368  1.00  0.00              
ATOM     20  O   LYS    39     -84.933   1.566 -18.505  1.00  0.00              
ATOM     21  N   ARG    40     -85.570   2.230 -20.573  1.00  0.00              
ATOM     22  CA  ARG    40     -84.303   2.866 -20.903  1.00  0.00              
ATOM     23  C   ARG    40     -83.973   3.978 -19.913  1.00  0.00              
ATOM     24  O   ARG    40     -82.819   4.077 -19.450  1.00  0.00              
ATOM     25  N   PHE    41     -84.977   4.794 -19.581  1.00  0.00              
ATOM     26  CA  PHE    41     -84.834   5.900 -18.599  1.00  0.00              
ATOM     27  C   PHE    41     -84.506   5.446 -17.155  1.00  0.00              
ATOM     28  O   PHE    41     -83.664   6.054 -16.470  1.00  0.00              
ATOM     29  N   LYS    42     -85.180   4.392 -16.696  1.00  0.00              
ATOM     30  CA  LYS    42     -84.850   3.760 -15.413  1.00  0.00              
ATOM     31  C   LYS    42     -83.405   3.223 -15.395  1.00  0.00              
ATOM     32  O   LYS    42     -82.694   3.399 -14.422  1.00  0.00              
ATOM     33  N   PRO    43     -82.979   2.572 -16.477  1.00  0.00              
ATOM     34  CA  PRO    43     -81.610   2.038 -16.564  1.00  0.00              
ATOM     35  C   PRO    43     -80.561   3.137 -16.501  1.00  0.00              
ATOM     36  O   PRO    43     -79.538   3.002 -15.822  1.00  0.00              
ATOM     37  N   LEU    44     -80.780   4.227 -17.216  1.00  0.00              
ATOM     38  CA  LEU    44     -79.839   5.365 -17.175  1.00  0.00              
ATOM     39  C   LEU    44     -79.909   6.057 -15.808  1.00  0.00              
ATOM     40  O   LEU    44     -78.890   6.317 -15.168  1.00  0.00              
ATOM     41  N   ALA    45     -81.121   6.296 -15.324  1.00  0.00              
ATOM     42  CA  ALA    45     -81.282   6.930 -14.001  1.00  0.00              
ATOM     43  C   ALA    45     -80.414   6.248 -12.965  1.00  0.00              
ATOM     44  O   ALA    45     -79.601   6.899 -12.335  1.00  0.00              
ATOM     45  N   LEU    46     -80.563   4.939 -12.802  1.00  0.00              
ATOM     46  CA  LEU    46     -79.838   4.196 -11.754  1.00  0.00              
ATOM     47  C   LEU    46     -78.445   3.697 -12.099  1.00  0.00              
ATOM     48  O   LEU    46     -77.672   3.338 -11.197  1.00  0.00              
ATOM     49  N   GLY    47     -78.099   3.710 -13.396  1.00  0.00              
ATOM     50  CA  GLY    47     -76.774   3.268 -13.835  1.00  0.00              
ATOM     51  C   GLY    47     -75.727   4.314 -14.215  1.00  0.00              
ATOM     52  O   GLY    47     -74.525   4.016 -14.131  1.00  0.00              
ATOM     53  N   ILE    48     -76.132   5.529 -14.614  1.00  0.00              
ATOM     54  CA  ILE    48     -75.144   6.500 -15.156  1.00  0.00              
ATOM     55  C   ILE    48     -74.038   6.875 -14.201  1.00  0.00              
ATOM     56  O   ILE    48     -72.884   6.894 -14.606  1.00  0.00              
ATOM     57  N   ASP    49     -74.379   7.148 -12.922  1.00  0.00              
ATOM     58  CA  ASP    49     -73.342   7.426 -11.923  1.00  0.00              
ATOM     59  C   ASP    49     -72.435   6.255 -11.537  1.00  0.00              
ATOM     60  O   ASP    49     -71.269   6.482 -11.255  1.00  0.00              
ATOM     61  N   GLN    50     -72.937   5.025 -11.466  1.00  0.00              
ATOM     62  CA  GLN    50     -72.051   3.887 -11.285  1.00  0.00              
ATOM     63  C   GLN    50     -71.046   3.866 -12.460  1.00  0.00              
ATOM     64  O   GLN    50     -69.845   3.645 -12.270  1.00  0.00              
ATOM     65  N   ASP    51     -71.553   4.075 -13.668  1.00  0.00              
ATOM     66  CA  ASP    51     -70.659   4.030 -14.856  1.00  0.00              
ATOM     67  C   ASP    51     -69.663   5.194 -14.788  1.00  0.00              
ATOM     68  O   ASP    51     -68.465   5.032 -15.060  1.00  0.00              
ATOM     69  N   LEU    52     -70.158   6.362 -14.374  1.00  0.00              
ATOM     70  CA  LEU    52     -69.327   7.555 -14.267  1.00  0.00              
ATOM     71  C   LEU    52     -68.155   7.350 -13.305  1.00  0.00              
ATOM     72  O   LEU    52     -67.019   7.694 -13.617  1.00  0.00              
ATOM     73  N   ILE    53     -68.453   6.816 -12.118  1.00  0.00              
ATOM     74  CA  ILE    53     -67.436   6.659 -11.098  1.00  0.00              
ATOM     75  C   ILE    53     -66.466   5.533 -11.422  1.00  0.00              
ATOM     76  O   ILE    53     -65.332   5.603 -11.029  1.00  0.00              
ATOM     77  N   ALA    54     -66.903   4.503 -12.138  1.00  0.00              
ATOM     78  CA  ALA    54     -65.965   3.484 -12.704  1.00  0.00              
ATOM     79  C   ALA    54     -64.965   4.074 -13.728  1.00  0.00              
ATOM     80  O   ALA    54     -63.748   3.753 -13.680  1.00  0.00              
ATOM     81  N   ALA    55     -65.460   4.908 -14.647  1.00  0.00              
ATOM     82  CA  ALA    55     -64.611   5.572 -15.683  1.00  0.00              
ATOM     83  C   ALA    55     -63.734   6.693 -15.138  1.00  0.00              
ATOM     84  O   ALA    55     -62.655   6.983 -15.684  1.00  0.00              
ATOM     85  N   LEU    56     -64.188   7.319 -14.050  1.00  0.00              
ATOM     86  CA  LEU    56     -63.362   8.252 -13.283  1.00  0.00              
ATOM     87  C   LEU    56     -61.962   7.688 -12.978  1.00  0.00              
ATOM     88  O   LEU    56     -60.957   8.395 -13.103  1.00  0.00              
ATOM     89  N   PRO    57     -61.902   6.426 -12.574  1.00  0.00              
ATOM     90  CA  PRO    57     -60.639   5.772 -12.248  1.00  0.00              
ATOM     91  C   PRO    57     -59.611   5.910 -13.373  1.00  0.00              
ATOM     92  O   PRO    57     -58.430   6.036 -13.108  1.00  0.00              
ATOM     93  N   GLN    58     -60.081   5.897 -14.619  1.00  0.00              
ATOM     94  CA  GLN    58     -59.241   6.050 -15.813  1.00  0.00              
ATOM     95  C   GLN    58     -58.423   7.333 -15.852  1.00  0.00              
ATOM     96  O   GLN    58     -57.355   7.360 -16.465  1.00  0.00              
ATOM     97  N   TYR    59     -57.692   9.262 -13.033  1.00  0.00              
ATOM     98  CA  TYR    59     -57.264   9.512 -11.661  1.00  0.00              
ATOM     99  C   TYR    59     -55.913   8.825 -11.380  1.00  0.00              
ATOM    100  O   TYR    59     -55.598   7.775 -11.961  1.00  0.00              
ATOM    101  N   ASP    60     -55.088   9.473 -10.563  1.00  0.00              
ATOM    102  CA  ASP    60     -54.055   8.778  -9.805  1.00  0.00              
ATOM    103  C   ASP    60     -54.173   9.237  -8.331  1.00  0.00              
ATOM    104  O   ASP    60     -55.047  10.072  -8.007  1.00  0.00              
ATOM    105  N   ALA    61     -53.333   8.692  -7.443  1.00  0.00              
ATOM    106  CA  ALA    61     -53.361   9.034  -6.011  1.00  0.00              
ATOM    107  C   ALA    61     -53.253  10.543  -5.754  1.00  0.00              
ATOM    108  O   ALA    61     -53.625  11.018  -4.684  1.00  0.00              
ATOM    109  N   ALA    62     -52.744  11.272  -6.753  1.00  0.00              
ATOM    110  CA  ALA    62     -52.428  12.708  -6.657  1.00  0.00              
ATOM    111  C   ALA    62     -53.530  13.662  -7.150  1.00  0.00              
ATOM    112  O   ALA    62     -53.495  14.862  -6.866  1.00  0.00              
ATOM    113  N   LEU    63     -54.476  13.158  -7.938  1.00  0.00              
ATOM    114  CA  LEU    63     -55.427  14.069  -8.596  1.00  0.00              
ATOM    115  C   LEU    63     -56.048  13.515  -9.854  1.00  0.00              
ATOM    116  O   LEU    63     -55.980  12.320 -10.102  1.00  0.00              
ATOM    117  N   ILE    64     -56.685  14.378 -10.641  1.00  0.00              
ATOM    118  CA  ILE    64     -57.429  13.897 -11.803  1.00  0.00              
ATOM    119  C   ILE    64     -57.313  14.812 -13.005  1.00  0.00              
ATOM    120  O   ILE    64     -57.278  16.030 -12.851  1.00  0.00              
ATOM    121  N   ALA    65     -57.250  14.220 -14.194  1.00  0.00              
ATOM    122  CA  ALA    65     -57.305  14.994 -15.443  1.00  0.00              
ATOM    123  C   ALA    65     -58.664  15.637 -15.681  1.00  0.00              
ATOM    124  O   ALA    65     -59.693  14.979 -15.523  1.00  0.00              
ATOM    125  N   ARG    66     -58.664  16.904 -16.095  1.00  0.00              
ATOM    126  CA  ARG    66     -59.885  17.603 -16.476  1.00  0.00              
ATOM    127  C   ARG    66     -59.768  18.170 -17.899  1.00  0.00              
ATOM    128  O   ARG    66     -58.664  18.204 -18.479  1.00  0.00              
ATOM    129  N   VAL    67     -60.906  18.577 -18.458  1.00  0.00              
ATOM    130  CA  VAL    67     -60.981  19.174 -19.801  1.00  0.00              
ATOM    131  C   VAL    67     -60.126  18.485 -20.863  1.00  0.00              
ATOM    132  O   VAL    67     -59.218  19.084 -21.441  1.00  0.00              
END
