
#######################################################
#                                                     #
#                        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   47 (  188),  selected   47 , name T0350AL381_3
# Molecule2: number of CA atoms  109 ( 1798),  selected  109 , name T0350.pdb
# PARAMETERS: T0350AL381_3.T0350.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      N       2           -
LGA    -       -      I       3           -
LGA    -       -      E       4           -
LGA    -       -      R       5           -
LGA    -       -      L       6           -
LGA    -       -      T       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      Q      10           -
LGA    -       -      P      11           -
LGA    -       -      V      12           -
LGA    -       -      W      13           -
LGA    -       -      D      14           -
LGA    -       -      R      15           -
LGA    -       -      Y      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      Q      19           -
LGA    -       -      I      20           -
LGA    -       -      H      21           -
LGA    -       -      N      22           -
LGA    -       -      Q      23           -
LGA    -       -      K      24           -
LGA    -       -      D      25           -
LGA    -       -      N      26           -
LGA    -       -      D      27           -
LGA    -       -      N      28           -
LGA    -       -      E      29           -
LGA    -       -      V      30           -
LGA    -       -      P      31           -
LGA    -       -      V      32           -
LGA    -       -      H      33           -
LGA    -       -      Q      34           -
LGA    -       -      V      35           -
LGA    V      35      S      36          4.688
LGA    S      36      Y      37          2.422
LGA    Y      37      -       -           -
LGA    T      38      T      38          1.373
LGA    N      39      N      39          1.035
LGA    L      40      L      40          0.286
LGA    A      41      A      41          0.776
LGA    E      42      E      42          1.029
LGA    M      43      M      43          1.110
LGA    V      44      V      44          1.272
LGA    G      45      G      45          1.621
LGA    E      46      E      46          0.906
LGA    M      47      M      47          1.054
LGA    N      48      N      48          1.182
LGA    K      49      K      49          2.318
LGA    L      50      L      50          2.736
LGA    L      51      L      51          3.422
LGA    E      52      E      52          3.624
LGA    -       -      P      53           -
LGA    -       -      S      54           -
LGA    -       -      Q      55           -
LGA    -       -      V      56           -
LGA    P      53      H      57          3.510
LGA    S      54      L      58          4.787
LGA    Q      55      K      59          2.351
LGA    V      56      F      60          1.900
LGA    H      57      E      61          1.941
LGA    L      58      L      62          0.864
LGA    F      60      H      63          1.848
LGA    E      61      D      64          1.544
LGA    L      62      K      65          1.473
LGA    H      63      L      66          1.013
LGA    D      64      -       -           -
LGA    K      65      -       -           -
LGA    L      66      -       -           -
LGA    N      67      -       -           -
LGA    E      68      -       -           -
LGA    Y      69      N      67          2.610
LGA    Y      70      E      68          2.401
LGA    V      71      Y      69          2.250
LGA    K      72      Y      70          1.816
LGA    V      73      V      71          0.886
LGA    I      74      K      72          1.788
LGA    E      75      V      73          2.091
LGA    D      76      I      74          1.772
LGA    S      77      E      75          0.304
LGA    T      78      D      76          2.829
LGA    -       -      S      77           -
LGA    -       -      T      78           -
LGA    N      79      N      79          0.846
LGA    E      80      E      80          1.679
LGA    V      81      V      81          1.281
LGA    I      82      I      82          3.119
LGA    -       -      R      83           -
LGA    -       -      E      84           -
LGA    -       -      I      85           -
LGA    -       -      P      86           -
LGA    -       -      P      87           -
LGA    -       -      K      88           -
LGA    -       -      R      89           -
LGA    -       -      W      90           -
LGA    -       -      L      91           -
LGA    -       -      D      92           -
LGA    -       -      F      93           -
LGA    -       -      Y      94           -
LGA    -       -      A      95           -
LGA    -       -      A      96           -
LGA    -       -      M      97           -
LGA    -       -      T      98           -
LGA    -       -      E      99           -
LGA    -       -      F     100           -
LGA    -       -      L     101           -
LGA    -       -      G     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      V     105           -
LGA    -       -      D     106           -
LGA    -       -      E     107           -
LGA    -       -      K     108           -
LGA    -       -      K     109           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   47  109    5.0     41    2.17    51.22     29.952     1.809

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.447582 * X  +  -0.489622 * Y  +   0.748292 * Z  +  33.825493
  Y_new =  -0.762376 * X  +   0.646286 * Y  +  -0.033129 * Z  +  -5.442805
  Z_new =  -0.467389 * X  +  -0.585308 * Y  +  -0.662542 * Z  +   1.415709 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.418009    0.723584  [ DEG:  -138.5417     41.4583 ]
  Theta =   0.486335    2.655257  [ DEG:    27.8650    152.1350 ]
  Phi   =  -2.101668    1.039925  [ DEG:  -120.4167     59.5833 ]
 
# 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: T0350AL381_3                                  
REMARK     2: T0350.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350AL381_3.T0350.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   47  109   5.0   41   2.17   51.22  29.952
REMARK  ---------------------------------------------------------- 
MOLECULE T0350AL381_3
REMARK Aligment from pdb entry: 1ylxA
ATOM      1  N   VAL    35       1.100  11.843 -36.221  1.00  0.00              
ATOM      2  CA  VAL    35      -0.017  11.579 -35.320  1.00  0.00              
ATOM      3  C   VAL    35       0.338  10.460 -34.347  1.00  0.00              
ATOM      4  O   VAL    35       0.077  10.560 -33.150  1.00  0.00              
ATOM      5  N   SER    36       0.935   9.395 -34.871  1.00  0.00              
ATOM      6  CA  SER    36       1.335   8.260 -34.044  1.00  0.00              
ATOM      7  C   SER    36       2.382   8.683 -33.015  1.00  0.00              
ATOM      8  O   SER    36       2.269   8.355 -31.828  1.00  0.00              
ATOM      9  N   TYR    37       3.392   9.421 -33.466  1.00  0.00              
ATOM     10  CA  TYR    37       4.445   9.885 -32.570  1.00  0.00              
ATOM     11  C   TYR    37       3.862  10.731 -31.441  1.00  0.00              
ATOM     12  O   TYR    37       4.197  10.534 -30.279  1.00  0.00              
ATOM     13  N   THR    38       2.988  11.673 -31.780  1.00  0.00              
ATOM     14  CA  THR    38       2.386  12.517 -30.756  1.00  0.00              
ATOM     15  C   THR    38       1.600  11.717 -29.720  1.00  0.00              
ATOM     16  O   THR    38       1.560  12.090 -28.551  1.00  0.00              
ATOM     17  N   ASN    39       0.973  10.618 -30.133  1.00  0.00              
ATOM     18  CA  ASN    39       0.227   9.807 -29.183  1.00  0.00              
ATOM     19  C   ASN    39       1.200   9.140 -28.207  1.00  0.00              
ATOM     20  O   ASN    39       0.894   8.973 -27.025  1.00  0.00              
ATOM     21  N   LEU    40       2.374   8.756 -28.697  1.00  0.00              
ATOM     22  CA  LEU    40       3.360   8.146 -27.813  1.00  0.00              
ATOM     23  C   LEU    40       3.917   9.225 -26.893  1.00  0.00              
ATOM     24  O   LEU    40       4.201   8.973 -25.723  1.00  0.00              
ATOM     25  N   ALA    41       4.069  10.436 -27.421  1.00  0.00              
ATOM     26  CA  ALA    41       4.584  11.533 -26.612  1.00  0.00              
ATOM     27  C   ALA    41       3.609  11.874 -25.484  1.00  0.00              
ATOM     28  O   ALA    41       4.034  12.225 -24.381  1.00  0.00              
ATOM     29  N   GLU    42       2.309  11.748 -25.743  1.00  0.00              
ATOM     30  CA  GLU    42       1.312  12.053 -24.714  1.00  0.00              
ATOM     31  C   GLU    42       1.435  11.155 -23.489  1.00  0.00              
ATOM     32  O   GLU    42       1.142  11.573 -22.371  1.00  0.00              
ATOM     33  N   MET    43       1.861   9.916 -23.702  1.00  0.00              
ATOM     34  CA  MET    43       1.996   8.962 -22.610  1.00  0.00              
ATOM     35  C   MET    43       3.362   9.023 -21.927  1.00  0.00              
ATOM     36  O   MET    43       3.550   8.461 -20.848  1.00  0.00              
ATOM     37  N   VAL    44       4.301   9.736 -22.540  1.00  0.00              
ATOM     38  CA  VAL    44       5.657   9.850 -22.008  1.00  0.00              
ATOM     39  C   VAL    44       5.734  10.347 -20.559  1.00  0.00              
ATOM     40  O   VAL    44       6.233   9.639 -19.685  1.00  0.00              
ATOM     41  N   GLY    45       5.248  11.559 -20.306  1.00  0.00              
ATOM     42  CA  GLY    45       5.283  12.128 -18.957  1.00  0.00              
ATOM     43  C   GLY    45       4.505  11.282 -17.945  1.00  0.00              
ATOM     44  O   GLY    45       4.982  11.041 -16.835  1.00  0.00              
ATOM     45  N   GLU    46       3.293  10.830 -18.305  1.00  0.00              
ATOM     46  CA  GLU    46       2.522  10.011 -17.364  1.00  0.00              
ATOM     47  C   GLU    46       3.265   8.728 -16.987  1.00  0.00              
ATOM     48  O   GLU    46       3.260   8.306 -15.828  1.00  0.00              
ATOM     49  N   MET    47       3.907   8.115 -17.976  1.00  0.00              
ATOM     50  CA  MET    47       4.652   6.884 -17.754  1.00  0.00              
ATOM     51  C   MET    47       5.867   7.142 -16.871  1.00  0.00              
ATOM     52  O   MET    47       6.179   6.353 -15.979  1.00  0.00              
ATOM     53  N   ASN    48       6.556   8.250 -17.126  1.00  0.00              
ATOM     54  CA  ASN    48       7.735   8.592 -16.344  1.00  0.00              
ATOM     55  C   ASN    48       7.363   8.843 -14.888  1.00  0.00              
ATOM     56  O   ASN    48       8.070   8.414 -13.978  1.00  0.00              
ATOM     57  N   LYS    49       6.247   9.529 -14.668  1.00  0.00              
ATOM     58  CA  LYS    49       5.805   9.824 -13.310  1.00  0.00              
ATOM     59  C   LYS    49       5.366   8.552 -12.596  1.00  0.00              
ATOM     60  O   LYS    49       5.705   8.337 -11.437  1.00  0.00              
ATOM     61  N   LEU    50       4.618   7.705 -13.295  1.00  0.00              
ATOM     62  CA  LEU    50       4.124   6.465 -12.706  1.00  0.00              
ATOM     63  C   LEU    50       5.225   5.499 -12.280  1.00  0.00              
ATOM     64  O   LEU    50       5.091   4.808 -11.266  1.00  0.00              
ATOM     65  N   LEU    51       6.314   5.449 -13.041  1.00  0.00              
ATOM     66  CA  LEU    51       7.406   4.533 -12.723  1.00  0.00              
ATOM     67  C   LEU    51       8.663   5.208 -12.182  1.00  0.00              
ATOM     68  O   LEU    51       9.698   4.559 -12.005  1.00  0.00              
ATOM     69  N   GLU    52       8.567   6.504 -11.903  1.00  0.00              
ATOM     70  CA  GLU    52       9.702   7.242 -11.371  1.00  0.00              
ATOM     71  C   GLU    52      10.915   7.224 -12.280  1.00  0.00              
ATOM     72  O   GLU    52      12.050   7.098 -11.817  1.00  0.00              
ATOM     73  N   PRO    53      10.677   7.360 -13.581  1.00  0.00              
ATOM     74  CA  PRO    53      11.756   7.345 -14.561  1.00  0.00              
ATOM     75  C   PRO    53      12.284   8.753 -14.781  1.00  0.00              
ATOM     76  O   PRO    53      11.514   9.706 -14.919  1.00  0.00              
ATOM     77  N   SER    54      13.605   8.871 -14.822  1.00  0.00              
ATOM     78  CA  SER    54      14.268  10.157 -14.997  1.00  0.00              
ATOM     79  C   SER    54      14.550  10.550 -16.447  1.00  0.00              
ATOM     80  O   SER    54      14.457  11.723 -16.804  1.00  0.00              
ATOM     81  N   GLN    55      14.895   9.577 -17.282  1.00  0.00              
ATOM     82  CA  GLN    55      15.220   9.871 -18.673  1.00  0.00              
ATOM     83  C   GLN    55      14.621   8.855 -19.639  1.00  0.00              
ATOM     84  O   GLN    55      15.033   7.696 -19.678  1.00  0.00              
ATOM     85  N   VAL    56      13.646   9.306 -20.421  1.00  0.00              
ATOM     86  CA  VAL    56      12.974   8.445 -21.389  1.00  0.00              
ATOM     87  C   VAL    56      12.715   9.235 -22.661  1.00  0.00              
ATOM     88  O   VAL    56      12.418  10.430 -22.613  1.00  0.00              
ATOM     89  N   HIS    57      12.827   8.565 -23.801  1.00  0.00              
ATOM     90  CA  HIS    57      12.577   9.237 -25.061  1.00  0.00              
ATOM     91  C   HIS    57      11.813   8.331 -26.005  1.00  0.00              
ATOM     92  O   HIS    57      11.578   7.164 -25.687  1.00  0.00              
ATOM     93  N   LEU    58      11.415   8.869 -27.155  1.00  0.00              
ATOM     94  CA  LEU    58      10.687   8.092 -28.155  1.00  0.00              
ATOM     95  C   LEU    58      11.665   7.318 -29.028  1.00  0.00              
ATOM     96  O   LEU    58      12.707   7.834 -29.425  1.00  0.00              
ATOM     97  N   PHE    60      11.302   6.077 -29.330  1.00  0.00              
ATOM     98  CA  PHE    60      12.114   5.178 -30.142  1.00  0.00              
ATOM     99  C   PHE    60      11.374   4.791 -31.419  1.00  0.00              
ATOM    100  O   PHE    60      10.176   4.508 -31.385  1.00  0.00              
ATOM    101  N   GLU    61      12.092   4.783 -32.539  1.00  0.00              
ATOM    102  CA  GLU    61      11.516   4.385 -33.824  1.00  0.00              
ATOM    103  C   GLU    61      12.533   3.564 -34.599  1.00  0.00              
ATOM    104  O   GLU    61      13.725   3.854 -34.582  1.00  0.00              
ATOM    105  N   LEU    62      12.062   2.531 -35.280  1.00  0.00              
ATOM    106  CA  LEU    62      12.950   1.728 -36.098  1.00  0.00              
ATOM    107  C   LEU    62      12.208   1.349 -37.366  1.00  0.00              
ATOM    108  O   LEU    62      11.034   0.979 -37.316  1.00  0.00              
ATOM    109  N   HIS    63      12.888   1.484 -38.500  1.00  0.00              
ATOM    110  CA  HIS    63      12.301   1.148 -39.793  1.00  0.00              
ATOM    111  C   HIS    63      12.723  -0.280 -40.092  1.00  0.00              
ATOM    112  O   HIS    63      13.903  -0.545 -40.319  1.00  0.00              
ATOM    113  N   ASP    64      11.760  -1.195 -40.079  1.00  0.00              
ATOM    114  CA  ASP    64      12.064  -2.592 -40.334  1.00  0.00              
ATOM    115  C   ASP    64      12.068  -2.944 -41.808  1.00  0.00              
ATOM    116  O   ASP    64      11.950  -2.070 -42.666  1.00  0.00              
ATOM    117  N   LYS    65      12.211  -4.231 -42.102  1.00  0.00              
ATOM    118  CA  LYS    65      12.220  -4.694 -43.484  1.00  0.00              
ATOM    119  C   LYS    65      10.788  -4.774 -43.993  1.00  0.00              
ATOM    120  O   LYS    65       9.856  -4.989 -43.214  1.00  0.00              
ATOM    121  N   LEU    66      10.613  -4.602 -45.297  1.00  0.00              
ATOM    122  CA  LEU    66       9.281  -4.659 -45.866  1.00  0.00              
ATOM    123  C   LEU    66       8.422  -3.526 -45.338  1.00  0.00              
ATOM    124  O   LEU    66       8.835  -2.369 -45.353  1.00  0.00              
ATOM    125  N   ASN    67       7.231  -3.855 -44.856  1.00  0.00              
ATOM    126  CA  ASN    67       6.332  -2.834 -44.330  1.00  0.00              
ATOM    127  C   ASN    67       6.398  -2.710 -42.809  1.00  0.00              
ATOM    128  O   ASN    67       5.542  -2.071 -42.196  1.00  0.00              
ATOM    129  N   GLU    68       7.419  -3.305 -42.198  1.00  0.00              
ATOM    130  CA  GLU    68       7.549  -3.266 -40.744  1.00  0.00              
ATOM    131  C   GLU    68       8.110  -1.949 -40.198  1.00  0.00              
ATOM    132  O   GLU    68       9.042  -1.365 -40.755  1.00  0.00              
ATOM    133  N   TYR    69       7.525  -1.489 -39.097  1.00  0.00              
ATOM    134  CA  TYR    69       7.956  -0.254 -38.446  1.00  0.00              
ATOM    135  C   TYR    69       7.740  -0.462 -36.955  1.00  0.00              
ATOM    136  O   TYR    69       6.768  -1.095 -36.546  1.00  0.00              
ATOM    137  N   TYR    70       8.638   0.069 -36.136  1.00  0.00              
ATOM    138  CA  TYR    70       8.512  -0.115 -34.702  1.00  0.00              
ATOM    139  C   TYR    70       8.553   1.215 -33.975  1.00  0.00              
ATOM    140  O   TYR    70       9.379   2.076 -34.280  1.00  0.00              
ATOM    141  N   VAL    71       7.641   1.384 -33.026  1.00  0.00              
ATOM    142  CA  VAL    71       7.584   2.612 -32.245  1.00  0.00              
ATOM    143  C   VAL    71       7.446   2.281 -30.773  1.00  0.00              
ATOM    144  O   VAL    71       6.698   1.381 -30.385  1.00  0.00              
ATOM    145  N   LYS    72       8.172   3.019 -29.946  1.00  0.00              
ATOM    146  CA  LYS    72       8.102   2.776 -28.523  1.00  0.00              
ATOM    147  C   LYS    72       8.894   3.793 -27.736  1.00  0.00              
ATOM    148  O   LYS    72       8.981   4.961 -28.111  1.00  0.00              
ATOM    149  N   VAL    73       9.491   3.328 -26.648  1.00  0.00              
ATOM    150  CA  VAL    73      10.268   4.187 -25.770  1.00  0.00              
ATOM    151  C   VAL    73      11.611   3.570 -25.441  1.00  0.00              
ATOM    152  O   VAL    73      11.756   2.355 -25.434  1.00  0.00              
ATOM    153  N   ILE    74      12.595   4.422 -25.178  1.00  0.00              
ATOM    154  CA  ILE    74      13.894   3.936 -24.746  1.00  0.00              
ATOM    155  C   ILE    74      14.112   4.617 -23.415  1.00  0.00              
ATOM    156  O   ILE    74      14.018   5.838 -23.300  1.00  0.00              
ATOM    157  N   GLU    75      14.358   3.795 -22.405  1.00  0.00              
ATOM    158  CA  GLU    75      14.571   4.256 -21.048  1.00  0.00              
ATOM    159  C   GLU    75      16.043   4.153 -20.702  1.00  0.00              
ATOM    160  O   GLU    75      16.689   3.150 -21.006  1.00  0.00              
ATOM    161  N   ASP    76      16.569   5.200 -20.081  1.00  0.00              
ATOM    162  CA  ASP    76      17.955   5.198 -19.651  1.00  0.00              
ATOM    163  C   ASP    76      17.882   4.959 -18.153  1.00  0.00              
ATOM    164  O   ASP    76      17.610   5.882 -17.386  1.00  0.00              
ATOM    165  N   SER    77      18.087   3.714 -17.747  1.00  0.00              
ATOM    166  CA  SER    77      18.055   3.363 -16.336  1.00  0.00              
ATOM    167  C   SER    77      19.495   3.203 -15.866  1.00  0.00              
ATOM    168  O   SER    77      20.112   2.155 -16.061  1.00  0.00              
ATOM    169  N   THR    78      20.024   4.261 -15.264  1.00  0.00              
ATOM    170  CA  THR    78      21.391   4.272 -14.763  1.00  0.00              
ATOM    171  C   THR    78      22.379   3.828 -15.840  1.00  0.00              
ATOM    172  O   THR    78      23.120   2.862 -15.663  1.00  0.00              
ATOM    173  N   ASN    79      22.368   4.547 -16.958  1.00  0.00              
ATOM    174  CA  ASN    79      23.256   4.275 -18.084  1.00  0.00              
ATOM    175  C   ASN    79      22.879   3.054 -18.916  1.00  0.00              
ATOM    176  O   ASN    79      23.397   2.875 -20.018  1.00  0.00              
ATOM    177  N   GLU    80      21.994   2.209 -18.398  1.00  0.00              
ATOM    178  CA  GLU    80      21.568   1.043 -19.166  1.00  0.00              
ATOM    179  C   GLU    80      20.396   1.464 -20.046  1.00  0.00              
ATOM    180  O   GLU    80      19.420   2.033 -19.557  1.00  0.00              
ATOM    181  N   VAL    81      20.495   1.183 -21.340  1.00  0.00              
ATOM    182  CA  VAL    81      19.440   1.548 -22.279  1.00  0.00              
ATOM    183  C   VAL    81      18.497   0.370 -22.487  1.00  0.00              
ATOM    184  O   VAL    81      18.915  -0.702 -22.921  1.00  0.00              
ATOM    185  N   ILE    82      17.223   0.570 -22.165  1.00  0.00              
ATOM    186  CA  ILE    82      16.224  -0.476 -22.334  1.00  0.00              
ATOM    187  C   ILE    82      15.137   0.086 -23.235  1.00  0.00              
ATOM    188  O   ILE    82      14.622   1.178 -22.992  1.00  0.00              
END
