
#######################################################
#                                                     #
#                        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   42 (  168),  selected   42 , name T0350AL381_1
# Molecule2: number of CA atoms  109 ( 1798),  selected  109 , name T0350.pdb
# PARAMETERS: T0350AL381_1.T0350.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N      22      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    -       -      S      36           -
LGA    -       -      Y      37           -
LGA    Q      23      T      38           #
LGA    K      24      N      39          4.657
LGA    D      25      L      40          0.708
LGA    N      26      A      41          0.510
LGA    -       -      E      42           -
LGA    -       -      M      43           -
LGA    D      27      V      44          1.012
LGA    N      28      G      45           #
LGA    E      29      E      46           -
LGA    V      30      M      47           -
LGA    -       -      N      48           -
LGA    -       -      K      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      E      52           -
LGA    -       -      P      53           -
LGA    -       -      S      54           -
LGA    -       -      Q      55           -
LGA    -       -      V      56           -
LGA    -       -      H      57           -
LGA    -       -      L      58           -
LGA    -       -      K      59           -
LGA    P      31      F      60          1.259
LGA    V      32      E      61          1.457
LGA    -       -      L      62           -
LGA    -       -      H      63           -
LGA    -       -      D      64           -
LGA    -       -      K      65           -
LGA    -       -      L      66           -
LGA    -       -      N      67           -
LGA    -       -      E      68           -
LGA    -       -      Y      69           -
LGA    -       -      Y      70           -
LGA    H      33      V      71          2.162
LGA    -       -      K      72           -
LGA    -       -      V      73           -
LGA    -       -      I      74           -
LGA    -       -      E      75           -
LGA    -       -      D      76           -
LGA    -       -      S      77           -
LGA    -       -      T      78           -
LGA    -       -      N      79           -
LGA    -       -      E      80           -
LGA    -       -      V      81           -
LGA    -       -      I      82           -
LGA    -       -      R      83           -
LGA    -       -      E      84           -
LGA    Q      34      I      85          3.137
LGA    V      35      P      86          5.281
LGA    -       -      P      87           -
LGA    -       -      K      88           -
LGA    -       -      R      89           -
LGA    S      36      W      90          1.770
LGA    Y      37      L      91          0.636
LGA    T      38      D      92          0.812
LGA    N      39      F      93          1.044
LGA    L      40      Y      94          0.972
LGA    A      41      A      95          1.014
LGA    E      42      A      96          0.748
LGA    M      43      M      97          0.979
LGA    V      44      T      98          1.061
LGA    G      45      E      99          1.023
LGA    E      46      F     100          0.697
LGA    M      47      L     101          0.429
LGA    N      48      G     102          0.674
LGA    K      49      L     103          1.307
LGA    L      50      F     104          1.682
LGA    L      51      V     105          2.547
LGA    E      52      -       -           -
LGA    P      53      -       -           -
LGA    S      54      -       -           -
LGA    Q      55      -       -           -
LGA    V      56      -       -           -
LGA    H      57      -       -           -
LGA    L      58      D     106          2.891
LGA    K      59      E     107          2.377
LGA    F      60      K     108           #
LGA    E      61      K     109           -
LGA    L      62      -       -           -
LGA    H      63      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   42  109    5.0     27    1.99     7.41     21.119     1.293

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.951671 * X  +   0.302355 * Y  +   0.053893 * Z  +  -7.990067
  Y_new =  -0.198774 * X  +  -0.740148 * Y  +   0.642393 * Z  +  28.152317
  Z_new =   0.234119 * X  +   0.600634 * Y  +   0.764478 * Z  + -32.308292 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.665948   -2.475645  [ DEG:    38.1560   -141.8440 ]
  Theta =  -0.236313   -2.905280  [ DEG:   -13.5397   -166.4603 ]
  Phi   =  -2.935684    0.205908  [ DEG:  -168.2023     11.7977 ]
 
# 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_1                                  
REMARK     2: T0350.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350AL381_1.T0350.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   42  109   5.0   27   1.99    7.41  21.119
REMARK  ---------------------------------------------------------- 
MOLECULE T0350AL381_1
REMARK Aligment from pdb entry: 1t6sA
ATOM      1  N   ASN    22      -1.531  12.747 -20.796  1.00  0.00              
ATOM      2  CA  ASN    22      -0.413  12.288 -21.623  1.00  0.00              
ATOM      3  C   ASN    22      -0.718  10.920 -22.197  1.00  0.00              
ATOM      4  O   ASN    22      -1.085  10.013 -21.463  1.00  0.00              
ATOM      5  N   GLN    23      -0.518  10.760 -23.499  1.00  0.00              
ATOM      6  CA  GLN    23      -0.798   9.492 -24.141  1.00  0.00              
ATOM      7  C   GLN    23       0.398   8.561 -24.286  1.00  0.00              
ATOM      8  O   GLN    23       1.542   8.919 -23.992  1.00  0.00              
ATOM      9  N   LYS    24       0.108   7.356 -24.761  1.00  0.00              
ATOM     10  CA  LYS    24       1.118   6.334 -24.988  1.00  0.00              
ATOM     11  C   LYS    24       2.225   6.811 -25.942  1.00  0.00              
ATOM     12  O   LYS    24       3.400   6.499 -25.746  1.00  0.00              
ATOM     13  N   ASP    25       1.852   7.537 -26.994  1.00  0.00              
ATOM     14  CA  ASP    25       2.840   8.025 -27.960  1.00  0.00              
ATOM     15  C   ASP    25       3.867   8.960 -27.319  1.00  0.00              
ATOM     16  O   ASP    25       5.070   8.820 -27.528  1.00  0.00              
ATOM     17  N   ASN    26       3.377   9.917 -26.543  1.00  0.00              
ATOM     18  CA  ASN    26       4.241  10.875 -25.881  1.00  0.00              
ATOM     19  C   ASN    26       5.123  10.218 -24.818  1.00  0.00              
ATOM     20  O   ASN    26       6.332  10.461 -24.764  1.00  0.00              
ATOM     21  N   ASP    27       4.527   9.386 -23.972  1.00  0.00              
ATOM     22  CA  ASP    27       5.301   8.708 -22.940  1.00  0.00              
ATOM     23  C   ASP    27       6.394   7.789 -23.510  1.00  0.00              
ATOM     24  O   ASP    27       7.482   7.701 -22.937  1.00  0.00              
ATOM     25  N   ASN    28       6.119   7.103 -24.620  1.00  0.00              
ATOM     26  CA  ASN    28       7.122   6.211 -25.218  1.00  0.00              
ATOM     27  C   ASN    28       8.260   7.013 -25.881  1.00  0.00              
ATOM     28  O   ASN    28       9.420   6.603 -25.838  1.00  0.00              
ATOM     29  N   GLU    29       7.929   8.146 -26.490  1.00  0.00              
ATOM     30  CA  GLU    29       8.951   8.962 -27.150  1.00  0.00              
ATOM     31  C   GLU    29       9.911   9.578 -26.148  1.00  0.00              
ATOM     32  O   GLU    29      11.120   9.582 -26.361  1.00  0.00              
ATOM     33  N   VAL    30       9.381  10.098 -25.048  1.00  0.00              
ATOM     34  CA  VAL    30      10.240  10.744 -24.058  1.00  0.00              
ATOM     35  C   VAL    30      11.093   9.771 -23.234  1.00  0.00              
ATOM     36  O   VAL    30      12.253  10.055 -22.943  1.00  0.00              
ATOM     37  N   PRO    31      10.533   8.622 -22.876  1.00  0.00              
ATOM     38  CA  PRO    31      11.277   7.638 -22.096  1.00  0.00              
ATOM     39  C   PRO    31      12.112   6.741 -23.010  1.00  0.00              
ATOM     40  O   PRO    31      12.837   5.861 -22.546  1.00  0.00              
ATOM     41  N   VAL    32      12.013   6.980 -24.316  1.00  0.00              
ATOM     42  CA  VAL    32      12.737   6.190 -25.301  1.00  0.00              
ATOM     43  C   VAL    32      12.483   4.699 -25.059  1.00  0.00              
ATOM     44  O   VAL    32      13.394   3.879 -25.206  1.00  0.00              
ATOM     45  N   HIS    33      11.249   4.366 -24.677  1.00  0.00              
ATOM     46  CA  HIS    33      10.828   2.979 -24.433  1.00  0.00              
ATOM     47  C   HIS    33       9.622   2.659 -25.319  1.00  0.00              
ATOM     48  O   HIS    33       8.627   3.385 -25.292  1.00  0.00              
ATOM     49  N   GLN    34       9.718   1.576 -26.094  1.00  0.00              
ATOM     50  CA  GLN    34       8.640   1.159 -26.989  1.00  0.00              
ATOM     51  C   GLN    34       7.500   0.444 -26.263  1.00  0.00              
ATOM     52  O   GLN    34       7.287  -0.761 -26.436  1.00  0.00              
ATOM     53  N   VAL    35       6.772   1.206 -25.455  1.00  0.00              
ATOM     54  CA  VAL    35       5.637   0.698 -24.695  1.00  0.00              
ATOM     55  C   VAL    35       4.513   0.130 -25.529  1.00  0.00              
ATOM     56  O   VAL    35       4.114   0.730 -26.520  1.00  0.00              
ATOM     57  N   SER    36       3.993  -1.022 -25.109  1.00  0.00              
ATOM     58  CA  SER    36       2.834  -1.613 -25.767  1.00  0.00              
ATOM     59  C   SER    36       1.670  -1.017 -24.950  1.00  0.00              
ATOM     60  O   SER    36       1.854  -0.632 -23.792  1.00  0.00              
ATOM     61  N   TYR    37       0.474  -0.898 -25.546  1.00  0.00              
ATOM     62  CA  TYR    37      -0.658  -0.335 -24.799  1.00  0.00              
ATOM     63  C   TYR    37      -0.962  -1.110 -23.523  1.00  0.00              
ATOM     64  O   TYR    37      -1.401  -0.543 -22.517  1.00  0.00              
ATOM     65  N   THR    38      -0.696  -2.408 -23.560  1.00  0.00              
ATOM     66  CA  THR    38      -0.935  -3.249 -22.414  1.00  0.00              
ATOM     67  C   THR    38       0.173  -3.066 -21.375  1.00  0.00              
ATOM     68  O   THR    38      -0.089  -3.008 -20.168  1.00  0.00              
ATOM     69  N   ASN    39       1.415  -2.971 -21.845  1.00  0.00              
ATOM     70  CA  ASN    39       2.551  -2.777 -20.948  1.00  0.00              
ATOM     71  C   ASN    39       2.438  -1.445 -20.208  1.00  0.00              
ATOM     72  O   ASN    39       2.725  -1.372 -19.017  1.00  0.00              
ATOM     73  N   LEU    40       1.987  -0.398 -20.902  1.00  0.00              
ATOM     74  CA  LEU    40       1.863   0.921 -20.275  1.00  0.00              
ATOM     75  C   LEU    40       0.815   0.923 -19.172  1.00  0.00              
ATOM     76  O   LEU    40       1.019   1.497 -18.101  1.00  0.00              
ATOM     77  N   ALA    41      -0.321   0.297 -19.444  1.00  0.00              
ATOM     78  CA  ALA    41      -1.393   0.242 -18.460  1.00  0.00              
ATOM     79  C   ALA    41      -0.957  -0.539 -17.226  1.00  0.00              
ATOM     80  O   ALA    41      -1.357  -0.216 -16.106  1.00  0.00              
ATOM     81  N   GLU    42      -0.139  -1.570 -17.450  1.00  0.00              
ATOM     82  CA  GLU    42       0.387  -2.428 -16.381  1.00  0.00              
ATOM     83  C   GLU    42       1.344  -1.638 -15.490  1.00  0.00              
ATOM     84  O   GLU    42       1.405  -1.859 -14.283  1.00  0.00              
ATOM     85  N   MET    43       2.101  -0.719 -16.088  1.00  0.00              
ATOM     86  CA  MET    43       3.040   0.098 -15.321  1.00  0.00              
ATOM     87  C   MET    43       2.228   1.091 -14.501  1.00  0.00              
ATOM     88  O   MET    43       2.534   1.355 -13.340  1.00  0.00              
ATOM     89  N   VAL    44       1.185   1.638 -15.112  1.00  0.00              
ATOM     90  CA  VAL    44       0.326   2.586 -14.431  1.00  0.00              
ATOM     91  C   VAL    44      -0.377   1.896 -13.264  1.00  0.00              
ATOM     92  O   VAL    44      -0.508   2.484 -12.196  1.00  0.00              
ATOM     93  N   GLY    45      -0.826   0.652 -13.468  1.00  0.00              
ATOM     94  CA  GLY    45      -1.490  -0.105 -12.398  1.00  0.00              
ATOM     95  C   GLY    45      -0.562  -0.266 -11.195  1.00  0.00              
ATOM     96  O   GLY    45      -1.001  -0.117 -10.055  1.00  0.00              
ATOM     97  N   GLU    46       0.711  -0.575 -11.447  1.00  0.00              
ATOM     98  CA  GLU    46       1.676  -0.743 -10.359  1.00  0.00              
ATOM     99  C   GLU    46       1.818   0.541  -9.541  1.00  0.00              
ATOM    100  O   GLU    46       1.816   0.499  -8.308  1.00  0.00              
ATOM    101  N   MET    47       1.928   1.679 -10.227  1.00  0.00              
ATOM    102  CA  MET    47       2.044   2.957  -9.536  1.00  0.00              
ATOM    103  C   MET    47       0.791   3.151  -8.671  1.00  0.00              
ATOM    104  O   MET    47       0.895   3.470  -7.483  1.00  0.00              
ATOM    105  N   ASN    48      -0.387   2.971  -9.263  1.00  0.00              
ATOM    106  CA  ASN    48      -1.634   3.127  -8.509  1.00  0.00              
ATOM    107  C   ASN    48      -1.662   2.166  -7.314  1.00  0.00              
ATOM    108  O   ASN    48      -2.230   2.488  -6.268  1.00  0.00              
ATOM    109  N   LYS    49      -1.050   0.993  -7.460  1.00  0.00              
ATOM    110  CA  LYS    49      -1.004   0.058  -6.340  1.00  0.00              
ATOM    111  C   LYS    49      -0.134   0.644  -5.222  1.00  0.00              
ATOM    112  O   LYS    49      -0.479   0.537  -4.038  1.00  0.00              
ATOM    113  N   LEU    50       0.976   1.284  -5.586  1.00  0.00              
ATOM    114  CA  LEU    50       1.851   1.910  -4.588  1.00  0.00              
ATOM    115  C   LEU    50       1.167   3.087  -3.888  1.00  0.00              
ATOM    116  O   LEU    50       1.410   3.336  -2.701  1.00  0.00              
ATOM    117  N   LEU    51       0.332   3.819  -4.632  1.00  0.00              
ATOM    118  CA  LEU    51      -0.402   4.966  -4.070  1.00  0.00              
ATOM    119  C   LEU    51      -1.381   4.447  -3.023  1.00  0.00              
ATOM    120  O   LEU    51      -1.529   5.024  -1.944  1.00  0.00              
ATOM    121  N   GLU    52      -2.058   3.355  -3.357  1.00  0.00              
ATOM    122  CA  GLU    52      -3.001   2.742  -2.433  1.00  0.00              
ATOM    123  C   GLU    52      -2.257   2.246  -1.190  1.00  0.00              
ATOM    124  O   GLU    52      -2.706   2.450  -0.069  1.00  0.00              
ATOM    125  N   PRO    53      -1.109   1.615  -1.413  1.00  0.00              
ATOM    126  CA  PRO    53      -0.273   1.054  -0.353  1.00  0.00              
ATOM    127  C   PRO    53       0.295   2.063   0.648  1.00  0.00              
ATOM    128  O   PRO    53       0.302   1.804   1.856  1.00  0.00              
ATOM    129  N   SER    54       0.780   3.195   0.142  1.00  0.00              
ATOM    130  CA  SER    54       1.376   4.230   0.977  1.00  0.00              
ATOM    131  C   SER    54       0.370   5.277   1.479  1.00  0.00              
ATOM    132  O   SER    54       0.730   6.176   2.233  1.00  0.00              
ATOM    133  N   GLN    55      -0.886   5.158   1.066  1.00  0.00              
ATOM    134  CA  GLN    55      -1.900   6.082   1.535  1.00  0.00              
ATOM    135  C   GLN    55      -1.950   7.443   0.866  1.00  0.00              
ATOM    136  O   GLN    55      -2.264   8.438   1.521  1.00  0.00              
ATOM    137  N   VAL    56      -1.653   7.487  -0.429  1.00  0.00              
ATOM    138  CA  VAL    56      -1.687   8.737  -1.191  1.00  0.00              
ATOM    139  C   VAL    56      -3.141   9.115  -1.492  1.00  0.00              
ATOM    140  O   VAL    56      -4.015   8.254  -1.583  1.00  0.00              
ATOM    141  N   HIS    57      -3.394  10.408  -1.654  1.00  0.00              
ATOM    142  CA  HIS    57      -4.749  10.895  -1.900  1.00  0.00              
ATOM    143  C   HIS    57      -5.101  11.102  -3.373  1.00  0.00              
ATOM    144  O   HIS    57      -6.118  11.718  -3.695  1.00  0.00              
ATOM    145  N   LEU    58      -4.259  10.581  -4.260  1.00  0.00              
ATOM    146  CA  LEU    58      -4.483  10.714  -5.695  1.00  0.00              
ATOM    147  C   LEU    58      -4.234   9.403  -6.441  1.00  0.00              
ATOM    148  O   LEU    58      -3.621   8.470  -5.906  1.00  0.00              
ATOM    149  N   LYS    59      -4.714   9.344  -7.679  1.00  0.00              
ATOM    150  CA  LYS    59      -4.562   8.154  -8.524  1.00  0.00              
ATOM    151  C   LYS    59      -4.448   8.557  -9.974  1.00  0.00              
ATOM    152  O   LYS    59      -4.962   9.602 -10.374  1.00  0.00              
ATOM    153  N   PHE    60      -3.780   7.718 -10.760  1.00  0.00              
ATOM    154  CA  PHE    60      -3.661   7.959 -12.190  1.00  0.00              
ATOM    155  C   PHE    60      -4.864   7.289 -12.884  1.00  0.00              
ATOM    156  O   PHE    60      -5.176   6.119 -12.642  1.00  0.00              
ATOM    157  N   GLU    61      -5.533   8.060 -13.736  1.00  0.00              
ATOM    158  CA  GLU    61      -6.700   7.616 -14.489  1.00  0.00              
ATOM    159  C   GLU    61      -6.487   7.689 -16.005  1.00  0.00              
ATOM    160  O   GLU    61      -5.936   8.666 -16.540  1.00  0.00              
ATOM    161  N   LEU    62      -6.950   6.653 -16.692  1.00  0.00              
ATOM    162  CA  LEU    62      -6.861   6.576 -18.141  1.00  0.00              
ATOM    163  C   LEU    62      -8.164   7.140 -18.684  1.00  0.00              
ATOM    164  O   LEU    62      -9.198   6.467 -18.645  1.00  0.00              
ATOM    165  N   HIS    63      -8.129   8.376 -19.170  1.00  0.00              
ATOM    166  CA  HIS    63      -9.335   8.992 -19.722  1.00  0.00              
ATOM    167  C   HIS    63      -9.138   9.256 -21.211  1.00  0.00              
ATOM    168  O   HIS    63      -8.283  10.052 -21.592  1.00  0.00              
END
