
#######################################################
#                                                     #
#                        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   97 (   97),  selected   97 , name T0359TS393_1
# Molecule2: number of CA atoms   93 (  690),  selected   93 , name T0359.pdb
# PARAMETERS: T0359TS393_1.T0359.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1           #
LGA    M       2      M       2          6.353
LGA    S       3      S       3          2.446
LGA    E       4      E       4          2.881
LGA    T       5      T       5          1.219
LGA    F       6      F       6          0.458
LGA    D       7      D       7          1.087
LGA    V       8      V       8          1.532
LGA    E       9      E       9          1.350
LGA    L      10      L      10          1.638
LGA    T      11      T      11          2.338
LGA    K      12      K      12          0.511
LGA    N      13      N      13          1.388
LGA    V      14      V      14          1.658
LGA    Q      15      Q      15          4.508
LGA    G      16      G      16          1.538
LGA    L      17      L      17          2.467
LGA    G      18      G      18          0.930
LGA    I      19      I      19          1.185
LGA    T      20      T      20          2.130
LGA    I      21      I      21          2.107
LGA    A      22      A      22          1.556
LGA    G      23      G      23          3.676
LGA    Y      24      Y      24          4.077
LGA    I      25      -       -           -
LGA    G      26      I      25          3.846
LGA    D      27      G      26          4.358
LGA    K      28      D      27           -
LGA    K      29      -       -           -
LGA    L      30      P      32          3.580
LGA    E      31      S      33          3.491
LGA    P      32      -       -           -
LGA    S      33      -       -           -
LGA    G      34      G      34          2.369
LGA    I      35      I      35          1.294
LGA    F      36      F      36          0.925
LGA    V      37      V      37          1.215
LGA    K      38      K      38          2.068
LGA    S      39      S      39          1.337
LGA    I      40      I      40          1.480
LGA    T      41      T      41          1.547
LGA    K      42      K      42          1.522
LGA    S      43      S      43          1.743
LGA    S      44      S      44          2.681
LGA    A      45      A      45          2.423
LGA    V      46      V      46          0.524
LGA    E      47      E      47          1.737
LGA    H      48      H      48          2.377
LGA    D      49      D      49          1.246
LGA    G      50      G      50          3.030
LGA    R      51      R      51          0.992
LGA    I      52      I      52          0.949
LGA    Q      53      Q      53          2.223
LGA    I      54      I      54          1.486
LGA    G      55      G      55          1.544
LGA    D      56      D      56          1.644
LGA    Q      57      Q      57          1.810
LGA    I      58      I      58          1.681
LGA    I      59      I      59          1.084
LGA    A      60      A      60          1.117
LGA    V      61      V      61          1.368
LGA    D      62      D      62          1.012
LGA    G      63      G      63          1.276
LGA    T      64      T      64          1.504
LGA    N      65      N      65          1.393
LGA    L      66      L      66          1.134
LGA    Q      67      Q      67          1.597
LGA    G      68      G      68          2.391
LGA    F      69      F      69          2.162
LGA    T      70      T      70          3.177
LGA    N      71      N      71          3.274
LGA    Q      72      Q      72          2.735
LGA    Q      73      Q      73          2.300
LGA    A      74      A      74          2.674
LGA    V      75      V      75          3.020
LGA    E      76      E      76          2.442
LGA    V      77      V      77          1.864
LGA    L      78      L      78          2.097
LGA    R      79      R      79          2.960
LGA    H      80      H      80          2.676
LGA    T      81      T      81          2.027
LGA    G      82      G      82          1.621
LGA    Q      83      Q      83          2.682
LGA    T      84      T      84          1.821
LGA    V      85      V      85          1.216
LGA    L      86      L      86          0.618
LGA    L      87      L      87          1.123
LGA    T      88      T      88          2.247
LGA    L      89      L      89          2.297
LGA    M      90      M      90          1.244
LGA    R      91      R      91          1.582
LGA    R      92      R      92          2.540
LGA    G      93      G      93          2.685
LGA    E      94      E      94          4.619
LGA    T      95      -       -           -
LGA    S      96      -       -           -
LGA    V      97      T      95          4.101
LGA    -       -      S      96           -
LGA    -       -      V      97           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   93    5.0     89    2.31    94.38     74.203     3.688

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.530605 * X  +  -0.815211 * Y  +  -0.232141 * Z  +  -4.460286
  Y_new =   0.076205 * X  +  -0.318646 * Y  +   0.944806 * Z  +  13.890660
  Z_new =  -0.844187 * X  +   0.483628 * Y  +   0.231198 * Z  +  -7.198997 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.124863   -2.016730  [ DEG:    64.4499   -115.5501 ]
  Theta =   1.005046    2.136546  [ DEG:    57.5849    122.4151 ]
  Phi   =   2.998948   -0.142644  [ DEG:   171.8271     -8.1729 ]
 
# 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: T0359TS393_1                                  
REMARK     2: T0359.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0359TS393_1.T0359.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   97   93   5.0   89   2.31   94.38  74.203
REMARK  ---------------------------------------------------------- 
MOLECULE T0359TS393_1
PFRMAT TS
TARGET T0359
MODEL 1
PARENT N/A
ATOM      1  CA  SER     1      10.154   1.044   0.052  1.00 25.00           C
ATOM      2  CA  MET     2       6.410   0.921  -0.511  1.00 25.00           C
ATOM      3  CA  SER     3       6.534   4.139  -2.519  1.00 25.00           C
ATOM      4  CA  GLU     4       5.477   6.202   0.454  1.00 25.00           C
ATOM      5  CA  THR     5       1.943   7.575   0.513  1.00 25.00           C
ATOM      6  CA  PHE     6       1.306  11.319   1.182  1.00 25.00           C
ATOM      7  CA  ASP     7      -1.294  13.565   2.882  1.00 25.00           C
ATOM      8  CA  VAL     8      -2.164  16.844   1.239  1.00 25.00           C
ATOM      9  CA  GLU     9      -4.965  17.765   3.659  1.00 25.00           C
ATOM     10  CA  LEU    10      -6.010  20.439   1.174  1.00 25.00           C
ATOM     11  CA  THR    11      -8.028  23.681   0.934  1.00 25.00           C
ATOM     12  CA  LYS    12     -11.071  24.822  -0.916  1.00 25.00           C
ATOM     13  CA  ASN    13     -11.741  28.494  -0.519  1.00 25.00           C
ATOM     14  CA  VAL    14     -11.775  29.986  -3.999  1.00 25.00           C
ATOM     15  CA  GLN    15     -14.661  28.160  -5.670  1.00 25.00           C
ATOM     16  CA  GLY    16     -12.116  25.672  -7.046  1.00 25.00           C
ATOM     17  CA  LEU    17     -10.057  22.580  -6.311  1.00 25.00           C
ATOM     18  CA  GLY    18      -7.088  24.382  -7.861  1.00 25.00           C
ATOM     19  CA  ILE    19      -6.044  20.975  -9.088  1.00 25.00           C
ATOM     20  CA  THR    20      -6.678  18.702 -12.049  1.00 25.00           C
ATOM     21  CA  ILE    21      -7.304  15.333 -13.633  1.00 25.00           C
ATOM     22  CA  ALA    22      -6.609  14.084 -17.196  1.00 25.00           C
ATOM     23  CA  GLY    23      -3.320  12.747 -18.709  1.00 25.00           C
ATOM     24  CA  TYR    24      -2.683   9.142 -17.538  1.00 25.00           C
ATOM     25  CA  ILE    25      -5.149   6.231 -17.177  1.00 25.00           C
ATOM     26  CA  GLY    26      -7.899   5.045 -19.489  1.00 25.00           C
ATOM     27  CA  ASP    27      -6.689   7.148 -22.427  1.00 25.00           C
ATOM     28  CA  LYS    28      -2.902   7.696 -22.517  1.00 25.00           C
ATOM     29  CA  LYS    29      -2.278   3.963 -22.194  1.00 25.00           C
ATOM     30  CA  LEU    30      -0.792   2.438 -18.997  1.00 25.00           C
ATOM     31  CA  GLU    31      -4.127   1.192 -17.620  1.00 25.00           C
ATOM     32  CA  PRO    32      -4.793   1.202 -13.878  1.00 25.00           C
ATOM     33  CA  SER    33      -2.313   3.890 -13.020  1.00 25.00           C
ATOM     34  CA  GLY    34      -4.929   5.600 -10.916  1.00 25.00           C
ATOM     35  CA  ILE    35      -5.247   9.267 -11.883  1.00 25.00           C
ATOM     36  CA  PHE    36      -2.970  12.288 -12.291  1.00 25.00           C
ATOM     37  CA  VAL    37      -2.296  15.978 -12.090  1.00 25.00           C
ATOM     38  CA  LYS    38      -2.804  17.929 -15.366  1.00 25.00           C
ATOM     39  CA  SER    39      -1.697  20.971 -13.317  1.00 25.00           C
ATOM     40  CA  ILE    40      -1.307  22.530  -9.822  1.00 25.00           C
ATOM     41  CA  THR    41      -1.847  26.256 -10.104  1.00 25.00           C
ATOM     42  CA  LYS    42       0.092  29.469  -9.198  1.00 25.00           C
ATOM     43  CA  SER    43      -2.157  31.605  -6.942  1.00 25.00           C
ATOM     44  CA  SER    44      -5.011  29.205  -7.310  1.00 25.00           C
ATOM     45  CA  ALA    45      -4.926  27.358  -3.936  1.00 25.00           C
ATOM     46  CA  VAL    46      -3.105  24.061  -3.407  1.00 25.00           C
ATOM     47  CA  GLU    47       0.303  24.706  -5.031  1.00 25.00           C
ATOM     48  CA  HIS    48       1.441  26.643  -1.929  1.00 25.00           C
ATOM     49  CA  ASP    49      -0.382  25.465   1.196  1.00 25.00           C
ATOM     50  CA  GLY    50       1.386  22.162   1.175  1.00 25.00           C
ATOM     51  CA  ARG    51       2.483  19.633  -1.420  1.00 25.00           C
ATOM     52  CA  ILE    52       0.952  18.200  -4.625  1.00 25.00           C
ATOM     53  CA  GLN    53       1.701  18.451  -8.364  1.00 25.00           C
ATOM     54  CA  ILE    54       2.332  18.169 -12.163  1.00 25.00           C
ATOM     55  CA  GLY    55       2.927  14.524 -13.106  1.00 25.00           C
ATOM     56  CA  ASP    56       1.996  12.795  -9.846  1.00 25.00           C
ATOM     57  CA  GLN    57       0.291   9.452  -9.367  1.00 25.00           C
ATOM     58  CA  ILE    58      -2.934  10.388  -7.548  1.00 25.00           C
ATOM     59  CA  ILE    59      -4.233   7.262  -5.847  1.00 25.00           C
ATOM     60  CA  ALA    60      -7.111   8.243  -3.534  1.00 25.00           C
ATOM     61  CA  VAL    61     -10.387   9.954  -2.447  1.00 25.00           C
ATOM     62  CA  ASP    62     -11.882  10.697   1.010  1.00 25.00           C
ATOM     63  CA  GLY    63     -12.318   6.957   1.619  1.00 25.00           C
ATOM     64  CA  THR    64     -13.086   5.314  -1.769  1.00 25.00           C
ATOM     65  CA  ASN    65     -10.183   3.830  -3.727  1.00 25.00           C
ATOM     66  CA  LEU    66      -8.700   4.788  -7.105  1.00 25.00           C
ATOM     67  CA  GLN    67      -7.382   1.408  -8.148  1.00 25.00           C
ATOM     68  CA  GLY    68      -9.583   1.307 -11.198  1.00 25.00           C
ATOM     69  CA  PHE    69     -10.898   4.828 -11.688  1.00 25.00           C
ATOM     70  CA  THR    70      -9.922   6.709 -14.808  1.00 25.00           C
ATOM     71  CA  ASN    71     -10.791  10.450 -14.650  1.00 25.00           C
ATOM     72  CA  GLN    72     -14.532  11.264 -14.768  1.00 25.00           C
ATOM     73  CA  GLN    73     -15.038   9.538 -11.386  1.00 25.00           C
ATOM     74  CA  ALA    74     -12.131  11.540  -9.901  1.00 25.00           C
ATOM     75  CA  VAL    75     -13.643  14.787 -11.256  1.00 25.00           C
ATOM     76  CA  GLU    76     -17.034  13.874  -9.727  1.00 25.00           C
ATOM     77  CA  VAL    77     -15.353  13.161  -6.361  1.00 25.00           C
ATOM     78  CA  LEU    78     -13.555  16.539  -6.516  1.00 25.00           C
ATOM     79  CA  ARG    79     -16.870  18.296  -7.286  1.00 25.00           C
ATOM     80  CA  HIS    80     -18.526  16.525  -4.322  1.00 25.00           C
ATOM     81  CA  THR    81     -15.763  17.383  -1.801  1.00 25.00           C
ATOM     82  CA  GLY    82     -16.596  20.820  -0.400  1.00 25.00           C
ATOM     83  CA  GLN    83     -14.534  21.649   2.722  1.00 25.00           C
ATOM     84  CA  THR    84     -11.235  19.741   2.682  1.00 25.00           C
ATOM     85  CA  VAL    85     -10.514  17.384  -0.178  1.00 25.00           C
ATOM     86  CA  LEU    86      -8.489  14.623   1.590  1.00 25.00           C
ATOM     87  CA  LEU    87      -6.944  13.703  -1.754  1.00 25.00           C
ATOM     88  CA  THR    88      -3.747  11.877  -2.726  1.00 25.00           C
ATOM     89  CA  LEU    89      -0.184  13.082  -3.565  1.00 25.00           C
ATOM     90  CA  MET    90       1.857   9.969  -4.386  1.00 25.00           C
ATOM     91  CA  ARG    91       4.982  11.615  -5.750  1.00 25.00           C
ATOM     92  CA  ARG    92       7.228   8.567  -5.565  1.00 25.00           C
ATOM     93  CA  GLY    93      10.980   8.315  -5.079  1.00 25.00           C
ATOM     94  CA  GLU    94      14.413   7.019  -5.989  1.00 25.00           C
ATOM     95  CA  THR    95      17.713   5.695  -7.367  1.00 25.00           C
ATOM     96  CA  SER    96      16.598   3.687 -10.365  1.00 25.00           C
ATOM     97  CA  VAL    97      13.652   4.306 -12.601  1.00 25.00           C
TER
END
