
#######################################################
#                                                     #
#                        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  117 (  117),  selected  117 , name T0350TS393_4
# Molecule2: number of CA atoms  109 ( 1798),  selected  109 , name T0350.pdb
# PARAMETERS: T0350TS393_4.T0350.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    N       2      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    I       3      W      13           #
LGA    E       4      D      14           -
LGA    R       5      R      15           -
LGA    -       -      Y      16           -
LGA    L       6      D      17          4.018
LGA    T       7      T      18          3.380
LGA    T       8      Q      19          1.833
LGA    L       9      I      20          3.493
LGA    -       -      H      21           -
LGA    -       -      N      22           -
LGA    Q      10      Q      23          1.473
LGA    P      11      K      24          1.696
LGA    V      12      D      25          4.645
LGA    W      13      -       -           -
LGA    D      14      -       -           -
LGA    R      15      -       -           -
LGA    Y      16      N      26          3.498
LGA    D      17      D      27           -
LGA    T      18      -       -           -
LGA    Q      19      N      28          3.560
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    T      38      -       -           -
LGA    N      39      -       -           -
LGA    L      40      E      29           #
LGA    A      41      V      30           -
LGA    E      42      -       -           -
LGA    M      43      P      31          4.745
LGA    V      44      V      32          3.066
LGA    G      45      H      33          3.382
LGA    E      46      -       -           -
LGA    M      47      -       -           -
LGA    N      48      Q      34          1.749
LGA    K      49      V      35          3.016
LGA    L      50      -       -           -
LGA    L      51      -       -           -
LGA    E      52      S      36          3.368
LGA    P      53      Y      37          2.325
LGA    S      54      T      38           -
LGA    Q      55      N      39           -
LGA    V      56      -       -           -
LGA    H      57      -       -           -
LGA    L      58      -       -           -
LGA    K      59      L      40          2.869
LGA    F      60      A      41          1.921
LGA    E      61      E      42          3.359
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      M      43          3.451
LGA    V      71      V      44           #
LGA    K      72      -       -           -
LGA    V      73      -       -           -
LGA    I      74      -       -           -
LGA    E      75      -       -           -
LGA    D      76      -       -           -
LGA    S      77      -       -           -
LGA    T      78      -       -           -
LGA    N      79      G      45           #
LGA    E      80      E      46           #
LGA    V      81      M      47           #
LGA    I      82      N      48          4.069
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    R      83      F      60           #
LGA    E      84      E      61           -
LGA    I      85      L      62           #
LGA    -       -      H      63           -
LGA    -       -      D      64           -
LGA    -       -      K      65           -
LGA    -       -      L      66           -
LGA    -       -      N      67           -
LGA    -       -      E      68           -
LGA    -       -      Y      69           -
LGA    P      86      Y      70          4.128
LGA    -       -      V      71           -
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    -       -      I      85           -
LGA    -       -      P      86           -
LGA    P      87      P      87          2.317
LGA    K      88      K      88          2.848
LGA    R      89      R      89          1.783
LGA    W      90      W      90          1.464
LGA    L      91      L      91          1.289
LGA    D      92      D      92          1.002
LGA    F      93      F      93          0.891
LGA    Y      94      Y      94          0.865
LGA    A      95      A      95          0.742
LGA    A      96      A      96          0.949
LGA    M      97      M      97          1.325
LGA    T      98      T      98          0.685
LGA    E      99      E      99          0.513
LGA    F     100      F     100          0.880
LGA    L     101      L     101          1.496
LGA    G     102      G     102          1.687
LGA    L     103      L     103          1.336
LGA    F     104      F     104          1.066
LGA    V     105      V     105           #
LGA    D     106      D     106           -
LGA    E     107      E     107           -
LGA    K     108      K     108           -
LGA    K     109      K     109           -
LGA    L     110      -       -           -
LGA    E     111      -       -           -
LGA    H     112      -       -           -
LGA    H     113      -       -           -
LGA    H     114      -       -           -
LGA    H     115      -       -           -
LGA    H     116      -       -           -
LGA    H     117      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  117  109    5.0     40    2.60    55.00     25.033     1.479

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.196706 * X  +  -0.198091 * Y  +   0.960243 * Z  +  -1.562529
  Y_new =  -0.838223 * X  +  -0.542029 * Y  +   0.059894 * Z  +  -0.292830
  Z_new =   0.508615 * X  +  -0.816679 * Y  +  -0.272664 * Z  + -19.007795 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.893029    1.248563  [ DEG:  -108.4626     71.5374 ]
  Theta =  -0.533576   -2.608017  [ DEG:   -30.5716   -149.4284 ]
  Phi   =  -1.340297    1.801296  [ DEG:   -76.7934    103.2066 ]
 
# 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: T0350TS393_4                                  
REMARK     2: T0350.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350TS393_4.T0350.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  117  109   5.0   40   2.60   55.00  25.033
REMARK  ---------------------------------------------------------- 
MOLECULE T0350TS393_4
PFRMAT TS
TARGET T0350
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      20.692  -9.415 -20.216  1.00 25.00           C
ATOM      2  CA  ASN     2      17.311 -10.593 -18.991  1.00 25.00           C
ATOM      3  CA  ILE     3      14.583 -13.293 -19.188  1.00 25.00           C
ATOM      4  CA  GLU     4      12.580 -16.533 -18.759  1.00 25.00           C
ATOM      5  CA  ARG     5       9.272 -16.392 -20.588  1.00 25.00           C
ATOM      6  CA  LEU     6       9.219 -12.639 -21.240  1.00 25.00           C
ATOM      7  CA  THR     7       5.631 -12.001 -20.066  1.00 25.00           C
ATOM      8  CA  THR     8       1.875 -12.565 -20.138  1.00 25.00           C
ATOM      9  CA  LEU     9       0.022 -12.056 -23.464  1.00 25.00           C
ATOM     10  CA  GLN    10      -2.455 -14.128 -25.499  1.00 25.00           C
ATOM     11  CA  PRO    11      -6.161 -13.357 -25.838  1.00 25.00           C
ATOM     12  CA  VAL    12      -6.818 -14.911 -22.481  1.00 25.00           C
ATOM     13  CA  TRP    13      -5.103 -12.187 -20.526  1.00 25.00           C
ATOM     14  CA  ASP    14      -7.165 -13.241 -17.476  1.00 25.00           C
ATOM     15  CA  ARG    15      -8.464  -9.660 -17.086  1.00 25.00           C
ATOM     16  CA  TYR    16      -9.422  -9.577 -20.793  1.00 25.00           C
ATOM     17  CA  ASP    17     -11.262 -12.915 -20.418  1.00 25.00           C
ATOM     18  CA  THR    18     -13.136 -11.566 -17.363  1.00 25.00           C
ATOM     19  CA  GLN    19     -14.116  -8.423 -19.322  1.00 25.00           C
ATOM     20  CA  ILE    20     -15.372 -10.591 -22.218  1.00 25.00           C
ATOM     21  CA  HIS    21     -17.427 -12.708 -19.776  1.00 25.00           C
ATOM     22  CA  ASN    22     -18.929  -9.532 -18.250  1.00 25.00           C
ATOM     23  CA  GLN    23     -22.199 -11.150 -19.335  1.00 25.00           C
ATOM     24  CA  LYS    24     -23.774 -14.106 -17.531  1.00 25.00           C
ATOM     25  CA  ASP    25     -23.388 -14.264 -13.797  1.00 25.00           C
ATOM     26  CA  ASN    26     -21.355 -14.754 -10.570  1.00 25.00           C
ATOM     27  CA  ASP    27     -19.026 -14.298  -7.563  1.00 25.00           C
ATOM     28  CA  ASN    28     -21.596 -11.703  -6.351  1.00 25.00           C
ATOM     29  CA  GLU    29     -19.551  -8.615  -5.618  1.00 25.00           C
ATOM     30  CA  VAL    30     -16.581  -6.429  -6.756  1.00 25.00           C
ATOM     31  CA  PRO    31     -17.380  -2.975  -8.220  1.00 25.00           C
ATOM     32  CA  VAL    32     -15.417  -2.605 -11.391  1.00 25.00           C
ATOM     33  CA  HIS    33     -17.334  -0.061 -13.547  1.00 25.00           C
ATOM     34  CA  GLN    34     -18.789   1.208 -16.824  1.00 25.00           C
ATOM     35  CA  VAL    35     -17.137   1.509 -20.238  1.00 25.00           C
ATOM     36  CA  SER    36     -20.200   2.238 -22.268  1.00 25.00           C
ATOM     37  CA  TYR    37     -17.741   2.307 -25.145  1.00 25.00           C
ATOM     38  CA  THR    38     -16.730   5.859 -26.160  1.00 25.00           C
ATOM     39  CA  ASN    39     -14.018   5.886 -23.456  1.00 25.00           C
ATOM     40  CA  LEU    40     -12.711   2.507 -24.699  1.00 25.00           C
ATOM     41  CA  ALA    41     -12.618   3.837 -28.290  1.00 25.00           C
ATOM     42  CA  GLU    42     -10.697   6.936 -27.120  1.00 25.00           C
ATOM     43  CA  MET    43      -8.198   4.713 -25.254  1.00 25.00           C
ATOM     44  CA  VAL    44      -7.727   2.568 -28.392  1.00 25.00           C
ATOM     45  CA  GLY    45      -7.130   5.719 -30.485  1.00 25.00           C
ATOM     46  CA  GLU    46      -4.550   6.952 -27.939  1.00 25.00           C
ATOM     47  CA  MET    47      -2.783   3.556 -28.048  1.00 25.00           C
ATOM     48  CA  ASN    48      -2.718   3.684 -31.876  1.00 25.00           C
ATOM     49  CA  LYS    49      -1.248   7.219 -31.756  1.00 25.00           C
ATOM     50  CA  LEU    50       1.437   6.045 -29.289  1.00 25.00           C
ATOM     51  CA  LEU    51       2.293   3.101 -31.584  1.00 25.00           C
ATOM     52  CA  GLU    52       2.571   5.480 -34.573  1.00 25.00           C
ATOM     53  CA  PRO    53       4.877   7.781 -32.559  1.00 25.00           C
ATOM     54  CA  SER    54       7.552   6.506 -30.130  1.00 25.00           C
ATOM     55  CA  GLN    55      11.061   5.251 -29.284  1.00 25.00           C
ATOM     56  CA  VAL    56      10.984   5.619 -25.441  1.00 25.00           C
ATOM     57  CA  HIS    57      11.058   8.817 -23.369  1.00 25.00           C
ATOM     58  CA  LEU    58       9.138  10.333 -26.284  1.00 25.00           C
ATOM     59  CA  LYS    59       5.460   9.968 -27.089  1.00 25.00           C
ATOM     60  CA  PHE    60       3.570  11.542 -24.168  1.00 25.00           C
ATOM     61  CA  GLU    61       1.368  14.054 -22.379  1.00 25.00           C
ATOM     62  CA  LEU    62      -1.290  11.775 -20.847  1.00 25.00           C
ATOM     63  CA  HIS    63      -5.051  12.497 -20.429  1.00 25.00           C
ATOM     64  CA  ASP    64      -5.382  14.518 -17.183  1.00 25.00           C
ATOM     65  CA  LYS    65      -4.457  13.949 -13.526  1.00 25.00           C
ATOM     66  CA  LEU    66      -5.346  10.320 -14.422  1.00 25.00           C
ATOM     67  CA  ASN    67      -1.695   9.995 -15.441  1.00 25.00           C
ATOM     68  CA  GLU    68      -0.418   7.255 -17.761  1.00 25.00           C
ATOM     69  CA  TYR    69      -2.711   4.753 -19.415  1.00 25.00           C
ATOM     70  CA  TYR    70      -1.304   5.958 -22.690  1.00 25.00           C
ATOM     71  CA  VAL    71      -0.426   8.642 -25.219  1.00 25.00           C
ATOM     72  CA  LYS    72       0.224  11.131 -27.977  1.00 25.00           C
ATOM     73  CA  VAL    73       1.348  14.783 -27.569  1.00 25.00           C
ATOM     74  CA  ILE    74       4.552  15.826 -29.408  1.00 25.00           C
ATOM     75  CA  GLU    75       7.016  15.570 -26.522  1.00 25.00           C
ATOM     76  CA  ASP    76       9.641  17.227 -28.768  1.00 25.00           C
ATOM     77  CA  SER    77       9.725  19.888 -26.041  1.00 25.00           C
ATOM     78  CA  THR    78      11.742  17.645 -23.769  1.00 25.00           C
ATOM     79  CA  ASN    79       8.953  18.178 -21.165  1.00 25.00           C
ATOM     80  CA  GLU    80       6.594  15.256 -20.602  1.00 25.00           C
ATOM     81  CA  VAL    81       4.119  13.796 -18.103  1.00 25.00           C
ATOM     82  CA  ILE    82       5.083  10.339 -19.509  1.00 25.00           C
ATOM     83  CA  ARG    83       5.608   7.189 -21.589  1.00 25.00           C
ATOM     84  CA  GLU    84       5.288   3.449 -22.087  1.00 25.00           C
ATOM     85  CA  ILE    85       5.763   4.177 -25.775  1.00 25.00           C
ATOM     86  CA  PRO    86       5.376   1.787 -28.693  1.00 25.00           C
ATOM     87  CA  PRO    87       3.112  -0.950 -29.992  1.00 25.00           C
ATOM     88  CA  LYS    88       0.956  -3.579 -28.231  1.00 25.00           C
ATOM     89  CA  ARG    89       3.876  -4.460 -25.917  1.00 25.00           C
ATOM     90  CA  TRP    90       4.385  -0.752 -25.106  1.00 25.00           C
ATOM     91  CA  LEU    91       0.653  -0.387 -24.326  1.00 25.00           C
ATOM     92  CA  ASP    92       0.807  -3.449 -22.032  1.00 25.00           C
ATOM     93  CA  PHE    93       3.851  -1.980 -20.232  1.00 25.00           C
ATOM     94  CA  TYR    94       2.005   1.345 -19.775  1.00 25.00           C
ATOM     95  CA  ALA    95      -1.031  -0.508 -18.357  1.00 25.00           C
ATOM     96  CA  ALA    96       1.235  -2.417 -15.930  1.00 25.00           C
ATOM     97  CA  MET    97       2.851   0.871 -14.814  1.00 25.00           C
ATOM     98  CA  THR    98      -0.611   2.410 -14.253  1.00 25.00           C
ATOM     99  CA  GLU    99      -1.659  -0.640 -12.187  1.00 25.00           C
ATOM    100  CA  PHE   100       1.533  -0.347 -10.091  1.00 25.00           C
ATOM    101  CA  LEU   101       0.838   3.373  -9.508  1.00 25.00           C
ATOM    102  CA  GLY   102      -2.747   2.560  -8.431  1.00 25.00           C
ATOM    103  CA  LEU   103      -1.440  -0.107  -6.012  1.00 25.00           C
ATOM    104  CA  PHE   104       1.057   2.405  -4.552  1.00 25.00           C
ATOM    105  CA  VAL   105       4.508   2.515  -6.170  1.00 25.00           C
ATOM    106  CA  ASP   106       7.901   1.020  -6.882  1.00 25.00           C
ATOM    107  CA  GLU   107       8.736  -1.788  -4.380  1.00 25.00           C
ATOM    108  CA  LYS   108       8.081   0.281  -1.224  1.00 25.00           C
ATOM    109  CA  LYS   109       7.839  -2.925   0.857  1.00 25.00           C
ATOM    110  CA  LEU   110      10.474  -5.437  -0.202  1.00 25.00           C
ATOM    111  CA  GLU   111       8.444  -7.654  -2.594  1.00 25.00           C
ATOM    112  CA  HIS   112      10.773 -10.470  -1.402  1.00 25.00           C
ATOM    113  CA  HIS   113       8.549 -12.718   0.653  1.00 25.00           C
ATOM    114  CA  HIS   114       8.520 -15.512  -1.968  1.00 25.00           C
ATOM    115  CA  HIS   115       5.591 -16.797   0.028  1.00 25.00           C
ATOM    116  CA  HIS   116       2.888 -17.416  -2.550  1.00 25.00           C
ATOM    117  CA  HIS   117       0.825 -18.405  -5.561  1.00 25.00           C
TER
END
