
#######################################################
#                                                     #
#                        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  119 (  119),  selected  119 , name T0322TS677_2-D1
# Molecule2: number of CA atoms  128 (  980),  selected  128 , name T0322_D1.pdb
# PARAMETERS: T0322TS677_2-D1.T0322_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G      16      G      16           -
LGA    F      17      F      17           -
LGA    S      18      S      18           -
LGA    Q      19      Q      19           -
LGA    N      21      -       -           -
LGA    W      22      -       -           -
LGA    S      23      -       -           -
LGA    R      24      L      20           #
LGA    G      25      N      21          4.958
LGA    F      26      W      22          5.179
LGA    -       -      S      23           -
LGA    -       -      R      24           -
LGA    -       -      G      25           -
LGA    -       -      F      26           -
LGA    G      27      G      27          4.667
LGA    R      28      R      28          5.143
LGA    Q      29      Q      29          4.862
LGA    -       -      I      30           -
LGA    I      30      G      31          1.131
LGA    P      32      P      32          0.973
LGA    L      33      L      33          1.048
LGA    F      34      F      34          0.831
LGA    E      35      E      35          0.982
LGA    H      36      H      36          1.551
LGA    -       -      R      37           -
LGA    -       -      E      38           -
LGA    -       -      G      39           -
LGA    -       -      P      40           -
LGA    R      37      G      41          3.125
LGA    G      39      Q      42          4.984
LGA    P      40      -       -           -
LGA    G      41      -       -           -
LGA    Q      42      -       -           -
LGA    A      43      A      43          0.951
LGA    R      44      R      44          0.570
LGA    L      45      L      45          1.086
LGA    A      46      A      46          1.044
LGA    -       -      F      47           -
LGA    R      48      R      48          0.335
LGA    V      49      V      49          0.281
LGA    E      50      E      50          0.757
LGA    E      51      E      51          1.789
LGA    H      52      H      52          1.962
LGA    -       -      H      53           -
LGA    T      54      T      54          1.368
LGA    N      55      N      55          1.130
LGA    G      56      G      56          4.979
LGA    L      57      L      57          4.817
LGA    G      58      G      58          3.183
LGA    N      59      N      59          1.482
LGA    C      60      C      60          0.810
LGA    H      61      H      61          0.929
LGA    G      62      G      62          1.593
LGA    G      63      G      63          1.800
LGA    M      64      M      64          1.085
LGA    L      65      L      65          0.719
LGA    M      66      M      66          1.447
LGA    S      67      S      67          1.829
LGA    F      68      F      68          1.376
LGA    A      69      A      69          1.305
LGA    D      70      D      70          1.765
LGA    M      71      M      71          1.685
LGA    A      72      A      72          1.338
LGA    W      73      W      73          2.467
LGA    G      74      G      74          3.173
LGA    R      75      R      75          1.886
LGA    I      76      I      76          1.232
LGA    I      77      I      77          0.822
LGA    S      78      S      78          0.675
LGA    Q      80      L      79          0.590
LGA    K      81      Q      80          1.430
LGA    S      82      K      81          1.512
LGA    -       -      S      82           -
LGA    Y      83      Y      83          3.695
LGA    S      84      S      84          2.936
LGA    W      85      W      85          1.815
LGA    V      86      V      86          1.093
LGA    T      87      T      87          0.883
LGA    V      88      V      88          0.980
LGA    R      89      R      89          1.200
LGA    L      90      L      90          0.945
LGA    M      91      M      91          0.788
LGA    C      92      C      92          0.561
LGA    D      93      D      93          0.628
LGA    F      94      F      94          0.610
LGA    L      95      L      95          0.640
LGA    S      96      S      96          0.709
LGA    G      97      G      97          0.697
LGA    A      98      A      98          0.781
LGA    K      99      K      99          0.508
LGA    L     100      L     100          0.368
LGA    G     101      G     101          0.614
LGA    D     102      D     102          0.370
LGA    W     103      W     103          0.298
LGA    V     104      V     104          0.213
LGA    E     105      E     105          0.620
LGA    G     106      G     106          0.616
LGA    E     107      E     107          0.995
LGA    G     108      G     108          1.762
LGA    E     109      E     109          1.826
LGA    L     110      L     110          1.204
LGA    I     111      I     111          1.256
LGA    S     112      S     112          1.049
LGA    E     113      E     113          1.257
LGA    E     114      E     114          1.303
LGA    D     115      D     115          1.204
LGA    M     116      M     116          2.618
LGA    L     117      L     117          0.946
LGA    F     118      F     118          1.607
LGA    T     119      T     119          0.841
LGA    V     120      V     120          0.914
LGA    R     121      R     121          1.795
LGA    G     122      G     122          2.011
LGA    R     123      R     123          0.666
LGA    I     124      I     124          0.715
LGA    W     125      W     125          0.622
LGA    A     126      A     126          0.459
LGA    G     127      G     127          2.836
LGA    E     128      E     128          1.992
LGA    R     129      R     129          1.124
LGA    T     130      T     130          0.238
LGA    L     131      L     131          0.772
LGA    I     132      I     132          0.927
LGA    T     133      T     133          1.328
LGA    G     134      G     134          2.370
LGA    T     135      T     135          0.591
LGA    G     136      G     136          0.778
LGA    V     137      V     137          1.349
LGA    F     138      F     138          1.449
LGA    K     139      K     139          1.500
LGA    A     140      A     140          2.352
LGA    -       -      L     141           -
LGA    -       -      S     142           -
LGA    -       -      A     143           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  119  128    5.0    108    1.93    92.59     76.621     5.328

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.871264 * X  +   0.207421 * Y  +  -0.444832 * Z  +  38.881004
  Y_new =   0.490672 * X  +  -0.346241 * Y  +   0.799599 * Z  + -52.465637
  Z_new =   0.011835 * X  +  -0.914928 * Y  +  -0.403443 * Z  +  63.477257 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.986104    1.155489  [ DEG:  -113.7954     66.2046 ]
  Theta =  -0.011835   -3.129758  [ DEG:    -0.6781   -179.3219 ]
  Phi   =   0.512900   -2.628692  [ DEG:    29.3870   -150.6130 ]
 
# 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: T0322TS677_2-D1                               
REMARK     2: T0322_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0322TS677_2-D1.T0322_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  119  128   5.0  108   1.93   92.59  76.621
REMARK  ---------------------------------------------------------- 
MOLECULE T0322TS677_2-D1
PFRMAT TS
TARGET T0322
MODEL  2  REFINED
PARENT 2fs2_A
ATOM      8  CA  GLY    16      23.801  -1.753 -13.843  1.00 77.00
ATOM      9  CA  PHE    17      23.765  -2.650 -10.183  1.00 81.00
ATOM     10  CA  SER    18      21.764   0.485  -9.418  1.00 76.00
ATOM     11  CA  GLN    19      19.159  -0.311 -12.160  1.00 99.00
ATOM     13  CA  ASN    21      18.317  -2.675  -7.257  1.00 78.00
ATOM     14  CA  TRP    22      15.532  -0.439  -8.500  1.00 90.00
ATOM     15  CA  SER    23      13.835  -3.074 -10.534  1.00 73.00
ATOM     16  CA  ARG    24      14.016  -5.483  -7.596  1.00 62.00
ATOM     17  CA  GLY    25      12.371  -2.950  -5.292  1.00 32.00
ATOM     18  CA  PHE    26       9.430  -2.530  -7.639  1.00 52.00
ATOM     19  CA  GLY    27       9.122  -6.300  -8.001  1.00 44.00
ATOM     20  CA  ARG    28       9.137  -6.777  -4.256  1.00 47.00
ATOM     21  CA  GLN    29       6.434  -4.156  -3.884  1.00 59.00
ATOM     22  CA  ILE    30       4.304  -5.840  -6.514  1.00 60.00
ATOM     23  CA  PRO    32       4.944  -9.429  -5.346  1.00 85.00
ATOM     24  CA  LEU    33       6.840 -10.426  -8.485  1.00 83.00
ATOM     25  CA  PHE    34       9.314 -13.264  -8.521  1.00 99.00
ATOM     26  CA  GLU    35      12.059 -14.063 -11.127  1.00 99.00
ATOM     27  CA  HIS    36      11.749 -17.578 -12.491  1.00 99.00
ATOM     28  CA  ARG    37      14.224 -17.578 -15.402  1.00 76.00
ATOM     30  CA  GLY    39      19.147 -14.743 -19.427  1.00 54.00
ATOM     31  CA  PRO    40      20.458 -12.629 -22.180  1.00 44.00
ATOM     32  CA  GLY    41      17.629 -10.442 -23.472  1.00 54.00
ATOM     33  CA  GLN    42      14.803 -12.216 -21.682  1.00 62.00
ATOM     34  CA  ALA    43      13.092 -12.665 -18.350  1.00 61.00
ATOM     35  CA  ARG    44      10.194 -14.749 -17.081  1.00 73.00
ATOM     36  CA  LEU    45       8.687 -13.425 -13.800  1.00 70.00
ATOM     37  CA  ALA    46       5.500 -14.519 -11.882  1.00 73.00
ATOM     39  CA  ARG    48      -0.305 -14.010  -7.983  1.00 97.00
ATOM     40  CA  VAL    49      -3.412 -11.845  -8.438  1.00 97.00
ATOM     41  CA  GLU    50      -4.734 -10.968  -4.931  1.00 99.00
ATOM     42  CA  GLU    51      -8.195  -9.643  -4.130  1.00 99.00
ATOM     43  CA  HIS    52      -6.603  -6.180  -3.666  1.00 99.00
ATOM     45  CA  THR    54      -9.484  -6.549  -8.624  1.00 69.00
ATOM     46  CA  ASN    55     -11.528  -4.038 -10.567  1.00 97.00
ATOM     47  CA  GLY    56     -15.374  -3.990 -10.384  1.00 67.00
ATOM     48  CA  LEU    57     -15.750  -7.027 -12.642  1.00 74.00
ATOM     49  CA  GLY    58     -13.491  -8.990 -10.216  1.00 58.00
ATOM     50  CA  ASN    59     -10.457  -9.215 -12.535  1.00 76.00
ATOM     51  CA  CYS    60      -6.974  -7.884 -12.426  1.00 31.00
ATOM     52  CA  HIS    61      -6.897  -4.165 -13.218  1.00 31.00
ATOM     53  CA  GLY    62      -5.128  -3.285 -16.461  1.00 43.00
ATOM     54  CA  GLY    63      -2.570  -1.188 -14.511  1.00 47.00
ATOM     55  CA  MET    64      -1.363  -4.090 -12.521  1.00 68.00
ATOM     56  CA  LEU    65      -1.082  -6.153 -15.623  1.00 78.00
ATOM     57  CA  MET    66       0.846  -3.194 -17.159  1.00 72.00
ATOM     58  CA  SER    67       3.228  -3.159 -14.173  1.00 46.00
ATOM     59  CA  PHE    68       3.812  -6.794 -14.143  1.00 57.00
ATOM     60  CA  ALA    69       4.735  -6.543 -17.881  1.00 20.00
ATOM     61  CA  ASP    70       6.880  -3.323 -17.232  1.00 22.00
ATOM     62  CA  MET    71       8.817  -5.118 -14.561  1.00 18.00
ATOM     63  CA  ALA    72       9.482  -8.173 -16.862  1.00  6.00
ATOM     64  CA  TRP    73      10.598  -5.712 -19.497  1.00  2.00
ATOM     65  CA  GLY    74      12.977  -3.874 -17.117  1.00  5.00
ATOM     66  CA  ARG    75      14.469  -7.216 -16.176  1.00  0.00
ATOM     67  CA  ILE    76      14.971  -8.144 -19.863  1.00 20.00
ATOM     68  CA  ILE    77      16.787  -4.707 -20.465  1.00 37.00
ATOM     69  CA  SER    78      18.873  -5.263 -17.342  1.00 41.00
ATOM     70  CA  GLN    80      19.853  -8.846 -18.294  1.00 51.00
ATOM     71  CA  LYS    81      22.216  -7.125 -20.749  1.00 42.00
ATOM     72  CA  SER    82      23.034  -3.867 -19.048  1.00 47.00
ATOM     73  CA  TYR    83      20.749  -1.798 -21.316  1.00 33.00
ATOM     74  CA  SER    84      18.688   0.202 -18.964  1.00 57.00
ATOM     75  CA  TRP    85      15.771   1.763 -20.911  1.00 53.00
ATOM     76  CA  VAL    86      12.290   3.265 -20.542  1.00 80.00
ATOM     77  CA  THR    87       9.270   2.553 -22.580  1.00 95.00
ATOM     78  CA  VAL    88       8.337   5.233 -24.978  1.00 98.00
ATOM     79  CA  ARG    89       5.257   3.447 -26.447  1.00 99.00
ATOM     80  CA  LEU    90       3.374   0.224 -25.675  1.00 95.00
ATOM     81  CA  MET    91       0.617  -1.768 -27.429  1.00 83.00
ATOM     82  CA  CYS    92      -1.460  -4.324 -25.402  1.00 60.00
ATOM     83  CA  ASP    93      -4.080  -6.916 -26.402  1.00 89.00
ATOM     84  CA  PHE    94      -6.094  -8.204 -23.378  1.00 57.00
ATOM     85  CA  LEU    95      -7.333 -11.748 -24.294  1.00 60.00
ATOM     86  CA  SER    96      -8.711 -13.117 -20.977  1.00 61.00
ATOM     87  CA  GLY    97      -8.984 -11.559 -17.549  1.00 66.00
ATOM     88  CA  ALA    98      -6.668 -12.492 -14.765  1.00 66.00
ATOM     89  CA  LYS    99      -8.742 -13.453 -11.744  1.00 50.00
ATOM     90  CA  LEU   100      -7.964 -13.407  -8.100  1.00 66.00
ATOM     91  CA  GLY   101      -5.711 -16.335  -7.307  1.00 84.00
ATOM     92  CA  ASP   102      -4.325 -16.820 -10.839  1.00 73.00
ATOM     93  CA  TRP   103      -0.564 -17.087 -11.076  1.00 69.00
ATOM     94  CA  VAL   104       0.444 -15.007 -14.007  1.00 69.00
ATOM     95  CA  GLU   105       3.761 -15.481 -15.789  1.00 70.00
ATOM     96  CA  GLY   106       5.068 -12.658 -17.792  1.00 40.00
ATOM     97  CA  GLU   107       7.855 -13.398 -20.379  1.00 54.00
ATOM     98  CA  GLY   108       9.716 -10.489 -21.875  1.00 29.00
ATOM     99  CA  GLU   109      11.996 -10.896 -24.917  1.00 70.00
ATOM    100  CA  LEU   110      14.009  -8.417 -26.837  1.00 72.00
ATOM    101  CA  ILE   111      12.986  -8.456 -30.521  1.00 99.00
ATOM    102  CA  SER   112      15.122  -5.631 -31.832  1.00 99.00
ATOM    103  CA  GLU   113      17.832  -3.580 -30.210  1.00 99.00
ATOM    104  CA  GLU   114      19.009  -0.499 -32.178  1.00 99.00
ATOM    105  CA  ASP   115      21.546   2.180 -31.148  1.00 99.00
ATOM    106  CA  MET   116      19.122   4.191 -29.025  1.00 99.00
ATOM    107  CA  LEU   117      15.954   2.142 -29.195  1.00 93.00
ATOM    108  CA  PHE   118      14.564  -1.362 -28.989  1.00 78.00
ATOM    109  CA  THR   119      11.390  -3.420 -29.253  1.00 47.00
ATOM    110  CA  VAL   120      10.427  -5.956 -26.583  1.00 19.00
ATOM    111  CA  ARG   121       7.517  -8.409 -26.629  1.00 19.00
ATOM    112  CA  GLY   122       5.891  -9.510 -23.408  1.00 11.00
ATOM    113  CA  ARG   123       3.314 -12.323 -23.104  1.00  9.00
ATOM    114  CA  ILE   124       1.389 -12.856 -19.826  1.00 13.00
ATOM    115  CA  TRP   125      -0.129 -16.323 -19.393  1.00 13.00
ATOM    116  CA  ALA   126      -2.109 -17.940 -16.556  1.00 26.00
ATOM    118  CA  GLY   127      -3.427 -23.062 -17.325  1.00 53.00
ATOM    119  CA  GLU   128      -0.886 -21.717 -19.777  1.00 74.00
ATOM    120  CA  ARG   129      -3.616 -19.624 -21.498  1.00 78.00
ATOM    121  CA  THR   130      -2.735 -16.133 -22.744  1.00 81.00
ATOM    122  CA  LEU   131      -3.997 -13.335 -20.703  1.00 81.00
ATOM    123  CA  ILE   132      -2.342 -10.406 -22.468  1.00 50.00
ATOM    124  CA  THR   133       0.252  -9.536 -25.242  1.00 41.00
ATOM    125  CA  GLY   134       2.441  -6.401 -25.096  1.00 25.00
ATOM    126  CA  THR   135       4.826  -5.024 -27.587  1.00 45.00
ATOM    127  CA  GLY   136       6.947  -2.143 -26.258  1.00 26.00
ATOM    128  CA  VAL   137       9.313   0.316 -27.950  1.00 39.00
ATOM    129  CA  PHE   138      12.121   1.264 -25.583  1.00 40.00
ATOM    130  CA  LYS   139      14.519   4.109 -25.269  1.00 40.00
ATOM    131  CA  ALA   140      18.272   3.923 -24.185  1.00 40.00
TER
END
