
#######################################################
#                                                     #
#                        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   84 (   84),  selected   84 , name T0299TS677_1-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299TS677_1-D2.T0299_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L      79      -       -           -
LGA    E      80      -       -           -
LGA    D      81      -       -           -
LGA    F      82      -       -           -
LGA    E      83      -       -           -
LGA    A      84      -       -           -
LGA    E      85      -       -           -
LGA    L      86      -       -           -
LGA    E      87      -       -           -
LGA    N      88      -       -           -
LGA    A      91      L      79          3.204
LGA    W      92      E      80          5.597
LGA    W      93      -       -           -
LGA    S      94      -       -           -
LGA    R      95      D      81           #
LGA    D      96      -       -           -
LGA    L      97      -       -           -
LGA    A      98      -       -           -
LGA    R      99      -       -           -
LGA    K     100      -       -           -
LGA    D     101      -       -           -
LGA    F     102      F      82          2.668
LGA    L     103      E      83           #
LGA    -       -      A      84           -
LGA    F     104      E      85          1.789
LGA    -       -      L      86           -
LGA    -       -      E      87           -
LGA    Y     105      N      88          3.699
LGA    T     106      L      89          3.047
LGA    E     107      P      90          3.018
LGA    G     108      A      91           #
LGA    L     109      W      92           -
LGA    D     110      W      93           -
LGA    V     111      S      94           -
LGA    D     112      R      95           -
LGA    Q     113      D      96           -
LGA    V     114      L      97           -
LGA    I     115      A      98           -
LGA    A     116      R      99           -
LGA    T     117      K     100           -
LGA    V     118      D     101           -
LGA    E     119      -       -           -
LGA    S     120      -       -           -
LGA    L     121      -       -           -
LGA    E     122      -       -           -
LGA    L     123      -       -           -
LGA    K     124      -       -           -
LGA    D     125      -       -           -
LGA    E     126      -       -           -
LGA    V     127      -       -           -
LGA    L     128      F     102          5.330
LGA    Y     129      L     103           #
LGA    F     130      -       -           -
LGA    G     131      -       -           -
LGA    K     132      -       -           -
LGA    G     134      F     104          0.549
LGA    -       -      Y     105           -
LGA    -       -      T     106           -
LGA    -       -      E     107           -
LGA    -       -      G     108           -
LGA    -       -      L     109           -
LGA    -       -      D     110           -
LGA    -       -      V     111           -
LGA    -       -      D     112           -
LGA    -       -      Q     113           -
LGA    -       -      V     114           -
LGA    -       -      I     115           -
LGA    -       -      A     116           -
LGA    -       -      T     117           -
LGA    -       -      V     118           -
LGA    -       -      E     119           -
LGA    -       -      S     120           -
LGA    -       -      L     121           -
LGA    -       -      E     122           -
LGA    -       -      L     123           -
LGA    -       -      K     124           -
LGA    -       -      D     125           -
LGA    -       -      E     126           -
LGA    -       -      V     127           -
LGA    -       -      L     128           -
LGA    -       -      Y     129           -
LGA    -       -      F     130           -
LGA    -       -      G     131           -
LGA    -       -      K     132           -
LGA    -       -      L     133           -
LGA    -       -      G     134           -
LGA    I     135      I     135          2.773
LGA    F     136      F     136          2.641
LGA    W     137      W     137          2.334
LGA    G     138      G     138          1.571
LGA    K     139      K     139          1.480
LGA    F     140      F     140          2.630
LGA    S     141      S     141          3.092
LGA    E     142      E     142          3.476
LGA    E     143      E     143          4.514
LGA    S     144      S     144          3.009
LGA    Y     145      Y     145          2.650
LGA    S     146      S     146          2.511
LGA    -       -      K     147           -
LGA    K     147      T     148          3.295
LGA    T     148      A     149          2.826
LGA    -       -      Y     150           -
LGA    A     149      H     151          0.220
LGA    Y     150      K     152          1.256
LGA    H     151      Y     153          2.770
LGA    K     152      L     154          2.709
LGA    Y     153      L     155          2.305
LGA    L     154      K     156          2.983
LGA    L     155      V     157          3.960
LGA    K     156      -       -           -
LGA    V     157      P     158          4.469
LGA    P     158      F     159          2.009
LGA    F     159      Y     160          3.190
LGA    -       -      R     161           -
LGA    -       -      H     162           -
LGA    Y     160      I     163          2.994
LGA    R     161      T     164          2.880
LGA    H     162      I     165          2.726
LGA    I     163      R     166          2.761
LGA    T     164      N     167          3.138
LGA    I     165      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   84   89    5.0     38    3.04    34.21     25.082     1.211

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.118648 * X  +   0.878214 * Y  +  -0.463318 * Z  +  27.708136
  Y_new =  -0.120627 * X  +   0.475906 * Y  +   0.871185 * Z  +  40.960594
  Z_new =   0.985582 * X  +  -0.047476 * Y  +   0.162401 * Z  +  24.711592 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.284411    2.857182  [ DEG:   -16.2956    163.7045 ]
  Theta =  -1.400780   -1.740813  [ DEG:   -80.2588    -99.7412 ]
  Phi   =  -0.793668    2.347925  [ DEG:   -45.4738    134.5262 ]
 
# 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: T0299TS677_1-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS677_1-D2.T0299_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   84   89   5.0   38   3.04   34.21  25.082
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS677_1-D2
PFRMAT     TS
TARGET     T0299
MODEL      1
PARENT     1lf1A
ATOM    112  CA  LEU    79      -2.860  71.399  -2.529  1.00 36.00
ATOM    113  CA  GLU    80      -6.320  72.900  -2.423  1.00 29.00
ATOM    114  CA  ASP    81      -6.782  72.019  -6.063  1.00 29.00
ATOM    115  CA  PHE    82      -5.313  68.542  -5.370  1.00 48.00
ATOM    116  CA  GLU    83      -7.912  68.035  -2.679  1.00 76.00
ATOM    117  CA  ALA    84     -10.825  68.973  -4.927  1.00 65.00
ATOM    118  CA  GLU    85      -9.515  66.777  -7.755  1.00 87.00
ATOM    119  CA  LEU    86      -9.013  63.658  -5.573  1.00 83.00
ATOM    120  CA  GLU    87     -12.394  64.219  -3.860  1.00 76.00
ATOM    121  CA  ASN    88     -13.988  64.093  -7.325  1.00 31.00
ATOM    123  CA  ALA    91     -12.535  58.970  -5.355  1.00 30.00
ATOM    124  CA  TRP    92     -16.240  59.780  -5.383  1.00 23.00
ATOM    125  CA  TRP    93     -16.584  58.621  -8.997  1.00 19.00
ATOM    126  CA  SER    94     -14.439  55.479  -8.871  1.00 25.00
ATOM    127  CA  ARG    95     -13.739  54.625  -5.226  1.00 54.00
ATOM    128  CA  ASP    96     -16.031  51.591  -5.330  1.00 73.00
ATOM    129  CA  LEU    97     -13.878  49.879  -7.974  1.00 71.00
ATOM    130  CA  ALA    98     -10.689  47.942  -7.066  1.00 99.00
ATOM    131  CA  ARG    99      -8.923  49.133 -10.249  1.00 99.00
ATOM    132  CA  LYS   100      -7.923  52.578  -8.946  1.00 98.00
ATOM    133  CA  ASP   101      -4.563  53.538  -7.383  1.00 79.00
ATOM    134  CA  PHE   102      -3.998  57.189  -6.434  1.00 66.00
ATOM    135  CA  LEU   103      -0.560  58.829  -6.900  1.00  0.00
ATOM    136  CA  PHE   104      -0.979  62.114  -5.107  1.00  0.00
ATOM    137  CA  TYR   105       2.334  63.884  -5.812  1.00  9.00
ATOM    138  CA  THR   106       4.578  62.559  -8.621  1.00  8.00
ATOM    139  CA  GLU   107       8.038  64.023  -7.869  1.00 59.00
ATOM    140  CA  GLY   108       8.617  66.411  -5.007  1.00 80.00
ATOM    141  CA  LEU   109      12.025  68.041  -5.512  1.00 99.00
ATOM    142  CA  ASP   110      14.297  70.815  -4.238  1.00 99.00
ATOM    155  CA  VAL   111      -0.183  63.626   2.479  1.00 99.00
ATOM    156  CA  ASP   112      -1.955  63.937   5.811  1.00 86.00
ATOM    157  CA  GLN   113      -4.229  66.541   4.225  1.00 96.00
ATOM    158  CA  VAL   114      -5.010  64.751   0.941  1.00 86.00
ATOM    159  CA  ILE   115      -5.391  61.147   2.161  1.00 79.00
ATOM    160  CA  ALA   116      -8.390  61.888   4.466  1.00 59.00
ATOM    161  CA  THR   117     -10.329  63.521   1.622  1.00 84.00
ATOM    162  CA  VAL   118      -9.859  60.326  -0.419  1.00 71.00
ATOM    163  CA  GLU   119     -10.586  58.141   2.525  1.00 68.00
ATOM    164  CA  SER   120     -14.026  59.667   3.116  1.00 99.00
ATOM    165  CA  LEU   121     -15.004  58.233  -0.321  1.00 99.00
ATOM    166  CA  GLU   122     -12.655  55.300  -0.761  1.00 99.00
ATOM    167  CA  LEU   123     -11.516  53.643   2.458  1.00 99.00
ATOM    168  CA  LYS   124      -9.176  50.998   1.054  1.00 99.00
ATOM    169  CA  ASP   125      -7.639  51.617  -2.368  1.00 90.00
ATOM    170  CA  GLU   126      -3.885  52.123  -2.471  1.00 61.00
ATOM    171  CA  VAL   127      -2.341  55.563  -2.282  1.00 36.00
ATOM    172  CA  LEU   128       1.170  56.131  -3.674  1.00 22.00
ATOM    173  CA  TYR   129       2.987  59.093  -2.044  1.00  6.00
ATOM    174  CA  PHE   130       5.994  60.790  -3.710  1.00 10.00
ATOM    175  CA  GLY   131       9.270  61.214  -1.893  1.00  3.00
ATOM    176  CA  LYS   132      12.079  63.733  -1.865  1.00 10.00
ATOM    196  CA  GLY   134       3.112  53.008  -0.639  1.00 10.00
ATOM    197  CA  ILE   135       6.114  55.272  -1.203  1.00  9.00
ATOM    198  CA  PHE   136       7.271  56.099  -4.719  1.00  0.00
ATOM    199  CA  TRP   137      10.737  55.248  -5.984  1.00 17.00
ATOM    200  CA  GLY   138      11.849  56.523  -9.426  1.00 66.00
ATOM    201  CA  LYS   139      15.116  55.859 -11.249  1.00 80.00
ATOM    202  CA  PHE   140      16.932  56.116 -14.562  1.00 99.00
ATOM    203  CA  SER   141      18.925  53.033 -15.550  1.00 99.00
ATOM    204  CA  GLU   142      21.611  55.063 -17.286  1.00 99.00
ATOM    205  CA  GLU   143      22.169  57.253 -14.165  1.00 88.00
ATOM    206  CA  SER   144      21.194  55.479 -10.932  1.00 88.00
ATOM    207  CA  TYR   145      23.349  52.996  -9.085  1.00 91.00
ATOM    208  CA  SER   146      23.940  50.817  -6.033  1.00 90.00
ATOM    209  CA  LYS   147      23.491  53.556  -3.439  1.00 99.00
ATOM    210  CA  THR   148      19.842  53.848  -4.589  1.00 99.00
ATOM    211  CA  ALA   149      19.338  50.078  -4.379  1.00 99.00
ATOM    212  CA  TYR   150      20.802  50.110  -0.866  1.00 99.00
ATOM    213  CA  HIS   151      18.361  52.914   0.030  1.00 99.00
ATOM    214  CA  LYS   152      15.436  50.930  -1.335  1.00 99.00
ATOM    215  CA  TYR   153      16.495  47.881   0.676  1.00 99.00
ATOM    216  CA  LEU   154      16.720  49.949   3.804  1.00 99.00
ATOM    217  CA  LEU   155      13.155  51.273   3.409  1.00 99.00
ATOM    218  CA  LYS   156      11.864  47.761   2.800  1.00 91.00
ATOM    219  CA  VAL   157      13.682  46.611   5.950  1.00 99.00
ATOM    220  CA  PRO   158      11.769  49.315   7.813  1.00 99.00
ATOM    221  CA  PHE   159       8.488  47.760   6.673  1.00 99.00
ATOM    222  CA  TYR   160       7.718  50.426   4.069  1.00 99.00
ATOM    223  CA  ARG   161       5.966  49.368   0.839  1.00 99.00
ATOM    224  CA  HIS   162       7.460  50.806  -2.318  1.00 99.00
ATOM    225  CA  ILE   163       5.956  51.241  -5.832  1.00 85.00
ATOM    226  CA  THR   164       8.315  52.050  -8.646  1.00 85.00
ATOM    227  CA  ILE   165       5.708  54.229 -10.404  1.00 85.00
TER
END
