
#######################################################
#                                                     #
#                        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   15 (  120),  selected   15 , name T0318TS174_1u-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected  154 , name T0318_D1.pdb
# PARAMETERS: T0318TS174_1u-D1.T0318_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      T       2           -
LGA    -       -      Q       3           -
LGA    -       -      V       4           -
LGA    -       -      L       5           -
LGA    -       -      V       6           -
LGA    I     141      R       7          4.417
LGA    -       -      N       8           -
LGA    -       -      G       9           -
LGA    -       -      I      10           -
LGA    -       -      Q      11           -
LGA    -       -      A      12           -
LGA    -       -      V      13           -
LGA    -       -      G      14           -
LGA    -       -      D      15           -
LGA    -       -      G      16           -
LGA    -       -      L      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      L      20           -
LGA    -       -      I      21           -
LGA    -       -      I      22           -
LGA    -       -      V      23           -
LGA    -       -      G      24           -
LGA    -       -      K      25           -
LGA    -       -      K      26           -
LGA    -       -      S      27           -
LGA    -       -      V      28           -
LGA    -       -      L      29           -
LGA    -       -      K      30           -
LGA    -       -      N      31           -
LGA    -       -      V      32           -
LGA    -       -      T      33           -
LGA    -       -      F      34           -
LGA    -       -      E      35           -
LGA    -       -      G      36           -
LGA    -       -      K      37           -
LGA    -       -      F      38           -
LGA    -       -      K      39           -
LGA    -       -      E      40           -
LGA    -       -      V      41           -
LGA    -       -      A      42           -
LGA    -       -      Q      43           -
LGA    -       -      K      44           -
LGA    -       -      F      45           -
LGA    -       -      V      46           -
LGA    -       -      T      47           -
LGA    -       -      D      48           -
LGA    -       -      G      49           -
LGA    -       -      D      50           -
LGA    -       -      S      51           -
LGA    -       -      W      52           -
LGA    -       -      N      53           -
LGA    -       -      S      54           -
LGA    -       -      M      55           -
LGA    -       -      I      56           -
LGA    -       -      S      57           -
LGA    -       -      R      58           -
LGA    -       -      I      59           -
LGA    -       -      P      60           -
LGA    -       -      A      61           -
LGA    -       -      S      62           -
LGA    -       -      G      63           -
LGA    -       -      R      64           -
LGA    -       -      H      65           -
LGA    -       -      P      66           -
LGA    -       -      L      67           -
LGA    -       -      H      68           -
LGA    -       -      Y      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      A      72           -
LGA    -       -      H      73           -
LGA    -       -      L      74           -
LGA    -       -      I      75           -
LGA    -       -      T      76           -
LGA    -       -      V      77           -
LGA    -       -      P      78           -
LGA    -       -      D      79           -
LGA    -       -      A      80           -
LGA    -       -      S      81           -
LGA    -       -      S      82           -
LGA    -       -      R      83           -
LGA    -       -      G      84           -
LGA    -       -      N      85           -
LGA    -       -      T      86           -
LGA    -       -      P      87           -
LGA    -       -      T      88           -
LGA    -       -      N      89           -
LGA    -       -      A      90           -
LGA    -       -      H      91           -
LGA    -       -      S      92           -
LGA    -       -      I      93           -
LGA    -       -      Y      94           -
LGA    -       -      K      95           -
LGA    -       -      E      96           -
LGA    -       -      L      97           -
LGA    -       -      K      98           -
LGA    -       -      P      99           -
LGA    -       -      I     100           -
LGA    -       -      N     101           -
LGA    -       -      Y     102           -
LGA    -       -      P     103           -
LGA    -       -      E     104           -
LGA    -       -      D     105           -
LGA    -       -      T     106           -
LGA    -       -      K     107           -
LGA    -       -      N     108           -
LGA    -       -      V     109           -
LGA    -       -      H     110           -
LGA    -       -      F     111           -
LGA    -       -      V     112           -
LGA    -       -      L     113           -
LGA    -       -      F     114           -
LGA    -       -      A     115           -
LGA    -       -      E     116           -
LGA    -       -      Y     117           -
LGA    -       -      P     118           -
LGA    -       -      D     119           -
LGA    -       -      V     120           -
LGA    -       -      L     121           -
LGA    -       -      S     122           -
LGA    -       -      H     123           -
LGA    -       -      V     124           -
LGA    -       -      A     125           -
LGA    -       -      A     126           -
LGA    -       -      I     127           -
LGA    -       -      A     128           -
LGA    -       -      R     129           -
LGA    -       -      T     130           -
LGA    -       -      F     131           -
LGA    -       -      C     132           -
LGA    -       -      K     133           -
LGA    -       -      F     134           -
LGA    -       -      S     135           -
LGA    -       -      M     136           -
LGA    -       -      K     137           -
LGA    -       -      T     138           -
LGA    -       -      S     139           -
LGA    -       -      G     140           -
LGA    R     142      I     141          1.203
LGA    E     143      R     142          1.711
LGA    L     144      E     143          2.795
LGA    N     145      L     144          1.842
LGA    V     146      N     145          1.343
LGA    N     147      V     146          2.049
LGA    I     148      N     147          1.962
LGA    D     149      I     148          1.625
LGA    V     150      D     149          2.170
LGA    V     151      V     150          0.983
LGA    C     152      V     151          1.366
LGA    D     153      C     152          3.709
LGA    K     154      D     153          0.846
LGA    L     155      K     154          3.198
LGA    -       -      L     155           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15  154    5.0     15    2.31     6.67      8.232     0.623

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.120573 * X  +   0.269982 * Y  +  -0.955286 * Z  +  71.520927
  Y_new =   0.441741 * X  +   0.847190 * Y  +   0.295186 * Z  +   3.252233
  Z_new =   0.889004 * X  +  -0.457580 * Y  +  -0.017114 * Z  +  69.369278 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.608180    1.533413  [ DEG:   -92.1419     87.8581 ]
  Theta =  -1.095164   -2.046428  [ DEG:   -62.7483   -117.2517 ]
  Phi   =   1.304338   -1.837255  [ DEG:    74.7331   -105.2669 ]
 
# 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: T0318TS174_1u-D1                              
REMARK     2: T0318_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS174_1u-D1.T0318_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15  154   5.0   15   2.31    6.67   8.232
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS174_1u-D1
PFRMAT TS
TARGET T0318
MODEL 1  UNREFINED
PARENT 1lcp_A 
ATOM   1089  N   ILE   141      33.207  35.113   8.452  1.00  1.00
ATOM   1090  CA  ILE   141      33.026  34.631   9.816  1.00  1.00
ATOM   1091  C   ILE   141      34.395  34.166  10.321  1.00  1.00
ATOM   1092  O   ILE   141      35.056  33.356   9.657  1.00  1.00
ATOM   1093  CB  ILE   141      32.070  33.451   9.786  1.00  1.00
ATOM   1094  CG1 ILE   141      31.864  33.038  11.238  1.00  1.00
ATOM   1095  CG2 ILE   141      32.650  32.271   9.022  1.00  1.00
ATOM   1096  CD1 ILE   141      31.139  34.070  12.103  1.00  1.00
ATOM   1097  N   ARG   142      34.229  60.199  11.783  1.00  1.00
ATOM   1098  CA  ARG   142      33.584  59.803  10.529  1.00  1.00
ATOM   1099  C   ARG   142      34.112  58.444  10.105  1.00  1.00
ATOM   1100  O   ARG   142      33.397  57.658   9.489  1.00  1.00
ATOM   1101  CB  ARG   142      33.911  60.778   9.398  1.00  1.00
ATOM   1102  CG  ARG   142      33.226  60.409   8.243  1.00  1.00
ATOM   1103  CD  ARG   142      31.720  60.542   8.439  1.00  1.00
ATOM   1104  NE  ARG   142      30.997  60.209   7.386  1.00  1.00
ATOM   1105  CZ  ARG   142      30.614  58.953   7.092  1.00  1.00
ATOM   1106  NH1 ARG   142      29.887  58.736   6.005  1.00  1.00
ATOM   1107  NH2 ARG   142      31.114  57.996   8.107  1.00  1.00
ATOM   1108  N   GLU   143      35.391  58.204  10.361  1.00  1.00
ATOM   1109  CA  GLU   143      36.020  56.950   9.986  1.00  1.00
ATOM   1110  C   GLU   143      36.170  56.031  11.182  1.00  1.00
ATOM   1111  O   GLU   143      36.824  56.368  12.176  1.00  1.00
ATOM   1112  CB  GLU   143      37.346  57.227   9.294  1.00  1.00
ATOM   1113  CG  GLU   143      37.208  57.937   7.970  1.00  1.00
ATOM   1114  CD  GLU   143      37.154  59.443   8.114  1.00  1.00
ATOM   1115  OE1 GLU   143      37.205  60.006   9.160  1.00  1.00
ATOM   1116  OE2 GLU   143      37.040  60.039   6.946  1.00  1.00
ATOM   1117  N   LEU   144      35.546  54.864  11.081  1.00  1.00
ATOM   1118  CA  LEU   144      35.558  53.904  12.172  1.00  1.00
ATOM   1119  C   LEU   144      35.872  52.497  11.701  1.00  1.00
ATOM   1120  O   LEU   144      35.559  52.136  10.563  1.00  1.00
ATOM   1121  CB  LEU   144      34.181  53.888  12.833  1.00  1.00
ATOM   1122  CG  LEU   144      34.140  52.949  14.043  1.00  1.00
ATOM   1123  CD1 LEU   144      35.020  53.364  15.206  1.00  1.00
ATOM   1124  CD2 LEU   144      32.660  52.809  14.450  1.00  1.00
ATOM   1125  N   ASN   145      36.439  51.692  12.598  1.00  1.00
ATOM   1126  CA  ASN   145      36.754  50.305  12.293  1.00  1.00
ATOM   1127  C   ASN   145      35.424  49.561  12.193  1.00  1.00
ATOM   1128  O   ASN   145      34.388  50.062  12.634  1.00  1.00
ATOM   1129  CB  ASN   145      37.621  49.687  13.401  1.00  1.00
ATOM   1130  CG  ASN   145      36.873  49.687  14.729  1.00  1.00
ATOM   1131  OD1 ASN   145      36.324  50.699  15.147  1.00  1.00
ATOM   1132  ND2 ASN   145      36.863  48.528  15.364  1.00  1.00
ATOM   1133  N   VAL   146      35.450  48.380  11.592  1.00  1.00
ATOM   1134  CA  VAL   146      34.246  47.564  11.438  1.00  1.00
ATOM   1135  C   VAL   146      33.742  47.128  12.812  1.00  1.00
ATOM   1136  O   VAL   146      34.548  46.788  13.685  1.00  1.00
ATOM   1137  CB  VAL   146      34.557  46.306  10.578  1.00  1.00
ATOM   1138  CG1 VAL   146      33.364  45.379  10.501  1.00  1.00
ATOM   1139  CG2 VAL   146      34.983  46.724   9.179  1.00  1.00
ATOM   1140  N   ASN   147      32.426  47.162  13.019  1.00  1.00
ATOM   1141  CA  ASN   147      31.852  46.734  14.297  1.00  1.00
ATOM   1142  C   ASN   147      31.890  45.208  14.358  1.00  1.00
ATOM   1143  O   ASN   147      31.337  44.534  13.487  1.00  1.00
ATOM   1144  CB  ASN   147      30.393  47.224  14.462  1.00  1.00
ATOM   1145  CG  ASN   147      29.833  46.910  15.847  1.00  1.00
ATOM   1146  OD1 ASN   147      29.419  45.790  16.123  1.00  1.00
ATOM   1147  ND2 ASN   147      29.846  47.918  16.695  1.00  1.00
ATOM   1148  N   ILE   148      32.550  44.665  15.372  1.00  1.00
ATOM   1149  CA  ILE   148      32.662  43.214  15.503  1.00  1.00
ATOM   1150  C   ILE   148      31.729  42.621  16.552  1.00  1.00
ATOM   1151  O   ILE   148      31.654  43.104  17.683  1.00  1.00
ATOM   1152  CB  ILE   148      34.130  42.771  15.818  1.00  1.00
ATOM   1153  CG1 ILE   148      35.084  43.269  14.741  1.00  1.00
ATOM   1154  CG2 ILE   148      34.199  41.251  15.872  1.00  1.00
ATOM   1155  CD1 ILE   148      34.772  42.776  13.324  1.00  1.00
ATOM   1156  N   ASP   149      31.026  41.561  16.175  1.00  1.00
ATOM   1157  CA  ASP   149      30.132  40.876  17.093  1.00  1.00
ATOM   1158  C   ASP   149      30.799  39.570  17.537  1.00  1.00
ATOM   1159  O   ASP   149      30.903  38.619  16.750  1.00  1.00
ATOM   1160  CB  ASP   149      28.785  40.584  16.423  1.00  1.00
ATOM   1161  CG  ASP   149      27.790  39.934  17.377  1.00  1.00
ATOM   1162  OD1 ASP   149      27.324  40.401  18.315  1.00  1.00
ATOM   1163  OD2 ASP   149      27.511  38.736  16.970  1.00  1.00
ATOM   1164  N   VAL   150      31.314  39.565  18.769  1.00  1.00
ATOM   1165  CA  VAL   150      31.971  38.396  19.364  1.00  1.00
ATOM   1166  C   VAL   150      30.983  37.526  20.155  1.00  1.00
ATOM   1167  O   VAL   150      30.181  38.043  20.944  1.00  1.00
ATOM   1168  CB  VAL   150      33.127  38.846  20.278  1.00  1.00
ATOM   1169  CG1 VAL   150      34.180  39.628  19.518  1.00  1.00
ATOM   1170  CG2 VAL   150      33.726  37.624  20.939  1.00  1.00
ATOM   1171  N   VAL   151      31.048  36.210  19.950  1.00  1.00
ATOM   1172  CA  VAL   151      30.170  35.264  20.645  1.00  1.00
ATOM   1173  C   VAL   151      30.933  33.995  21.038  1.00  1.00
ATOM   1174  O   VAL   151      31.972  33.683  20.456  1.00  1.00
ATOM   1175  CB  VAL   151      28.977  34.880  19.753  1.00  1.00
ATOM   1176  CG1 VAL   151      29.418  34.164  18.491  1.00  1.00
ATOM   1177  CG2 VAL   151      28.181  36.125  19.431  1.00  1.00
ATOM   1178  N   CYS   152      30.433  33.283  22.044  1.00  1.00
ATOM   1179  CA  CYS   152      31.047  32.033  22.490  1.00  1.00
ATOM   1180  C   CYS   152      31.083  30.968  21.381  1.00  1.00
ATOM   1181  O   CYS   152      30.115  30.815  20.635  1.00  1.00
ATOM   1182  CB  CYS   152      30.253  31.458  23.675  1.00  1.00
ATOM   1183  SG  CYS   152      31.102  29.945  24.265  1.00  1.00
ATOM   1184  N   ASP   153      32.211  30.271  21.257  1.00  1.00
ATOM   1185  CA  ASP   153      32.335  29.172  20.305  1.00  1.00
ATOM   1186  C   ASP   153      31.866  27.938  21.096  1.00  1.00
ATOM   1187  O   ASP   153      32.469  27.562  22.104  1.00  1.00
ATOM   1188  CB  ASP   153      33.789  28.994  19.863  1.00  1.00
ATOM   1189  CG  ASP   153      33.950  27.906  18.809  1.00  1.00
ATOM   1190  OD1 ASP   153      33.533  27.909  17.740  1.00  1.00
ATOM   1191  OD2 ASP   153      34.664  26.935  19.287  1.00  1.00
ATOM   1192  N   LYS   154      30.764  27.342  20.670  1.00  1.00
ATOM   1193  CA  LYS   154      30.230  26.187  21.366  1.00  1.00
ATOM   1194  C   LYS   154      29.012  26.595  22.179  1.00  1.00
ATOM   1195  O   LYS   154      28.614  27.765  22.194  1.00  1.00
ATOM   1196  CB  LYS   154      29.840  25.040  21.549  1.00  1.00
ATOM   1197  CG  LYS   154      29.260  23.974  22.232  1.00  1.00
ATOM   1198  CD  LYS   154      29.150  22.747  21.322  1.00  1.00
ATOM   1199  CE  LYS   154      28.507  21.577  22.073  1.00  1.00
ATOM   1200  NZ  LYS   154      28.399  20.382  21.199  1.00  1.00
ATOM   1201  N   LEU   155      28.440  25.636  22.897  1.00  1.00
ATOM   1202  CA  LEU   155      27.241  25.884  23.683  1.00  1.00
ATOM   1203  C   LEU   155      27.304  25.411  25.128  1.00  1.00
ATOM   1204  O   LEU   155      26.281  25.407  25.810  1.00  1.00
ATOM   1205  CB  LEU   155      26.071  25.181  23.006  1.00  1.00
ATOM   1206  CG  LEU   155      26.143  23.657  22.926  1.00  1.00
ATOM   1207  CD1 LEU   155      25.833  22.927  24.228  1.00  1.00
ATOM   1208  CD2 LEU   155      25.213  23.215  21.775  1.00  1.00
TER
END
