// Conversion PDB-Intervor // all amino acids names on 3 chars, CAPITAL letters // AA are the standard ones + MSE (seleno-MET) + HOH + UNK // // annotations of atoms: 2->4 chars, beginning with a capital letter // annotations of pairs: 3-4 chars, lowercase //hydrogens not included since Intervor cares for heavy atoms only //BEGIN ATOMS ANNOTATIONS //Cali 2.0 //Caro 1.75 //Cpep 1.55 //Nhbd 1.55 //Naro 1.55 //NchP 1.44 //Ohbd 1.4 //Opep 1.4 //OchM 1.4 //Owat 1.4 //Sh 2.0 //Unk 2.0 //END ATOMS ANNOTATIONS BEGIN ATOMS ANNOTATIONS Cali 1.87 Caro 1.76 Cpep 1.76 Nhbd 1.65 Naro 1.65 NchP 1.50 Ohbd 1.4 Opep 1.4 OchM 1.4 Owat 1.4 Sh 1.85 Unk 2.0 END ATOMS ANNOTATIONS BEGIN PAIRS ANNOTATIONS ali aro hbd elf elu ssb unk hbw unkw END PAIRS ANNOTATIONS BEGIN ATOM ANNOTATIONS RESIDUE UNK ATOM " C " Cali ATOM " O " Ohbd ATOM " N " Nhbd ATOM " S " Sh ATOM " P " Unk ATOM " F " Unk ATOM " X " Unk END RESIDUE GLY ATOM " C " Cpep ATOM " CA " Cali ATOM " O " Opep ATOM " N " Nhbd ATOM " OXT" Ohbd END RESIDUE ALA ATOM " C " Cpep ATOM " CB " Cali ATOM " CA " Cali ATOM " O " Opep ATOM " N " Nhbd ATOM " OXT" Ohbd END RESIDUE LEU ATOM " C " Cpep ATOM " CB " Cali ATOM " CA " Cali ATOM " CG " Cali ATOM " O " Opep ATOM " N " Nhbd ATOM " CD1" Cali ATOM " CD2" Cali ATOM " OXT" Ohbd END RESIDUE ILE ATOM " C " Cpep ATOM " N " Nhbd ATOM " CB " Cali ATOM " CA " Cali ATOM " O " Opep ATOM " CD " Cali ATOM " CD1" Cali ATOM " CG1" Cali ATOM " CG2" Cali ATOM " OXT" Ohbd END RESIDUE VAL ATOM " C " Cpep ATOM " CB " Cali ATOM " CA " Cali ATOM " O " Opep ATOM " N " Nhbd ATOM " CG1" Cali ATOM " CG2" Cali ATOM " OXT" Ohbd END RESIDUE ASP ATOM " C " Cpep ATOM " CB " Cali ATOM " CA " Cali ATOM " CG " Caro ATOM " O " Opep ATOM " N " Nhbd ATOM " OD1" OchM ATOM " OD2" OchM ATOM " OXT" Ohbd END RESIDUE GLU ATOM " C " Cpep ATOM " CB " Cali ATOM " CA " Cali ATOM " CG " Cali ATOM " O " Opep ATOM " CD " Caro ATOM " N " Nhbd ATOM " OE2" OchM ATOM " OE1" OchM ATOM " OXT" Ohbd END RESIDUE ASN ATOM " C " Cpep ATOM " ND2" Nhbd ATOM " CB " Cali ATOM " CA " Cali ATOM " CG " Caro ATOM " O " Opep ATOM " N " Nhbd ATOM " OD1" Ohbd ATOM " OXT" Ohbd END RESIDUE GLN ATOM " C " Cpep ATOM " CB " Cali ATOM " CA " Cali ATOM " CG " Cali ATOM " O " Opep ATOM " CD " Caro ATOM " N " Nhbd ATOM " NE2" Nhbd ATOM " OE1" Ohbd ATOM " OXT" Ohbd END RESIDUE HIS ATOM " C " Cpep ATOM " CD2" Caro ATOM " CB " Cali ATOM " CA " Cali ATOM " CG " Caro ATOM " O " Opep ATOM " N " Nhbd ATOM " CE1" Caro ATOM " ND1" Naro ATOM " NE2" Naro ATOM " OXT" Ohbd END RESIDUE HSE ATOM " C " Cpep ATOM " CD2" Caro ATOM " CB " Cali ATOM " CA " Cali ATOM " CG " Caro ATOM " O " Opep ATOM " N " Nhbd ATOM " CE1" Caro ATOM " ND1" Naro ATOM " NE2" Naro ATOM " OXT" Ohbd END RESIDUE SER ATOM " C " Cpep ATOM " OG " Ohbd ATOM " CB " Cali ATOM " CA " Cali ATOM " O " Opep ATOM " N " Nhbd ATOM " OXT" Ohbd END RESIDUE THR ATOM " C " Cpep ATOM " CB " Cali ATOM " CA " Cali ATOM " OG1" Ohbd ATOM " O " Opep ATOM " N " Nhbd ATOM " CG2" Cali ATOM " OXT" Ohbd END RESIDUE CYS ATOM " C " Cpep ATOM " CB " Cali ATOM " CA " Cali ATOM " O " Opep ATOM " N " Nhbd ATOM " SG " Sh ATOM " OXT" Ohbd END RESIDUE MET ATOM " C " Cpep ATOM " CB " Cali ATOM " CA " Cali ATOM " CG " Cali ATOM " CE " Cali ATOM " N " Nhbd ATOM " SD " Sh ATOM " O " Opep ATOM " OXT" Ohbd END RESIDUE MSE ATOM " C " Cpep ATOM " CB " Cali ATOM " CA " Cali ATOM " CG " Cali ATOM " CE " Cali ATOM " N " Nhbd ATOM " SD " Sh ATOM " O " Opep ATOM " OXT" Ohbd ATOM "SE " Sh END RESIDUE PRO ATOM " C " Cpep ATOM " CB " Cali ATOM " CA " Cali ATOM " CG " Cali ATOM " O " Opep ATOM " CD " Cali ATOM " N " Nhbd ATOM " OXT" Ohbd END RESIDUE ARG ATOM " NE " NchP ATOM " C " Cpep ATOM " CB " Cali ATOM " CA " Cali ATOM " CG " Cali ATOM " O " Opep ATOM " CD " Cali ATOM " CZ " Caro ATOM " NH1" NchP ATOM " NH2" NchP ATOM " N " Nhbd ATOM " OXT" Ohbd END RESIDUE LYS ATOM " NZ " NchP ATOM " C " Cpep ATOM " CB " Cali ATOM " CA " Cali ATOM " CG " Cali ATOM " CE " Cali ATOM " CD " Cali ATOM " O " Opep ATOM " N " Nhbd ATOM " OXT" Ohbd END RESIDUE PHE ATOM " C " Cpep ATOM " CD2" Caro ATOM " CB " Cali ATOM " CA " Cali ATOM " CG " Caro ATOM " O " Opep ATOM " CZ " Caro ATOM " N " Nhbd ATOM " CD1" Caro ATOM " CE1" Caro ATOM " CE2" Caro ATOM " OXT" Ohbd END RESIDUE TYR ATOM " C " Cpep ATOM " CD2" Caro ATOM " OH " Ohbd ATOM " N " Nhbd ATOM " CB " Cali ATOM " CA " Cali ATOM " CG " Caro ATOM " O " Opep ATOM " CZ " Caro ATOM " CD1" Caro ATOM " CE1" Caro ATOM " CE2" Caro ATOM " OXT" Ohbd END RESIDUE TRP ATOM " CZ2" Caro ATOM " CZ3" Caro ATOM " CD1" Caro ATOM " CD2" Caro ATOM " CH2" Caro ATOM " C " Cpep ATOM " CB " Cali ATOM " CA " Cali ATOM " CG " Caro ATOM " O " Opep ATOM " N " Nhbd ATOM " CE3" Caro ATOM " CE2" Caro ATOM " NE1" Naro ATOM " OXT" Ohbd END RESIDUE HOH ATOM " O " Owat END END ATOM ANNOTATIONS BEGIN ANNOTATED PAIRS MATRIX Cali Cali ali Cali Caro ali Cali Cpep ali Cali Nhbd unk Cali Naro unk Cali NchP unk Cali Ohbd unk Cali Opep unk Cali OchM unk Cali Owat unkw Cali Sh unk Cali Unk unk Caro Caro aro Caro Cpep ali Caro Nhbd unk Caro Naro aro Caro NchP unk Caro Ohbd unk Caro Opep unk Caro OchM unk Caro Owat unkw Caro Sh unk Caro Unk unk Cpep Cpep ali Cpep Nhbd unk Cpep Naro unk Cpep NchP unk Cpep Ohbd unk Cpep Opep unk Cpep OchM unk Cpep Owat unkw Cpep Sh unk Cpep Unk unk Nhbd Nhbd hbd Nhbd Naro hbd Nhbd NchP hbd Nhbd Ohbd hbd Nhbd Opep hbd Nhbd OchM hbd Nhbd Owat hbw Nhbd Sh hbd Nhbd Unk unk Naro Naro hbd Naro NchP hbd Naro Ohbd hbd Naro Opep hbd Naro OchM hbd Naro Owat hbw Naro Sh hbd Naro Unk unk NchP NchP elu NchP Ohbd hbd NchP Opep hbd NchP OchM elf NchP Owat hbw NchP Sh hbd NchP Unk unk Ohbd Ohbd hbd Ohbd Opep hbd Ohbd OchM hbd Ohbd Owat hbw Ohbd Sh hbd Ohbd Unk unk Opep Opep unk Opep OchM unk Opep Owat hbw Opep Sh hbd Opep Unk unk OchM OchM elu OchM Owat hbw OchM Sh hbd OchM Unk unk Owat Owat hbw Owat Sh hbw Owat Unk unk Sh Sh ssb Sh Unk unk Unk Unk unk END ANNOTATED PAIRS MATRIX