If you simply want a list of modified residues, here is one that I
compiled a while ago. More details on each can be found at LigandExpo.
'0CS' => 'ALA', '0NC' => 'ALA', 'AA3' => 'ALA',
'AA4' => 'ALA', 'ABA' => 'ALA', 'AHO' => 'ALA', 'AHP' => 'ALA', 'AIB' =>
'ALA',
'ALC' => 'ALA', 'ALM' => 'ALA', 'ALN' => 'ALA', 'ALS' => 'ALA', 'APH' =>
'ALA',
'AYA' => 'ALA', 'B2A' => 'ALA', 'B3A' => 'ALA', 'BAL' => 'ALA', 'BNN' =>
'ALA',
'CAB' => 'ALA', 'CHG' => 'ALA', 'CLB' => 'ALA', 'CLD' => 'ALA', 'DAB' =>
'ALA',
'DAL' => 'ALA', 'DBU' => 'ALA', 'DBZ' => 'ALA', 'DHA' => 'ALA', 'DNP' =>
'ALA',
'DPP' => 'ALA', 'FLA' => 'ALA', 'HAC' => 'ALA', 'HMF' => 'ALA', 'HV5' =>
'ALA',
'IAM' => 'ALA', 'KYN' => 'ALA', 'LAL' => 'ALA', 'MAA' => 'ALA', 'NAL' =>
'ALA',
'NAM' => 'ALA', 'NCB' => 'ALA', 'ORN' => 'ALA', 'PAU' => 'ALA', 'PRR' =>
'ALA',
'PYA' => 'ALA', 'SEC' => 'ALA', 'SEG' => 'ALA', 'TIH' => 'ALA', 'UMA' =>
'ALA',
'CLV' => 'ALA,PHE,GLY', 'X9Q' => 'ALA,PHE,GLY', '175' => 'ALA,SER,GLY',
'CRW' => 'ALA,SER,GLY', 'CRX' => 'ALA,SER,GLY
',
'MDO' => 'ALA,SER,GLY', 'AYG' => 'ALA,TYR,GLY', '2MR' => 'ARG', 'AAR' =>
'ARG', 'ACL' => 'ARG',
'AGM' => 'ARG', 'ALG' => 'ARG', 'ARM' => 'ARG', 'BOR' => 'ARG', 'CIR' =>
'ARG',
'DAR' => 'ARG', 'DIR' => 'ARG', 'HAR' => 'ARG', 'HMR' => 'ARG', 'HRG' =>
'ARG',
'MAI' => 'ARG', 'MGG' => 'ARG', 'NMM' => 'ARG', 'NNH' => 'ARG', 'OPR' =>
'ARG',
'ORQ' => 'ARG', '0A5' => 'ASN', 'AFA' => 'ASN', 'AHB' => 'ASN', 'B3X' =>
'ASN',
'DMH' => 'ASN', 'DSG' => 'ASN', 'MEN' => 'ASN', 'NYG' => 'ASN,TYR,GLY',
'0A0' => 'ASP',
'0AK' => 'ASP', '2AS' => 'ASP', '3MD' => 'ASP', 'ACB' => 'ASP', 'AEI' =>
'ASP',
'AKL' => 'ASP', 'ASA' => 'ASP', 'ASB' => 'ASP', 'ASI' => 'ASP', 'ASK' =>
'ASP',
'ASL' => 'ASP', 'ASQ' => 'ASP', 'B3D' => 'ASP', 'BFD' => 'ASP', 'BHD' =>
'ASP',
'DAS' => 'ASP', 'DMK' => 'ASP', 'DOH' => 'ASP', 'DSP' => 'ASP', 'IAS' =>
'ASP',
'LAA' => 'ASP', 'OHS' => 'ASP', 'OXX' => 'ASP', 'PAS' => 'ASP', 'PHD' =>
'ASP',
'TAV' => 'ASP', 'SUI' => 'ASP,GLY', 'DYG' => 'ASP,TYR,GLY', 'XYG' =>
'ASP,TYR,GLY', '0A8' => 'CYS',
'5CS' => 'CYS', 'BBC' => 'CYS', 'BCS' => 'CYS', 'BCX' => 'CYS', 'BPE' =>
'CYS',
'BTC' => 'CYS', 'BUC' => 'CYS', 'C3Y' => 'CYS', 'C5C' => 'CYS', 'C6C' =>
'CYS',
'CAF' => 'CYS', 'CAS' => 'CYS', 'CCS' => 'CYS', 'CEA' => 'CYS', 'CME' =>
'CYS',
'CMH' => 'CYS', 'CML' => 'CYS', 'CMT' => 'CYS', 'CS0' => 'CYS', 'CS1' =>
'CYS',
'CS3' => 'CYS', 'CS4' => 'CYS', 'CSA' => 'CYS', 'CSB' => 'CYS', 'CSD' =>
'CYS',
'CSE' => 'CYS', 'CSO' => 'CYS', 'CSP' => 'CYS', 'CSR' => 'CYS', 'CSS' =>
'CYS',
'CSU' => 'CYS', 'CSW' => 'CYS', 'CSX' => 'CYS', 'CSZ' => 'CYS', 'CY0' =>
'CYS',
'CY1' => 'CYS', 'CY3' => 'CYS', 'CY4' => 'CYS', 'CYA' => 'CYS', 'CYD' =>
'CYS',
'CYF' => 'CYS', 'CYG' => 'CYS', 'CYM' => 'CYS', 'CYQ' => 'CYS', 'CYR' =>
'CYS',
'CZ2' => 'CYS', 'CZZ' => 'CYS', 'DCY' => 'CYS', 'EFC' => 'CYS', 'FOE' =>
'CYS',
'GT9' => 'CYS', 'HTI' => 'CYS', 'K1R' => 'CYS', 'M0H' => 'CYS', 'MCS' =>
'CYS',
'NPH' => 'CYS', 'OCS' => 'CYS', 'OCY' => 'CYS', 'P1L' => 'CYS', 'PBB' =>
'CYS',
'PEC' => 'CYS', 'PR3' => 'CYS', 'PYX' => 'CYS', 'R1A' => 'CYS', 'R1B' =>
'CYS',
'R1F' => 'CYS', 'R7A' => 'CYS', 'RCY' => 'CYS', 'SAH' => 'CYS', 'SCH' =>
'CYS',
'SCS' => 'CYS', 'SCY' => 'CYS', 'SHC' => 'CYS', 'SIB' => 'CYS', 'SMC' =>
'CYS',
'SNC' => 'CYS', 'SOC' => 'CYS', 'TNB' => 'CYS', 'YCM' => 'CYS', 'GYC' =>
'CYS,TYR,GLY',
'DGN' => 'GLN', 'GHG' => 'GLN', 'GLH' => 'GLN', 'MEQ' => 'GLN', 'MGN' =>
'GLN',
'NLQ' => 'GLN', 'QLG' => 'GLN,LEU,GLY', 'CRQ' => 'GLN,TYR,GLY', '5HP' =>
'GLU', 'AR4' => 'GLU',
'B3E' => 'GLU', 'CGA' => 'GLU', 'CGU' => 'GLU', 'CRU' => 'GLU', 'DGL' =>
'GLU',
'GAU' => 'GLU', 'GGL' => 'GLU', 'GLQ' => 'GLU', 'GMA' => 'GLU', 'GSU' =>
'GLU',
'ILG' => 'GLU', 'LME' => 'GLU', 'MEG' => 'GLU', 'NHL' => 'GLU', 'PCA' =>
'GLU',
'0AC' => 'GLY', 'CHP' => 'GLY', 'CR5' => 'GLY', 'CSI' => 'GLY', 'FGL' =>
'GLY',
'GHP' => 'GLY', 'GLZ' => 'GLY', 'GSC' => 'GLY', 'IGL' => 'GLY', 'LPG' =>
'GLY',
'LVG' => 'GLY', 'MEU' => 'GLY', 'MGY' => 'GLY', 'MPQ' => 'GLY', 'NMC' =>
'GLY',
'PG9' => 'GLY', 'PGY' => 'GLY', 'SAR' => 'GLY', 'SHP' => 'GLY', 'TBG' =>
'GLY',
'4F3' => 'GLY,TYR,GLY', 'CR2' => 'GLY,TYR,GLY', 'CRO' => 'GLY,TYR,GLY',
'MFC' => 'GLY,TYR,GLY', '3AH' => 'HIS',
'DDE' => 'HIS', 'DHI' => 'HIS', 'HBN' => 'HIS', 'HIA' => 'HIS', 'HIC' =>
'HIS',
'HIP' => 'HIS', 'HIQ' => 'HIS', 'HSO' => 'HIS', 'MHS' => 'HIS', 'NEM' =>
'HIS',
'NEP' => 'HIS', 'NZH' => 'HIS', 'OHI' => 'HIS', 'PSH' => 'HIS', 'PVH' =>
'HIS',
'CR8' => 'HIS,TYR,GLY', 'RC7' => 'HIS,TYR,GLY', 'B2I' => 'ILE', 'DIL' =>
'ILE', 'IIL' => 'ILE',
'ILX' => 'ILE', 'IML' => 'ILE', '0AG' => 'LEU', '1LU' => 'LEU', '2LU' =>
'LEU',
'2ML' => 'LEU', 'BLE' => 'LEU', 'BTA' => 'LEU', 'BUG' => 'LEU', 'CL0' =>
'LEU',
'CLE' => 'LEU', 'DLE' => 'LEU', 'DNE' => 'LEU', 'DNG' => 'LEU', 'DNM' =>
'LEU',
'DON' => 'LEU', 'FLE' => 'LEU', 'HLU' => 'LEU', 'LED' => 'LEU', 'LEF' =>
'LEU',
'MHL' => 'LEU', 'MLE' => 'LEU', 'MLL' => 'LEU', 'MNL' => 'LEU', 'NLE' =>
'LEU',
'NLN' => 'LEU', 'NLO' => 'LEU', 'NLP' => 'LEU', 'PLE' => 'LEU', 'PPH' =>
'LEU',
'LNT' => 'LEU,THR', '0A2' => 'LYS', '0AY' => 'LYS', '6CL' => 'LYS',
'ALY' => 'LYS',
'API' => 'LYS', 'APK' => 'LYS', 'AZK' => 'LYS', 'B3K' => 'LYS', 'BLY' =>
'LYS',
'C1X' => 'LYS', 'CCL' => 'LYS', 'CLG' => 'LYS', 'CLH' => 'LYS', 'DLS' =>
'LYS',
'DLY' => 'LYS', 'DM0' => 'LYS', 'DNL' => 'LYS', 'DNS' => 'LYS', 'GPL' =>
'LYS',
'I58' => 'LYS', 'IT1' => 'LYS', 'KCX' => 'LYS', 'KGC' => 'LYS', 'KST' =>
'LYS',
'LA2' => 'LYS', 'LCK' => 'LYS', 'LCX' => 'LYS', 'LDH' => 'LYS', 'LLP' =>
'LYS',
'LLY' => 'LYS', 'LYM' => 'LYS', 'LYN' => 'LYS', 'LYR' => 'LYS', 'LYX' =>
'LYS',
'LYZ' => 'LYS', 'M3L' => 'LYS', 'MCL' => 'LYS', 'MLY' => 'LYS', 'MLZ' =>
'LYS',
'SHR' => 'LYS', 'SLZ' => 'LYS', 'TRG' => 'LYS', 'XX1' => 'LYS', 'CH7' =>
'LYS,TYR,GLY',
'CR7' => 'LYS,TYR,GLY', '2FM' => 'MET', 'CXM' => 'MET', 'FME' => 'MET',
'KOR' => 'MET',
'MHO' => 'MET', 'MME' => 'MET', 'MSE' => 'MET', 'MSL' => 'MET', 'MSO' =>
'MET',
'OMT' => 'MET', 'SME' => 'MET', 'CH6' => 'MET,TYR,GLY', 'CRK' =>
'MET,TYR,GLY', 'NRQ' => 'MET,TYR,GLY',
'0A9' => 'PHE', '1PA' => 'PHE', '200' => 'PHE', '23F' => 'PHE', '4PH' =>
'PHE',
'B1F' => 'PHE', 'B2F' => 'PHE', 'BIF' => 'PHE', 'DAH' => 'PHE', 'DPH' =>
'PHE',
'DPN' => 'PHE', 'FCL' => 'PHE', 'FPA' => 'PHE', 'HPC' => 'PHE', 'HPE' =>
'PHE',
'HPQ' => 'PHE', 'IOY' => 'PHE', 'MEA' => 'PHE', 'NDF' => 'PHE', 'NFA' =>
'PHE',
'PBF' => 'PHE', 'PCS' => 'PHE', 'PF5' => 'PHE', 'PFF' => 'PHE', 'PHA' =>
'PHE',
'PHI' => 'PHE', 'PHL' => 'PHE', 'PHM' => 'PHE', 'PM3' => 'PHE', 'PPN' =>
'PHE',
'PSA' => 'PHE', 'SMF' => 'PHE', 'T11' => 'PHE', 'TFQ' => 'PHE', 'CFY' =>
'PHE,CYS,TYR,GLY',
'0AZ' => 'PRO', '2MT' => 'PRO', '4FB' => 'PRO', 'DPL' => 'PRO', 'DPR' =>
'PRO',
'H5M' => 'PRO', 'HY3' => 'PRO', 'HYP' => 'PRO', 'LPD' => 'PRO', 'N7P' =>
'PRO',
'P2Y' => 'PRO', 'PCC' => 'PRO', 'POM' => 'PRO', 'PRS' => 'PRO', '0AH' =>
'SER',
'B3S' => 'SER', 'BSE' => 'SER', 'CWR' => 'SER', 'DBS' => 'SER', 'DSE' =>
'SER',
'DSN' => 'SER', 'FGP' => 'SER', 'HSE' => 'SER', 'HSL' => 'SER', 'LPS' =>
'SER',
'MC1' => 'SER', 'MIS' => 'SER', 'N10' => 'SER', 'NC1' => 'SER', 'OAS' =>
'SER',
'OSE' => 'SER', 'PG1' => 'SER', 'SAC' => 'SER', 'SBD' => 'SER', 'SBL' =>
'SER',
'SDP' => 'SER', 'SEB' => 'SER', 'SEL' => 'SER', 'SEP' => 'SER', 'SET' =>
'SER',
'SOY' => 'SER', 'SVA' => 'SER', 'TNR' => 'SER', 'IIC' => 'SER,HIS,GLY',
'CSY' => 'SER,TYR,GLY',
'GYS' => 'SER,TYR,GLY', 'D11' => 'T', 'ALO' => 'THR', 'BMT' => 'THR',
'CTH' => 'THR',
'DTH' => 'THR', 'IYT' => 'THR', 'TBM' => 'THR', 'THC' => 'THR', 'TMB' =>
'THR',
'TMD' => 'THR', 'TPO' => 'THR', 'XXY' => 'THR,HIS,GLY', 'CR0' =>
'THR,LEU,GLY', 'C99' => 'THR,PHE,GLY',
'CRF' => 'THR,TRP,GLY', 'C12' => 'THR,TYR,GLY', '0AF' => 'TRP', '1TQ' =>
'TRP', '4DP' => 'TRP',
'4FW' => 'TRP', '4HT' => 'TRP', '6CW' => 'TRP', 'DTR' => 'TRP', 'FT6' =>
'TRP',
'FTR' => 'TRP', 'HRP' => 'TRP', 'HTR' => 'TRP', 'LTR' => 'TRP', 'PAT' =>
'TRP',
'TOX' => 'TRP', 'TPL' => 'TRP', 'TQQ' => 'TRP', 'TRN' => 'TRP', 'TRO' =>
'TRP',
'TRQ' => 'TRP', 'TRW' => 'TRP', 'TRX' => 'TRP', 'TTQ' => 'TRP', '0A1' =>
'TYR',
'1TY' => 'TYR', '2TY' => 'TYR', 'AZY' => 'TYR', 'B3Y' => 'TYR', 'DBY' =>
'TYR',
'DPQ' => 'TYR', 'DTY' => 'TYR', 'FTY' => 'TYR', 'IYR' => 'TYR', 'MBQ' =>
'TYR',
'NBQ' => 'TYR', 'NIY' => 'TYR', 'NTY' => 'TYR', 'OTY' => 'TYR', 'PAQ' =>
'TYR',
'PTH' => 'TYR', 'PTM' => 'TYR', 'PTR' => 'TYR', 'STY' => 'TYR', 'TPQ' =>
'TYR',
'TTS' => 'TYR', 'TYB' => 'TYR', 'TYI' => 'TYR', 'TYN' => 'TYR', 'TYO' =>
'TYR',
'TYQ' => 'TYR', 'TYS' => 'TYR', 'TYT' => 'TYR', 'TYY' => 'TYR', '0AA' =>
'VAL',
'0AB' => 'VAL', '2VA' => 'VAL', 'B2V' => 'VAL', 'DHN' => 'VAL', 'DIV' =>
'VAL',
'DVA' => 'VAL', 'MNV' => 'VAL', 'MVA' => 'VAL', 'NVA' => 'VAL', 'VAD' =>
'VAL',
'VAF' => 'VAL',
Thanks,
Abhinav
JCSG@SSRL, SLAC
Phone: (650) 926-2992
Fax: (650) 926-3292
On 07/26/2011 10:46 AM, Bernhard Rupp (Hofkristallrat a.D.) wrote:
Dear All,
Is there a simple way (or already an existing list) to extract/parse from
the heterodictionaries or monomer libraries which 3-letter symbols are
actually modified standard amino acids (as compared to bona fide ligands,
solvent molecules etc)?
Thx!!
BR
-----------------------------------------------------------------
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
------------------------------------------------------------------
Knowledge: When you know a thing, to know that you know it,
and when you do not know a thing, to recognize that you
do not know it.
Conficius.
------------------------------------------------------------------
