REMARK REMARK Residues.dat REMARK REMARK REMARK REMARK Residues.dat is immediately read by Vince when the application is run. REMARK The data is scanned in and stored for future use as reference data for REMARK the residues in the sequence. This file REMARK contains the data for the standard twenty residues. The user can add REMARK data for any unusual residues that occur in the sequence. Use the REMARK format of the standard twenty residues as a guide to the format. REMARK REMARK REMARK The data format is described as follows. For each residue, the data REMARK begins on the Residue Declaration Line. This line begins with the REMARK token "RESIDUE" followed by a space or tab. Then follows the Three REMARK Letter Code for that residue immediately followed by a colon. REMARK Immediately after the colon follows the residue's One Letter Code. REMARK The One Letter Code is also immediately followed by a colon. That REMARK colon is then followed immediately by the name of the residue. This REMARK can be multiple tokens and is taken between the colon and the end of REMARK the line. REMARK REMARK REMARK The next line is the string MW followed by a few spaces or a tab REMARK character. The molecular weight then folows, then some blank lines. REMARK REMARK REMARK The next four lines begin with the strings, "C-alpha", "C-prime", REMARK "C-beta", and "Proton". After each string is the corresponding REMARK reference chemical shift relative to TSP, separated by a few spaces REMARK or a tab. Then follows a few more spaces or a tab, then a Delta REMARK value, which is a floating point number. Delta is added to the REMARK reference shift and subtracted from the reference REMARK shift to obtain a reference range for the chemical shift. REMARK REMARK REMARK Whether an observed shift is greater than or less than this range REMARK determines if the chemical shift index is one or minus one. A shift REMARK within the range corresponds to an index of zero. This process is REMARK described fully in the Journal of Biomolecular NMR, 4( 1994 ) REMARK 171 - 180, in the article "The 13C Chemical Shift Index...", by REMARK David S. Wishart and Brian D. Sykes. REMARK REMARK REMARK Then follow a few blank lines. Then follow a sequence of lines REMARK beginning with the string "ATOM". On each of these lines are a REMARK sequence of strings that represent atoms that exist in that residue. REMARK The first string after "ATOM" is the most REMARK common name of an atom appearing in the residue. Any strings that REMARK follow that name are synonyms ( up to ten ) for that name that could be REMARK found in any of the files that Vince might read. Look at the data for REMARK the standard twenty residues to get examples of these synonyms. REMARK REMARK REMARK After a blank line comes the METHYL line. After "METHYL" follows REMARK up to ten atoms which are methyl protons. These are names which the REMARK application will find invalid. These tokens are separated REMARK by spaces or tabs. These are the literal names for protons in the REMARK residue which should not appear without a wildcard in an NOE file. REMARK Example: HG11 in VAL should appear as HG1* or HG1#, not HG11. Vince REMARK will use these to determine if invalid methyl protons have been REMARK included in NOE's in the NOE file. REMARK REMARK REMARK After the METHYL line, the residue section may contain several REMARK additional lines whether it is hydrophobic, hydrophyllic, or aromatic. REMARK Simply add a line containing only the key word HYDROPHOBIC, REMARK HYDROPHYLLIC, or AROMATIC. REMARK REMARK REMARK Then after some blank lines, the Residue Declaration Line is found for REMARK the next residue. The user can add their own unusual residues to REMARK this file by adding an entry in the preceding format. This entry REMARK should be appended to the file several blank lines past the end of REMARK the currently last residue entry. REMARK REMARK REMARK Note: The first twenty residues in the file must be the standard REMARK twenty. Append other residues (up to 50) at the end of the file. REMARK REMARK RESIDUE ALA:A:Alanyl MW 71.1 C-alpha 52.5 0.7 C-prime 177.1 0.5 C-beta 19.0 0.7 Proton 4.35 0.10 ATOM HT+ ATOM C ATOM O ATOM CA ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB1 1HB ATOM HB2 2HB ATOM HB3 3HB ATOM HB# CB #HB 1HB 2HB 3HB HB* HB+ METHYL HB1 HB2 HB3 RESIDUE ARG:R:Arginyl MW 156.2 C-alpha 56.3 0.7 C-prime 176.5 0.5 C-beta 30.3 0.7 Proton 4.38 0.10 ATOM HT+ ATOM C ATOM O ATOM CA ATOM NE ATOM NH1 ATOM NH2 ATOM NH* NH+ ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB1 1HB ATOM HB2 2HB ATOM HB# CB #HB 1HB 2HB HB* HB+ ATOM HG1 1HG ATOM HG2 2HG ATOM HG# CG #HG 1HG 2HG HG* HG+ ATOM HD1 1HD ATOM HD2 2HD ATOM HD# CD #HD 1HD 2HD HD* HD+ ATOM HE HE ATOM HH11 1HH1 ATOM HH12 2HH1 ATOM HH21 1HH2 ATOM HH22 2HH2 ATOM HH1# NH1 #HH1 1HH1 2HH1 HH1* HH1+ ATOM HH2# NH2 #HH2 1HH2 2HH2 HH2* HH2+ ATOM HH* CZ #HH# 1HH1 2HH1 1HH2 2HH2 HH# HH++ METHYL RESIDUE ASN:N:Asparaginyl MW 114.1 C-alpha 53.6 0.7 C-prime 175.1 0.5 C-beta 39.0 0.7 Proton 4.75 0.10 ATOM HT+ ATOM C ATOM O ATOM CA ATOM CG ATOM OD1 OD# OD* OD+ ATOM ND2 ND# ND+ ND* ATOM HND1 HND* HND# HND+ ATOM HND2 ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB1 1HB ATOM HB2 2HB ATOM HB# CB #HB 1HB 2HB HB+ HB* ATOM HD1 1HD2 ATOM HD2 2HD2 ATOM HD# ND2 #HD2 1HD2 2HD2 HD+ HD* ATOM HD2# ND2 #HD2 1HD2 2HD2 HD2* HD2+ METHYL RESIDUE ASP:D:Aspartyl MW 115.1 C-alpha 54.1 0.7 C-prime 177.2 0.5 C-beta 40.8 0.7 Proton 4.76 0.10 ATOM HT+ ATOM CA ATOM C ATOM O ATOM CG ATOM OD1 OD# OD* OD+ ATOM OD2 ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB1 1HB ATOM HB2 2HB ATOM HB# CB #HB 1HB 2HB HB* HB+ METHYL RESIDUE CYS:C:Cysteinyl MW 103.2 C-alpha 58.3 0.7 C-prime 174.8 0.5 C-beta 28.6 0.7 Proton 4.65 0.10 ATOM HT+ ATOM C ATOM O ATOM CA ATOM SG ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB1 1HB ATOM HB2 2HB ATOM HB# CB #HB 1HB 2HB HB* HB+ ATOM HG HG METHYL RESIDUE GLN:Q:Glutaminyl MW 128.1 C-alpha 56.2 0.7 C-prime 176.3 0.5 C-beta 30.1 0.7 Proton 4.37 0.10 ATOM HT+ ATOM C ATOM O ATOM CA ATOM CD ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB1 1HB ATOM HB2 2HB ATOM HB# CB #HB 1HB 2HB HB* HB+ ATOM HG1 1HG ATOM HG2 2HG ATOM HG# CG #HG 1HG 2HG HG* HG+ ATOM HNE1 1HE2 ATOM HNE2 2HE2 ATOM HNE# NE2 #HE2 1HE2 2HE2 HNE* HNE+ ATOM HE2# NE2 #HE2 1HE2 2HE2 HE2* HE2+ ATOM OE1 OE* OE# OE+ ATOM NE2 NE* NE# NE+ METHYL RESIDUE GLU:E:Glutamyl MW 129.1 C-alpha 56.7 0.7 C-prime 176.1 0.5 C-beta 29.7 0.7 Proton 4.29 0.10 ATOM HT+ ATOM C ATOM O ATOM CA ATOM CD ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB1 1HB ATOM HB2 2HB ATOM HB# CB #HB 1HB 2HB HB* HB+ ATOM HG1 1HG ATOM HG2 2HG ATOM HG# CG #HG 1HG 2HG HG* HG+ ATOM OE1 OE# OE+ OE* ATOM OE2 METHYL RESIDUE GLY:G:Glycyl MW 57.1 C-alpha 45.0 0.7 C-prime 173.6 0.5 C-beta 3.97 0.10 !! These are for H !! Proton 3.97 0.10 !! These are for H !! ATOM HT+ ATOM C ATOM O ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA1 1HA ATOM HA2 2HA ATOM HA# CA #HA 1HA 2HA HA* HA+ ATOM CB ATOM CG METHYL RESIDUE HIS:H:Histidyl MW 137.2 C-alpha 55.8 0.7 C-prime 175.1 0.5 C-beta 32.0 0.7 Proton 4.63 0.10 ATOM HT+ ATOM C ATOM O ATOM CA ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB1 1HB ATOM HB2 2HB ATOM HB# CB #HB 1HB 2HB HB* HB+ ATOM HD1 HD1 ATOM HD2 HD2 HD+ HD* ATOM HE1 HE1 HE* HE+ ATOM ND1 ND+ ND# ND* ATOM CD2 CD+ CD* CD# ATOM CE1 CE# CE* CE+ ATOM NE2 NE# NE+ NE* METHYL AROMATIC RESIDUE ILE:I:Isoleucyl MW 113.2 C-alpha 62.6 0.7 C-prime 176.9 0.5 C-beta 37.5 0.7 Proton 3.95 0.10 ATOM HT+ ATOM C ATOM O ATOM CA ATOM CB ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB HB ATOM HG11 1HG1 ATOM HG# HG* HG++ ATOM HG12 2HG1 ATOM HG1* HG2* HG1+ HG2+ HG1# HG2# ATOM HG1# CG1 #HG1 1HG1 2HG1 ATOM HG21 1HG2 ATOM HG22 2HG2 ATOM HG23 3HG2 ATOM HG2# CG2 #HG2 1HG2 2HG2 3HG2 ATOM HD1 1HD1 HD# HD+ HD* ATOM HD2 2HD1 ATOM HD3 3HD1 ATOM HD# CD1 #HD1 1HD1 2HD1 3HD1 ATOM HD1# CD1 #HD1 1HD1 2HD1 3HD1 HD1* HD1+ ATOM HD11 HD12 HD13 METHYL HG21 HG22 HG23 HD11 HD12 HD13 RESIDUE LEU:L:Leucyl MW 113.2 C-alpha 55.7 0.7 C-prime 177.1 0.5 C-beta 41.9 0.7 Proton 4.17 0.10 ATOM HT+ ATOM C ATOM O ATOM CA ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB1 1HB ATOM HB2 2HB ATOM HB# CB #HB 1HB 2HB HB* HB+ ATOM HG HG ATOM HD11 1HD1 HD1+ HD1# HD1* ATOM HD12 2HD1 HD++ HD# HD* ATOM HD13 3HD1 ATOM HD1# CD1 #HD1 1HD1 2HD1 3HD1 ATOM HD21 1HD2 HD2+ HD2# HD2* ATOM HD22 2HD2 ATOM HD23 3HD2 ATOM HD2# CD2 CD+ CD* CD# #HD2 1HD2 2HD2 3HD2 ATOM HD* CG #HD# 1HD1 2HD1 3HD1 1HD2 2HD2 3HD2 METHYL HD21 HD22 HD23 HD11 HD12 HD13 RESIDUE LYS:K:Lysyl MW 128.2 C-alpha 56.7 0.7 C-prime 176.5 0.5 C-beta 32.2 0.7 Proton 4.36 0.10 ATOM HT+ ATOM C ATOM O ATOM CA ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB1 1HB ATOM HB2 2HB ATOM HB# CB #HB 1HB 2HB HB* HB+ ATOM HG1 1HG ATOM HG2 2HG ATOM HG# CG #HG 1HG 2HG HG* HG+ ATOM HD1 1HD ATOM HD2 2HD ATOM HD# CD #HD 1HD 2HD HD* HD+ HD# ATOM HE1 1HE ATOM HE2 2HE ATOM HE# CE #HE 1HE 2HE HE# HE* HE+ ATOM HZ1 1HZ ATOM HZ2 2HZ ATOM HZ3 3HZ HZ* HZ+ ATOM HZ# NZ #HZ 1HZ 2HZ 3HZ METHYL HZ1 HZ2 HZ3 RESIDUE MET:M:Methionyl MW 131.2 C-alpha 56.6 0.7 C-prime 175.8 0.5 C-beta 32.8 0.7 Proton 4.52 0.10 ATOM HT+ ATOM C ATOM O ATOM CA ATOM SD ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB1 1HB ATOM HB2 2HB ATOM HB# CB #HB 1HB 2HB HB* HB+ ATOM HG1 1HG ATOM HG2 2HG ATOM HG# CG #HG 1HG 2HG HG* HG+ ATOM HE1 1HE ATOM HE2 2HE ATOM HE3 3HE HE* HE+ ATOM HE# CE #HE 1HE 2HE 3HE METHYL HE1 HE2 HE3 RESIDUE PHE:F:Phenylalanyl MW 147.2 C-alpha 57.9 0.7 C-prime 175.8 0.5 C-beta 39.3 0.7 Proton 4.66 0.10 ATOM HT+ ATOM C ATOM O ATOM CA ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB1 1HB ATOM HB2 2HB ATOM HB# CB #HB 1HB 2HB HB* HB+ ATOM HD1 HD1 ATOM HD2 HD2 HD+ HD* ATOM HD# CG HD# HD1 HD2 ATOM HE1 HE1 ATOM HE2 HE2 HE* HE+ ATOM HE# CZ HE# HE1 HE* HE+ HE2 ATOM HZ HZ ATOM CD1 ATOM CD2 CD+ CD* CD# ATOM CE1 CE# CE* CE+ ATOM CE2 METHYL AROMATIC RESIDUE PRO:P:Prolyl MW 97.1 C-alpha 62.9 4.0 C-prime 176.0 4.0 C-beta 31.7 4.0 Proton 4.44 0.10 ATOM C ATOM O ATOM CA ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HA HA ATOM HB1 1HB ATOM HB2 2HB ATOM HB# CB #HB 1HB 2HB HB* HB+ ATOM HG1 1HG ATOM HG2 2HG ATOM HG# CG #HG 1HG 2HG HG* HG+ ATOM HD1 1HD ATOM HD2 2HD ATOM HD# CD #HD 1HD 2HD HD* HD+ METHYL RESIDUE SER:S:Seryl MW 87.1 C-alpha 58.3 0.7 C-prime 173.7 0.5 C-beta 62.7 0.7 Proton 4.50 0.10 ATOM HT+ ATOM C ATOM O ATOM CA ATOM OG ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB1 1HB ATOM HB2 2HB ATOM HB# CB #HB 1HB 2HB HB* HB+ ATOM HG HG METHYL RESIDUE THR:T:Threonyl MW 101.1 C-alpha 63.1 0.7 C-prime 175.2 0.5 C-beta 68.1 0.7 Proton 4.35 0.10 ATOM HT+ ATOM C ATOM O ATOM CA ATOM CB ATOM OG1 OG# OG* OG+ ATOM HG ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB HB ATOM HG1 HG* HG# HG+ HG1 ATOM HG21 1HG2 HG2* HG2+ HG2# ATOM HG22 2HG2 ATOM HG23 3HG2 ATOM HG2# CG2 #HG2 1HG2 2HG2 3HG2 METHYL HG21 HG22 HG23 RESIDUE TRP:W:Tryptophyl MW 186.2 C-alpha 57.8 0.7 C-prime 175.8 0.5 C-beta 28.3 0.7 Proton 4.70 0.10 ATOM HT+ ATOM C ATOM O ATOM CA ATOM CG ATOM CD1 ATOM CD2 CD+ CD* CD# ATOM NE1 NE# NE* NE+ ATOM HE1 HE# HE* HE+ ATOM CE2 ATOM CE3 CE# CE* CE+ ATOM HE3 ATOM CZ2 CZ# CZ* CZ+ ATOM HH ATOM CZ3 ATOM CH2 CH# CH* CH+ ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB1 1HB ATOM HB2 2HB ATOM HB# CB #HB 1HB 2HB HB* HB+ ATOM HD1 HD1 HD# HD* HD+ ATOM HE1 HE1 ATOM HE3 HE3 ATOM HZ2 HZ2 HZ# HZ* HZ+ ATOM HZ3 HZ3 ATOM HH2 HH2 HH# HH* HH+ METHYL AROMATIC RESIDUE TYR:Y:Tyrosyl MW 163.2 C-alpha 58.6 0.7 C-prime 175.7 0.5 C-beta 38.7 0.7 Proton 4.60 0.10 ATOM HT+ ATOM C ATOM O ATOM CA ATOM CD1 ATOM CD2 CD+ CD* CD# ATOM CE1 CE# CE* CE+ ATOM CE2 ATOM OH ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB1 1HB ATOM HB2 2HB ATOM HB# CB #HB 1HB 2HB HB* HB+ ATOM HD1 HD1 ATOM HD2 HD2 ATOM HD# CG HD# HD1 HD2 HD+ HD* ATOM HE1 HE1 HE# HE* HE+ ATOM HE2 HE2 HE* HE+ ATOM HE# CZ HE# HE1 HE2 ATOM HH HH METHYL AROMATIC RESIDUE VAL:V:Valyl MW 99.1 C-alpha 63.0 0.7 C-prime 177.1 0.5 C-beta 31.7 0.7 Proton 3.95 0.10 ATOM HT+ ATOM C ATOM O ATOM CA ATOM HN1 1H ATOM HN2 2H ATOM HN3 3H ATOM HN# N #HN 1H 2H 3H HN* HN+ ATOM HN HN ATOM HA HA ATOM HB HB ATOM HG11 1HG1 HG# HG* HG++ ATOM HG12 2HG1 HG1# HG1* HG1+ ATOM HG13 3HG1 ATOM HG1# CG1 #HG1 1HG1 2HG1 3HG1 ATOM HG21 1HG2 ATOM HG22 2HG2 ATOM HG23 3HG2 HG2# HG2* HG2+ ATOM HG2# CG2 #HG2 1HG2 2HG2 3HG2 ATOM HG* CG2 #HG# 1HG1 2HG1 3HG1 1HG2 2HG2 ATOM N ATOM CA ATOM CB ATOM CG1 CG# CG* CG+ ATOM CG2 ATOM C ATOM O METHYL HG21 HG22 HG23 HG11 HG12 HG13