FOR CODE NOTES FOR DIPEPTIDES, SEE DIPEPS.TXT --------------------- FOR ALL SB makeCatPiSBSpt() (scripts.js) is called by the link in tools (control2.js). makeCatPiSBSpt2() (scripts.js) is called next selectedFound is set and can be reported by alert #32 in scripts.js It is residues and not backbone for sidechains, and Residues and backbone for termini. Search for SALT in scripts.js to find the code. --------------------- Version 2.9 showed SB only between SideChains (SC) of AA in chains of length 3 or longer (ATOM). Version 3.0 added SB involving: Chain ends (including end to end), including C-termini missing OXT. HETERO monoAA and dipeptide ligands, sidechains and ends. PDB FG contacts target ~targ_current ~cont_current 6qf3 2.9 2x Asp monomers 427-8 18 29 6qf3 3.0 2x Asp monomers 427-8 18 31 (2 spurious extra, see below) CHECKS FOR 3.0: Include sidechains of HETERO monoAA and dipeptides for SB. Examples 6qf3, target = 2x ASP monomer ligands: Asp428 monomer=ligand SC- to Arg203 SC + In ~targ/cont_sb. SEEMS TO BE WORKING. Asp427 monomer both N and Cterm to Zn++. SC to Na+. 4oem Gly-Lys dipeptide. CHG OK. No end SB. Lys SC SB to Asp 1: OK in Cont. Include ends of HETERO monoAA and dipeptides Examples 6qf3, target = 2x ASP monomer ligands: Asp427.N end to Asp428.O/OXT end 3.61 Å Asp427.N end to Glu143 SC, 2.51, 2.71 Å. In ~targ/cont_hbonds but not ~targ/cont_sb. 3der AlaLys dipep:C N-term SB 2.9 Asp317; C-term SB 3.2 3.6 to Lys265 & 2.6 to Mg. (CHG OK) Find: Ala411:c,Lys412:c BUG (NOT SB) FIX NEEDED: Exclude altloc when looking for end blockage. Example: Leu1 in 6qf3 is not blocked (but FG says it is). ––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– Examples: --MONOPEPTIDES = MONOAA = SINGLE AMINO ACIDS-- RCSB Advanced Search: Chemical Attribute, Chemical Components, Chemical ID(s) setting "polymer type" to "free". 4cpa 4cpa G OXT SB:Gly308:A Nterm to Val38 Cterm Chains AU=4 BU=2 4reo 4reo G x3 OXT SB:Gly307:A Nterm to Glu197:A Chains AU=1 BU=1 Gly307:A Cterm to Lys200:A Gly308:A none Gly309:A none 6qf3 6qf3 D see above Chains: AU=1 BU=1 4ffL 4ffL K OXT SB: Lys901:A Nterm to Glu72:A (and phosphate) Chains: AU=1 BU=1 Lys901:A SC to Glu302:A (and phosphate) 6nie 6nie K x4 SC SB to Glu120 (x4). Chains: AU=4 BU=1 N term no SB. C term SB to Arg74 chain C only. --DIPEPTIDES-- Assemblies: 4oem 4oem Gly-Lys Chains: AU=2, BU=4. Two dipeptides, one with chain A1. See notes.htm#aalig which include 2cyh AP OXT A no SB. P SB to Arg55:A. (Chain termini SB to each other) 1dpp GL x4 OXT G SB to Asp408. L SB to Arg355. (Chain termini SB to each other) See examples in moltab.js which include 3deq 3deq AL x4 OXT. N-term SB to Asp319. C-term SB to Lys159, 165, 265 & Mg++! 2whz 2whz IY OXT I SB to Glu143. Y no SB. 1e8k 1e8k AP OXT A no SB. P SB to Arg62. 2hnu 2hnu FY x5 OXT F SB to Glu47. Y no SB. 4d2c 4d2c AF x1 OXT A SB to Glu400. F SB to Arg26/Lys126. Examples found at RCSB using Chemical ID, polymer type "free": 4n1m 4n1m GP OXT SB: Pro202:A Cterm to Arg55 Misc: 6gb6 6gb6 GL x2 OXT: No SB to either end. ---TRIPEPTIDES--- See notes.htm#aalig which include 4q1L 4q1L QSW OXT N-term no SB. C-term bound to Zn (not "blocked" due to OXT I think). See examples in moltab.js which include 1hqw 1hqw YPY OXT No SB either end. 5mxo 5mxo F-K-TPO(phosphothreonine) no-OXT. N-term SB Glu182. C-term SC-PO3, no SB. 2xdw 2xdw PHQ-PRO-YCP NO-OXT The Pro is not hetero, but the other two are. All Ligands+. Unique chain name P. Ends not found. ----TETRAPEPTIDES---- 5fpk 5fpk ACE-FATA-amide Paper says "All peptides prepared and used in the study were N‐acetylated and C‐amide terminated." 4P9V 4P9V PHQ-PTR(phospho-tyrosine)-02K-ASN(amidated-blocked) ----COMPLEX---- 4cvk 4cvk Uridine-5'-diphosphate UDPpp-MUB-ALA-FGA-API ––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– CATION DISTANCE TO C-TERMINAL CARBON WHEN OXT IS MISSING. INCREASE THE 4.0 SALT BRIDGE DISTANCE FOR C-TERMINI TO 4.0+1.2=5.2 Å BETWEEN THE CATIONIC NITROGEN AND THE CARBOXY CARBON. Distance ––––––––––––––––––––––––– c-term oxt sb-to closestO C of COOH Diff –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– 1hxw phe99 OXT pro1.n 2.45 3.4 1.05 2nm1 lys60:b OXT lys60.nz 3.49 4.63 1.14 internal SB lys60.ce 2.97 3.9 0.93 9ins ala30 OXT gly1.n 3.61 4.65 1.04 asn21 OXT arg22.ne 2.93 3.82 0.89 arg22.cz 3.78 4.98 1.2 1zms asp210 OXT arg393.cz 3.31 4.29 0.98 1hho his146 OXT lys144.nz 3.09 4.28 1.19 6ef8 asp407 OXT arg151.nh2 2.55 3.47 0.92 2vaa met99 OXt arg202.ne 2.9 3.95 1.05 –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– OTHER SB –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– cooh OO? sb-to closestO C of COOH Diff –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– 1zms asp210.od1 OO arg393.cz 3.94 4.53 0.59 –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– PDB FILES WITH MISSING OXT (NO C-TERMINAL SB) 1bl8: all 4 identical chains. 2xy9: single chain ending ALA624. –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– SALT BRIDGES INVOLVING C-TERMINI MISSING ONE OXYGEN. To find these, I listed >33,000 entries lacking REMARK 465, thus guaranteeing the C-terminal residues to be present. That list was pasted in to RCSB's advanced search, and anded with must have protein only, method X-ray, resolution >= 2.5 Å. I examined the first 50 of the several thousand hits. 5j0z: 5 C-term SB! F315:R119. F315 is also involved in a CatPi. The one O present points AWAY from the cation. Distance from the terminal carboxy carbon to the nearest cationic nitrogen is 4.23 Å. Distance from cation to the one oxygen is 5.33 Å. 5mxo: Chain P (3 residues, seq 385-387) ends in phospho-threonine (TPO). C-term SB to one of 2 altlocs of Lys49, 4.69 Å carbon to nitrogen, 4.39 carbon to oxygen. The N-terminus of this tri-peptide, Phe385, has SB with Glu182, and meets the 6A rule for catpi to itself but is off the edge of the ring. 5jy0: Chain B (tripeptide, seq 1-3), N terminus is in both CatPi to W218:B and SB to D669:A. But the C-term (no OXT) does nothing. 5mx3: Arg220:A COO- is SB to its own sidechain. Nearest N to C 4.19 Å. Identical chain H: 5.1 Å. N termini of chains B and L are Asp with internal SB. 5Lum has an end to end SB from Ala149 (no OXT) to G72, in chains A, E, D. But the one oxygen is also 3.49 Å from the cation. 5v33: Yes but poor angle / atoms intervening. Not convincing. 5uvk: Yes but also the one oxygen is 3.99 Å to the cation. –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– ––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––