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--

  4cpa  4cpa G OXT SB:Gly308:A Nterm to Val38 Cterm
	4reo  4reo G x3 OXT SB:Gly307:A Nterm to Glu197:A
                          Gly307:A Cterm to Lys200:A
                          Gly308:A none
                          Gly309:A none
  6qf3  6qf3 D see above
	4ffL  4ffL K OXT SB: Lys901:A Nterm to Glu72:A (and phosphate)
                       Lys901:A SC to Glu302:A (and phosphate)
  6nie  6nie K x4 SC SB to Glu120 (x4). N term no SB. C term SB to Arg74 chain C only.

--DIPEPTIDES--

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.

––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
