Tutorials

STING short tutorial

STING: Charge complementarity on molecular interfaces
STING: Protein/DNA Interface and Structural Waters
STING: Ligand Pocket and Coordinating Residues
STING: Enzyme/Inhibitor Interface and Structural Waters
STING: Charge complementarity on molecular interfaces

In this example, we will look at the charge complementarity of two protein chains at their interface!


Step by step instructions


  • First of all, open the pdb file 1avp, by typing-in this 4 letter code and then pressing "Enter" key on the keyboard, at entry STING page (simply click on the STING It icon, and you will be in familiar area).
  • You will get screen as shown below:


  • Press:{Shift left mouse button}: enlarge image a little!
  • Observe: in the Sequence Frame that sequence of the B chain starts with residue number 205, causing STING to show long stretch of "------" as indication of missing residues!
  • Slide: mouse over sequence residues at Sequence Frame! Residue numbers will appear on the STING's Status Frame!
  • Press:[HOH off]!
  • Press:[Color by chain]!
  • Press:[Interface on]!
  • Press:[HOH+Interface]!
  • Observe:very few water molecules are placed in vicinity of Interface Forming Residues (IFR)!
  • Press:[Interface: 1st half ]!
  • Observe:verify position of the peptide (it is positioned at the interface in its entire length)
  • Press:[Interface: 2nd half ]!
  • Observe:Chain A with IFR presented in CPK!
  • Press:[Colour CPK]!
  • Observe:IFR are now colored by their default CPK colors.
  • Press: [Charged residues]!
  • Observe:all charged residues are colored on both protein and peptide chains; Protein chain (chain A) has its charged residues presented in CPK with positively charged R and K in blue color, negativly charged residues E and D in red color, and H in cyan. At the same time, charged residues of the chain B are color coded in identical way, but presented using dots at van der Waals radius around atom center. This CPK/dots combination allows user to get very direct graphics presentation on how complementary are charges at the interface! One can clearly see that residues of the chain B: 210, 211, 212 and 213 (K,R,R,R respectively) are very much complementing negatively charged residues of chain A at interface: E_108, D_77, E_89, and D_102. At the same time, positively charged residues of the B chain, effectively are avoiding contacts with positively charged residues of the A chain at interface: K_109, R_93 and R_103! All this analysis is possible by using combination of very few, carefully designed STING scripts.
  • Final Screen: You will get screen as shown below:


  • And Beyond: Use [HOH + 1st half] and [HOH + 2nd half] to get exclusive view on first half and then second half of the complementary Interface Forming Residues (IFR) with water molecules in their vicinity! See FEATURES chapter for explanation of this command, as well as differences with [Interface: 1st half] and [Interface: 2nd half]! Very useful STING command will be [Charged residues]: user can see how charge is distributed and how complemented at Interface halves!



    STING: Protein/DNA interface and structural waters

    In this example, we will look at the interaction of Protein and DNA chains.


    Step by step instructions


  • First of all, open the pdb file 2dgc, by typing-in this 4 letter code and then pressing "Enter" key on the keyboard, at entry STING page (simply click on the STING It icon, and you will be in familiar area).
  • You will get screen as shown below:


  • Press:{Shift left mouse button}: enlarge image a little!
  • Observe: in the Sequence Frame that sequence of the A chain starts with residue number 229, causing STING to show long stretch of "------" as indication of missing residues!
  • Press: [Charged residues] button on STING control panel
  • Observe: all charged residues are colored on the protein chain, clearly indicating positively charged moiety engaged in DNA binding. Curiously, there is also negatively charged Glutamic acid in this region: E, chain A,#237.
  • Slide: mouse over sequence residues at Sequence Frame! Residue numbers will appear on the STING's Status Frame!
    Note that STING handles well negative residue numbers for DNA chain
  • Press:[HOH off]!
  • Press:[Color by chain]!
  • Press:[Interface on]!
  • Press:[HOH+Interface]!
  • Observe:water molecules in-between protein and DNA surface, clearly involved in H-bond network formed among two molecules!
  • Click:(Sequence Frame) on B chain, nucleotide G,#1.
  • Observe:this is a central nucleotide of the DNA bound stretch!
  • Final Screen: You will get screen as shown below:

  • And Beyond: Use [Interface: 1st half] and [Interface: 2nd half] to get exclusive view on first half and then second half of the complementary Interface Forming Residues (IFR)! Continuing, use [Interface: 1st half] to get again exclusive look at the first half of the interface... Such iterative procedure allows users to get better glimpse at IFR. Very useful STING command will be [Charged residues]: user can see how charge is distributed and how complemented at Interface halves!



    STING: Ligand Pocket and Coordinating Residues

    In this example, we will look at the Ligand Pocket within Protein Fold


    Step by step instructions


  • First of all, open the pdb file 1ytc, by typing in this 4 letter code and then pressing "Enter" key on the keyboard, at entry STING page (simply click on STING It icon, and you will be in familiar area).
  • You will get screen as shown below:

  • Press:{Shift left mouse button}: enlarge image a little! Turn it to get most pleasing view on the molecule!
  • Observe: in the Sequence Frame: there are 3 Histidine residues! Click on each of them to see 3D position with respect to HEME. Clearly, HIS #18 is the one coordinated to Fe of the HEME ligand!
  • Press: [Charged residues] button on STING control panel
  • Observe: all charged residues are colored on the protein chain, clearly indicating Histidine residue (cyan color) engaged in HEME (LIGAND) binding.
  • Slide: mouse over sequence residues at LF! Residue numbers will appear on the browser's lower border! Observe HIS sequence numbers! Again, HIS #18 is the one coordinated to Fe of the HEME ligand!
    Note that STING handles well negative residue numbers for protein chain!
  • Press:[ribbon] button on STING control panel!
  • Press:[ligand off]
  • Press:[ligand on]
  • Observe: Histidins placed appropriately around Ligand for coordination.
  • Press:[Ligand Pocket]
  • Press:[ligand off]
  • Press:[ligand on]
  • Observe: only atoms in contact with LIGAND are presented in CPK graphics format.

  • Click: with mouse on each HIS (cyan) residue on the Graphics Frame.
  • Observe: within STING's Status Frame residue number!

  • Final Screen: You will get screen as shown below:



    STING: Enzyme/Inhibitor Interface and Structural Waters

    In this example, we will look at the Enzyme Inhibitor Interface


    Step by step instructions


  • First of all, open the pdb file 1slu, by typing in this 4 letter code and then pressing "Enter" key on the keyboard, at entry STING page (simply click on the STING It icon, and you will be in familiar area).
  • You will get screen as shown below:

  • Press:{Shift left mouse button}: enlarge image a little!
  • Observe: in the Sequence Frame that both chains do not start with residue number 1, causing STING to show a stretch of "------" as indication of missing residues! Also present are gaps in the sequence, easily identified in the Sequence Frame.
  • Slide: mouse over sequence residues at Sequence Frame! Residue numbers will appear on the STING's Status Frame!
  • Press:[HOH off]!
  • Press:[Ligand Pocket]
  • Press:[HOH + Ligand]
  • Adjust: for the best view!
  • Press:[ligand off]
  • Press:[ligand on]
  • Observe: Ligand pocket and residues creating it, as well as structural water molecules.!
  • Press:[Color by chain]
  • Press:[Interface on]!
  • Press:[HOH+Interface]!
  • Observe:water molecules in-between Enzyme and Inhibitor surface, some of which are involved in H-bond network formed among two molecules!
  • Click:Sequence Frame Arginin on B chain, residue #96.
  • Observe: position of this residue w/r/t interface!
  • Click:(UR) frame, pointer BLOCKS
  • Type_in: CHYMOTRYPSIN in the separate BLOCKS browser search area!
  • Click: on BLOCKS browser Edit menu option and then type in TRY1 at FIND option!
  • Observe: following sequence profile: ( 43) GGSLINDQWVVSAAHC
  • Click: on boxes bellow GGSLINDQWVVTAAHC sequence, starting at position B#43.

  • Mouse Mark: residues GGSLINDQWVVTAAHC by sliding mouse above these residues in the (LF) with left mouse button pressed.

  • Observe: Identify visually 3D position of this stretch! Obviously, one can see that very preserved CONTIGUOUS stretch of the sequence within CHYMOTRYPSIN family of proteins, is not participating in Interface Forming (IF) area! Only initial and ending residues are 3D_positioned within IF moiety. Thus, STING helped us to quickly locate BLOCK of the conserved sequence stretch out of IF area!
  • Final Screen: You will get screen as shown below: