Tutorials

We encourage the user to see our:
Samples of BLUE STAR STING application

STING short tutorial

• 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 BLUE STAR STING page (or simply click on the STING It button, and you will be in familiar area).
• You will get screen as shown on Fig. 1. below.
• By pressing REFRESH button, BLUE STAR STING will produce image as on Fig.2. bellow.
  
  

  1	2

  
  

  3

  
  
• Press:{Shift left mouse button within the Graphics Window}: enlarge image a little!
• Slide: mouse over sequence residues at Sequence Frame! Residue numbers will appear on the BLUE STAR STING Status Frame!
• Press:[ACTION:Structural Waters:HOH off]!
• Press:[ACTION:Structural Presentation:Color by chain]!
• Press:[Windows:Interface chain...]!
• Follow red line instruction on the Fig. 3 above.
• Observe:very few water molecules are placed in vicinity of Interface Forming Residues (IFR)!
• Press:[Int Surface:Interface Component: View 1st half ]!
• Observe:verify position of the peptide (it is positioned at the interface in its entire length)
• Press:[Int Surface:Interface Component: View 2nd half ]!
• Observe:Chain A with IFR presented in CPK!
• Press: [Int Surface:Interface component: Charged Residues on Interface]!
• 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, negatively 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 BLUE STAR STING scripts.

• Final Screen: You will get screen as shown on fig.4. below:
  
  

  4

  
  
• And Beyond: Use [Int Surface:1st Half HOH on] and [ Int Surface:2nd Half HOH on] 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 the explanation of these commands, as well as differences between [Int Surface:Interface component: View 1st half] and [Int Surface:Interface component: View 2nd half]! Very useful BLUE STAR STING command is [Int Surface:Interface component: Charges on Interface]; here the user can see how charge (and not charged residues, as in above example) is distributed and how it is complemented at Interface halves!
  

• 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 BLUE STAR STING page (simply click on the STING It button, and you will be in familiar area).
• You will get screen as shown on the Fig.5. Below
• By pressing REFRESH button, BLUE STAR STING will produce image as on Fig.6. Bellow
  

5	6

• Press:{Shift left mouse button within the Graphics Window}: enlarge image a little!
• Observe: in the Sequence Window that sequence of the A chain starts with residue number 229, causing BLUE STAR STING to show long stretch of "------" as indication of missing residues!
  

7	8

• Press: [Action:Structure Presentation:Charged Residues] on BLUE STAR STING menu option
• Observe: [fig.7.] 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 the Sequence Window! Residue numbers will appear on the BLUE STAR STING Status Frame!
  Note that BLUE STAR STING handles well negative residue numbers for DNA chain
• Press:[Windows: Interface Chain]! [Fig.8.]
• Press:[Int Surface: 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. [Fig.9.]
• Observe:this is a central nucleotide of the DNA bound stretch!
• Final Screen: You will get screen as shown bellow:
  
  

  9

  
  
• And Beyond: Use [Int Surface:1st Half HOH on] and [ Int Surface:2nd Half HOH on] 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 the explanation of these commands, as well as differences between [Int Surface:Interface component: View 1st half] and [Int Surface:Interface component: View 2nd half]! Very useful BLUE STAR STING command is [Int Surface:Interface component: Charges on Interface]; here the user can see how charge (and not charged residues, as in above example) is distributed and how it is 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 BLUE STAR STING page (simply click on the STING It button, and you will be in familiar area).
  • You will get screen as shown below [fig.10.], rotate the molecule until you get the view as in Fig.11.:
    
    

    10	11

    
    

    12	13

    
    

    14

    
    
  • Press:{Shift left mouse button within the Graphics Window}: enlarge image a little! Turn it to get most pleasing view on the molecule! [fig.11.]
  • Observe: in the Sequence Window: there are 3 Histidine residues! Click on each of them (choosing indicated colors and WS presentation) to see 3D position with respect to HEME. Clearly, HIS #18 is the one coordinated to Fe of the HEME ligand! [Fig.12.]
  • Press: [Action: Structure Presentation:Charged Residues] on BLUE STAR STING menu options.
  • Observe: all charged residues are colored (blue=positively charged amino acids, red=negatively charged amino acids and cyan=hysitdine) and presented in dotted spheres on the protein chain, clearly indicating Histidine residue engaged in HEME (LIGAND) binding.
  • Press:[Action: Structure Presentation:Ribbon] on BLUE STAR STING menu options. [Fig.14.]
  • Press:[Action: Ligand:Ligand off]
  • Press:[Action: Ligand:Ligand on]
  • Observe: Histidins placed appropriately around Ligand for coordination.
  • Press:[Action: Ligand:Ligand Pocket]
  • Press:[Action: Ligand:Ligand off]
  • Press:[Action: Ligand:Ligand on]
  • Observe: only atoms in contact with LIGAND are presented in WS graphics format.
    
  • Final Screen: You will get screen as shown on Fig.15. Below:
  • Possible STING responses that might be confusing: sometimes you might see Pocket but not the LIgand! See for the example here!
    
    

    15

    
    
  
  BLUE STAR STING: Ramachandran plot
  
  
  Step by step instructions
  
  
  • No text! Just follow the graphical instructions and get acquainted with Ramachandran plot.
    
    

    16	17

    
    

    18	19

    
    

    20