Interaction Types

How to use PICI server?

How to interpret the data file?

Release notes

 

Hydrogen Bond

Default parameters for PICI server

D-H···Π   Hydrogen bond
D-H···A dD-A (Å) ∠D-H-A
N-H···O ≤ 3.5 (1) ≥ 110 ° (2)
N-H···N ≤ 3.5 (1)
N-H···S ≤ 4.1  (3)
O-H···N ≤ 3.5 (1)
O-H···O ≤ 3.5 (1)
O-H···S ≤ 4.1 (3)
S-H···O ≤ 4.3 (3)
S-H···N ≤ 4.3 (3)
S-H···S ≤ 4.5 (3)
C-H···O ≤ 3.5 (4)
C-H···N ≤ 3.5 (4)
C-H···S ≤ 4.1 (3)
N-H···π < 4.3 (5)
O-H···π < 4.3 (5)
S-H···π ≤ 4.5 (3)
C-H···π ≤ 4.5 (6-8)

Reference:

1.   Baker, E.N., Hubbard, R.E. (1984) Hydrogen bonding in globular proteins. Prog Biophys Mol Biol, 44, 97-179.
2.   Arunan, E., Desiraju, G.R., Klein, R.A., et al. (2011) Definition of the hydrogen bond (IUPAC Recommendations 2011). Pure and Applied Chemistry, 83, 1637-1641.
3.   Zhou, P., Tian, F., Lv, F., Shang, Z. (2009) Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins. Proteins, 76, 151-63.
4.   Weiss, M.S., Brandl, M., Suhnel, J., Pal, D., Hilgenfeld, R. (2001) More hydrogen bonds for the (structural) biologist. Trends Biochem Sci, 26, 521-3.
5.   Steiner, T., Koellner, G. (2001) Hydrogen bonds with pi-acceptors in proteins: frequencies and role in stabilizing local 3D structures. J Mol Biol, 305, 535-57.
6.   Brandl, M., Weiss, M.S., Jabs, A., Suhnel, J., Hilgenfeld, R. (2001) C-H...pi-interactions in proteins. J Mol Biol, 307, 357-77.
7.   Steiner, T., Desiraju, G.R. (1998) Distinction between the weak hydrogen bond and the van der Waals interaction. Chemical Communications, 891-892.
8.   Nishio, M., Umezawa, Y., Fantini, J., Weiss, M.S., Chakrabarti, P. (2014) CH-pi hydrogen bonds in biological macromolecules. Phys Chem Chem Phys, 16, 12648-83.

 


Aromatic-aromatic (Π-Π)   interaction

 


Cation-aromatic   interaction

 


Anion-aromatic   interaction

 


Lone pair-aromatic (Lp-Π)   interaction

 

How to use PICI server?

User can upload his/her protein structure file in pdb format at index page for calculation by PICI server. Pdb files can be uploaded to server by browsing to your file.

  1. Click Browse / Choose File button (depends upon web browser type)

  2. Click Submit button. (It will open the data processing page)

  3. Select the radio button for your chain of interest.

  4. Click Go button.

  5. Calculation process will take few seconds for different types of interactions.

  6. Result page will open after finishing the calculation. (description and image below.)

    a. Buttons for different interactions.

    b. Chain information of protein structure

    c. Interacting residues in protein structure by JSmol visualizaton tool.

    d. Interaction details in text.

    e. Interacting residues in protein sequence.

  7. Click download button to download the interaction file in txt format.

How to interpret data file?

Interaction data files are being generated for each calculation and stored on the server.

(Note: Interaction files will be stored upto 15 days)

Users can download their data files by following URL: http://www.pici.bicpu.edu.in/download.php?accid=[ accession id ]&chain=[ chain id ]

 

Interaction File Description

Record: HBOND

Contains: Hydrogen bond description

 

COLUMNS CONTENT
0 - 6 bond type
7 - 8 selected chain
9 - 12 residue
13 - 18 residue number
19 - 20 donor/acceptor type
21 - 26 atom
27 - 28 other chain
29 - 32 residue
33 - 38 residue number
39 - 40 donor/acceptor type
41 - 46 atom
47 - 52 donor-acceptor distance (Å)
53 - 58 hydrogen-acceptor distance(Å)
59 - 66 d-h⋯a angle Θ°
67 - 69 inter-chain type
70 - 74 h-bond type
  MM - Main chain to Main chain; SM - Main chain to Side chain; SS - Side chain to Side chain

Example:
          1         2         3         4         5         6         7         8
012345678901234567890123456789012345678901234567890123456789012345678901234567890

HBOND  P SER 2     d OG    A TYR 9     a O     3.35  2.63  145.30  SM OH⋯O
HBOND  P SER 2     d N     A TYR 9     a O     2.97  2.13  165.62  MM NH⋯O
HBOND  P GLN 3     d N     B GLU 74    a OE2   3.21  2.43  151.09  SM NH⋯O
HBOND  P TYR 4     d N     A ASN 62    a OD1   2.70  1.92  151.20  SM NH⋯O
HBOND  P ARG 5     d N     B TYR 30    a OH    2.99  2.21  151.97  SM NH⋯O
HBOND  P SER 7     d N     A ASN 69    a OD1   3.20  2.35  170.23  SM NH⋯O

 

Record: HPHOB

Contains: Hydrophobic interaction description

COLUMNS CONTENT
0 - 6 bond type
7 - 8 selected chain
9 - 12 residue
13 - 18 residue number
19 - 20 other chain
21 - 24 residue
25 - 30 residue number

Example:
          1         2         3
0123456789012345678901234567890

HPHOB  A CYS 293   B TRP 539   
HPHOB  A LEU 295   B TRP 334   
HPHOB  A LEU 295   B TRP 539   
HPHOB  A PRO 297   B PRO 333   
HPHOB  A LEU 298   B TYR 434   
HPHOB  A LEU 298   B VAL 329   
HPHOB  A PHE 299   B LEU 331   
HPHOB  A PHE 299   B VAL 329   
HPHOB  A LEU 312   B TRP 539

 

Record: SSBOND / IONIC

Contains: Disulfide bond (SSBOND), Electrostatic interactions (IONIC)

COLUMNS CONTENT
0 - 6 bond type
7 - 8 selected chain
9 - 12 residue
13 - 18 residue number
19 - 23 atom
24 - 30 atom number
31 - 32 other chain
33 - 36 residue
37 - 42 residue number
43 - 47 atom
48 - 54 atom number
55 - 60 distance (Å)

Example:
          1         2         3         4         5         6      
0123456789012345678901234567890123456789012345678901234567890

SSBOND A CYS 293   SG   1024   B CYS 439   SG   2243   2.01  
...
...
IONIC  A ASP 225   OD2  479    B ARG 409   NH2  1986   2.73  
IONIC  A ASP 239   OD1  585    B LYS 413   NZ   2029   3.87  
IONIC  A GLU 241   OE2  606    B LYS 413   NZ   2029   3.10  
IONIC  A ASP 292   OD2  1018   B HIS 436   NE2  2223   3.13  
IONIC  A GLU 311   OE2  1176   B LYS 455   NZ   2365   2.83  
IONIC  A ASP 306   OD1  1132   B ARG 457   NH1  2379   3.93

 

Record: PIPI

Contains: Aromatic ring - aromatic ring interaction

COLUMNS CONTENT
0 - 6 bond type
7 - 8 selected chain
9 - 12 residue
13 - 18 residue number
19 - 20 other chain
21 - 24 residue
25 - 30 residue number
31 - 36 distance (Å) [centroid - centroid]
37 - 42 dihedral angle

Example:
          1         2         3         4  
0123456789012345678901234567890123456789012

PIPI   A TRP 4     B PHE 88    5.84  65.56 
PIPI   A TYR 316   B PHE 454   5.18  97.24

 

Record: CATPI / ANPI / SPI

Contains: Cation - aromatic ring (CATPI), Anion - aromatic ring (CATPI), Sulfur - aromatic ring (SPI) interactions

COLUMNS CONTENT
0 - 6 bond type
7 - 8 selected chain
9 - 12 residue
13 - 18 residue number
19 - 23 atom
24 - 30 atom number
31 - 32 other chain
33 - 36 residue
37 - 42 residue number
43 - 47 atom
48 - 54 atom number
55 - 60 distance (Å)
60 - 66 angle

Example:
          1         2         3         4         5         6      
0123456789012345678901234567890123456789012345678901234567890123456
 
CATPI  A ARG 296   CZ   1045   B TRP 539   RING -      4.74  64.56 
CATPI  A TRP 230   RING -      B ARG 409   CZ   1984   3.49  24.49 
CATPI  A PHE 240   RING -      B ARG 409   CZ   1984   4.02  33.68 
...
...
ANPI   A ASP 306   OD2  1133   B TRP 539   RING -      5.71  61.58 
ANPI   A GLU 309   OE1  1157   B TRP 539   RING -      5.98  77.39 
ANPI   A TYR 242   RING -      B GLU 414   OE1  2037   4.66  69.21 
ANPI   A TYR 242   RING -      B GLU 414   OE2  2038   5.59  84.88 
ANPI   A PHE 281   RING -      B ASP 575   OD1  3319   5.78  89.89 
...
...
SPI    A PHE 277   RING -      B CYS 439   SG   2243   5.26  68.49 
SPI    A TRP 285   RING -      B MET 120   SD   1822   4.86  29.54

Release notes

PICI version 3.2 (released in Dec 2015)

  • Improved to calculate non-standard amino acids.

  • XML files are improved to handle data more efficiently.

  • Several bug fix for fast and accurate calculation.

  • Bug fix to remove false positive.

 

Older versions:

PICI version 3.1 (released in Sep 2015)

  • Calculation for interface area with NACCESS.

  • Improved interaction viewer with data display in tabular form or an interactive matrix.

  • Interaction files in downloadable XML and TXT file format.

  • Bug fix for hydrogen atom addition.

 

PICI version 2.9 (released in May 2015)

  • Hydrogen bond calculation now includes CH···O, CH···N, CH···S, OH···Π, NH···Π, SH···Π, CH···Π, types

  • Integration of HAAD and REDUCE programs to fix hydrogen atom positions in pdb files.

  • Calculation for aromatic ring – aromatic ring interactions with θ, Φ1 and Φ2 angles

  • Calculation for cation – aromatic ring interactions with θ

  • Calculation for anion – aromatic ring interactions with θ

  • Calculation for Lone pair – aromatic ring interactions with θ

  • Changed interaction file format

  • Changed JSmol view

  • Faster data processing and calculation

  • Visualization of interacting aminoacids on interaction matrix for each type of interactions

  • Improved user interface

 

PICI version 2.1 (released in 2014)

  • Hydrogen bond calculation now includes OH···O, OH···S, SH···O, SH···N, NH···S types apart from NH···O and OH···N types

  • For hydrophobic interactions hydrophobicities are based on solvent transfer free energies from octanol to water as mentioned by Brian W Mattews (1)

  • Calculation for aromatic ring – aromatic ring interactions

  • Calculation for cation – aromatic ring interactions

  • Calculation for anion – aromatic ring interactions

  • Calculation for sulfur – aromatic ring interactions

  • Changed interaction file format

  • Faster data processing and calculation

  • Integrated JSmol molecular visualization tool

  • Visualization of interacting aminoacids on an interaction matrix

  • Improved user interface

Reference:

1.  Matthews, B.W. (2001) Hydrophobic Interactions in Proteins.  Encyclopedia of life sciences. John Wiley & Sons, Inc.

 

PICI version 1.2 (released in 2011)

Integrated in PepBind database for calculating interaction interface in protein-peptide complexes.

  • NH···O and OH···N type hydrogen bond calculation.

  • For hydrophobic interactions hydrophobicities are based on Kyte-Doolittle hydropathy scale.

  • Calculation of disulfide bridges.

  • Calculation of ionic interactions (salt bridges).

  • Integrated Jmol molecular visualization tool.

  • Sequence display with highlighted interacting residues.

Citation: Das, A.A., Sharma, O.P., Kumar, M.S., Krishna, R., Mathur, P.P. (2013) PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions. Genomics Proteomics Bioinformatics, 11, 241-6.