Areaimol

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Summary

CCP4 program that computes solvent-exposed surface area (SA) and reduction in SA resulting from various protein-protein contacts including interfaces and lattice contacts.

Representative run files

Use, e.g.:
arn_narl.sh > arn_narl.html
Then edit arn_narl.html to add a <tt> tag after the first <!--SUMMARY_END--></FONT></B> in the file and a  </tt> tag before final </html> tag.  This will create a fixed width font instead of variable width which makes the tables of numbers aligned properly in the browser.

Output files


ARN:  Protection of N-domain by C-domain
ARC:  Protection of C-domain by N-domain
ARI:  Protection of assymetric unit (AU) by lattice contacts
ARA:  Protection of A by B (AU = A + B)
ARB:  Protection of B by A (AU = A + B)
ARAB:  Protection of A by BC
ARBC:  Protection of C by AB
ARB(FixJ):  Protection of B by A..C

NarL(1A04): A,B segments, space group C121 (#5)
CheB(1A2O): A,B segments, space group C121 (#5)
DrrD(MI3N): One segment, space group P21 (#4)
FixJNP(1D5W):  A,B,C segments, space group C121 (#5), segments arranged linearly A-B-C, proposed functional dimeric interface at B-C
 

Summary of results comparing NarL, CheB, FixJ and DrrD interdomain and lattice contacts

 
NARL (1A04) A,B
CHEB (1A2O) A,B
DRRD (MI3N)
FIXJ (1DCK) A,B,C
Total SA (A, B separate)
ASU SA (A-B comb)
20,313
19,653
29,116
28,099
11,679
19,985 
16,108 
N-Domain SA (A)
6,508
7,090
6,640
(A) 6,775 
(B) 6,647 
(C) 6,563 
C-Domain SA (A)
5,490
9,076
5,530
  
N-Domain buried by C-Domain
948
782
238
  
C-Domain buried by N-Domain
996
872
253
  
A buried by B
339
495
  
(A by BC) 941 
(C by AB) 604 
(B by A C) 1,360 
B buried by A
321
522
    
ASU buried by lattice contacts
3,819
3,061
2,109
1,162 
Total buried by A-B + lattice
4,149
3,570
2109
2,707 
Ratio:  (buried)/(tot SA)
0.211
0.123
0.180
0.135 

Notes:

1.  Total SA in above Ratio calculation is:

tot SA = sum of SA for A, B, C in isolation from ASU partners


2.  (buried) above in Ratio calculation is:

buried = 0.5[(A buried by B)+(B buried by A)] + (ASU buried by lattice contacts)

buried(FixJ) = [(A by BC)+(C by AB)] + (ASU buried by lattice contacts)

3.  Calculation for fractional buried by lattice contacts for OmpRc (1OPC) was 2342/5909 = 0.396

4.  See O. Carugo & P. Argos (1997) Protein Science 6: 2261-2263, "Protein-protein crystal-packing contacts" for general, useful principles.
For example, analysis of 78 representative structures from PDB gave:
average percentage of protein surface buried by crystal contacts:  mean=27%, sd=2% (range = 15% to 49%)