Contacts of the helix formed by residues 375 - 398 (chain A) in PDB entry 3BNF
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 375 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A GLY 4.1 7.2 - - - +
374A ALA* 1.3 75.2 - - - +
376A ASP* 1.3 66.1 + - - +
377A ALA* 3.5 8.8 + - - +
378A GLU* 2.8 41.0 + - - +
379A LEU* 3.1 26.9 + - - +
435A TYR* 4.5 3.1 - - - +
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Residues in contact with ASP 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ALA 5.5 0.2 - - - +
375A THR* 1.3 70.8 - - - +
377A ALA* 1.3 61.7 + - - +
379A LEU* 3.0 1.0 + - - +
380A LYS* 2.7 34.0 + - - +
383A ARG* 2.9 29.3 + - - +
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Residues in contact with ALA 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A THR* 3.2 8.7 + - - +
376A ASP* 1.3 79.3 - - - +
378A GLU* 1.3 61.7 + - + +
379A LEU 3.2 0.3 + - - -
380A LYS* 3.5 15.7 + - - +
381A GLU* 4.9 1.2 + - - +
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Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ALA* 3.2 5.1 - - + -
375A THR* 2.8 44.6 + - - +
377A ALA* 1.3 75.8 - - + +
379A LEU* 1.3 61.0 + - + +
381A GLU* 5.3 1.3 + - - +
382A ILE* 4.2 4.9 + - - +
431A VAL* 3.9 26.9 - - + +
434A LYS* 2.8 39.0 + - - +
435A TYR* 2.7 29.5 + - - -
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A THR* 4.3 10.3 - - + +
369A ALA* 4.3 4.0 - - + -
370A MET* 3.7 29.6 - - + +
374A ALA* 4.2 15.9 - - + +
375A THR 3.3 15.9 - - - +
376A ASP* 3.0 2.2 + - - +
378A GLU* 1.3 84.1 - - - +
380A LYS* 1.3 66.1 + - - +
381A GLU 3.3 2.9 - - - -
382A ILE* 3.2 22.4 + - + +
383A ARG* 2.8 53.9 + - + +
428A LEU* 4.2 14.8 - - + -
431A VAL* 4.3 15.3 - - + -
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Residues in contact with LYS 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ASP 2.7 16.7 + - - +
377A ALA* 3.5 11.3 + - - +
379A LEU* 1.3 78.0 - - - +
381A GLU* 1.3 58.1 + - + +
383A ARG* 3.7 7.9 - - - +
384A THR* 2.9 37.9 + - - +
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Residues in contact with GLU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ALA 4.9 1.2 + - - -
378A GLU 5.3 1.2 + - - +
379A LEU 3.3 0.6 - - - -
380A LYS* 1.3 76.8 - - + +
382A ILE* 1.3 67.8 + - + +
384A THR* 3.3 8.0 + - - -
385A HIS* 3.0 30.3 + - + +
427A LYS* 3.1 35.0 + - + +
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Residues in contact with ILE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A THR* 3.5 28.9 - - + +
378A GLU 4.2 6.5 + - - +
379A LEU* 3.2 16.0 + - + +
381A GLU* 1.3 78.6 - - - +
383A ARG* 1.3 58.5 + - - +
385A HIS* 3.0 12.8 + - - +
386A ILE* 2.9 32.5 + - + +
424A ALA* 3.9 8.2 - - + +
427A LYS* 3.5 39.3 - - + -
428A LEU* 3.7 34.3 - - + -
431A VAL* 3.8 18.8 - - + -
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Residues in contact with ARG 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A SER 2.8 26.9 + - - +
269A LYS* 3.6 23.7 + - - +
270A THR* 3.1 36.9 - - + +
271A PRO* 4.5 9.0 - - + -
366A THR* 4.2 10.5 - - + +
370A MET* 3.3 30.3 - - - +
376A ASP* 2.9 35.8 + - - +
379A LEU* 2.8 43.7 + - - +
380A LYS* 3.7 6.3 - - - +
382A ILE* 1.3 72.4 - - + +
384A THR* 1.3 58.5 + - - +
386A ILE* 3.1 3.4 + - - +
387A ARG* 2.8 27.6 + - - +
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Residues in contact with THR 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PRO* 6.1 0.9 - - - +
380A LYS* 2.9 24.4 + - - +
381A GLU* 3.6 10.8 - - - -
382A ILE 3.3 0.2 - - - -
383A ARG* 1.3 76.1 - - - +
385A HIS* 1.3 64.5 + - + +
387A ARG* 3.4 11.0 + - - +
388A HIS* 3.0 50.7 + - + +
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Residues in contact with HIS 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A GLU* 3.0 27.6 + - - +
382A ILE* 3.0 9.7 + - - +
384A THR* 1.3 78.4 - - + +
386A ILE* 1.3 58.5 + - - +
388A HIS* 3.8 0.2 - - - -
389A ALA* 2.8 30.3 + - - +
420A GLU* 2.7 50.3 + - - +
423A LYS* 3.9 27.5 - - + +
424A ALA* 3.7 13.0 - - + -
427A LYS* 2.8 40.1 + - + -
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Residues in contact with ILE 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A SER* 4.5 0.4 - - - -
270A THR* 4.0 18.4 - - + +
272A MET* 4.4 1.6 - - + -
359A ILE* 5.0 7.2 - - + +
362A ALA* 3.8 29.6 - - + +
363A HIS* 3.3 39.3 - - + +
366A THR* 3.4 27.8 - - - +
382A ILE* 2.9 23.0 + - + +
383A ARG* 3.6 7.2 - - - +
385A HIS* 1.3 72.4 - - - +
387A ARG* 1.3 67.4 + - - +
389A ALA* 3.6 6.6 - - + +
390A GLN* 2.9 25.3 + - - +
421A ALA* 5.6 0.4 - - - +
424A ALA* 4.0 8.3 - - + -
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Residues in contact with ARG 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A TYR 3.5 16.4 + - - -
256A ASP* 2.8 31.9 + - - +
259A ASN* 4.7 2.0 - - - +
260A PHE 2.8 31.3 + - - +
261A ALA* 4.3 0.2 - - - +
270A THR* 3.8 6.2 - - + +
271A PRO* 3.0 57.6 + - - +
272A MET* 4.5 7.9 - - - +
273A LEU* 3.8 31.3 + - + +
383A ARG 2.8 20.0 + - - +
384A THR* 3.6 10.5 - - - +
386A ILE* 1.3 73.6 - - - +
388A HIS* 1.3 68.3 + - + +
390A GLN* 4.1 0.9 - - - +
391A TRP* 3.0 29.6 + - - +
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Residues in contact with HIS 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A GLU* 3.4 37.3 - - + +
256A ASP* 2.8 27.8 + - - -
384A THR* 3.0 42.8 + - + +
385A HIS 3.9 2.5 - - - +
387A ARG* 1.3 88.6 + - + +
389A ALA* 1.3 64.9 + - - +
391A TRP* 3.7 1.5 - - + +
392A ARG* 3.0 47.3 + - - +
420A GLU* 4.0 13.1 + - - +
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Residues in contact with ALA 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A ILE* 4.0 8.1 - - + -
385A HIS 2.8 22.3 + - - +
386A ILE* 3.6 7.0 - - - +
388A HIS* 1.3 72.3 - - - +
390A GLN* 1.3 59.7 + - - +
392A ARG 3.4 0.2 + - - -
393A ALA* 2.9 27.2 + - - +
417A GLY* 3.1 35.3 - - - +
420A GLU* 3.6 9.5 - - + +
421A ALA* 3.6 19.1 - - + +
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Residues in contact with GLN 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ALA* 3.0 29.9 + - - +
87A TRP* 3.5 22.8 - - - +
263A TRP* 3.6 6.9 - - - -
272A MET* 3.2 22.9 - - + +
273A LEU 4.8 4.5 + - - +
356A PHE* 4.5 11.7 - - + -
359A ILE* 3.2 24.7 - - + +
363A HIS* 2.8 28.6 + - - -
386A ILE 2.9 16.3 + - - +
389A ALA* 1.3 75.3 - - - +
391A TRP* 1.3 62.0 + - - +
394A ASP* 2.8 39.4 + - + +
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Residues in contact with TRP 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A GLU* 3.2 26.9 - - + -
248A THR* 3.0 29.7 + - + +
251A MET* 3.8 22.2 - - + -
252A GLU* 3.3 38.5 - - + +
255A TYR* 3.6 11.9 - + - -
273A LEU* 3.5 42.0 + - + -
274A LYS 3.6 22.9 - - - -
275A ALA* 3.7 10.8 - - + -
387A ARG 3.0 19.9 + - - +
388A HIS* 3.7 4.0 - - - +
390A GLN* 1.3 77.3 - - - +
392A ARG* 1.3 58.7 + - - +
394A ASP* 4.7 0.7 - - - -
395A MET* 3.0 53.0 + - + +
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Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A THR* 4.1 20.9 - - + -
249A GLU* 4.9 13.7 + - - +
252A GLU* 2.9 39.3 + - - +
388A HIS* 3.0 27.9 + - - +
389A ALA 3.8 2.5 - - - +
391A TRP* 1.3 74.4 - - - +
393A ALA* 1.3 66.7 + - - +
395A MET* 3.4 2.8 + - - +
396A ALA* 3.1 21.5 + - - +
413A LEU* 3.9 24.9 - - + +
416A SER* 3.0 31.0 + - - -
417A GLY* 4.1 7.2 - - - +
420A GLU* 3.4 29.2 + - - +
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Residues in contact with ALA 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A ALA* 4.1 8.1 - - + -
356A PHE* 3.7 20.9 - - + -
359A ILE* 3.7 16.6 - - + -
389A ALA 2.9 20.1 + - - +
390A GLN 4.2 0.2 - - - +
392A ARG* 1.3 73.7 - - - +
394A ASP* 1.3 62.1 + - - +
396A ALA* 3.2 5.4 + - - +
397A ILE* 3.2 25.5 + - - +
413A LEU 4.4 3.3 + - - -
414A LEU* 3.9 18.2 - - + -
417A GLY* 4.7 4.0 - - - -
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Residues in contact with ASP 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TRP* 3.5 25.7 + - - -
273A LEU 4.5 2.6 - - - +
274A LYS* 2.8 35.3 + - - +
275A ALA* 3.1 23.5 + - + +
356A PHE* 3.9 7.0 - - + -
390A GLN* 2.8 26.6 + - + +
391A TRP* 4.1 2.5 - - - +
393A ALA* 1.3 67.9 - - - +
395A MET* 1.3 61.2 + - - +
397A ILE* 3.0 12.2 + - - +
398A ALA* 2.7 43.0 + - - +
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Residues in contact with MET 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLU* 4.5 3.6 - - - -
246A ILE 5.2 1.3 - - - +
248A THR* 3.5 31.0 - - + +
251A MET* 3.9 25.1 - - + +
275A ALA* 3.4 11.6 - - + +
278A PRO* 3.4 53.2 - - + +
281A GLU* 5.3 0.2 - - + -
282A LEU* 3.6 20.7 - - + +
391A TRP* 3.0 61.4 + - + +
392A ARG 3.6 4.5 - - - +
393A ALA 3.3 0.2 - - - -
394A ASP* 1.3 79.1 - - - +
396A ALA* 1.3 59.0 + - - +
398A ALA 4.2 0.9 + - - -
399A GLY 4.6 0.5 + - - -
413A LEU* 4.5 2.0 - - + -
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Residues in contact with ALA 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LEU* 4.6 0.4 - - - -
348A LYS* 5.4 1.0 - - - +
392A ARG 3.1 12.9 + - - +
393A ALA 3.3 11.0 - - - +
395A MET* 1.3 79.9 - - - +
397A ILE* 1.3 60.3 + - - +
399A GLY 4.2 1.5 - - - +
402A SER* 4.1 8.8 - - - -
403A PHE 5.2 0.9 + - - -
410A VAL* 3.7 38.9 - - + +
413A LEU* 3.9 15.0 - - + +
414A LEU* 3.6 27.8 - - + -
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Residues in contact with ILE 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.6 24.2 - - + -
87A TRP* 5.1 2.2 - - + -
96A TYR* 4.7 3.8 + - + +
348A LYS* 4.4 11.2 - - + +
352A GLN* 3.4 40.8 - - + +
356A PHE* 3.5 26.0 - - + -
393A ALA 3.3 18.2 - - - +
394A ASP* 3.0 15.1 + - - +
396A ALA* 1.3 77.5 - - + +
398A ALA* 1.3 66.7 + - - +
399A GLY 3.2 10.6 + - - +
400A HIS* 4.3 13.7 + - - -
414A LEU* 3.9 17.9 - - + -
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Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 4.5 8.2 + - - +
274A LYS* 4.9 1.6 - - - +
275A ALA* 3.7 20.2 - - + +
276A GLN* 4.2 0.2 - - - -
277A HIS* 3.4 30.0 + - - +
278A PRO* 3.7 8.3 - - + -
394A ASP* 2.7 29.5 + - - +
395A MET 4.2 0.2 + - - -
396A ALA 3.6 0.4 - - - -
397A ILE* 1.3 74.5 - - - +
399A GLY* 1.3 58.1 + - - +
400A HIS* 3.6 6.5 + - - -
508A HEM 3.5 13.9 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il