Contacts of the helix formed by residues 406 - 435 (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 ALA 406 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ACT 4.2 1.8 - - + -
282A LEU* 3.2 34.3 - - + +
285A THR* 3.6 16.6 - - + -
286A GLY* 3.8 9.2 - - - -
402A SER 2.8 10.7 + - - +
405A HIS* 1.3 77.7 - - - +
407A PRO* 1.3 62.6 - - - +
408A GLU 3.3 2.0 - - - -
409A GLU* 3.2 6.1 + - + -
410A VAL* 2.9 30.4 + - + +
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Residues in contact with PRO 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ACT 3.0 23.6 - - - +
287A ILE* 6.0 0.2 - - + -
344A LYS* 3.7 27.8 - - + +
347A ARG* 5.8 1.8 - - - +
403A PHE 3.2 27.6 - - - +
404A PHE 3.3 13.9 - - - +
405A HIS 3.7 1.3 - - - +
406A ALA* 1.3 88.0 - - - +
408A GLU* 1.3 63.8 + - + +
410A VAL* 3.3 4.7 + - + +
411A LEU* 3.1 34.0 + - + +
512A HEM 3.8 9.0 - - - +
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Residues in contact with GLU 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A Y1 2.3 32.1 - - - -
5A ACT 3.1 21.0 + - + +
406A ALA 3.3 0.2 - - - -
407A PRO* 1.3 79.9 - - + +
409A GLU* 1.3 56.5 + - - +
411A LEU* 3.5 10.7 + - + +
412A ARG* 3.0 29.9 + - - +
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Residues in contact with GLU 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ACT 5.0 2.0 - - - +
247A SER* 5.7 2.3 - - - -
248A THR* 4.6 5.1 + - - +
249A GLU* 4.3 4.5 - - - +
282A LEU* 4.9 6.5 - - + -
285A THR* 3.8 29.8 - - + -
406A ALA* 3.2 9.6 + - + +
408A GLU* 1.3 75.9 - - - +
410A VAL* 1.3 54.1 + - + +
412A ARG* 2.9 44.0 + - - -
413A LEU* 2.8 52.6 + - + +
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Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LEU* 4.1 8.7 - - + -
348A LYS* 3.6 32.3 - - + -
396A ALA* 3.7 21.5 - - + +
402A SER* 3.4 44.0 - - - +
403A PHE* 4.3 6.1 - - - -
406A ALA 2.9 12.7 + - - +
407A PRO 3.6 6.1 - - - +
408A GLU 3.2 0.2 - - - -
409A GLU* 1.3 75.5 - - - +
411A LEU* 1.3 65.1 + - + +
413A LEU* 3.2 4.9 + - - +
414A LEU* 3.1 31.4 + - + +
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LYS 5.4 0.4 - - - +
347A ARG* 3.8 55.2 - - + +
348A LYS* 3.9 12.3 - - + +
351A LEU* 3.8 24.0 - - + +
407A PRO* 3.1 23.6 + - + +
408A GLU* 4.0 9.2 - - + +
410A VAL* 1.3 75.8 - - + +
412A ARG* 1.3 64.4 + - - +
414A LEU* 3.3 2.1 + - + -
415A ALA* 2.9 26.4 + - - +
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Residues in contact with ARG 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A GLU* 2.7 35.8 + - - -
408A GLU 3.0 19.6 + - - +
409A GLU* 2.9 37.5 + - - +
411A LEU* 1.3 76.7 - - - +
413A LEU* 1.3 63.7 + - - +
415A ALA* 3.6 6.5 - - - +
416A SER* 2.8 51.2 + - - -
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Residues in contact with LEU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A THR* 3.4 36.1 - - + +
249A GLU* 3.5 11.2 - - - +
282A LEU* 4.4 11.7 - - + -
392A ARG* 3.9 24.1 - - + +
395A MET 4.5 0.9 - - - -
396A ALA* 3.9 24.2 - - + +
409A GLU* 2.8 39.3 + - + +
410A VAL 3.6 4.0 - - - +
412A ARG* 1.3 101.5 - - - +
414A LEU* 1.3 56.0 + - - +
416A SER* 3.2 3.6 + - - -
417A GLY* 2.8 32.4 + - - -
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Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LYS* 3.8 28.3 - - + +
351A LEU* 3.9 22.2 - - + +
352A GLN* 3.9 15.5 - - + +
355A ALA* 3.9 8.5 - - + +
356A PHE* 4.7 1.3 - - + -
393A ALA* 3.8 26.7 - - + +
396A ALA* 3.6 18.4 - - + -
397A ILE* 3.9 10.8 - - + -
410A VAL* 3.1 36.0 + - + +
411A LEU* 3.8 4.9 - - - +
413A LEU* 1.3 73.6 - - - +
415A ALA* 1.3 61.6 + - - +
417A GLY* 3.5 0.7 + - - +
418A ASN* 2.9 31.4 + - - +
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Residues in contact with ALA 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 4.6 13.4 - - + +
411A LEU 2.9 17.6 + - - +
412A ARG* 3.6 7.2 - - - +
414A LEU* 1.3 79.8 - - - +
416A SER* 1.3 61.1 + - - +
418A ASN* 3.5 5.7 + - - +
419A GLU* 3.1 23.6 + - - +
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Residues in contact with SER 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A GLU* 5.0 2.1 + - - -
392A ARG* 3.0 31.7 + - - -
412A ARG* 2.8 35.7 + - - -
413A LEU* 3.6 8.3 - - - -
415A ALA* 1.3 70.8 - - - +
417A GLY* 1.3 63.6 + - - +
419A GLU* 3.3 7.6 + - - +
420A GLU* 3.1 24.3 + - - +
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Residues in contact with GLY 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ALA* 4.9 2.7 - - - -
359A ILE* 5.3 1.3 - - - -
389A ALA* 3.1 38.0 - - - +
392A ARG* 4.1 7.0 - - - +
393A ALA* 4.5 3.8 - - - -
413A LEU 2.8 19.4 + - - -
414A LEU 3.8 1.3 - - - -
416A SER* 1.3 69.3 - - - +
418A ASN* 1.3 64.4 + - - +
420A GLU 3.0 3.3 + - - -
421A ALA* 2.9 18.5 + - - +
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Residues in contact with ASN 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU 5.5 0.4 - - - +
354A ILE* 3.5 23.6 - - + +
355A ALA* 3.6 19.1 - - - +
358A ASN* 2.7 30.3 + - - +
414A LEU 2.9 18.1 + - - +
415A ALA* 3.8 6.0 + - - +
417A GLY* 1.3 73.5 - - - +
419A GLU* 1.3 53.1 + - - +
421A ALA* 2.8 9.0 + - - +
422A GLN* 2.7 45.3 + - - +
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Residues in contact with GLU 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ALA 3.1 17.2 + - - +
416A SER* 3.6 7.6 - - - +
417A GLY 3.2 0.2 - - - -
418A ASN* 1.3 79.0 - - - +
420A GLU* 1.3 63.5 + - + +
422A GLN* 3.5 9.8 + - - +
423A LYS* 3.0 48.6 + - + +
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Residues in contact with GLU 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A HIS* 2.7 60.5 + - - +
388A HIS* 4.0 11.9 + - + +
389A ALA* 3.6 11.4 - - + +
392A ARG* 3.4 35.2 + - - +
416A SER 3.1 9.8 + - - +
417A GLY 3.0 9.4 + - - +
419A GLU* 1.3 77.3 - - + +
421A ALA* 1.3 57.1 + - - +
423A LYS* 3.4 24.5 + - - +
424A ALA 3.0 22.2 + - - -
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Residues in contact with ALA 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ASN* 4.0 9.4 - - + -
359A ILE* 3.8 33.2 - - + +
362A ALA* 4.5 2.8 - - + +
386A ILE* 5.6 0.7 - - - +
389A ALA* 3.9 13.0 - - + -
417A GLY 2.9 10.5 + - - +
418A ASN* 2.8 11.3 + - - +
420A GLU* 1.3 74.6 - - - +
422A GLN* 1.3 59.4 + - - +
424A ALA* 3.1 11.3 + - - +
425A ARG* 2.9 31.6 + - - +
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Residues in contact with GLN 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ASN* 3.4 25.7 + - - +
418A ASN* 2.7 37.5 + - - +
419A GLU* 3.9 13.2 - - - +
421A ALA* 1.3 69.0 - - - +
423A LYS* 1.3 65.2 + - - +
425A ARG* 3.0 39.4 + - - +
426A ILE* 2.9 36.9 + - + +
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Residues in contact with LYS 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A HIS* 3.9 25.4 - - + +
419A GLU* 3.0 43.4 + - + +
420A GLU* 3.4 30.2 + - - +
422A GLN* 1.3 75.0 - - - +
424A ALA* 1.3 62.2 + - - +
426A ILE* 3.6 9.8 + - + +
427A LYS* 3.3 31.8 + - - +
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Residues in contact with ALA 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ALA* 4.4 4.9 - - + -
382A ILE* 3.9 11.5 - - + +
385A HIS* 3.7 21.5 - - + +
386A ILE* 4.0 23.8 - - + -
420A GLU 3.0 14.0 + - - +
421A ALA* 3.1 15.0 - - - +
423A LYS* 1.3 75.2 - - - +
425A ARG* 1.3 54.3 + - - +
427A LYS* 3.3 5.0 + - - +
428A LEU* 2.9 32.3 + - - +
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Residues in contact with ARG 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ASN* 3.2 39.9 + - - -
361A LYS* 3.5 27.7 - - - +
362A ALA* 3.9 11.9 - - + -
365A GLU* 2.8 40.9 + - - +
421A ALA 2.9 18.7 + - - +
422A GLN* 3.0 28.4 + - - +
424A ALA* 1.3 72.3 - - - +
426A ILE* 1.3 65.9 + - + +
428A LEU* 3.2 8.9 + - - +
429A VAL* 3.0 31.2 + - + +
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Residues in contact with ILE 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A GLN* 2.9 28.1 + - + +
423A LYS* 4.0 9.0 - - + +
424A ALA 3.4 0.2 - - - -
425A ARG* 1.3 76.8 - - + +
427A LYS* 1.3 62.0 + - + +
429A VAL* 3.2 23.5 + - + +
430A LYS* 3.6 14.4 + - + +
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Residues in contact with LYS 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A GLU* 3.1 31.6 + - + +
382A ILE* 3.5 24.5 - - + -
385A HIS* 2.8 37.6 + - + -
423A LYS* 3.3 16.6 + - - +
424A ALA 3.5 2.7 - - - +
426A ILE* 1.3 79.1 - - + +
428A LEU* 1.3 61.1 + - - +
430A LYS* 3.4 15.4 + - + +
431A VAL* 3.2 23.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ALA* 3.6 21.5 - - + +
365A GLU* 3.9 25.6 - - + +
366A THR* 3.3 42.0 - - - +
369A ALA* 4.5 6.3 - - + -
379A LEU* 4.2 9.0 - - + -
382A ILE* 3.7 27.4 - - + -
424A ALA 2.9 24.7 + - - +
425A ARG* 3.5 7.4 - - - +
426A ILE 3.2 0.2 - - - -
427A LYS* 1.3 74.8 - - - +
429A VAL* 1.3 57.5 + - - +
431A VAL* 3.0 2.9 + - + +
432A LEU* 2.8 41.0 + - + +
----------------------------------------------------------
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Residues in contact with VAL 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLU* 6.0 2.5 - - - +
425A ARG* 3.0 24.3 + - + +
426A ILE* 3.2 12.8 + - + +
428A LEU* 1.3 75.3 - - - +
430A LYS* 1.3 55.1 + - + +
432A LEU* 3.5 11.2 - - + +
433A ALA* 2.7 33.1 + - - +
438A ILE* 3.9 31.0 - - + +
----------------------------------------------------------
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Residues in contact with LYS 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ILE* 3.6 16.1 + - + +
427A LYS* 3.5 13.7 - - + +
429A VAL* 1.3 78.1 - - + +
431A VAL* 1.3 59.9 + - + +
433A ALA* 3.3 7.8 + - - +
434A LYS* 2.9 27.5 + - - +
----------------------------------------------------------
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Residues in contact with VAL 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ALA* 3.8 15.0 - - + -
374A ALA* 3.7 30.7 - - + -
378A GLU* 3.9 21.3 - - + +
379A LEU* 4.3 4.0 - - + -
382A ILE* 3.8 18.2 - - + -
427A LYS 3.2 13.4 + - - +
428A LEU* 3.0 9.6 + - + +
430A LYS* 1.3 74.4 - - + +
432A LEU* 1.3 67.8 + - - +
434A LYS* 3.1 14.8 + - - +
435A TYR* 3.2 26.1 - - + -
----------------------------------------------------------
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Residues in contact with LEU 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLU* 3.9 32.5 - - + +
368A LYS* 3.8 28.7 - - + -
369A ALA* 3.9 14.1 - - + +
372A LEU* 4.1 9.4 - - + -
428A LEU* 2.8 24.2 + - + +
429A VAL* 3.5 9.2 - - + +
431A VAL* 1.3 76.9 - - - +
433A ALA* 1.3 62.2 + - - +
435A TYR* 3.0 9.4 + - - -
436A GLY 3.2 0.2 + - - -
437A ALA* 2.9 41.7 + - - +
438A ILE* 4.5 4.3 - - - +
440A TYR* 4.2 20.9 - - + +
----------------------------------------------------------
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Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A VAL 2.7 21.7 + - - +
430A LYS* 3.5 9.9 - - - +
431A VAL 3.2 0.2 - - - -
432A LEU* 1.3 72.2 - - - +
434A LYS* 1.3 65.5 + - - +
436A GLY* 3.0 14.9 + - - -
437A ALA 4.5 0.2 - - - +
438A ILE* 3.7 35.6 - - + +
----------------------------------------------------------
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Residues in contact with LYS 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLU* 2.8 31.9 + - - +
430A LYS 2.9 13.3 + - - +
431A VAL* 3.1 11.8 + - - +
433A ALA* 1.3 76.8 - - - +
435A TYR* 1.3 80.9 + - + +
436A GLY 3.7 1.0 + - - -
----------------------------------------------------------
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Residues in contact with TYR 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ALA* 5.1 0.9 - - + -
372A LEU* 3.6 59.2 - - + +
373A GLY* 3.6 12.1 + - - -
374A ALA* 3.5 22.4 - - + -
375A THR* 4.5 3.6 - - - +
378A GLU* 2.7 43.2 + - - -
431A VAL* 3.2 24.1 + - + +
432A LEU 3.0 5.0 + - - +
434A LYS* 1.3 99.5 + - + +
436A GLY* 1.3 57.8 + - - +
437A ALA 3.4 2.8 + - - -
----------------------------------------------------------
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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