Contacts of the helix formed by residues 415 - 443 (chain A) in PDB entry 2YEV
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 ASP 415 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A TYR* 1.3 77.9 - - - +
416A GLU* 1.3 63.2 + - - +
417A ARG* 2.8 59.9 + - - +
418A LEU* 3.1 34.5 + - + +
419A GLY 3.0 18.2 + - - -
483A THR* 4.4 3.7 + - - +
486A LYS* 4.2 21.0 + - + +
487A SER* 5.2 1.4 - - - +
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LYS* 3.8 26.7 - - + +
345A THR* 2.8 33.8 + - - -
413A MET* 5.8 0.2 - - - +
414A TYR* 3.0 37.8 + - + +
415A ASP* 1.3 73.6 + - - +
417A ARG* 1.3 58.3 + - - +
419A GLY 3.4 0.3 + - - -
420A ARG* 3.0 53.6 + - - +
499A TRP* 3.6 15.8 - - - -
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Residues in contact with ARG 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASP* 2.8 36.7 + - - +
416A GLU* 1.3 75.1 - - - +
418A LEU* 1.3 60.3 + - + +
420A ARG* 3.6 27.5 + - - +
421A LEU* 3.1 25.1 + - - +
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Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASP* 3.1 27.6 + - + +
417A ARG* 1.3 77.5 - - + +
419A GLY* 1.3 60.0 + - - +
421A LEU* 3.1 18.1 + - + +
422A HIS* 2.9 31.0 + - - +
479A VAL* 3.8 6.6 - - + +
482A TYR* 3.7 38.1 - - + -
483A THR* 3.1 26.9 - - + +
486A LYS* 3.7 20.6 - - + -
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Residues in contact with GLY 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A THR* 3.7 27.7 - - - +
349A TRP* 4.6 1.0 + - - -
403A TYR* 4.2 20.8 + - - -
414A TYR* 4.8 1.1 - - - -
415A ASP 3.0 13.2 + - - -
416A GLU 3.8 0.4 - - - -
417A ARG 3.3 0.2 - - - -
418A LEU* 1.3 78.3 - - - +
420A ARG* 1.3 60.2 + - - +
422A HIS* 3.3 4.2 - - - +
423A PHE* 3.0 21.5 + - - +
483A THR* 4.3 1.0 - - - +
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Residues in contact with ARG 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A MET 4.8 5.9 + - - -
345A THR* 3.9 10.8 - - - +
348A TYR* 3.6 41.9 + - + -
416A GLU* 3.0 48.0 + - - +
417A ARG* 3.6 31.4 - - - +
419A GLY* 1.3 73.9 - - - +
421A LEU* 1.3 64.9 + - - +
423A PHE* 3.0 8.1 + - - +
424A TRP* 3.0 40.4 + - + +
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Residues in contact with LEU 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ARG 3.1 15.4 + - - +
418A LEU* 3.1 17.9 + - + +
420A ARG* 1.3 75.3 - - - +
422A HIS* 1.3 64.5 + - - +
424A TRP* 3.4 7.2 + - + -
425A LEU* 3.1 49.6 + - + +
479A VAL* 3.9 26.2 - - + -
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Residues in contact with HIS 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A TRP* 3.5 11.7 - + - -
399A PHE* 3.6 22.2 - + - -
403A TYR* 2.7 22.5 + - - +
418A LEU 2.9 13.3 + - - +
419A GLY 3.3 8.7 - - - +
421A LEU* 1.3 78.0 - - - +
423A PHE* 1.3 63.9 + - - +
425A LEU* 3.8 2.1 - - - +
426A PHE* 3.0 53.0 + + - +
476A GLY 3.5 17.7 - - - -
479A VAL* 3.8 14.7 - - + +
480A TRP* 3.3 34.0 - + + +
483A THR* 5.2 0.2 - - - +
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Residues in contact with PHE 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A THR* 5.5 0.2 - - + -
348A TYR* 3.1 48.9 - + + -
349A TRP* 3.7 48.9 - + + +
351A LEU* 5.8 0.7 - - + -
352A GLY* 4.1 17.3 - - - -
396A PHE* 4.5 7.6 - + - -
419A GLY 3.0 12.9 + - - +
420A ARG* 3.0 11.9 + - - +
422A HIS* 1.3 76.7 - - - +
424A TRP* 1.3 90.9 + + - +
426A PHE* 3.1 5.2 + - - +
427A LEU* 2.7 48.9 + - + +
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Residues in contact with TRP 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A TYR* 4.1 28.0 - + - -
420A ARG* 3.0 36.6 + - + +
421A LEU* 4.2 7.9 - - + +
423A PHE* 1.3 90.2 - + - +
425A LEU* 1.3 58.3 + - + +
427A LEU* 3.4 35.2 - - + -
428A VAL* 2.8 44.1 + - + +
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Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LEU* 3.1 37.7 + - + +
422A HIS 3.8 0.7 - - - +
424A TRP* 1.3 77.7 - - + +
426A PHE* 1.3 58.5 + - - +
428A VAL* 4.9 1.6 - - + -
429A GLY* 2.8 29.6 + - - -
472A ILE* 3.7 25.5 - - + +
473A LEU* 4.0 2.0 - - - +
475A LEU* 4.2 12.6 - - + -
476A GLY* 3.7 26.9 - - - +
479A VAL* 3.7 29.8 - - + -
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Residues in contact with PHE 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 3.9 25.1 - + - -
349A TRP* 3.6 28.5 - + + -
391A MET* 3.9 16.4 - - + -
396A PHE* 3.9 9.3 - + + -
399A PHE* 3.5 22.7 - + - -
422A HIS* 3.0 37.4 + + - +
423A PHE 3.5 6.7 - - - +
425A LEU* 1.3 79.1 - - - +
427A LEU* 1.3 55.2 + - - +
430A TYR* 2.8 32.6 + - - +
473A LEU* 3.5 39.5 - - + +
476A GLY* 3.8 14.8 - - - -
477A GLY* 3.8 7.0 - - - -
480A TRP* 5.4 0.7 - + - -
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Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLY* 4.8 3.6 - - - -
356A ASN* 3.5 28.5 - - - +
396A PHE* 4.1 15.6 - - + -
423A PHE* 2.7 37.3 + - + +
424A TRP* 3.4 39.0 - - + +
425A LEU 3.3 0.2 - - - -
426A PHE* 1.3 72.6 - - - +
428A VAL* 1.3 65.7 + - + +
430A TYR* 3.2 4.7 + - + +
431A LEU* 3.1 42.4 + - + +
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Residues in contact with VAL 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A TRP* 2.8 32.9 + - + +
425A LEU* 4.3 3.6 - - + +
427A LEU* 1.3 74.6 - - + +
429A GLY* 1.3 65.8 + - - +
431A LEU* 3.3 12.0 + - + +
432A LEU* 3.0 29.6 + - + +
472A ILE* 4.5 19.5 - - + -
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Residues in contact with GLY 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LEU 2.8 23.4 + - - -
428A VAL* 1.3 74.3 - - - +
430A TYR* 1.3 61.8 + - - +
432A LEU* 3.3 0.7 + - - -
433A THR* 2.9 28.9 + - - -
469A GLY* 3.8 12.4 - - - +
472A ILE* 3.8 17.4 - - - +
473A LEU* 3.8 11.2 - - - -
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Residues in contact with TYR 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ASN* 3.2 28.5 - - - -
359A LEU* 5.6 0.2 - - - +
387A HIS 3.9 11.2 - - - -
388A ASN* 2.7 38.5 + - - +
391A MET* 4.2 11.7 - - + -
392A ALA* 3.4 27.6 - - + -
396A PHE* 4.4 9.4 - + + -
426A PHE 2.8 21.3 + - - +
427A LEU* 3.2 4.2 + - + +
429A GLY* 1.3 78.0 - - - +
431A LEU* 1.3 79.0 + - + +
433A THR 3.2 0.2 + - - -
434A PHE* 3.1 55.4 + + + +
435A LEU* 5.3 6.8 - - + +
438A TYR* 5.1 2.1 - - - -
473A LEU* 3.6 11.0 - - + +
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Residues in contact with LEU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ASN* 3.7 24.2 - - - +
427A LEU* 3.1 31.3 + - + +
428A VAL* 3.7 10.3 - - + +
430A TYR* 1.3 86.9 - - + +
432A LEU* 1.3 59.8 + - + +
435A LEU* 3.1 62.0 + - + +
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Residues in contact with LEU 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A VAL* 3.0 23.4 + - + +
429A GLY* 4.7 0.4 - - - -
431A LEU* 1.3 77.4 - - + +
433A THR* 1.3 57.7 + - - +
436A PRO* 3.1 25.9 - - + +
465A LEU* 3.6 23.8 - - + +
466A SER* 3.5 8.7 - - - -
468A ILE* 3.8 18.2 - - + -
469A GLY* 3.6 30.1 - - - +
472A ILE* 4.1 12.3 - - + -
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Residues in contact with THR 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 4.3 8.7 - - - -
429A GLY 2.9 21.9 + - - -
432A LEU* 1.3 78.3 - - - +
434A PHE* 1.3 96.2 + - + +
436A PRO* 4.0 1.4 - - - +
437A GLN* 3.5 10.4 - - - +
466A SER* 2.7 44.8 + - - +
469A GLY 2.9 1.7 + - - -
470A ALA* 2.9 28.7 + - + +
473A LEU* 3.8 5.8 - - + +
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Residues in contact with PHE 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL* 5.0 0.2 - - + -
384A ALA* 3.6 17.1 - - + +
387A HIS* 3.2 54.7 - + + -
391A MET* 4.4 11.0 - - + -
430A TYR* 3.1 50.0 + + + +
433A THR* 1.3 99.1 - - + +
435A LEU* 1.3 68.2 + - - +
436A PRO 3.3 1.8 - - - -
437A GLN* 3.0 41.5 + - - +
438A TYR* 3.3 10.2 + - + -
473A LEU* 4.6 9.0 - - + -
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Residues in contact with LEU 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A LEU* 4.1 26.2 - - + -
430A TYR* 5.3 7.0 - - + +
431A LEU* 3.1 51.6 + - + +
434A PHE* 1.3 77.6 - - - +
436A PRO* 1.3 65.7 - - + +
438A TYR* 3.2 30.4 + - + +
439A ALA* 3.5 5.4 + - - +
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Residues in contact with PRO 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LEU 3.5 2.5 - - - +
432A LEU* 3.1 30.1 - - + +
433A THR 4.4 0.2 - - - +
434A PHE 3.5 3.6 - - - +
435A LEU* 1.3 96.3 - - + +
437A GLN* 1.3 56.6 + - - +
439A ALA* 3.2 7.4 + - + +
440A LEU* 2.9 30.5 + - - +
462A LEU* 3.6 39.5 - - + +
465A LEU* 4.2 18.4 - - + -
466A SER* 4.4 5.8 - - - +
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Residues in contact with GLN 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 3.3 18.4 - - - +
380A TYR* 3.5 34.0 - - + +
383A VAL* 3.4 22.7 - - - +
384A ALA* 4.0 7.6 + - + -
433A THR* 3.5 14.5 + - - +
434A PHE* 3.0 40.2 + - - +
436A PRO* 1.3 76.1 - - - +
438A TYR* 1.3 63.9 + - - +
440A LEU* 3.2 16.9 + - + +
441A GLY 3.1 18.4 + - - -
466A SER* 3.0 23.5 + - - +
----------------------------------------------------------
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Residues in contact with TYR 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A LEU* 4.0 14.4 - - + -
363A THR* 3.0 39.5 + - + +
381A PHE* 3.6 32.5 - + + +
384A ALA* 3.4 28.2 - - + +
385A HIS* 3.5 9.8 - - - -
388A ASN* 2.7 40.2 + - + +
430A TYR* 5.1 1.8 - - - -
434A PHE* 3.3 13.1 + - + -
435A LEU* 3.2 22.5 + - + +
437A GLN* 1.3 76.6 - - - +
439A ALA* 1.3 62.6 + - - +
441A GLY* 3.2 10.9 + - - -
442A TYR* 3.3 20.8 + - + -
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Residues in contact with ALA 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A LEU 3.5 5.2 + - - +
436A PRO* 3.2 13.4 + - + +
437A GLN 3.2 0.4 - - - -
438A TYR* 1.3 80.0 - - - +
440A LEU* 1.3 61.4 + - - +
442A TYR* 3.1 12.2 + - - +
443A LEU* 2.9 27.5 + - + +
462A LEU* 3.7 22.0 - - + -
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Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 6.0 0.2 - - - +
380A TYR* 4.0 11.7 - - + -
436A PRO 2.9 19.0 + - - +
437A GLN* 3.2 25.3 + - + +
439A ALA* 1.3 75.7 - - - +
441A GLY* 1.3 59.1 + - - +
443A LEU* 3.1 11.7 + - - +
444A GLY 3.1 0.3 + - - -
445A MET* 2.9 39.3 + - + +
459A TRP* 3.9 25.6 - - + -
462A LEU* 3.7 28.3 - - + +
463A ASN* 3.7 41.5 - - - +
466A SER* 5.4 0.7 - - - -
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Residues in contact with GLY 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLN 5.6 0.3 - - - +
376A PHE* 5.1 1.3 - - - -
379A SER* 3.9 15.1 + - - -
380A TYR* 4.1 4.4 - - - +
381A PHE* 3.6 28.9 - - - -
437A GLN 3.1 9.9 + - - -
438A TYR 3.2 3.5 + - - -
440A LEU* 1.3 76.5 - - - +
442A TYR* 1.3 57.2 + - - +
444A GLY* 2.9 19.6 + - - -
445A MET 4.5 0.7 - - - -
24B ILE* 3.7 11.6 - - - +
165B TRP* 4.7 0.2 - - - -
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Residues in contact with TYR 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A MET* 3.6 14.2 - - - +
376A PHE* 4.0 6.1 - + - -
381A PHE* 3.7 26.7 - + - -
438A TYR* 3.3 23.9 + - + -
439A ALA* 3.1 12.2 + - - +
441A GLY* 1.3 75.4 - - - +
443A LEU* 1.3 61.2 + - + +
444A GLY 3.2 0.4 + - - -
23B ALA* 3.2 6.1 - - - +
24B ILE* 2.9 46.0 + - + +
25B THR* 4.2 15.6 + - + -
39B PHE* 3.3 25.5 - + - -
43B TYR* 3.0 31.7 + + - -
----------------------------------------------------------
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Residues in contact with LEU 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ALA* 2.9 12.8 + - + +
440A LEU* 3.1 10.7 + - - +
442A TYR* 1.3 81.7 - - + +
444A GLY* 1.3 58.2 + - - +
445A MET 3.4 0.2 - - - -
457A ALA 3.9 19.3 - - - +
458A GLY* 4.1 9.6 - - - -
459A TRP* 3.0 26.9 + - + +
462A LEU* 3.6 30.3 - - + -
22B VAL* 3.3 37.3 - - - +
23B ALA* 4.4 7.6 - - + -
----------------------------------------------------------
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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