Contacts of the helix formed by residues 402 - 431 (chain A) in PDB entry 5AVL
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 LEU 402 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ASP* 3.1 14.1 + - - +
401A ARG* 1.3 78.8 - - - +
403A MET* 1.3 64.7 + - - +
404A PHE 3.3 0.2 - - - -
405A PRO* 3.2 18.6 - - + +
406A ARG* 3.0 41.3 + - + +
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Residues in contact with MET 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 3.7 37.9 - - + +
393A VAL* 3.7 18.2 - - + -
397A HIS* 3.7 33.0 - - + +
400A ASP* 3.1 32.7 + - - +
402A LEU* 1.3 75.9 - - - +
404A PHE* 1.3 62.0 + - - +
406A ARG* 3.2 33.4 + - - +
407A MET* 3.1 41.4 + - + +
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Residues in contact with PHE 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A VAL* 3.7 30.3 - - + -
389A LEU* 4.1 14.4 - - + -
390A HIS* 3.5 59.9 - + + -
393A VAL* 3.7 21.8 - - + +
401A ARG 4.2 3.0 + - - +
403A MET* 1.3 78.8 - - - +
405A PRO* 1.4 77.1 - - + +
407A MET* 3.6 3.7 + - - +
408A LEU* 3.4 52.3 + - + +
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Residues in contact with PRO 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ARG 3.3 19.3 - - - +
402A LEU* 3.3 31.6 - - + +
404A PHE* 1.4 97.3 - - + +
406A ARG* 1.3 55.4 + - + +
408A LEU* 3.1 12.8 + - + +
409A MET* 2.9 37.6 + - + +
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Residues in contact with ARG 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A GLU* 5.6 8.1 + - - +
349A LEU* 3.5 34.8 - - + +
400A ASP* 4.5 8.9 + - - -
402A LEU* 3.0 41.7 + - + +
403A MET* 3.2 24.6 + - - +
405A PRO* 1.3 75.2 - - + +
407A MET* 1.3 61.2 + - - +
409A MET* 3.3 18.0 + - - +
410A LYS* 3.4 19.3 + - - +
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Residues in contact with MET 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 4.3 9.9 - - + -
351A LEU* 3.8 29.8 - - + -
355A GLU* 3.6 45.5 - - - +
359A LEU* 3.8 25.9 - - + +
389A LEU* 4.4 11.4 - - + -
393A VAL* 3.8 26.2 - - + -
397A HIS* 4.4 1.8 - - + +
403A MET* 3.1 32.3 + - + +
404A PHE* 3.8 5.4 - - - +
406A ARG* 1.3 76.2 - - - +
408A LEU* 1.3 62.8 + - - +
410A LYS* 3.2 20.1 + - - +
411A LEU 4.0 0.5 + - - -
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Residues in contact with LEU 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A LEU* 4.9 0.2 - - + -
362A ILE* 4.4 10.3 - - + -
386A VAL* 4.4 16.2 - - + -
389A LEU* 4.2 14.8 - - + -
404A PHE* 3.4 47.5 + - + +
405A PRO* 3.1 11.6 + - + +
407A MET* 1.3 73.6 - - - +
409A MET* 1.3 58.0 + - + +
410A LYS 3.0 5.6 - - - -
411A LEU* 2.7 51.6 + - + +
412A VAL* 3.8 4.5 + - - +
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Residues in contact with MET 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A PRO* 2.9 25.1 + - + +
406A ARG* 3.6 13.2 - - - +
407A MET 3.3 0.6 - - - -
408A LEU* 1.3 78.1 - - - +
410A LYS* 1.3 63.7 + - - +
411A LEU 3.2 0.2 - - - -
412A VAL* 3.3 41.1 - - + +
413A SER* 3.7 8.3 + - - -
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Residues in contact with LYS 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LEU* 5.8 0.9 - - + -
342A PHE* 3.7 27.2 - - + -
345A ALA* 3.8 43.6 + - - +
346A MET* 3.8 32.8 - - + +
349A LEU* 4.0 12.8 - - + +
359A LEU* 5.2 1.8 - - + -
406A ARG 3.4 14.8 + - - +
407A MET 3.2 12.7 + - - +
408A LEU 3.0 0.8 - - - -
409A MET* 1.3 80.2 + - - +
411A LEU* 1.3 60.1 + - + +
412A VAL 3.2 0.2 - - - -
413A SER* 3.6 9.1 + - - -
414A LEU* 2.9 27.9 + - - +
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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
----------------------------------------------------------
296A GLU* 5.5 0.5 - - - +
300A LEU* 5.2 1.8 - - + -
359A LEU* 3.8 48.2 - - + +
362A ILE* 3.6 26.5 - - + -
363A SER* 4.5 9.2 - - - -
408A LEU* 2.7 34.6 + - + +
410A LYS* 1.3 72.8 - - - +
412A VAL* 1.3 67.3 + - + +
414A LEU* 3.5 22.9 - - + +
415A ARG* 3.2 23.0 + - - +
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Residues in contact with VAL 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A LEU 4.3 2.2 - - - +
409A MET* 3.3 44.4 - - + +
411A LEU* 1.3 78.0 - - + +
413A SER* 1.3 58.8 + - - +
415A ARG* 2.9 29.8 + - - +
416A THR* 3.5 8.0 + - - +
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Residues in contact with SER 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A PHE* 4.0 20.6 - - - -
409A MET 3.7 8.7 + - - -
410A LYS* 3.6 15.7 + - - +
412A VAL* 1.3 76.3 - - - +
414A LEU* 1.3 64.1 + - - +
416A THR* 3.0 21.2 + - - +
417A LEU* 3.0 14.9 + - - +
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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
----------------------------------------------------------
296A GLU* 3.6 35.8 - - + +
299A LEU* 3.8 33.7 - - + -
300A LEU* 3.6 34.1 - - + -
342A PHE* 3.7 24.3 - - + -
363A SER* 4.6 1.8 - - - +
410A LYS 2.9 15.2 + - - +
411A LEU* 3.5 22.0 - - + +
412A VAL 3.3 0.2 - - - -
413A SER* 1.3 76.7 - - - +
415A ARG* 1.3 55.8 + - - +
417A LEU* 3.5 5.6 + - + +
418A SER* 3.0 26.5 + - - -
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Residues in contact with ARG 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLU* 3.6 16.3 + - - -
366A SER* 3.5 21.2 + - - -
368A ASP* 2.8 44.1 + - - -
369A ARG* 3.2 20.0 - - - +
411A LEU 3.2 15.4 + - - +
412A VAL* 2.9 16.7 + - - +
414A LEU* 1.3 69.9 - - - +
416A THR* 1.3 66.9 + - - +
418A SER* 3.3 7.2 - - - -
419A SER* 3.3 19.9 + - - -
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Residues in contact with THR 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A VAL* 3.5 8.9 + - - +
413A SER* 3.0 12.1 + - - -
415A ARG* 1.3 76.5 - - - +
417A LEU* 1.3 59.7 - - + +
419A SER* 3.0 12.4 + - - +
420A VAL* 3.0 40.4 + - + +
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Residues in contact with LEU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 3.8 27.6 - - + -
335A PHE* 4.1 15.0 - - + -
338A PRO* 3.7 36.3 - - + +
339A ILE* 4.1 5.2 - - - +
342A PHE* 3.7 43.5 - - + -
413A SER 3.0 11.7 + - - +
414A LEU* 3.6 12.6 - - + +
416A THR* 1.3 76.5 - - - +
418A SER* 1.3 56.3 + - - +
420A VAL* 3.1 9.2 + - + +
421A HIS* 2.9 30.3 + - - +
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Residues in contact with SER 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A THR* 4.3 10.4 + - - +
295A ILE* 3.6 21.6 - - - +
296A GLU* 3.4 29.5 + - - -
299A LEU* 4.6 1.6 - - - +
369A ARG* 5.2 0.2 + - - -
414A LEU 3.0 9.1 + - - -
415A ARG* 3.3 13.5 - - - -
417A LEU* 1.3 75.4 - - - +
419A SER* 1.3 58.3 + - - +
421A HIS* 3.4 13.0 + - - +
422A SER* 3.2 20.7 + - - -
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Residues in contact with SER 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ARG 3.3 8.0 + - - -
416A THR* 3.0 17.9 + - - +
418A SER* 1.3 76.4 - - - +
420A VAL* 1.3 61.4 + - - +
421A HIS 3.1 1.6 - - - -
422A SER* 2.8 26.3 + - - +
423A GLU* 3.0 21.9 + - - +
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Residues in contact with VAL 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A GLN* 5.4 0.7 + - - -
334A GLU 3.4 26.9 - - - +
335A PHE* 3.8 19.3 - - + +
338A PRO* 4.4 12.1 - - + -
416A THR* 3.0 32.8 + - + +
417A LEU* 3.1 14.1 + - + +
419A SER* 1.3 75.0 - - - +
421A HIS* 1.3 56.1 + - - +
423A GLU* 3.3 21.0 + - + +
424A GLN* 3.0 25.1 + - - +
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Residues in contact with HIS 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ILE* 3.7 26.7 - - + +
335A PHE* 3.7 18.1 - + + -
417A LEU 2.9 13.0 + - - +
418A SER 3.4 12.8 + - - +
420A VAL* 1.3 74.1 - - - +
422A SER* 1.3 60.9 + - - +
424A GLN* 3.2 6.3 + - + +
425A VAL* 3.0 41.4 + - + +
443A TRP* 3.3 56.3 - + - -
501A 4KQ 3.2 31.3 + - - -
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Residues in contact with SER 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A SER 3.2 12.1 + - - -
419A SER* 2.8 22.9 + - - -
421A HIS* 1.3 73.6 + - - +
423A GLU* 1.3 58.3 + - - +
425A VAL* 3.2 8.1 + - - +
426A PHE* 3.0 30.2 + - - +
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Residues in contact with GLU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A GLN* 3.9 9.5 + - - +
334A GLU* 6.1 1.6 - - - +
419A SER* 3.0 21.0 + - - +
420A VAL* 3.6 21.6 - - + +
422A SER* 1.3 74.9 - - - +
424A GLN* 1.3 57.6 + - - +
426A PHE* 3.7 10.2 + - - +
427A ALA* 3.1 27.9 + - - +
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Residues in contact with GLN 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLY 4.8 0.9 - - - +
331A LEU* 3.4 10.6 - - - +
332A GLN* 2.9 50.1 + - - +
335A PHE* 3.3 33.8 - - + +
420A VAL 3.0 13.6 + - - +
421A HIS* 3.3 14.6 - - - +
422A SER 3.1 0.2 - - - -
423A GLU* 1.3 73.7 - - - +
425A VAL* 1.3 64.8 + - - +
427A ALA* 3.1 12.3 + - - +
428A LEU* 3.2 21.4 + - + +
501A 4KQ 3.3 27.4 - - - -
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Residues in contact with VAL 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A HIS* 3.0 45.2 + - + +
422A SER* 3.2 9.8 + - - +
424A GLN* 1.3 74.5 - - - +
426A PHE* 1.3 63.2 + - - +
428A LEU* 3.3 20.7 + - - +
429A ARG* 3.3 14.8 + - + +
435A LEU* 4.1 10.5 - - + +
443A TRP* 3.6 27.6 - - + +
444A ASP* 3.5 23.6 - - - +
445A VAL* 5.5 3.1 - - + +
501A 4KQ 4.4 8.1 - - - -
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Residues in contact with PHE 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A SER 3.0 16.4 + - - +
423A GLU* 4.0 8.5 - - - +
425A VAL* 1.3 78.8 - - - +
427A ALA* 1.3 62.5 + - + +
429A ARG* 3.1 30.6 + - + +
430A LEU* 3.4 40.0 + - + +
445A VAL* 6.3 2.7 - - + -
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Residues in contact with ALA 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A GLN* 3.7 26.5 - - - +
423A GLU 3.1 19.6 + - - +
424A GLN* 3.1 7.1 + - - +
426A PHE* 1.3 74.6 - - + +
428A LEU* 1.3 63.8 + - - +
430A LEU* 3.3 18.6 + - + +
431A GLN* 3.2 29.9 + - - +
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Residues in contact with LEU 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A PHE* 4.2 8.3 - - + -
330A GLY 4.2 12.1 - - - +
331A LEU* 6.2 0.2 - - + -
424A GLN* 3.2 19.5 + - - +
425A VAL* 3.4 11.4 - - - +
426A PHE 3.3 0.2 - - - -
427A ALA* 1.3 74.2 - - - +
429A ARG* 1.3 61.2 + - + +
431A GLN* 2.9 48.2 + - - +
433A LYS* 3.3 40.0 + - + +
435A LEU* 3.9 20.6 - - + -
501A 4KQ 3.3 37.7 - - - -
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Residues in contact with ARG 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A VAL* 3.3 15.5 - - + +
426A PHE* 3.1 22.9 + - + +
428A LEU* 1.3 78.7 - - - +
430A LEU* 1.3 59.0 + - + +
431A GLN 3.0 13.2 - - - +
433A LYS 5.1 2.9 + - - -
434A LYS* 5.9 7.0 - - - +
435A LEU* 6.1 1.1 - - - -
444A ASP* 3.2 34.7 + - - +
445A VAL* 4.5 14.3 + - - +
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Residues in contact with LEU 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A PHE* 3.7 42.8 - - + +
427A ALA* 3.3 17.7 + - + +
429A ARG* 1.3 81.7 - - + +
431A GLN* 1.3 58.0 + - - +
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Residues in contact with GLN 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ARG* 5.2 2.8 - - - +
330A GLY 4.1 7.7 + - - -
332A GLN* 5.5 1.4 - - - +
427A ALA* 3.2 25.1 + - - +
428A LEU* 2.9 32.3 + - - +
429A ARG 3.0 10.7 - - - +
430A LEU* 1.3 76.6 - - - +
432A ASP* 1.3 60.7 + - - +
433A LYS* 3.2 41.0 + - + +
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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