Contacts of the helix formed by residues 395 - 423 (chain A) in PDB entry 6YB9
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 ASN 395 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A SER* 2.6 26.7 + - - +
263A GLU* 4.0 6.0 - - - +
264A SER* 3.0 25.3 + - - +
266A CYS* 3.9 12.2 - - - -
391A PHE 2.8 13.9 + - - +
392A GLY* 3.7 3.1 - - - +
394A SER* 1.3 77.9 - - - +
396A HIS* 1.3 58.0 + - - +
397A LEU* 2.9 35.2 + - - +
398A VAL* 3.1 23.1 + - + +
399A TRP* 3.0 27.2 + - - +
503A EDO 3.6 3.5 - - - -
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Residues in contact with HIS 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.7 0.7 - - + -
178A LYS* 4.0 20.4 - - + +
179A SER* 3.4 32.2 - - - +
182A PRO* 4.3 9.7 - - + +
258A LEU 4.8 0.9 - - - -
259A LEU* 2.8 29.2 + - - -
261A LYS 3.3 26.7 - - - -
263A GLU* 2.6 27.4 + - + +
395A ASN* 1.3 69.8 + - - +
397A LEU* 1.3 72.5 + - + +
399A TRP* 3.6 4.6 - - - +
400A SER* 2.6 37.8 + - - -
503A EDO 3.3 21.0 - - - +
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Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.8 22.9 - - + -
71A ALA* 5.4 0.3 - - - +
259A LEU 3.9 4.0 - - - +
260A LEU* 3.7 21.3 - - + +
262A SER* 3.7 32.1 - - - +
395A ASN* 2.9 8.5 + - - +
396A HIS* 1.3 99.2 - - + +
398A VAL* 1.3 66.0 + - + +
400A SER* 3.3 6.0 + - - -
401A LYS* 3.2 37.9 + - - +
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A CYS* 4.5 7.2 - - - -
291A PHE* 3.8 23.5 - - + +
292A GLY 5.6 1.6 - - - +
293A ILE* 4.1 18.2 - - + -
388A ALA* 3.2 46.4 - - + +
391A PHE* 4.5 1.1 - - + -
392A GLY* 4.0 3.1 - - - +
395A ASN* 3.1 30.6 + - + +
397A LEU* 1.3 72.0 - - + +
399A TRP* 1.3 67.0 + - - +
401A LYS* 3.1 15.1 + - - +
402A LEU* 3.1 14.3 + - + +
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Residues in contact with TRP 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLU* 3.7 37.9 - - + -
175A ILE* 4.1 4.7 - - - -
178A LYS* 3.5 35.0 - - + +
392A GLY* 3.6 26.7 - - - +
395A ASN 3.0 16.8 + - - +
396A HIS* 3.6 9.0 - - - +
397A LEU 3.3 0.2 - - - -
398A VAL* 1.3 76.4 - - - +
400A SER* 1.3 60.5 + - - +
402A LEU* 3.0 10.5 + - - +
403A ARG* 2.9 62.9 + - + -
503A EDO 4.1 0.9 - - - +
317B GLU* 6.0 7.9 - - + -
344B ALA* 3.4 30.8 - - + +
345B TYR* 3.7 27.5 - + - -
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Residues in contact with SER 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 5.7 3.4 - - - +
71A ALA* 3.8 14.2 - - - +
175A ILE* 3.6 32.4 + - - +
178A LYS* 5.3 0.3 - - - +
179A SER* 4.1 7.1 + - - -
396A HIS* 2.6 24.1 + - - +
397A LEU* 3.6 7.6 - - - -
398A VAL 3.2 0.4 - - - -
399A TRP* 1.3 85.1 - - - +
401A LYS* 1.3 61.1 + - - +
403A ARG* 3.3 1.2 + - - +
404A ALA* 2.9 31.7 + - - +
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Residues in contact with LYS 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLU* 3.2 27.8 + - - +
71A ALA* 3.5 22.7 - - - +
290A ASN 3.4 21.1 - - - +
291A PHE* 3.5 42.1 - - + +
292A GLY* 4.1 5.8 - - - +
397A LEU* 3.2 25.0 + - - +
398A VAL* 3.1 7.4 + - - +
400A SER* 1.3 74.8 - - - +
402A LEU* 1.3 57.9 + - - +
404A ALA* 3.9 1.2 - - - +
405A SER* 3.0 30.3 + - - -
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Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PHE* 3.4 28.9 - - + -
385A GLN* 4.2 13.5 - - + +
388A ALA* 3.7 19.3 - - + +
389A GLN* 3.6 41.5 - - + +
392A GLY* 4.6 2.0 - - - -
398A VAL* 3.1 17.2 + - + +
399A TRP* 3.0 16.2 + - - +
401A LYS* 1.3 76.1 - - - +
403A ARG* 1.4 56.2 + - - +
405A SER* 3.2 7.5 + - - -
406A ILE* 3.0 32.7 + - + +
344B ALA* 3.7 24.7 - - + +
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Residues in contact with ARG 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A HIS 4.8 2.4 + - - -
170A GLN* 4.4 8.9 + - - +
171A ALA* 3.6 35.0 - - + +
174A GLU* 2.9 34.5 + - + +
175A ILE* 4.1 13.5 - - + -
399A TRP* 2.9 50.4 + - + +
400A SER 3.3 4.9 + - - +
402A LEU* 1.4 73.4 - - - +
404A ALA* 1.3 63.9 + - - +
406A ILE* 3.4 32.6 + - - +
407A LEU* 3.3 14.9 + - - +
317B GLU* 6.2 0.2 - - - -
344B ALA* 4.2 3.9 - - - +
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Residues in contact with ALA 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA 3.4 25.1 - - - +
72A GLY* 4.2 6.7 - - - -
73A ILE* 3.7 30.5 - - + -
171A ALA* 5.6 0.4 - - - -
175A ILE* 4.3 3.1 - - + +
400A SER 2.9 17.6 + - - +
401A LYS 4.0 0.2 - - - +
403A ARG* 1.3 76.3 - - - +
405A SER* 1.3 58.0 + - - +
407A LEU* 3.1 6.0 + - - +
408A ASN* 2.8 33.6 + - - -
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Residues in contact with SER 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PHE* 5.3 8.5 - - - -
385A GLN* 5.7 4.2 + - - -
401A LYS 3.0 19.3 + - - -
402A LEU* 3.2 8.5 + - - -
404A ALA* 1.3 75.5 - - - +
406A ILE* 1.3 63.9 + - - +
408A ASN* 4.4 7.0 - - - +
409A THR* 2.9 38.6 + - - -
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Residues in contact with ILE 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLN* 6.0 4.3 - - - +
402A LEU 3.0 19.1 + - - +
403A ARG* 3.6 25.6 - - - +
404A ALA 3.3 0.2 - - - -
405A SER* 1.3 74.6 - - - +
407A LEU* 1.3 63.1 + - - +
409A THR* 3.9 4.0 - - - -
410A TRP* 3.1 24.3 + - + +
340B SER 5.3 0.7 - - - +
341B GLY 4.0 20.2 - - - +
342B ASN* 4.1 11.0 - - - +
343B THR* 3.5 42.8 - - - +
344B ALA* 3.7 9.6 - - + +
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Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 3.8 27.6 - - + -
167A HIS* 3.9 16.8 - - + +
168A ALA* 3.8 43.7 - - + +
171A ALA* 4.0 12.1 - - + -
403A ARG* 3.3 12.5 + - - +
404A ALA 3.1 9.0 + - - +
406A ILE* 1.3 79.8 - - - +
408A ASN* 1.3 56.7 + - - +
410A TRP* 3.0 9.7 + - + +
411A ILE* 2.8 59.2 + - + +
504A EDO 4.5 6.7 - - - -
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Residues in contact with ASN 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLY* 2.8 33.2 + - - +
73A ILE* 5.0 0.9 - - - +
74A LYS* 4.7 15.6 + - - +
404A ALA* 2.8 25.3 + - - +
405A SER* 4.2 6.3 - - - +
407A LEU* 1.3 79.3 - - - +
409A THR* 1.3 57.7 + - - +
411A ILE* 3.3 18.4 + - - +
412A SER* 2.9 31.0 + - - -
504A EDO 5.1 1.4 - - - -
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Residues in contact with THR 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A SER* 2.9 25.0 + - - -
406A ILE* 3.9 4.9 - - - -
408A ASN* 1.3 77.0 - - - +
410A TRP* 1.3 60.1 + - - +
412A SER* 3.4 9.5 + - - -
413A LEU* 3.2 33.2 + - + +
370B SER 6.1 0.9 - - - +
371B GLY* 6.0 7.8 - - - +
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Residues in contact with TRP 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASP* 3.7 22.9 - - - -
164A ILE* 4.0 14.1 - - + -
167A HIS* 3.5 63.0 + + + -
406A ILE* 3.1 15.6 + - + +
407A LEU* 3.0 12.0 + - + +
409A THR* 1.3 73.3 - - - +
411A ILE* 1.3 77.3 - - + +
413A LEU* 3.2 19.1 + - + +
414A LYS* 3.1 55.4 + - + +
342B ASN* 6.1 1.3 - - - -
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Residues in contact with ILE 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ILE* 4.0 25.8 - - + +
407A LEU* 2.8 37.4 + - + +
408A ASN* 3.5 16.2 - - - +
410A TRP* 1.3 92.2 - - + +
412A SER* 1.3 57.3 + - - +
414A LYS* 3.2 8.6 + - - +
415A GLN* 3.0 43.6 + - + +
504A EDO 3.5 29.4 - - - +
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Residues in contact with SER 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ASN 2.9 14.5 + - - -
409A THR* 3.5 12.9 - - - -
410A TRP 3.3 0.2 - - - -
411A ILE* 1.3 77.3 - - - +
413A LEU* 1.3 58.2 + - - +
415A GLN* 3.3 8.2 + - - +
416A ALA* 2.9 30.4 + - - +
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Residues in contact with LEU 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A THR* 3.2 23.3 + - + +
410A TRP* 3.2 19.6 + - + +
412A SER* 1.3 76.2 - - - +
414A LYS* 1.3 60.1 + - - +
416A ALA* 3.3 7.7 + - + +
417A ASP* 2.9 31.9 + - - +
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Residues in contact with LYS 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLN* 3.5 17.0 - - - +
160A THR* 4.1 38.1 + - + +
163A ASP* 3.0 28.5 + - - +
164A ILE* 4.6 5.2 - - + -
410A TRP* 3.1 48.6 + - + +
411A ILE* 3.4 8.1 - - - +
413A LEU* 1.3 77.5 - - + +
415A GLN* 1.3 57.4 + - - +
417A ASP* 3.4 6.5 + - - +
418A LYS* 3.0 28.4 + - - +
421A ARG* 4.7 5.2 + - - +
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Residues in contact with GLN 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A THR* 4.6 3.4 - - - +
161A GLU* 5.2 2.0 + - - +
164A ILE* 3.9 22.9 - - - +
411A ILE* 3.0 30.5 + - + +
412A SER* 3.7 9.6 - - - +
413A LEU 3.2 0.2 - - - -
414A LYS* 1.3 71.1 - - - +
416A ALA* 1.3 60.1 + - - +
418A LYS* 3.3 23.3 + - - +
419A LYS* 3.0 27.9 + - - +
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Residues in contact with ALA 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A SER 2.9 17.5 + - - +
413A LEU* 3.8 8.3 - - + +
415A GLN* 1.3 71.9 - - - +
417A ASP* 1.3 64.0 + - - +
419A LYS* 3.4 8.3 + - - +
420A ILE* 3.1 25.3 + - - +
----------------------------------------------------------
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Residues in contact with ASP 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A LEU 2.9 17.1 + - - +
414A LYS* 3.7 7.6 - - - +
416A ALA* 1.3 72.9 - - - +
418A LYS* 1.3 59.9 + - - +
420A ILE* 3.2 15.7 - - - +
421A ARG* 2.9 59.4 + - - +
----------------------------------------------------------
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Residues in contact with LYS 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 5.2 5.9 - - - +
156A LEU 5.3 1.2 + - - -
160A THR* 4.5 10.4 - - + +
161A GLU* 2.7 33.9 + - - +
414A LYS 3.0 18.1 + - - +
415A GLN* 3.3 22.6 + - - +
417A ASP* 1.3 77.0 - - - +
419A LYS* 1.3 62.8 + - - +
421A ARG* 3.4 41.7 + - - +
422A GLU* 3.5 30.3 + - - +
----------------------------------------------------------
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Residues in contact with LYS 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A GLN 3.0 13.6 + - - +
416A ALA* 3.6 10.8 - - - +
417A ASP 3.2 0.2 - - - -
418A LYS* 1.3 76.1 - - - +
420A ILE* 1.3 57.0 + - - +
422A GLU* 3.1 31.8 + - - +
423A CYS* 3.6 11.1 + - - -
----------------------------------------------------------
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Residues in contact with ILE 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ALA 3.1 13.7 + - - +
417A ASP* 3.2 24.0 - - - +
419A LYS* 1.3 74.8 - - - +
421A ARG* 1.3 68.7 + - - +
423A CYS* 3.2 31.6 + - + +
424A ASN* 3.7 8.4 + - - +
----------------------------------------------------------
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Residues in contact with ARG 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A THR* 3.4 25.3 + - - -
414A LYS* 4.7 4.4 + - - +
417A ASP* 2.9 44.0 + - - +
418A LYS* 3.4 39.9 + - - +
420A ILE* 1.3 79.1 - - - +
422A GLU* 1.3 58.7 + - + +
424A ASN* 3.0 39.0 - - - +
425A LEU* 4.6 5.5 - - - +
----------------------------------------------------------
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Residues in contact with GLU 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LYS* 3.6 36.9 - - - +
419A LYS* 3.1 14.5 + - - +
421A ARG* 1.3 72.4 - - + +
423A CYS* 1.3 58.3 + - - +
424A ASN 3.1 9.2 + - - -
425A LEU* 3.6 23.7 + - + +
----------------------------------------------------------
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Residues in contact with CYS 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A LYS* 3.9 17.9 - - - -
420A ILE* 3.2 21.9 + - + +
422A GLU* 1.3 73.4 - - - +
424A ASN* 1.3 58.1 + - - +
425A LEU 3.5 7.2 - - - +
----------------------------------------------------------
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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