Contacts of the helix formed by residues 483 - 506 (chain C) in PDB entry 1JIQ
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 483 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C HIS* 4.7 6.8 + - - +
171C LEU* 3.8 4.0 - - - +
174C TYR* 3.6 16.4 - - + +
481C LYS* 3.0 28.3 + - + +
482C LEU* 1.3 75.8 - - - +
484C PRO* 1.3 76.8 - - - +
485C PHE* 3.6 8.4 + - - +
486C MET* 3.2 22.1 + - - +
487C LEU* 2.9 22.5 + - - +
557D VAL* 4.4 14.8 - - + -
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Residues in contact with PRO 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C LEU* 3.8 28.7 - - + -
174C TYR* 3.7 27.1 - - + -
292C ASN* 3.6 48.9 - - + +
295C GLN* 4.0 7.2 - - + -
296C LEU* 3.4 16.1 - - - +
483C THR* 1.3 90.2 - - - +
485C PHE* 1.3 62.8 + - - +
487C LEU 3.5 0.2 + - - -
488C GLY 3.1 17.2 + - - -
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Residues in contact with PHE 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR* 3.5 31.9 - - + -
48C HIS* 3.5 42.6 - + + -
295C GLN* 3.3 40.8 + - + +
298C SER* 3.6 13.0 - - - -
299C GLY* 3.2 33.4 - - - -
302C TRP* 3.7 26.9 - + + -
483C THR* 3.2 7.5 + - - +
484C PRO* 1.3 79.6 - - - +
486C MET* 1.3 69.7 + - + +
488C GLY 3.1 2.4 + - - -
489C ALA* 3.0 21.1 + - + -
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Residues in contact with MET 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR* 4.5 5.4 - - + +
48C HIS 4.3 5.4 - - - +
49C GLY* 3.9 25.4 - - - +
50C HIS 3.8 14.1 - - - +
51C ILE* 3.6 40.6 - - + -
479C PHE* 3.8 25.4 - - + -
480C THR* 4.6 2.9 - - - +
481C LYS 3.3 26.5 - - - +
482C LEU* 4.6 0.9 - - + -
483C THR* 3.2 11.9 + - - +
485C PHE* 1.3 80.1 - - + +
487C LEU* 1.3 67.7 + - - +
489C ALA* 3.1 6.4 + - - +
490C LEU* 2.9 33.0 + - + +
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Residues in contact with LEU 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C MET* 4.4 4.3 - - - -
167C VAL* 3.9 23.3 - - + -
170C ALA* 3.7 24.0 - - + -
171C LEU* 3.8 20.9 - - + -
296C LEU* 4.2 5.2 - - + -
345C LEU* 4.2 23.1 - - + -
348C PHE* 4.3 8.7 - - + -
482C LEU* 3.9 16.0 - - + +
483C THR 2.9 16.7 + - - +
484C PRO 3.8 4.5 - - - +
486C MET* 1.3 75.9 - - - +
488C GLY* 1.3 62.1 + - - +
490C LEU* 3.3 4.3 + - + +
491C VAL* 3.0 46.8 + - + +
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Residues in contact with GLY 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C TRP* 3.7 8.1 - - - -
296C LEU* 3.5 33.6 - - - +
300C ALA* 3.4 16.8 - - - +
484C PRO 3.1 11.3 + - - -
485C PHE 3.1 1.7 + - - -
487C LEU* 1.3 75.6 - - - +
489C ALA* 1.3 62.2 + - - +
492C ALA* 3.1 18.9 + - - +
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Residues in contact with ALA 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR* 5.3 0.4 - - + -
51C ILE* 4.4 12.3 - - + -
299C GLY* 3.3 21.8 - - - +
302C TRP* 4.9 6.3 - - + -
303C MET* 3.5 24.9 - - + +
485C PHE* 3.0 17.0 + - + +
486C MET* 3.1 11.6 + - - +
488C GLY* 1.3 77.2 - - - +
490C LEU* 1.3 57.6 + - - +
492C ALA 3.5 0.2 + - - -
493C MET* 2.9 28.4 + - - +
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Residues in contact with LEU 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ILE* 4.5 16.2 - - + -
345C LEU* 5.6 2.9 - - + -
348C PHE* 4.7 15.3 - - + -
407C LEU* 5.0 7.2 - - + -
477C ILE* 4.3 9.4 - - + -
479C PHE* 3.7 45.5 - - + -
482C LEU* 3.9 18.4 - - + -
486C MET* 2.9 24.6 + - + +
487C LEU* 3.3 6.3 + - + +
489C ALA* 1.3 73.7 - - - +
491C VAL* 1.3 66.5 + - - +
493C MET* 3.2 31.7 + - + +
494C TYR* 3.3 19.9 + - + -
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Residues in contact with VAL 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C MET* 3.9 16.4 - - + -
167C VAL* 5.5 1.6 - - + -
276C LEU* 4.6 4.7 - - + -
277C TRP* 3.5 28.9 - - + -
296C LEU* 5.8 0.7 - - + -
348C PHE* 4.2 7.0 - - + -
351C TYR* 4.0 16.8 - - + +
352C PHE* 3.6 22.0 - - + -
487C LEU* 3.0 42.9 + - + +
488C GLY* 5.0 0.2 - - - -
490C LEU* 1.3 74.4 - - - +
492C ALA* 1.3 64.0 + - - +
494C TYR* 3.1 4.9 + - - -
495C GLU* 2.9 25.9 + - - +
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Residues in contact with ALA 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ARG* 3.7 20.6 - - - +
277C TRP* 4.4 0.8 - - - -
300C ALA* 3.7 24.5 - - + +
303C MET* 3.9 8.1 - - + -
304C ASP* 4.2 2.0 - - - +
488C GLY 3.1 17.1 + - - +
489C ALA 3.9 3.1 - - - +
491C VAL* 1.3 78.8 - - - +
493C MET* 1.3 61.0 + - - +
495C GLU* 3.2 12.8 + - - +
496C HIS* 3.0 28.6 + - - -
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Residues in contact with MET 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 5.8 0.2 - - - -
51C ILE* 5.3 2.7 - - - -
53C VAL* 4.4 9.2 - - - -
303C MET* 3.6 29.3 - - + +
316C ALA* 4.1 16.8 - - - -
317C PRO* 3.4 18.5 - - - +
320C LEU* 3.8 31.6 - - + -
477C ILE* 4.1 16.4 - - + -
489C ALA 2.9 14.7 + - - +
490C LEU* 3.4 26.5 - - + +
491C VAL 3.2 0.2 - - - -
492C ALA* 1.3 76.5 - - - +
494C TYR* 1.3 79.6 + - + +
496C HIS 3.3 0.3 + - - -
497C LYS* 2.9 25.1 + - - +
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Residues in contact with TYR 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C LEU* 4.7 6.1 - - + -
338C MET* 3.6 29.6 - - + +
348C PHE* 4.1 20.9 - + - -
352C PHE* 3.3 27.8 - + + -
405C ASP* 2.7 38.8 + - - +
407C LEU* 4.1 10.0 - - + +
477C ILE* 3.5 15.2 - - + +
490C LEU* 3.3 18.8 + - + -
491C VAL 3.1 2.2 + - - +
493C MET* 1.3 97.0 - - + +
495C GLU* 1.3 64.2 + - - +
497C LYS* 3.2 29.5 + - + +
498C ILE* 3.0 32.6 + - + +
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Residues in contact with GLU 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C HIS* 3.6 8.0 + - - +
104C ARG* 2.8 36.4 + - - -
273C ARG 5.7 0.2 - - - +
274C TYR* 3.6 45.3 + - + -
277C TRP* 2.9 30.3 + - - -
351C TYR* 4.3 5.5 + - + +
352C PHE* 4.4 6.5 - - + -
491C VAL* 2.9 22.0 + - + +
492C ALA* 3.2 9.0 + - - +
494C TYR* 1.3 75.6 - - - +
496C HIS* 1.3 67.3 + - - +
498C ILE* 3.3 8.9 + - + +
499C PHE* 3.1 21.1 + - - +
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Residues in contact with HIS 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C MET* 3.8 22.1 - - + +
100C HIS* 4.7 6.0 + - - -
101C VAL* 4.1 7.6 - - + -
104C ARG* 3.8 11.5 + - - -
303C MET* 4.5 4.7 - - + -
304C ASP* 2.7 34.9 + - - -
307C PHE* 3.3 47.6 - + + -
317C PRO* 3.5 20.6 - - + -
492C ALA 3.0 22.4 + - - +
495C GLU* 1.3 77.4 - - + +
497C LYS* 1.3 64.1 + - - +
499C PHE* 3.2 5.4 + - - +
500C VAL* 3.0 27.9 + - - +
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Residues in contact with LYS 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C PRO* 3.5 17.8 - - + +
320C LEU* 4.0 24.7 + - + +
321C ALA* 3.5 21.5 - - - +
324C GLY* 5.4 1.8 - - - -
336C HIS* 3.2 42.4 + - - -
356C ASP* 4.6 9.8 + - - +
377C PRO* 6.0 1.6 - - - +
405C ASP* 4.4 3.0 + - - -
493C MET 2.9 14.4 + - - +
494C TYR* 3.4 29.9 - - + +
496C HIS* 1.3 77.2 - - - +
498C ILE* 1.3 66.4 + - + +
500C VAL 3.3 0.3 + - - -
501C GLN* 3.1 46.8 + - - +
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Residues in contact with ILE 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C TYR* 3.7 12.6 - - + +
352C PHE* 3.9 19.5 - - + -
355C GLY 3.8 5.6 - - - +
356C ASP* 3.5 47.6 - - + +
359C SER* 3.6 26.9 - - - -
360C ASN* 2.9 33.0 - - - +
494C TYR* 3.0 22.2 + - + +
495C GLU* 3.6 8.1 - - - +
497C LYS* 1.3 80.2 - - + +
499C PHE* 1.3 63.4 + - - +
501C GLN* 3.4 5.1 + - - +
502C GLY 3.1 10.2 + - - -
509C SER* 3.8 4.2 + - - +
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Residues in contact with PHE 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C VAL* 4.8 2.9 - - + -
80C ALA* 3.6 26.0 - - + -
81C ARG* 3.7 21.5 - - + -
84C MET* 4.1 18.2 - - + -
90C ILE* 4.0 21.8 - - + -
100C HIS* 6.3 0.9 - - - +
274C TYR* 5.4 0.2 + - - -
307C PHE* 3.7 28.9 - + - -
495C GLU 3.1 14.1 + - - +
496C HIS* 3.5 11.2 - - - +
498C ILE* 1.3 76.0 - - - +
500C VAL* 1.3 67.2 + - + +
502C GLY* 3.2 2.4 + - - -
503C ILE* 3.1 53.0 + - + +
509C SER* 4.5 5.7 + - - -
510C PHE* 3.6 29.4 - + + -
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Residues in contact with VAL 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C VAL* 4.0 26.5 - - + -
307C PHE* 3.8 28.9 - - + -
318C VAL* 4.2 26.5 - - + +
321C ALA* 3.5 25.4 - - + -
322C LEU* 5.3 0.7 - - + +
496C HIS 3.0 21.1 + - - +
497C LYS 3.3 0.2 + - - -
499C PHE* 1.3 76.4 - - + +
501C GLN* 1.3 64.3 + - - +
503C ILE* 3.2 8.1 + - - +
504C ILE* 3.0 32.5 + - + +
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Residues in contact with GLN 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C ALA* 3.0 36.4 + - + +
324C GLY* 3.5 22.2 - - - -
325C ILE* 3.9 11.6 - - + +
328C ILE* 4.7 3.4 - - - +
356C ASP* 4.6 10.0 - - - +
360C ASN* 3.9 4.3 - - - +
377C PRO* 4.8 4.2 - - - +
497C LYS* 3.1 40.7 + - - +
498C ILE* 3.8 7.5 - - - +
499C PHE 3.2 0.4 - - - -
500C VAL* 1.3 77.8 - - - +
502C GLY* 1.3 61.2 + - - +
504C ILE* 3.2 3.6 + - - +
505C TRP* 3.0 55.8 + - + -
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Residues in contact with GLY 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C ASN* 3.8 2.1 + - - -
498C ILE 3.1 11.5 + - - -
499C PHE 3.2 1.3 + - - -
501C GLN* 1.3 75.8 - - - +
503C ILE* 1.3 53.7 + - - +
505C TRP* 3.2 1.5 + - - -
506C ASP 2.8 30.1 + - - -
507C ILE* 3.0 32.7 + - - +
509C SER* 3.5 22.2 - - - -
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Residues in contact with ILE 503 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ARG* 3.0 35.6 + - - +
77C VAL* 4.1 17.0 - - + -
80C ALA* 3.6 35.2 - - + -
83C ARG* 5.5 2.0 - - - +
90C ILE* 6.0 0.9 - - + -
499C PHE* 3.1 39.2 + - + +
500C VAL* 3.2 9.6 + - - +
502C GLY* 1.3 77.4 - - - +
504C ILE* 1.3 62.4 + - - +
506C ASP* 3.0 12.2 + - - +
507C ILE 5.2 4.0 - - - +
510C PHE* 6.1 0.7 - - + -
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Residues in contact with ILE 504 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 3.7 29.5 - - + +
71C LEU* 4.2 12.8 - - + -
72C ALA* 4.4 5.2 - - - -
75C ARG* 2.8 37.3 + - + +
77C VAL* 4.1 17.9 - - + -
322C LEU* 3.6 31.2 - - + -
325C ILE* 3.8 29.4 - - + -
500C VAL* 3.0 25.7 + - + +
501C GLN 3.6 6.7 - - - +
503C ILE* 1.3 74.1 - - - +
505C TRP* 1.3 61.4 + - - +
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Residues in contact with TRP 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ALA* 5.7 0.2 - - - +
4C LEU* 3.7 10.6 + - + +
325C ILE* 3.4 21.3 - - + +
328C ILE* 3.8 22.4 - - + -
329C ASN* 2.8 25.6 + - - -
360C ASN* 3.8 16.8 - - + -
365C THR* 4.1 4.7 - - - +
373C HIS* 3.7 30.9 + + + -
374C GLN 3.4 14.3 + - - -
375C THR* 3.6 31.6 - - + -
376C GLY* 3.6 22.4 - - - -
377C PRO* 4.4 0.2 - - + -
501C GLN* 3.0 49.5 + - + +
502C GLY* 3.8 7.0 - - - +
504C ILE* 1.3 74.8 - - - +
506C ASP* 1.3 68.7 + - - +
507C ILE* 3.4 18.6 + - + +
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Residues in contact with ASP 506 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ALA* 3.5 23.3 - - + +
75C ARG* 3.3 21.6 + - - +
92C TYR* 3.6 2.6 + - - -
365C THR* 3.2 13.7 + - + -
366C LYS* 3.0 51.6 + - - +
367C SER* 4.5 4.3 + - - -
502C GLY 2.8 9.0 + - - -
503C ILE* 3.0 9.5 + - - +
505C TRP* 1.3 80.9 - - - +
507C ILE* 1.3 58.1 + - - +
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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