Contacts of the helix formed by residues 482 - 505 (chain C) in PDB entry 1JLH
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 482 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C HIS 4.6 6.4 + - - -
170C LEU* 3.9 3.1 - - - -
173C TYR* 3.4 17.5 - - + +
480C LYS* 3.0 28.8 + - + +
481C LEU* 1.3 75.8 - - - +
483C PRO* 1.3 76.6 - - - +
484C PHE* 3.1 7.8 + - - +
485C MET* 3.2 20.1 + - - +
486C LEU* 3.0 21.0 + - - +
556D VAL* 4.6 21.9 - - + +
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Residues in contact with PRO 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C LEU* 3.7 31.8 - - + -
173C TYR* 3.6 26.0 - - + -
291C ASN* 3.5 48.0 - - + +
294C GLN* 4.0 6.7 - - + -
295C LEU* 3.3 18.1 - - - +
482C THR* 1.3 87.8 - - - +
484C PHE* 1.3 61.3 + - - +
486C LEU* 3.5 0.3 + - - +
487C GLY 3.2 16.8 + - - -
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Residues in contact with PHE 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C THR* 3.4 34.8 - - + -
47C HIS* 3.4 47.6 - + + -
294C GLN* 3.4 37.7 + - + +
297C SER* 3.7 11.4 - - - -
298C GLY* 3.2 34.1 - - - -
301C TRP* 3.8 18.8 - + + -
482C THR* 3.1 7.5 + - - +
483C PRO* 1.3 78.7 - - - +
485C MET* 1.3 70.3 + - + +
487C GLY 3.2 2.1 + - - -
488C ALA* 3.1 20.1 + - + +
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Residues in contact with MET 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C THR* 4.3 6.1 - - + +
47C HIS 4.1 5.4 - - - +
48C GLY* 3.7 38.1 - - - +
49C HIS 4.1 5.4 - - - +
50C ILE* 3.6 37.2 - - + -
478C PHE* 3.8 24.7 - - + -
479C THR 4.7 1.6 - - - +
480C LYS 3.2 30.1 - - - +
481C LEU* 4.4 1.1 - - - -
482C THR* 3.2 12.3 + - - +
484C PHE* 1.3 82.5 - - + +
486C LEU* 1.3 61.9 + - - +
488C ALA* 3.2 3.9 + - - -
489C LEU* 3.0 28.8 + - + +
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Residues in contact with LEU 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C MET* 4.5 7.2 - - - -
166C VAL* 3.8 35.4 - - + -
169C ALA* 4.0 11.7 - - + -
170C LEU* 3.9 18.6 - - + -
295C LEU* 4.1 6.1 - - + -
344C LEU* 4.2 17.3 - - + -
347C PHE* 4.5 7.4 - - + -
481C LEU* 3.8 24.4 - - + +
482C THR 3.0 16.5 + - - +
483C PRO 3.8 3.6 - - - +
485C MET* 1.3 77.3 - - - +
487C GLY* 1.3 63.7 + - - +
489C LEU* 3.4 4.8 + - + +
490C VAL* 3.0 45.3 + - + +
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Residues in contact with GLY 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C TRP* 3.6 10.5 - - - -
295C LEU* 3.5 33.0 - - - +
299C ALA* 3.5 9.7 - - - -
483C PRO 3.2 10.5 + - - -
484C PHE 3.2 2.2 + - - -
486C LEU* 1.3 77.8 - - - +
488C ALA* 1.3 55.2 + - - +
490C VAL 3.5 0.2 + - - -
491C ALA* 3.0 30.7 + - - +
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Residues in contact with ALA 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C THR* 5.0 0.9 - - + -
50C ILE* 4.4 11.4 - - + -
298C GLY* 3.4 21.0 - - - +
301C TRP* 5.0 4.5 - - + -
302C MET* 3.4 25.6 - - + +
484C PHE* 3.1 18.4 + - + +
485C MET* 3.2 11.2 + - - +
487C GLY* 1.3 77.7 - - - +
489C LEU* 1.3 57.0 + - - +
491C ALA 3.3 0.3 + - - -
492C MET* 2.8 30.5 + - - +
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Residues in contact with LEU 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 4.5 16.4 - - + -
344C LEU* 5.6 2.7 - - + -
347C PHE* 4.8 13.7 - - + -
406C LEU* 5.1 7.0 - - + -
476C ILE* 4.3 9.0 - - + -
478C PHE* 3.5 51.8 - - + -
481C LEU* 4.2 12.3 - - + -
485C MET* 3.0 24.6 + - + +
486C LEU* 3.8 5.8 - - + +
488C ALA* 1.3 76.8 - - - +
490C VAL* 1.3 62.0 + - + +
492C MET* 3.3 27.2 + - + +
493C TYR* 3.2 28.6 + - + -
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Residues in contact with VAL 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C MET* 4.0 23.6 - - + -
166C VAL* 5.7 1.3 - - + -
275C LEU* 4.7 4.7 - - + -
276C TRP* 3.5 25.8 - - + -
295C LEU* 5.9 0.7 - - + -
347C PHE* 4.0 12.3 - - + -
350C TYR* 4.0 17.0 - - + +
351C PHE* 3.5 22.3 - - + -
486C LEU* 3.0 30.8 + - + +
487C GLY 3.9 3.4 - - - +
489C LEU* 1.3 71.5 - - - +
491C ALA* 1.3 65.8 + - - +
493C TYR 3.3 1.7 + - - -
494C GLU* 3.1 28.9 + - + +
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Residues in contact with ALA 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ARG* 3.7 19.5 - - - +
276C TRP* 4.5 0.8 - - + -
299C ALA* 3.7 19.3 - - + +
302C MET* 3.8 12.3 - - + -
303C ASP* 4.0 2.0 - - - +
487C GLY 3.0 19.4 + - - +
488C ALA 3.7 3.4 - - - +
490C VAL* 1.3 74.6 - - - +
492C MET* 1.3 67.1 + - - +
494C GLU* 3.1 13.9 + - - +
495C HIS* 3.1 27.5 + - - -
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Residues in contact with MET 492 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 5.7 0.4 - - - -
50C ILE* 5.0 3.4 - - - -
52C VAL* 4.5 10.5 - - - -
302C MET* 3.4 30.7 - - + +
315C ALA* 4.3 15.0 - - - -
316C PRO* 3.7 20.3 - - + +
319C LEU* 3.8 30.3 - - + -
476C ILE* 3.9 16.8 - - + -
488C ALA 2.8 17.6 + - - +
489C LEU* 3.3 28.0 - - + +
490C VAL 3.2 0.2 - - - -
491C ALA* 1.3 78.6 - - - +
493C TYR* 1.3 79.4 + - + +
495C HIS 3.5 0.3 + - - -
496C LYS* 3.1 22.3 + - - +
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Residues in contact with TYR 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C LEU* 4.7 5.2 - - + -
337C MET* 3.5 33.7 - - + +
347C PHE* 4.2 11.0 - + - -
351C PHE* 3.3 26.5 - + + -
404C ASP* 2.9 34.1 + - - +
406C LEU* 3.8 17.9 - - + +
476C ILE* 3.5 19.7 - - + +
489C LEU* 3.2 22.1 + - + -
490C VAL 3.3 0.2 + - - -
491C ALA 3.2 0.4 - - - -
492C MET* 1.3 98.1 - - + +
494C GLU* 1.3 66.8 + - - +
496C LYS* 3.0 31.0 + - + +
497C ILE* 2.9 28.6 + - + +
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Residues in contact with GLU 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C HIS* 3.8 3.9 + - + -
103C ARG* 2.7 41.1 + - - -
273C TYR* 3.2 44.5 + - + -
276C TRP* 3.1 25.7 + - - -
350C TYR* 4.2 7.4 + - + +
351C PHE* 4.1 6.2 - - + -
490C VAL* 3.1 20.2 + - + +
491C ALA* 3.1 7.2 + - - +
493C TYR* 1.3 75.7 - - - +
495C HIS* 1.3 64.3 + - + +
497C ILE* 3.3 13.4 + - - +
498C PHE* 2.9 25.3 + - - +
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Residues in contact with HIS 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C MET* 5.2 4.3 - - - -
84C PHE* 4.4 4.2 - + - -
99C HIS* 4.9 7.4 - + - -
100C VAL* 3.9 12.9 - - + +
103C ARG* 3.7 10.7 + - - -
302C MET* 4.3 4.0 + - - +
303C ASP* 2.7 46.7 + - - -
306C PHE* 3.4 38.8 - + + +
316C PRO* 3.7 19.7 - - + +
491C ALA* 3.1 15.4 + - + +
492C MET 3.9 0.2 - - - +
494C GLU* 1.3 81.1 - - + +
496C LYS* 1.3 65.5 + - - +
498C PHE* 3.2 10.7 + - + +
499C VAL* 2.9 29.6 + - - +
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Residues in contact with LYS 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C PRO* 3.5 17.2 - - + +
319C LEU* 3.6 32.5 + - + +
320C ALA* 3.5 18.5 - - - +
323C GLY* 5.2 2.6 - - - -
335C HIS* 3.4 41.0 + - - -
355C ASP* 4.8 9.0 + - - +
404C ASP* 4.3 3.4 + - - -
492C MET 3.1 13.6 + - - +
493C TYR* 3.0 29.1 + - + +
495C HIS* 1.3 76.9 - - - +
497C ILE* 1.3 65.8 + - + +
499C VAL 3.2 0.7 + - - -
500C GLN* 3.1 44.1 + - - +
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Residues in contact with ILE 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C TYR* 3.7 20.9 - - + +
351C PHE* 3.9 19.1 - - + -
354C GLY* 3.7 5.6 - - - +
355C ASP* 3.5 47.8 - - + +
358C SER* 3.7 14.6 - - - -
359C ASN* 3.0 37.2 + - - +
493C TYR* 2.9 20.3 + - + +
494C GLU* 3.3 10.5 - - - +
496C LYS* 1.3 82.2 - - + +
498C PHE* 1.3 62.4 + - - +
500C GLN* 3.4 4.1 + - - +
501C GLY 3.1 8.5 + - - -
508C SER* 3.9 3.9 + - - +
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Residues in contact with PHE 498 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C VAL* 4.4 5.4 - - + -
79C ALA* 3.6 26.5 - - + -
80C ARG* 3.7 24.5 - - + -
83C MET* 3.9 15.7 - - + -
89C ILE* 4.1 22.7 - - + -
99C HIS* 6.5 0.2 - - + -
273C TYR* 5.9 0.2 - - - -
306C PHE* 3.9 21.3 - + - -
494C GLU 2.9 13.1 + - - +
495C HIS* 3.2 13.6 + - + +
497C ILE* 1.3 77.9 - - - +
499C VAL* 1.3 68.4 + - + +
501C GLY* 3.3 2.4 + - - -
502C ILE* 3.1 49.8 + - + +
508C SER* 4.6 5.5 + - - -
509C PHE* 3.5 29.2 - + + -
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Residues in contact with VAL 499 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C VAL* 4.0 21.3 - - + -
306C PHE* 3.8 31.0 - - + -
317C VAL* 4.1 16.8 - - + +
320C ALA* 3.5 24.2 - - + -
321C LEU* 4.2 8.3 - - + -
495C HIS 2.9 20.5 + - - +
496C LYS 3.2 1.1 + - - +
498C PHE* 1.3 78.0 - - + +
500C GLN* 1.3 62.7 + - - +
502C ILE* 3.4 6.2 + - - +
503C ILE* 3.1 36.7 + - + +
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Residues in contact with GLN 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C ALA* 3.2 32.1 + - + +
323C GLY* 3.6 20.8 - - - -
324C ILE* 4.0 10.6 - - + +
327C ILE* 4.6 4.2 - - - +
355C ASP* 4.4 11.8 - - - +
359C ASN* 3.9 5.8 + - - +
376C PRO* 4.7 4.0 - - - +
496C LYS* 3.1 36.8 + - - +
497C ILE* 3.8 7.3 - - - +
498C PHE 3.3 0.2 - - - -
499C VAL* 1.3 75.7 - - - +
501C GLY* 1.3 64.9 + - - +
503C ILE* 3.2 4.6 + - - +
504C TRP* 2.9 58.6 + - + -
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Residues in contact with GLY 501 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C ASN* 3.8 7.7 - - - +
497C ILE 3.1 10.3 + - - -
498C PHE 3.3 1.1 + - - -
500C GLN* 1.3 78.2 - - - +
502C ILE* 1.3 57.4 + - - +
504C TRP* 3.2 1.8 + - - -
505C ASP 2.8 24.1 + - - -
506C ILE* 3.1 25.4 + - - +
508C SER* 3.4 24.0 - - - -
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Residues in contact with ILE 502 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ARG* 3.1 38.8 + - - +
75C GLY 4.3 0.7 - - - +
76C VAL* 4.2 14.4 - - + -
79C ALA* 3.6 28.9 - - + -
82C ARG* 5.8 2.9 - - - +
89C ILE* 6.1 1.3 - - + -
365C LYS* 5.9 5.4 - - - +
498C PHE* 3.1 46.2 + - + +
499C VAL* 3.8 7.4 - - - +
500C GLN 3.3 0.2 - - - -
501C GLY* 1.3 75.7 - - - +
503C ILE* 1.3 62.8 + - - +
505C ASP* 3.1 6.8 + - - +
506C ILE 5.2 4.7 - - - +
509C PHE* 6.0 1.8 - - + -
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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
----------------------------------------------------------
3C LEU* 3.3 33.0 - - + +
70C LEU* 4.2 14.1 - - + -
71C ALA* 4.7 8.7 - - - +
74C ARG* 3.1 31.7 + - + +
76C VAL* 4.1 16.6 - - + -
320C ALA* 5.3 0.2 - - + -
321C LEU* 4.1 14.8 - - + -
324C ILE* 4.0 33.0 - - + -
499C VAL* 3.1 31.2 + - + +
500C GLN* 3.6 7.4 - - - +
502C ILE* 1.3 76.0 - - - +
504C TRP* 1.3 59.1 + - + +
505C ASP 3.2 0.4 - - - -
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Residues in contact with TRP 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C ALA* 5.7 0.2 - - - +
3C LEU* 4.5 7.6 + - + +
324C ILE* 3.5 22.3 - - + +
327C ILE* 4.0 18.8 - - + -
328C ASN* 2.8 25.8 + - - -
359C ASN* 3.6 15.5 - - + -
364C THR* 4.5 5.4 - - - +
372C HIS* 3.6 39.8 + + + -
373C GLN 3.4 5.1 + - - -
374C THR* 3.4 28.7 - - + -
375C GLY* 3.5 16.8 - - - -
376C PRO* 4.2 0.4 - - + -
500C GLN* 2.9 52.7 + - + +
501C GLY 3.8 3.4 - - - +
503C ILE* 1.3 78.4 - - + +
505C ASP* 1.3 68.5 + - - +
506C ILE* 3.4 32.5 + - + +
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Residues in contact with ASP 505 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ALA* 4.0 19.9 - - + +
3C LEU 5.2 0.4 - - - +
74C ARG* 3.2 22.8 + - - +
91C TYR* 3.8 1.8 + - - -
364C THR* 3.2 16.3 + - + -
365C LYS* 3.0 54.5 + - - +
366C SER* 4.2 5.4 + - - -
501C GLY 2.8 7.8 + - - -
502C ILE* 3.1 10.6 + - - +
503C ILE 3.2 0.4 - - - -
504C TRP* 1.3 81.2 - - - +
506C ILE* 1.3 56.9 + - - +
----------------------------------------------------------
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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