Contacts of the helix formed by residues 415 - 447 (chain C) in PDB entry 2W4V
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 415 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C GLU* 2.9 23.1 - - + +
371C GLN* 4.2 5.2 - - - +
372C ALA* 3.6 2.5 - - - +
414C GLN* 1.3 72.4 + - - +
416C MET* 1.3 58.9 + - - +
417C ASN* 2.4 44.8 + - - +
418C GLN* 2.6 36.0 - - - +
419C VAL* 2.8 28.6 + - - +
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Residues in contact with MET 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C PHE* 3.6 23.2 - - + -
364C LYS 3.4 3.8 - - - +
365C GLN* 2.5 59.0 - - + +
370C GLU* 2.2 51.7 + - + +
372C ALA* 3.7 10.8 - - + -
415C ASN* 1.3 70.1 - - - +
417C ASN* 1.3 53.7 + - + +
419C VAL* 2.6 26.7 - - - +
420C VAL* 3.3 12.5 - - - +
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Residues in contact with ASN 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C PHE* 5.7 0.2 - - - -
415C ASN* 2.4 26.4 + - - +
416C MET* 1.3 72.4 - - - +
418C GLN* 1.3 91.7 + - - +
419C VAL 2.7 7.0 + - - -
420C VAL* 3.0 10.3 - - + +
421C ASN* 2.5 45.2 + - - +
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Residues in contact with GLN 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C GLN* 2.4 45.5 - - + +
415C ASN* 2.6 28.9 - - - +
417C ASN* 1.3 91.0 - - - +
419C VAL* 1.3 57.3 + - - +
421C ASN* 4.2 4.9 - - - +
422C SER* 3.4 22.2 + - - -
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Residues in contact with VAL 419 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C PHE* 4.9 8.1 - - + -
372C ALA* 4.8 2.2 - - + -
398C LEU 3.8 8.3 - - - +
399C LEU* 3.3 31.0 - - + -
414C GLN* 3.8 14.6 - - + -
415C ASN 2.8 19.5 - - - +
416C MET* 2.6 35.9 - - - +
417C ASN 2.7 0.8 - - - -
418C GLN* 1.3 75.9 - - - +
420C VAL* 1.3 65.9 + - + +
421C ASN 2.7 5.6 + - - -
422C SER* 2.6 36.1 + - - -
423C VAL* 2.8 13.7 + - + +
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Residues in contact with VAL 420 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C MET 5.7 1.8 - - - +
363C PHE* 3.0 46.0 - - + -
416C MET 3.3 6.1 - - - +
417C ASN* 3.0 29.4 - - + +
419C VAL* 1.3 82.8 - - + +
421C ASN* 1.3 64.9 + - - +
423C VAL* 2.2 37.6 - - + +
424C GLY* 3.5 2.1 + - - -
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Residues in contact with ASN 421 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C ASN* 2.5 48.2 + - - +
418C GLN* 4.2 5.3 - - - +
419C VAL 2.7 2.4 + - - -
420C VAL* 1.3 81.8 - - - +
422C SER* 1.3 61.9 + - - +
423C VAL 3.1 1.8 - - - -
424C GLY* 3.5 2.7 + - - +
425C ALA* 3.0 22.9 + - - +
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Residues in contact with SER 422 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C LEU* 4.1 22.0 + - - +
414C GLN* 6.1 0.2 - - - +
418C GLN* 3.4 21.4 + - - -
419C VAL* 2.6 25.1 + - - -
421C ASN* 1.3 73.5 - - - +
423C VAL* 1.3 65.2 + - - +
425C ALA* 3.5 12.3 - - - +
426C LEU* 3.0 27.9 + - - +
601C PRO 4.9 3.1 - - - -
602C ILE* 5.4 0.3 - - - -
603C ASN* 5.3 11.8 + - - -
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Residues in contact with VAL 423 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C MET* 2.5 54.4 - - + +
359C GLY* 6.2 1.3 - - - -
361C MET* 5.7 11.2 - - + +
398C LEU* 5.2 11.9 - - + -
419C VAL* 2.8 23.8 + - + +
420C VAL* 2.2 42.0 - - + +
422C SER* 1.3 79.7 - - - +
424C GLY* 1.3 70.9 + - - +
426C LEU* 2.9 1.3 + - - -
427C ALA* 2.9 7.8 + - - -
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Residues in contact with GLY 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C THR* 4.0 20.4 - - - -
420C VAL 3.5 3.8 + - - -
421C ASN 3.5 4.0 + - - -
423C VAL* 1.3 90.2 - - - +
425C ALA* 1.3 61.2 + - - +
427C ALA* 3.2 2.0 + - - -
428C LYS* 3.0 36.0 + - - +
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Residues in contact with ALA 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C ASN 3.0 19.1 + - - +
422C SER* 3.5 10.8 - - - +
423C VAL 3.2 0.4 - - - -
424C GLY* 1.3 75.3 - - - +
426C LEU* 1.3 56.9 + - - +
428C LYS* 4.0 7.0 - - - +
429C SER* 3.1 29.1 + - - -
600C ASP* 5.1 1.6 - - - +
601C PRO* 2.9 38.1 - - + +
602C ILE* 3.3 8.1 - - + +
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Residues in contact with LEU 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C MET* 2.5 31.2 - - + -
394C LEU* 6.1 0.4 - - + -
398C LEU* 4.4 16.6 - - + -
422C SER 3.0 12.3 + - - +
423C VAL 2.9 1.0 + - - +
425C ALA* 1.3 76.8 - - - +
427C ALA* 1.3 64.0 + - - +
429C SER* 2.7 26.7 + - - +
430C LEU* 2.9 24.3 + - + +
602C ILE* 3.9 13.9 - - + -
603C ASN* 4.1 3.6 - - - +
606C VAL* 3.4 49.1 - - + -
607C VAL* 5.5 1.1 - - + -
610C LEU* 5.9 3.6 - - + -
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Residues in contact with ALA 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C VAL* 4.9 3.6 - - + -
273C THR* 3.9 18.4 - - + -
355C ILE* 4.6 28.8 - - + +
358C MET* 3.2 22.1 - - + -
423C VAL 2.9 8.8 + - - +
424C GLY* 3.2 6.9 + - - +
426C LEU* 1.3 78.0 - - - +
428C LYS* 1.3 65.0 + - - +
430C LEU* 3.0 10.9 + - - +
431C TYR* 3.1 15.5 + - - +
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Residues in contact with LYS 428 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C LYS* 3.7 15.9 - - + +
270C SER* 4.0 19.4 + - - +
272C VAL* 3.0 30.3 - - + +
273C THR* 3.0 28.8 + - + -
274C TYR* 5.7 1.6 - - - +
424C GLY* 3.0 20.1 + - - +
425C ALA* 4.0 6.1 - - - +
427C ALA* 1.3 75.0 - - - +
429C SER* 1.3 54.4 + - - +
431C TYR* 3.4 2.3 + - - +
432C ASP* 2.3 40.9 + - - +
600C ASP* 6.1 0.9 - - - +
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Residues in contact with SER 429 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C LYS* 5.8 0.7 - - - +
425C ALA 3.1 16.1 + - - -
426C LEU* 2.7 32.6 + - - +
428C LYS* 1.3 76.9 - - - +
430C LEU* 1.3 68.2 + - - +
432C ASP* 3.5 9.6 + - - +
433C ARG* 3.3 16.8 + - - +
600C ASP* 4.7 10.0 + - - -
602C ILE* 3.8 18.4 - - - +
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Residues in contact with LEU 430 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C CYS* 5.6 4.0 - - + +
354C SER* 6.4 2.0 - - - -
355C ILE* 4.9 18.4 - - + -
358C MET* 5.8 4.5 - - - -
387C CYS* 6.1 4.0 - - + -
426C LEU* 2.9 22.3 + - + +
427C ALA* 3.4 9.2 - - - +
429C SER* 1.3 77.8 + - - +
431C TYR* 1.3 57.2 + - - +
433C ARG* 2.6 60.2 + - + +
434C MET* 2.8 14.2 + - - +
610C LEU* 4.0 26.2 - - + -
618C VAL* 6.2 2.5 - - + -
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Residues in contact with TYR 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C TYR* 1.5 57.8 + + + +
230C GLY* 4.0 1.2 - - - -
242C ARG* 4.5 1.9 + - - -
267C LEU* 4.6 12.7 - - + +
268C GLU* 4.5 11.0 - - - -
269C LYS* 5.4 0.2 - - - -
272C VAL* 3.6 29.2 - - + -
282C TYR* 4.2 30.2 - + + +
352C THR* 5.6 4.5 - - + -
355C ILE* 5.2 13.1 - - + +
427C ALA 3.1 8.1 + - - +
428C LYS 3.7 7.0 - - - +
430C LEU* 1.3 80.0 - - - +
432C ASP* 1.3 70.5 + - - +
434C MET* 3.9 16.6 - - + -
435C PHE* 3.1 32.0 + - + +
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Residues in contact with ASP 432 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C LEU* 4.2 9.4 - - - +
269C LYS* 2.4 66.8 + - - +
428C LYS 2.3 35.1 + - - +
429C SER* 3.5 9.9 + - - +
430C LEU 3.1 0.2 - - - -
431C TYR* 1.3 83.6 - - - +
433C ARG* 1.6 40.5 + - - +
435C PHE* 3.5 5.7 + - - +
436C ASN* 2.4 46.8 + - - +
600C ASP* 5.5 0.2 - - - +
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Residues in contact with ARG 433 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C SER 3.3 12.2 + - - +
430C LEU* 2.6 43.1 + - + +
432C ASP* 1.6 49.1 - - - +
434C MET* 1.3 56.2 + - - +
436C ASN* 3.6 8.8 - - + +
437C TRP* 2.7 35.8 + - + +
440C ARG* 4.6 11.0 - - - +
610C LEU* 4.9 6.5 + - - +
617C LEU 3.9 5.4 + - - -
618C VAL* 2.4 58.0 + - - +
619C ALA 4.4 0.8 + - - -
620C GLU 3.9 20.5 - - - +
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Residues in contact with MET 434 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C TYR* 3.4 27.1 - - + -
348C MET* 3.4 34.4 - - + +
351C CYS* 2.8 33.7 - - - -
352C THR* 2.8 34.3 - - + -
355C ILE* 5.7 2.0 - - - -
430C LEU 2.8 10.8 + - - +
431C TYR* 3.8 18.4 - - + +
433C ARG* 1.3 79.0 - - - +
435C PHE* 1.3 54.6 + - - +
437C TRP* 3.1 4.7 + - - +
438C LEU* 2.6 37.1 + - + +
441C ARG* 5.3 0.3 + - - -
617C LEU* 6.4 0.7 - - + -
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Residues in contact with PHE 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C LEU* 3.5 37.0 - - + -
229C TYR* 4.3 20.2 - - + -
230C GLY* 4.5 4.0 - - - -
243C PHE* 4.0 9.6 - + - -
264C THR* 3.3 40.8 - - + -
267C LEU* 2.7 44.4 - - + -
431C TYR* 3.1 22.1 + - + +
432C ASP* 3.5 4.9 - - - +
434C MET* 1.3 79.1 - - - +
436C ASN* 1.3 73.3 + - - +
438C LEU* 3.5 8.1 - - + +
439C VAL* 3.1 34.8 + - + +
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Residues in contact with ASN 436 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C THR* 5.0 3.8 + - - -
432C ASP* 2.4 36.5 + - - +
433C ARG* 3.6 8.2 - - - +
434C MET 3.2 0.2 - - - -
435C PHE* 1.3 83.6 - - - +
437C TRP* 1.3 64.3 + - - +
439C VAL* 2.5 32.5 - - + +
440C ARG* 3.1 17.3 + - + +
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Residues in contact with TRP 437 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C GLU* 5.2 2.0 + - - -
433C ARG* 2.7 22.7 + - + +
434C MET* 3.6 4.9 - - - +
436C ASN* 1.3 70.1 - - - +
438C LEU* 1.3 64.1 + - - +
440C ARG* 2.4 68.2 + - + +
441C ARG* 2.7 67.0 + - + +
617C LEU* 3.5 20.2 - - + +
620C GLU* 2.8 67.1 - - + -
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Residues in contact with LEU 438 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C VAL* 4.4 9.0 - - + +
226C LEU* 3.8 28.7 - - + -
229C TYR* 3.7 39.3 - - + -
340C PHE* 5.3 1.3 - - + -
348C MET* 3.9 19.1 - - + -
434C MET* 2.6 22.1 + - + +
435C PHE* 3.5 9.6 - - - +
437C TRP* 1.3 74.2 - - - +
439C VAL* 1.3 60.6 + - - +
441C ARG* 3.4 16.7 - - - +
442C VAL* 3.1 42.4 + - + +
----------------------------------------------------------
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Residues in contact with VAL 439 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C LEU* 3.9 25.8 - - + -
262C ILE* 3.4 18.8 - - + +
264C THR* 4.0 26.0 - - + +
435C PHE* 3.1 18.6 - - + +
436C ASN* 2.5 38.8 - - - +
438C LEU* 1.3 75.6 - - - +
440C ARG* 1.3 74.5 + - + +
442C VAL* 2.7 29.1 - - - +
443C ASN* 3.1 5.5 + - - +
----------------------------------------------------------
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Residues in contact with ARG 440 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C ARG* 3.8 10.3 + - - +
436C ASN* 3.1 16.3 + - - +
437C TRP* 2.4 83.6 + - + +
439C VAL* 1.3 85.2 - - + +
441C ARG* 1.3 56.6 + - - +
443C ASN* 3.3 8.6 + - - +
444C LYS* 3.2 22.5 + - - +
620C GLU 5.6 1.0 + - - -
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Residues in contact with ARG 441 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C PHE* 3.9 2.8 - - - -
340C PHE* 3.2 38.2 - - + -
344C GLU* 4.1 21.7 + - - +
348C MET* 3.0 50.9 - - - +
437C TRP* 2.7 48.1 + - + +
438C LEU* 3.4 14.8 - - - +
440C ARG* 1.3 73.9 - - - +
442C VAL* 1.3 57.6 + - - +
443C ASN 3.0 4.7 - - - -
444C LYS* 2.9 37.4 + - + +
445C THR* 3.2 12.2 + - + +
617C LEU* 3.8 11.8 - - - +
----------------------------------------------------------
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Residues in contact with VAL 442 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C ALA* 4.9 10.5 - - + -
225C VAL* 4.6 6.7 - - + -
226C LEU* 5.2 5.6 - - + -
262C ILE* 3.4 18.6 - - + +
338C LEU* 3.8 27.5 - - + +
340C PHE* 3.8 8.3 - - + -
438C LEU* 3.1 28.0 + - + +
439C VAL* 2.7 35.2 - - + +
441C ARG* 1.3 73.8 - - - +
443C ASN* 1.3 57.7 + - - +
444C LYS 3.2 0.4 - - - -
445C THR* 2.6 27.1 + - - +
446C LEU* 3.4 13.2 + - - +
----------------------------------------------------------
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Residues in contact with ASN 443 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ALA 3.3 8.5 + - - -
261C ASP* 2.3 56.7 + - - +
262C ILE* 3.8 10.2 - - + +
439C VAL 3.1 11.2 + - - +
440C ARG* 3.4 12.6 - - - +
441C ARG 3.0 0.8 - - - -
442C VAL* 1.3 76.2 - - - +
444C LYS* 1.3 59.9 + - - +
445C THR 3.3 0.2 - - - -
446C LEU* 3.5 2.4 - - - +
447C ASP* 2.7 46.5 + - - +
----------------------------------------------------------
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Residues in contact with LYS 444 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C ARG 3.2 9.8 + - - +
441C ARG* 2.9 27.8 + - + +
443C ASN* 1.3 81.5 - - - +
445C THR* 1.3 61.1 + - + +
446C LEU 3.4 0.3 + - - -
447C ASP* 4.0 10.2 + - - +
----------------------------------------------------------
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Residues in contact with THR 445 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C GLN* 5.0 9.4 - - - +
338C LEU* 2.9 42.9 - - - +
339C GLY 4.7 5.6 - - - +
340C PHE* 4.6 9.0 - - + -
441C ARG* 3.4 14.4 - - + +
442C VAL* 2.6 28.7 + - - -
444C LYS* 1.3 79.4 - - + +
446C LEU* 1.7 51.7 + - - +
447C ASP 5.6 0.2 - - - -
448C THR* 4.6 8.1 - - - +
----------------------------------------------------------
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Residues in contact with LEU 446 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C GLN* 3.7 34.3 - - + +
219C ILE* 3.8 27.4 - - + -
222C ALA* 5.7 5.4 - - + -
259C GLY* 3.6 2.5 - - - -
260C ALA* 3.0 56.5 + - + +
261C ASP 4.8 0.4 - - - +
262C ILE* 5.0 13.0 - - + -
338C LEU* 6.4 0.2 - - + -
442C VAL 3.4 13.9 + - - +
443C ASN* 3.1 6.6 + - - +
445C THR* 1.7 60.4 + - - +
447C ASP* 1.3 52.3 + - - +
448C THR* 2.5 31.5 + - + +
----------------------------------------------------------
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Residues in contact with ASP 447 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ALA 3.9 3.7 + - - -
261C ASP* 4.9 5.2 - - - +
443C ASN* 2.7 34.5 + - - +
444C LYS* 4.0 8.6 + - - +
446C LEU* 1.3 68.6 - - - +
448C THR* 1.3 65.2 + - - +
449C LYS* 3.1 6.9 + - - +
452C ARG* 2.8 32.3 + - - +
----------------------------------------------------------
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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