Contacts of the helix formed by residues 407 - 437 (chain D) in PDB entry 2FRV
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 407 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D TRP* 4.7 9.4 - - + -
271D TRP* 4.1 20.2 - - + -
274D ILE 2.6 23.5 + - - -
275D GLY* 3.5 9.7 - - - -
406D SER* 1.3 68.9 - - - +
408D LEU* 1.3 63.9 + - - +
410D ARG* 3.2 21.9 + - - +
411D THR* 2.8 29.9 + - - +
522D ARG 3.6 29.2 - - - +
523D THR* 3.5 10.2 + - - -
526D SER* 3.7 10.3 + - - +
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Residues in contact with LEU 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D TRP* 5.1 10.1 - - + -
265D ALA* 4.0 40.4 - - + +
268D TYR* 3.7 27.1 - - + +
269D LYS* 4.1 6.5 - - + -
271D TRP* 3.1 27.8 + - + +
272D ALA* 3.6 22.0 - - + +
397D LEU* 4.9 12.1 - - + -
399D VAL* 6.5 0.4 - - + -
403D ALA 5.1 0.4 - - - +
407D THR* 1.3 80.2 - - - +
409D GLY* 1.3 55.9 - - - +
411D THR* 3.0 15.1 + - + -
412D ALA* 2.9 27.4 + - + +
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Residues in contact with GLY 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D LEU* 3.7 2.9 - - - +
403D ALA 3.8 6.9 + - - -
404D LEU* 3.5 34.9 - - - +
406D SER* 2.9 12.3 + - - -
408D LEU* 1.3 74.5 - - - +
410D ARG* 1.3 59.8 + - - +
412D ALA* 4.2 3.5 - - - +
413D ALA* 2.9 33.4 + - - +
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Residues in contact with ARG 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D GLY 2.7 24.9 + - - -
277D THR* 3.2 22.2 + - - +
368D GLU* 3.1 21.5 + - - +
371D PRO* 4.9 1.2 - - + +
372D LEU* 4.2 19.9 + - + +
404D LEU 4.2 0.6 + - - -
406D SER* 3.0 15.9 + - - +
407D THR* 3.2 34.2 + - - +
408D LEU 3.2 0.2 - - - -
409D GLY* 1.3 77.3 - - - +
411D THR* 1.3 60.3 - - - +
413D ALA* 4.1 2.6 - - - +
414D ARG* 3.7 26.6 + - - +
505D ALA* 4.4 1.6 - - - +
523D THR* 4.7 0.8 + - - +
526D SER* 3.3 38.8 + - - +
527D TYR* 3.3 37.0 + - - -
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Residues in contact with THR 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D PHE* 5.0 8.5 - - + -
116D HIS* 3.5 36.0 - - + +
120D TRP* 5.1 5.0 - - + +
257D TYR* 4.8 1.6 + - - -
261D LEU* 3.6 24.5 - - + +
265D ALA* 6.4 0.9 - - + -
407D THR* 2.8 19.4 + - - +
408D LEU* 3.0 16.3 + - + -
410D ARG* 1.3 77.8 - - - +
412D ALA* 1.3 66.0 + - - +
413D ALA 3.3 0.4 - - - -
414D ARG* 3.6 18.6 + - - +
415D GLY 3.7 4.2 + - - -
526D SER* 3.7 5.9 - - - -
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Residues in contact with ALA 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D LEU* 4.2 17.3 - - + +
262D LEU* 5.4 2.7 - - + -
265D ALA* 6.1 3.6 - - + -
393D VAL* 4.1 26.6 - - + +
397D LEU* 5.2 8.3 - - + -
404D LEU* 5.4 4.3 - - + -
408D LEU* 2.9 16.2 + - + +
409D GLY* 3.4 6.2 + - - +
411D THR* 1.3 75.3 - - - +
413D ALA* 1.3 53.6 + - - +
415D GLY* 2.7 24.6 + - - -
416D ILE* 3.0 16.7 + - + +
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Residues in contact with ALA 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371D PRO* 3.6 5.6 - - - +
372D LEU* 3.6 37.7 - - + +
375D VAL* 3.7 11.8 - - + +
404D LEU* 5.5 2.6 - - + +
409D GLY 2.9 18.8 + - - +
410D ARG 4.1 2.5 - - - +
412D ALA* 1.3 76.7 - - - +
414D ARG* 1.3 54.9 + - - +
416D ILE* 3.6 13.3 - - + +
417D GLN* 2.8 30.8 + - - +
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Residues in contact with ARG 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D HIS* 3.5 25.5 + - + +
111D HIS* 3.5 33.7 - - - -
112D PHE* 6.0 0.4 - - - -
116D HIS* 5.2 1.0 + - - -
257D TYR* 3.8 12.3 + - - +
371D PRO* 3.6 37.1 - - + +
410D ARG* 3.7 18.9 + - - +
411D THR* 3.6 15.0 + - - +
412D ALA 3.2 1.0 - - - -
413D ALA* 1.3 77.3 - - - +
415D GLY* 1.3 58.1 + - - +
417D GLN* 4.5 0.4 - - - -
418D CYS* 3.0 30.0 + - - +
462D PRO 5.5 0.4 + - - -
463D ARG* 5.7 1.2 - - - +
526D SER* 2.6 35.1 + - - +
527D TYR* 3.8 5.3 + - - +
528D ASP* 3.4 31.2 + - - +
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Residues in contact with GLY 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D TYR* 3.7 10.5 + - - -
258D ILE* 3.2 24.6 - - - +
261D LEU* 3.6 23.1 - - - -
411D THR 3.7 2.8 + - - -
412D ALA 2.7 10.3 + - - -
414D ARG* 1.3 81.3 - - - +
416D ILE* 1.3 59.3 - - - +
418D CYS* 3.5 2.9 + - - +
419D LEU* 3.3 16.1 + - - +
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Residues in contact with ILE 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D ILE* 5.4 0.2 - - - -
375D VAL* 4.0 21.3 - - + -
386D THR* 4.7 9.0 - - + +
389D ALA* 3.8 27.1 - - + +
390D VAL* 3.9 28.7 - - + -
393D VAL* 4.1 28.0 - - + -
404D LEU* 5.3 6.3 - - + -
412D ALA* 3.0 20.0 + - + +
413D ALA* 3.3 15.0 + - - +
415D GLY* 1.3 74.6 - - - +
417D GLN* 1.3 65.5 + - - +
419D LEU* 3.0 17.6 + - + +
420D THR* 3.2 21.5 + - + +
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Residues in contact with GLN 417 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D TYR* 3.7 25.3 + - + -
108D HIS* 2.8 30.7 + - + -
371D PRO* 3.5 25.2 - - + +
374D SER* 3.7 17.7 + - - -
375D VAL* 4.1 10.1 - - + +
413D ALA 2.8 20.4 + - - +
414D ARG 4.1 0.2 - - - +
416D ILE* 1.3 73.5 - - - +
418D CYS* 1.3 60.6 + - - +
419D LEU 3.4 0.3 + - - -
420D THR* 3.9 7.9 + - - -
421D ALA* 3.4 22.9 + - - +
460D ASN* 4.2 5.5 - - - +
461D ALA 4.5 1.2 + - - +
462D PRO* 3.1 24.2 + - - +
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Residues in contact with CYS 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D TYR* 4.1 5.2 - - - -
105D MET* 4.0 12.7 - - - +
108D HIS* 3.1 37.9 - - + +
253D ILE* 4.0 28.5 - - - -
257D TYR* 4.0 16.2 - - + -
414D ARG 3.0 14.6 + - - +
415D GLY 3.7 4.7 - - - +
416D ILE 3.1 0.4 - - - -
417D GLN* 1.3 79.8 - - - +
419D LEU* 1.3 56.5 + - - +
421D ALA* 4.0 3.6 - - - +
422D ALA* 3.4 21.7 + - - +
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Residues in contact with LEU 419 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D ILE* 4.5 13.2 - - + -
254D GLU* 3.5 41.5 - - + +
258D ILE* 4.6 16.4 - - + -
389D ALA* 4.7 18.8 - - + -
392D LEU* 5.6 8.3 - - + -
415D GLY 3.3 13.9 + - - +
416D ILE* 3.0 6.6 + - + +
418D CYS* 1.3 76.3 - - - +
420D THR* 1.3 55.9 + - + +
421D ALA 3.3 1.6 - - - -
422D ALA* 3.3 9.0 + - + +
423D GLN* 2.8 57.8 + - + +
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Residues in contact with THR 420 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D TYR* 3.2 26.3 + - - -
298D THR* 4.7 10.7 - - - +
375D VAL* 6.1 0.2 - - - +
383D HIS* 4.9 1.1 - - - -
385D PRO* 3.9 33.7 - - + +
386D THR* 4.0 15.6 + - - +
389D ALA* 4.5 6.1 - - + -
416D ILE* 3.2 22.4 + - + +
417D GLN* 3.9 9.2 + - - -
419D LEU* 1.3 73.2 - - + +
421D ALA* 1.3 67.2 + - - +
423D GLN* 3.2 11.5 + - - +
424D GLU* 3.0 19.4 + - - +
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Residues in contact with ALA 421 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D GLY* 4.7 5.8 - - - +
104D TYR* 3.7 33.9 - - + -
105D MET* 5.3 0.7 - - + -
286D PHE* 4.6 15.0 - - + -
297D TYR* 4.8 4.0 - - - -
417D GLN 3.4 16.9 + - - +
418D CYS 4.0 2.2 - - - +
420D THR* 1.3 80.4 + - - +
422D ALA* 1.3 63.5 + - - +
424D GLU* 3.0 16.7 + - - +
425D VAL* 3.2 17.8 + - - +
428D TRP* 4.6 1.4 - - - -
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Residues in contact with ALA 422 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D MET* 4.1 27.8 - - + +
246D TYR* 2.6 32.7 + - - -
250D ARG* 4.0 22.8 - - + +
253D ILE* 4.7 5.2 - - + -
418D CYS 3.4 14.9 + - - +
419D LEU* 3.4 15.5 - - + +
420D THR 3.3 0.2 - - - -
421D ALA* 1.3 79.1 - - - +
423D GLN* 1.3 57.2 + - - +
425D VAL* 3.6 2.9 + - - -
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Residues in contact with GLN 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D TYR* 4.0 0.3 + - - -
250D ARG* 3.5 32.3 + - - +
254D GLU* 4.6 1.0 - - - +
297D TYR* 4.7 2.0 + - - +
385D PRO* 3.9 27.5 + - - +
388D LYS* 5.6 3.4 - - - +
389D ALA* 6.0 0.3 - - - +
419D LEU* 2.8 53.3 + - + +
420D THR* 3.6 12.8 - - - +
421D ALA 3.1 0.6 - - - -
422D ALA* 1.3 76.7 - - - +
424D GLU* 1.3 65.4 + - - +
425D VAL 3.4 0.3 + - - -
426D GLU* 3.7 17.3 + - - +
427D VAL* 4.5 1.6 + - - +
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Residues in contact with GLU 424 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D TYR* 3.5 39.1 + - + -
420D THR 3.0 11.4 + - - +
421D ALA 3.0 8.9 + - - +
423D GLN* 1.3 76.7 - - - +
425D VAL* 1.3 63.0 + - - +
426D GLU 3.1 2.7 - - - -
427D VAL* 3.1 52.0 + - - +
428D TRP* 3.2 41.9 + - + +
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Residues in contact with VAL 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D LEU* 3.6 20.2 - - + +
101D GLY* 3.8 31.4 - - - -
102D ALA 4.4 1.8 - - - +
105D MET* 4.5 5.4 - - - -
242D PHE* 3.9 17.5 - - + -
246D TYR* 3.7 34.8 - - + -
421D ALA 3.2 16.6 + - - +
422D ALA 4.0 1.1 - - - +
423D GLN 3.3 1.4 - - - -
424D GLU* 1.3 75.6 - - - +
426D GLU* 1.3 60.9 + - - +
428D TRP* 3.5 14.7 + - + -
429D LEU* 3.1 22.8 + - + +
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Residues in contact with GLU 426 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D ARG* 3.4 22.7 + - - -
246D TYR* 2.9 40.3 + - - +
247D LYS* 3.9 22.1 + - - -
250D ARG* 4.0 11.4 + - - +
423D GLN 3.7 10.1 - - - +
425D VAL* 1.3 77.8 - - - +
427D VAL* 1.3 60.6 + - + +
429D LEU* 3.6 5.1 - - - +
430D ASP* 3.2 41.6 + - - +
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Residues in contact with VAL 427 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423D GLN 5.3 1.6 - - - +
424D GLU* 3.1 42.3 + - - +
426D GLU* 1.3 79.7 - - + +
428D TRP* 1.3 74.0 + - + +
430D ASP* 3.5 5.6 + - - +
431D LYS* 3.2 31.9 + - + +
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Residues in contact with TRP 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LEU* 4.0 29.0 - - + +
97D ASN* 3.3 45.7 - - + +
98D LEU* 3.8 20.4 - - + +
101D GLY* 4.4 1.8 - - - -
286D PHE* 3.1 52.8 + + + +
297D TYR* 4.6 3.7 - + + +
421D ALA* 4.6 2.5 - - - -
424D GLU* 3.2 38.6 + - + +
425D VAL* 3.7 33.4 - - + +
427D VAL* 1.3 83.1 - - + +
429D LEU* 1.3 60.9 + - - +
431D LYS* 3.7 1.8 - - + +
432D LEU* 2.8 30.7 + - - +
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Residues in contact with LEU 429 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D LEU* 4.0 21.0 - - + +
213D PHE* 4.3 8.3 - - + -
239D ILE* 4.1 18.3 - - + +
242D PHE* 3.9 29.2 - - + -
243D ARG* 3.4 54.1 - - + +
246D TYR* 4.9 7.0 - - + -
425D VAL* 3.1 18.8 + - + +
426D GLU* 3.6 6.3 - - - +
428D TRP* 1.3 78.1 - - - +
430D ASP* 1.3 55.6 + - - +
432D LEU* 3.2 3.5 + - + +
433D GLU* 2.7 37.7 + - - +
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Residues in contact with ASP 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D ARG* 2.9 33.0 + - - -
426D GLU* 3.2 28.1 - - - +
427D VAL* 3.5 6.5 - - - +
429D LEU* 1.3 81.3 - - - +
431D LYS* 1.3 55.7 + - - +
433D GLU* 3.3 8.1 + - - +
434D ALA* 3.0 27.5 + - - +
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Residues in contact with LYS 431 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D GLU* 5.2 13.7 - - - +
94D LEU* 3.9 28.0 - - + -
288D THR* 6.1 5.2 - - - -
427D VAL* 3.2 24.2 + - + +
428D TRP* 3.7 7.2 - - + +
430D ASP* 1.3 69.2 - - - +
432D LEU* 1.3 71.6 + - - +
433D GLU 3.0 1.6 - - - -
434D ALA* 4.4 6.1 - - - -
435D ASN* 2.9 32.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 432 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D ASN* 3.7 44.4 - - + +
94D LEU* 3.8 15.7 - - + +
95D MET* 4.4 6.3 - - + +
98D LEU* 4.5 9.9 - - + -
213D PHE* 4.4 18.4 - - + -
234D LEU* 3.9 24.5 - - + -
239D ILE* 3.6 26.0 - - + -
428D TRP 2.8 22.0 + - - +
429D LEU* 3.6 6.5 - - + +
431D LYS* 1.3 76.4 - - - +
433D GLU* 1.3 58.0 + - - +
435D ASN* 3.3 4.7 + - - +
436D VAL* 3.0 25.2 + - + +
----------------------------------------------------------
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Residues in contact with GLU 433 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D PRO* 5.1 9.1 - - + +
239D ILE* 3.7 31.4 - - + +
243D ARG* 3.0 25.1 + - - -
429D LEU 2.7 18.1 + - - +
430D ASP* 3.3 7.7 - - - +
432D LEU* 1.3 79.2 - - - +
434D ALA* 1.3 56.2 + - - +
436D VAL* 3.4 4.5 + - + +
437D LYS* 3.0 62.5 + - - +
----------------------------------------------------------
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Residues in contact with ALA 434 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D ASP 3.0 15.9 + - - +
431D LYS* 3.8 7.4 - - + +
433D GLU* 1.3 72.8 - - - +
435D ASN* 1.3 68.1 + - - +
437D LYS* 3.7 10.3 - - - +
438D ALA* 3.0 25.6 + - - +
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Residues in contact with ASN 435 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D GLU* 2.9 30.4 + - - +
91D ASN* 2.8 27.4 + - - +
94D LEU* 3.9 8.9 - - - +
431D LYS* 2.9 17.7 + - - +
432D LEU 3.4 8.7 - - - +
434D ALA* 1.3 79.0 - - - +
436D VAL* 1.3 65.0 + - - +
438D ALA* 3.4 7.1 + - - -
440D LYS* 2.8 49.6 + - + +
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Residues in contact with VAL 436 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D ASN* 4.1 4.5 - - - +
234D LEU* 3.3 55.0 - - + +
236D PRO* 5.6 5.6 - - + -
239D ILE* 5.3 2.7 - - + -
432D LEU* 3.0 20.2 + - + +
433D GLU* 3.4 6.7 + - - +
435D ASN* 1.3 81.4 - - - +
437D LYS* 1.3 59.0 + - + +
439D GLY* 3.0 19.9 + - - -
440D LYS 3.9 14.4 - - - +
441D ASP* 4.9 6.9 - - + +
----------------------------------------------------------
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Residues in contact with LYS 437 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D PRO* 4.8 18.2 - - - +
433D GLU* 3.0 52.7 + - - +
434D ALA* 3.7 9.4 - - - +
435D ASN 3.2 0.2 - - - -
436D VAL* 1.3 74.6 - - + +
438D ALA* 1.3 55.8 + - - +
439D GLY 3.0 8.5 + - - -
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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