Contacts of the helix formed by residues 404 - 426 (chain Q) in PDB entry 4UJ3
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 SER 404 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379Q CYS* 3.4 24.9 - - - -
382Q THR* 4.2 3.8 + - - -
384Q GLN* 5.1 3.9 + - - -
386Q LYS* 4.3 15.9 + - - -
388Q CYS* 3.5 8.4 - - - -
403Q ILE* 1.3 78.8 - - - +
405Q PRO* 1.3 77.5 - - - +
406Q PHE* 3.7 8.9 + - - +
407Q CYS* 3.1 25.6 + - - -
408Q ARG* 3.1 19.1 + - - +
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Residues in contact with PRO 405 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386Q LYS* 4.6 13.5 - - + -
387Q SER* 3.5 22.0 - - - +
388Q CYS* 4.9 0.4 - - - -
389Q LYS* 5.4 4.9 - - + +
390Q HIS* 5.1 9.0 - - + -
403Q ILE 3.9 0.4 - - - +
404Q SER* 1.3 88.7 - - - +
406Q PHE* 1.3 62.4 + - + +
408Q ARG* 3.5 10.2 + - + +
409Q TYR* 3.4 15.9 + - - +
456Q PHE* 3.9 19.1 - - + -
457Q LYS 4.9 2.4 - - - +
458Q GLU* 4.0 35.7 - - + +
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Residues in contact with PHE 406 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335Q PHE* 5.0 2.7 - + - -
382Q THR* 5.6 6.3 - - + -
384Q GLN* 5.7 5.4 - - - +
386Q LYS* 5.9 4.9 - - - +
404Q SER* 3.9 7.9 - - - +
405Q PRO* 1.3 79.7 - - + +
407Q CYS* 1.3 76.0 + - - +
409Q TYR* 3.2 13.2 + - - +
410Q ARG* 3.2 56.5 + - + +
451Q ALA 3.7 9.9 - - - -
452Q LYS 5.5 0.4 - - - -
454Q GLY* 3.6 29.8 - - - -
456Q PHE* 3.7 39.8 - + + -
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Residues in contact with CYS 407 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335Q PHE* 3.2 39.9 - - + -
379Q CYS* 3.9 7.6 - - - -
381Q LEU* 3.8 20.4 - - + -
382Q THR* 4.0 8.7 - - - -
403Q ILE* 3.2 24.5 - - + -
404Q SER* 3.1 15.4 + - - +
406Q PHE* 1.3 80.7 - - - +
408Q ARG* 1.3 65.6 + - - +
410Q ARG* 3.1 4.4 + - - +
411Q ILE* 2.9 26.6 + - - +
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Residues in contact with ARG 408 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130P HIS 4.0 11.1 + - - -
131P LEU* 4.6 13.9 - - - +
132P ARG 5.9 1.0 + - - -
355Q ILE* 4.6 11.3 - - + +
390Q HIS* 3.1 57.6 + - + -
403Q ILE* 3.5 9.6 - - + +
404Q SER 3.1 12.2 + - - +
405Q PRO* 3.6 9.3 + - - +
406Q PHE 3.2 0.2 - - - -
407Q CYS* 1.3 76.4 - - - +
409Q TYR* 1.3 71.9 + - - +
411Q ILE* 3.3 5.4 + - - +
412Q THR* 2.9 59.9 + - + +
457Q LYS 5.6 3.2 + - - -
459Q GLU 6.3 1.6 - - - -
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Residues in contact with TYR 409 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405Q PRO 3.4 6.9 + - - +
406Q PHE 3.2 10.4 + - - +
407Q CYS 3.2 0.6 - - - -
408Q ARG* 1.3 88.2 - - - +
410Q ARG* 1.3 57.5 + - + +
412Q THR* 3.1 9.3 + - - -
413Q SER* 2.6 46.0 + - - -
447Q GLU* 2.1 40.1 + - - +
450Q LEU* 4.8 4.3 - - + +
451Q ALA* 3.8 21.5 - - + -
455Q TYR 3.2 21.5 + - - -
456Q PHE* 3.0 34.8 - - + -
457Q LYS* 4.1 22.9 - - + +
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Residues in contact with ARG 410 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331Q PRO 2.8 28.9 + - - -
332Q CYS* 3.0 31.1 + - - +
333Q LEU* 4.9 1.1 - - - -
334Q THR* 4.0 12.0 + - - -
335Q PHE* 4.0 21.7 - - + -
382Q THR* 6.0 0.2 - - - +
406Q PHE* 3.2 53.2 + - + +
407Q CYS 3.1 7.0 + - - +
409Q TYR* 1.3 79.7 - - + +
411Q ILE* 1.3 61.0 + - - +
413Q SER* 3.5 2.6 - - - -
414Q VAL* 3.1 29.1 + - - +
451Q ALA* 3.6 32.3 + - + +
452Q LYS* 3.8 16.8 + - - +
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Residues in contact with ILE 411 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333Q LEU* 4.2 20.0 - - + -
335Q PHE* 4.8 2.5 - - + -
344Q VAL* 3.7 20.0 - - + -
348Q VAL* 4.6 2.9 - - + -
353Q LEU* 3.4 30.7 - - + -
355Q ILE* 4.1 11.0 - - + -
381Q LEU* 3.6 30.5 - - + -
392Q ILE* 4.2 19.1 - - + -
403Q ILE* 5.0 2.0 - - + -
407Q CYS 2.9 20.3 + - - +
408Q ARG* 3.9 3.6 - - - +
410Q ARG* 1.3 78.0 - - - +
412Q THR* 1.3 57.4 + - - +
414Q VAL* 3.2 4.0 + - - +
415Q CYS* 2.8 36.1 + - - -
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Residues in contact with THR 412 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130P HIS* 3.9 30.5 - - + +
131P LEU* 4.3 7.9 - - + -
355Q ILE* 4.3 7.4 - - + -
408Q ARG* 2.9 57.3 + - + +
409Q TYR* 3.1 16.8 + - - -
411Q ILE* 1.3 73.9 - - - +
413Q SER* 1.3 61.4 + - - +
415Q CYS* 3.7 1.0 - - - +
416Q ASN* 2.8 40.9 + - - +
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Residues in contact with SER 413 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409Q TYR* 2.6 49.4 + - - -
410Q ARG* 3.5 8.7 - - - -
412Q THR* 1.3 79.5 + - - +
414Q VAL* 1.3 60.2 + - - +
416Q ASN* 3.6 8.8 + - - +
417Q PHE* 3.5 14.6 + - - +
444Q LEU* 4.6 5.8 - - - +
447Q GLU* 4.1 9.7 + - - +
448Q MET* 3.7 34.0 - - - +
451Q ALA* 4.1 3.0 - - - +
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Residues in contact with VAL 414 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329Q ILE* 3.6 20.4 - - + +
332Q CYS* 3.7 28.5 - - + -
333Q LEU* 4.1 18.6 - - + -
348Q VAL* 4.2 8.1 - - + -
410Q ARG 3.1 16.4 - - - +
411Q ILE 3.2 7.5 + - - +
413Q SER* 1.3 75.5 - - - +
415Q CYS* 1.3 66.0 + - - +
417Q PHE* 3.2 4.0 + - - +
418Q PHE* 3.1 53.1 + - + -
448Q MET* 4.0 12.1 - - - -
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Residues in contact with CYS 415 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130P HIS* 3.3 39.3 - - + +
348Q VAL* 3.9 20.4 - - - -
353Q LEU* 3.6 31.6 - - - -
411Q ILE* 2.8 27.4 + - - +
412Q THR 3.7 0.2 - - - +
414Q VAL* 1.3 78.0 - - - +
416Q ASN* 1.3 56.0 + - - +
418Q PHE* 3.4 2.9 + - - +
419Q THR* 2.9 33.9 + - - -
422Q ARG* 4.9 0.9 + - - -
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Residues in contact with ASN 416 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130P HIS* 2.8 22.8 + - - -
131P LEU* 3.9 16.9 - - - +
412Q THR* 2.8 30.3 + - - +
413Q SER* 3.8 6.4 - - - +
414Q VAL 3.2 0.2 - - - -
415Q CYS* 1.3 73.7 - - - +
417Q PHE* 1.3 65.1 + - - +
419Q THR* 3.3 6.8 + - - +
420Q TYR* 3.1 23.7 + - - +
444Q LEU* 3.7 21.7 - - + +
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Residues in contact with PHE 417 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321Q LEU* 3.7 15.5 - - + -
324Q ILE* 3.2 37.2 - - + -
325Q TYR* 5.7 0.7 - + - -
329Q ILE* 4.0 27.8 - - + -
413Q SER 3.5 10.0 + - - +
414Q VAL 3.2 8.8 + - - +
416Q ASN* 1.3 79.0 - - - +
418Q PHE* 1.3 77.2 + + - +
420Q TYR* 3.2 4.9 + + + +
421Q ILE* 3.0 55.2 + - + +
441Q VAL* 4.2 12.8 - - + -
444Q LEU* 3.9 25.3 - - + +
445Q ARG* 5.1 0.9 - - + -
448Q MET* 4.2 21.8 - - + -
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Residues in contact with PHE 418 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314Q MET* 4.4 22.2 - - + -
321Q LEU* 6.1 2.2 - - + -
325Q TYR* 3.3 32.3 - + - -
329Q ILE* 3.7 24.9 - - + -
345Q LEU* 5.2 1.6 - - + -
348Q VAL* 3.4 24.5 - - + +
349Q GLU* 3.9 24.2 - - + -
414Q VAL* 3.1 43.2 + - + -
415Q CYS 3.8 6.3 - - - +
417Q PHE* 1.3 90.0 - + - +
419Q THR* 1.3 64.0 + - - +
421Q ILE* 3.3 5.8 + - + +
422Q ARG* 3.0 42.9 + - - +
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Residues in contact with THR 419 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P LEU* 4.8 9.6 - - + +
130P HIS* 3.5 17.0 - - + -
351Q ASN* 5.2 0.5 + - - -
415Q CYS 2.9 22.4 + - - -
416Q ASN* 3.5 10.5 - - - +
417Q PHE 3.2 0.2 - - - -
418Q PHE* 1.3 77.3 - - - +
420Q TYR* 1.3 57.8 + - + +
422Q ARG* 3.6 21.8 + - - +
423Q TYR* 3.1 68.3 + - + +
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Residues in contact with TYR 420 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P LEU* 5.4 4.7 - - + -
416Q ASN 3.1 15.7 + - - +
417Q PHE* 3.8 4.7 - + + +
419Q THR* 1.3 75.5 - - + +
421Q ILE* 1.3 70.7 + - + +
423Q TYR* 3.0 31.1 + + + +
424Q ILE* 3.0 40.5 + - + +
429Q VAL* 4.8 9.4 - - + +
432Q GLN* 3.1 28.2 + - - -
437Q MET* 3.6 22.8 - - - +
440Q GLU* 3.6 36.7 - - + +
441Q VAL* 4.0 19.7 - - + -
444Q LEU* 4.8 11.0 - - + -
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Residues in contact with ILE 421 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308Q TRP* 3.8 34.4 - - + -
314Q MET* 3.8 25.8 - - + -
320Q PHE* 3.9 20.6 - - + -
321Q LEU* 4.7 7.9 - - + -
417Q PHE* 3.0 50.3 + - + +
418Q PHE* 3.3 8.0 + - + +
420Q TYR* 1.3 80.2 - - + +
422Q ARG* 1.3 64.1 + - - +
424Q ILE* 3.1 20.6 + - + +
425Q GLN* 3.2 13.8 + - - +
441Q VAL* 5.1 3.4 - - + -
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Residues in contact with ARG 422 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314Q MET* 4.0 19.7 - - + +
348Q VAL 4.6 2.8 + - - -
349Q GLU 4.8 9.2 + - - -
350Q ASN 6.2 0.2 - - - -
351Q ASN* 3.2 49.5 + - - +
415Q CYS 4.9 0.6 + - - -
418Q PHE* 3.0 27.3 + - - +
419Q THR* 3.8 31.2 + - - +
421Q ILE* 1.3 73.8 - - - +
423Q TYR* 1.3 71.9 + - + +
425Q GLN* 3.4 25.5 - - - +
426Q GLN* 3.1 40.7 + - - +
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Residues in contact with TYR 423 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P LEU* 4.0 31.2 - - + -
127P ASP* 3.7 1.8 + - - -
128P LEU* 3.5 19.8 - - - +
156P LEU* 3.5 34.2 - - + +
200P GNP 3.7 2.8 + - - -
419Q THR* 3.1 46.9 + - + +
420Q TYR* 3.0 28.8 + + + +
422Q ARG* 1.3 83.5 - - + +
424Q ILE* 1.3 54.2 + - - +
426Q GLN* 3.4 1.3 - - - -
427Q GLY* 2.8 27.4 + - - -
428Q LEU* 3.2 29.3 - - + +
429Q VAL* 3.8 3.7 - - + +
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Residues in contact with ILE 424 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305Q PHE* 4.4 18.2 - - + -
308Q TRP* 4.3 14.4 - - + -
309Q LYS* 4.7 10.8 - - + +
312Q PRO* 4.1 18.0 - - + +
420Q TYR* 3.0 40.6 + - + +
421Q ILE* 3.1 11.1 + - + +
423Q TYR* 1.3 74.9 - - - +
425Q GLN* 1.3 61.2 + - - +
426Q GLN 3.2 1.3 - - - -
427Q GLY* 2.9 16.3 + - - -
429Q VAL* 4.0 14.3 - - + +
437Q MET* 3.2 36.1 - - + -
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Residues in contact with GLN 425 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312Q PRO* 3.3 32.3 - - + +
313Q THR* 4.1 4.7 + - - +
314Q MET* 2.9 54.1 + - - +
421Q ILE* 3.2 5.8 + - - +
422Q ARG* 3.4 21.9 - - - +
424Q ILE* 1.3 79.9 - - - +
426Q GLN* 1.3 83.2 + - + +
427Q GLY 3.1 2.0 + - - -
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Residues in contact with GLN 426 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422Q ARG* 3.1 30.5 + - - +
423Q TYR* 3.4 4.6 - - - +
425Q GLN* 1.3 100.8 - - + +
427Q GLY* 1.3 65.8 + - - +
428Q LEU* 3.1 22.1 + - + +
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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