Contacts of the helix formed by residues 339 - 364 (chain B) in PDB entry 3V4R
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 GLU 339 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B HIS* 3.6 25.1 - - + +
69B LEU* 5.6 3.1 - - + -
338B ASP* 1.4 72.5 - - + +
340B SER* 1.3 54.2 + - - +
341B HIS* 3.2 23.1 - - + -
342B VAL* 2.8 27.4 + - + +
343B THR* 3.1 9.9 + - - -
392B VAL* 2.9 12.2 + - - +
393B SER* 4.5 3.8 - - - +
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Residues in contact with SER 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B VAL* 3.7 23.6 - - - -
338B ASP 3.3 1.2 - - - -
339B GLU* 1.3 74.2 - - - +
341B HIS* 1.3 56.4 + - - +
342B VAL 3.0 0.9 + - - -
343B THR 4.3 0.2 - - - +
344B ILE* 2.8 35.3 + - - +
391B TYR* 3.6 27.5 - - - +
392B VAL 3.1 7.0 + - - -
393B SER* 3.4 16.2 - - - -
396B PRO* 4.6 1.2 - - - +
400B GLU* 2.8 29.8 + - - +
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Residues in contact with HIS 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLU* 3.8 13.2 - - + -
340B SER* 1.3 74.6 + - - +
342B VAL* 1.3 78.1 + - + +
345B PRO* 3.5 19.6 - - - +
393B SER* 2.7 23.9 + - - +
394B ALA* 5.2 2.2 - - + -
395B THR* 3.4 29.5 + - - +
397B GLY* 3.6 16.6 - - - +
400B GLU* 3.2 9.6 + - - -
532B ARG* 3.7 28.6 - - + +
536B GLN* 5.8 5.7 - - - +
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Residues in contact with VAL 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B HIS* 3.4 37.0 - - + +
339B GLU* 2.8 13.3 + - + +
341B HIS* 1.3 114.3 - - + +
343B THR* 1.3 62.7 + - - +
345B PRO* 3.3 11.2 - - - +
346B GLN* 3.4 15.7 + - + +
2C A 5.4 11.4 - - - +
3C C 5.8 6.3 - - + -
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Residues in contact with THR 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 3.8 30.7 - - + +
64B ALA 4.3 1.3 - - - +
65B HIS* 3.2 30.4 + - + +
337B VAL* 3.6 21.8 - - + -
338B ASP 2.7 22.9 + - - -
339B GLU 3.1 3.2 + - - -
342B VAL* 1.3 73.1 - - - +
344B ILE* 1.3 60.2 + - - +
346B GLN* 3.0 9.0 + - - +
347B VAL* 2.8 40.7 + - + +
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Residues in contact with ILE 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B VAL* 4.1 18.2 - - + -
340B SER* 2.8 28.3 + - - +
343B THR* 1.3 69.8 - - - +
345B PRO* 1.4 64.2 - - + +
347B VAL* 3.3 7.1 + - + +
348B ARG* 3.0 33.5 + - - +
379B PHE* 4.0 25.0 - - + -
382B PHE* 4.7 11.7 - - + -
389B ILE* 5.6 0.2 - - + -
391B TYR* 3.9 35.0 - - + -
399B TYR* 3.9 30.5 - - + -
400B GLU* 4.5 7.0 - - - +
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Residues in contact with PRO 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B SER 3.6 2.2 - - - +
341B HIS* 3.5 20.6 - - - +
342B VAL* 3.3 17.3 - - - +
344B ILE* 1.4 93.4 - - + +
346B GLN* 1.4 50.2 + - - +
348B ARG* 3.5 17.2 + - + +
349B GLY* 2.9 30.0 + - - -
400B GLU* 6.0 0.2 - - - +
2C A 6.4 0.2 - - - +
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Residues in contact with GLN 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA 4.2 2.3 - - - +
65B HIS* 3.1 40.7 + - - +
142B VAL* 3.4 26.7 - - + +
342B VAL* 3.4 13.9 + - + +
343B THR* 3.0 12.7 + - - +
345B PRO* 1.4 74.1 - - - +
347B VAL* 1.4 66.0 + - - +
349B GLY* 3.1 10.4 + - - -
350B MET* 3.2 34.3 + - + +
4C T 2.7 29.1 + - - -
5C G 3.2 14.1 + - + +
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Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 4.9 8.7 - - + -
142B VAL* 3.6 25.8 - - + -
145B ILE* 4.2 18.8 - - + +
343B THR* 2.8 34.6 + - + +
344B ILE* 3.7 8.1 - - + +
346B GLN* 1.4 70.4 - - - +
348B ARG* 1.3 62.4 + - - +
349B GLY 3.3 0.9 + - - -
350B MET* 3.3 18.3 + - - +
351B PHE* 4.7 1.2 + - - +
377B LEU 4.9 3.8 - - - +
379B PHE* 3.9 20.5 + - + +
382B PHE* 4.0 33.2 - - + -
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Residues in contact with ARG 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ILE* 3.0 21.7 + - - +
345B PRO* 3.6 14.6 - - - +
347B VAL* 1.3 76.5 - - - +
349B GLY* 1.3 57.7 + - - +
350B MET 3.7 0.3 + - - -
351B PHE* 4.6 4.9 + - - +
352B ASN* 3.3 20.1 + - - +
379B PHE* 3.8 48.4 + - + +
399B TYR* 3.9 33.8 - - - +
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Residues in contact with GLY 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B PRO 2.9 15.1 + - - -
346B GLN 3.1 5.7 + - - -
348B ARG* 1.3 77.5 - - - +
350B MET* 1.3 71.9 + - - +
351B PHE 3.5 0.7 - - - -
352B ASN* 3.6 10.2 + - - +
353B GLY* 3.5 14.0 + - - -
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Residues in contact with MET 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 4.3 20.6 - - + -
145B ILE* 3.8 23.8 - - + -
146B TYR* 3.8 19.9 + - + +
346B GLN* 3.2 33.8 + - + +
347B VAL* 3.3 13.5 + - - +
349B GLY* 1.3 83.1 - - - +
351B PHE* 1.3 65.5 + - - +
353B GLY* 3.2 8.7 + - - -
354B ASP* 3.3 12.6 + - - +
376B PRO* 3.9 11.0 - - + -
5C G 3.6 28.3 - - + +
6C T 3.9 13.5 - - - +
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Residues in contact with PHE 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B VAL 4.7 0.8 + - - +
348B ARG 4.6 4.1 + - - +
349B GLY 3.5 0.2 - - - -
350B MET* 1.3 77.0 - - - +
352B ASN* 1.3 78.5 + - - +
354B ASP* 3.4 2.1 + - - +
355B GLN* 3.0 61.8 + - + +
375B ARG* 3.5 35.0 - - + -
376B PRO* 3.8 17.6 - - + +
377B LEU 3.5 18.7 + - - +
378B ARG* 3.3 60.3 - - + -
379B PHE 5.3 0.9 - - - +
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Residues in contact with ASN 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ARG* 3.3 25.1 + - - +
349B GLY* 4.1 8.3 - - - +
350B MET 3.3 1.0 - - - -
351B PHE* 1.3 92.9 - - - +
353B GLY* 1.3 61.3 + - - +
355B GLN* 3.7 3.6 + - - +
356B ALA* 3.1 24.8 + - - +
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Residues in contact with GLY 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B GLY 3.5 6.4 + - - -
350B MET 3.2 7.0 + - - -
352B ASN* 1.3 75.6 - - - +
354B ASP* 1.3 64.2 + - - +
356B ALA* 3.3 7.8 + - - +
357B ARG* 3.1 30.9 + - - +
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Residues in contact with ASP 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B TYR* 5.2 4.7 - - + +
350B MET 3.3 9.1 + - - +
351B PHE 3.6 7.9 - - - +
353B GLY* 1.3 74.2 - - - +
355B GLN* 1.3 59.6 + - - +
357B ARG* 3.5 22.2 + - - +
358B LYS* 2.9 45.3 + - - +
376B PRO* 3.7 29.4 - - + -
7C T 5.4 2.0 - - - +
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Residues in contact with GLN 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B PHE* 3.0 58.8 + - + +
352B ASN* 4.0 4.0 - - - +
354B ASP* 1.3 75.8 - - - +
356B ALA* 1.4 52.3 + - - +
358B LYS* 3.3 8.5 + - - -
359B GLN* 2.7 41.3 + - + +
372B LEU* 3.1 49.3 + - + +
375B ARG* 3.6 14.4 - - - +
378B ARG* 5.6 1.4 - - - +
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Residues in contact with ALA 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B ASN 3.1 20.2 + - - +
353B GLY* 3.4 8.7 - - - +
355B GLN* 1.4 76.1 - - - +
357B ARG* 1.4 60.4 + - - +
359B GLN* 3.3 5.6 + - - +
360B VAL* 3.1 25.1 + - - +
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Residues in contact with ARG 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PRO* 3.7 27.8 - - - +
99B GLU 3.4 25.7 + - - +
100B ALA* 4.2 14.1 - - + -
101B TYR 5.8 0.3 + - - -
146B TYR* 5.8 1.0 + - - -
353B GLY 3.1 18.0 + - - +
354B ASP* 3.9 21.3 + - - +
356B ALA* 1.4 74.3 - - - +
358B LYS* 1.3 69.2 + - + +
359B GLN 3.4 0.2 + - - -
360B VAL* 3.4 12.6 + - - +
361B LEU* 3.4 24.5 + - + +
7C T 2.8 34.8 + - - +
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Residues in contact with LYS 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B ASN* 4.1 12.8 - - - +
354B ASP* 2.9 32.3 + - - +
355B GLN* 3.8 15.4 + - - -
357B ARG* 1.3 84.7 - - + +
359B GLN* 1.3 57.9 + - - +
361B LEU* 3.4 18.5 + - + +
362B VAL* 3.0 31.4 + - - +
367B ARG* 5.8 1.6 - - + -
371B ALA* 3.2 36.9 + - + +
372B LEU* 3.8 16.2 - - + +
374B ASN* 3.1 28.5 + - - -
375B ARG* 4.4 1.8 - - - +
7C T 5.7 2.7 - - - -
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Residues in contact with GLN 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLN* 2.7 24.0 + - + +
356B ALA* 3.7 6.7 - - - +
358B LYS* 1.3 69.7 - - - +
360B VAL* 1.4 59.5 + - - +
362B VAL* 3.1 16.2 + - - +
363B ASP* 2.9 63.7 + - - +
369B PRO* 5.9 0.4 - - - +
372B LEU* 3.5 31.9 - - + +
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Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TYR* 3.9 42.8 - - + +
103B PRO* 4.3 11.2 - - + -
356B ALA 3.1 17.7 - - - +
357B ARG* 3.5 13.9 - - - +
358B LYS 3.4 0.2 - - - -
359B GLN* 1.4 73.5 - - - +
361B LEU* 1.4 62.1 + - - +
363B ASP* 3.2 11.4 + - - +
364B HIS* 3.0 37.0 + - + +
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLU* 3.5 39.7 - - + +
100B ALA* 4.0 26.0 - - - -
101B TYR* 4.0 5.6 - - + +
108B PHE* 4.1 5.8 - - + -
357B ARG* 3.4 20.7 + - + +
358B LYS* 3.6 20.9 - - + +
359B GLN 3.3 0.4 - - - -
360B VAL* 1.4 75.8 - - - +
362B VAL* 1.4 59.1 + - - +
364B HIS* 3.5 1.0 + - - -
365B GLY 3.3 2.9 + - - -
366B PHE* 2.8 61.9 + - + +
367B ARG* 4.0 12.6 - - + -
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Residues in contact with VAL 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLN* 4.4 6.8 + - - +
274B MET* 4.3 8.7 - - - +
358B LYS 3.0 20.0 + - - +
359B GLN* 3.1 21.1 + - - +
361B LEU* 1.4 74.4 - - - +
363B ASP* 1.4 64.1 + - - +
365B GLY* 3.0 15.9 + - - -
367B ARG* 3.5 20.5 - - + +
368B LEU 3.6 20.0 - - - +
369B PRO* 4.0 25.1 - - + -
371B ALA* 4.8 3.1 - - + -
372B LEU* 4.0 19.5 - - + -
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Residues in contact with ASP 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B MET* 5.2 0.9 - - - +
279B LYS* 3.8 31.9 + - - +
282B GLU* 4.0 6.8 - - - +
359B GLN* 2.9 45.7 + - - +
360B VAL* 3.4 12.5 + - - +
362B VAL* 1.4 73.1 - - - +
364B HIS* 1.3 69.8 + - + +
365B GLY 3.4 0.9 + - - -
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Residues in contact with HIS 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TYR* 3.5 35.0 + + + -
103B PRO* 4.3 13.6 - - + +
282B GLU* 3.5 24.8 + - - +
285B ARG* 2.8 33.8 + - - +
360B VAL* 3.0 32.5 + - + +
361B LEU 3.5 0.2 + - - -
362B VAL 3.2 0.4 - - - -
363B ASP* 1.3 85.5 - - + +
365B GLY* 1.3 61.1 + - - +
366B PHE* 3.4 21.5 - - + -
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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