Contacts of the helix formed by residues 338 - 362 (chain B) in PDB entry 5DKG
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 338 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B ARG* 4.9 3.3 + - - -
336B PRO 4.6 2.6 + - - -
337B PHE* 1.3 76.0 - - - +
339B GLU* 1.3 59.6 + - - +
340B ALA* 3.7 8.0 + - - +
341B SER* 2.8 28.1 + - - -
342B MET* 2.8 36.5 + - - +
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Residues in contact with GLU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B SER* 1.3 71.9 - - - +
340B ALA* 1.3 63.2 + - - +
342B MET* 3.8 9.2 - - - +
343B MET* 3.1 30.0 + - - +
417B CYS* 3.4 24.2 - - - +
418B VAL* 3.5 16.2 - - + -
534B VAL* 5.6 0.9 - - - -
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Residues in contact with ALA 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B SER* 3.2 7.2 + - - +
339B GLU* 1.3 78.8 - - - +
341B SER* 1.3 57.8 + - - +
343B MET* 4.1 1.7 - - - +
344B GLY* 3.1 21.7 + - - -
533B VAL* 6.2 2.2 - - + -
534B VAL* 4.4 22.8 - - + +
535B PRO* 5.5 3.9 - - + +
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Residues in contact with SER 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ARG* 3.8 37.5 - - - +
336B PRO 4.3 0.9 + - - -
337B PHE* 3.9 5.7 - - - -
338B SER* 2.8 42.5 + - - -
340B ALA* 1.3 75.7 - - - +
342B MET* 1.3 60.4 + - - +
344B GLY* 3.2 2.0 + - - -
345B LEU* 2.8 37.7 + - - +
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Residues in contact with MET 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B PHE* 3.8 19.1 - - + -
338B SER* 2.8 45.2 + - - +
339B GLU* 3.8 6.5 - - - +
341B SER* 1.3 77.1 + - - +
343B MET* 1.3 61.0 + - - +
345B LEU* 3.2 13.5 + - + +
346B LEU* 3.1 31.0 + - + +
414B GLN* 3.9 22.7 - - - +
417B CYS* 3.6 33.2 - - + -
418B VAL* 5.7 0.9 - - + -
421B MET* 5.2 14.1 - - + +
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Residues in contact with MET 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLU 3.1 18.2 + - - +
340B ALA 4.3 1.1 - - - +
342B MET* 1.3 76.6 - - - +
344B GLY* 1.3 60.7 + - - +
346B LEU* 3.8 5.6 - - - +
347B THR* 2.8 40.8 + - - +
418B VAL* 4.1 15.7 - - + -
421B MET* 3.5 26.9 - - + -
525B LEU* 4.3 8.7 - - + -
528B MET* 3.8 30.7 - - + -
534B VAL* 4.0 21.1 - - + -
536B LEU* 6.0 0.4 - - + -
601B 5C7 3.7 44.6 - - + -
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Residues in contact with GLY 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLU* 4.7 1.1 - - - +
340B ALA 3.1 18.1 + - - -
341B SER* 3.2 5.8 + - - -
343B MET* 1.3 77.6 - - - +
345B LEU* 1.3 54.4 + - - +
347B THR* 3.9 4.3 - - - -
348B ASN* 3.0 32.4 + - - +
534B VAL* 4.8 4.2 - - - +
535B PRO* 5.6 8.3 - - - -
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Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B SER* 4.7 5.1 - - - +
330B GLU* 3.6 48.5 + - + +
331B TYR* 3.6 32.1 - - + +
332B ASP 5.2 1.1 - - - +
341B SER* 2.8 21.0 + - - +
342B MET* 3.2 15.2 + - + +
344B GLY* 1.3 77.1 - - - +
346B LEU* 1.3 62.5 + - - +
348B ASN* 3.8 4.4 + - - +
349B LEU* 3.2 23.9 + - - +
352B ARG* 5.5 0.2 + - - -
408B LEU* 4.5 17.9 - - + +
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B MET* 3.1 16.4 + - + +
343B MET* 3.9 4.9 - - - +
345B LEU* 1.3 73.9 - - + +
347B THR* 1.3 60.6 + - - +
349B LEU* 3.4 5.7 + - + +
350B ALA* 3.0 29.3 + - - +
404B PHE* 3.6 46.9 - - + -
408B LEU* 3.9 20.0 - - + -
410B LEU* 4.7 6.7 - - + -
421B MET* 4.1 28.9 - - + -
425B PHE* 4.9 2.2 - - + -
601B 5C7 3.5 35.9 - - + -
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Residues in contact with THR 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B MET* 2.8 27.6 + - - +
344B GLY* 3.9 4.0 - - - -
346B LEU* 1.3 74.4 - - - +
348B ASN* 1.3 67.0 + - - +
350B ALA* 3.3 2.4 + - - +
351B ASP* 3.0 22.7 + - - +
534B VAL* 4.7 2.8 - - - +
535B PRO 3.6 23.0 + - - +
536B LEU* 3.8 18.1 - - + +
537B SER* 4.2 5.8 - - - +
540B LEU* 3.7 18.5 - - + +
601B 5C7 2.8 22.9 + - - -
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Residues in contact with ASN 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLU* 3.0 38.9 + - - +
344B GLY 3.0 16.5 + - - +
345B LEU 4.1 2.2 - - - +
347B THR* 1.3 77.7 - - - +
349B LEU* 1.3 61.7 + - - +
351B ASP* 3.5 8.4 + - - +
352B ARG* 2.8 62.7 + - - +
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 4.1 23.3 - - + +
328B TYR 3.8 26.0 - - - +
329B SER* 4.7 6.7 - - - +
345B LEU 3.2 18.2 + - - +
346B LEU* 3.6 4.3 - - + +
347B THR 3.2 0.2 - - - -
348B ASN* 1.3 79.8 + - - +
350B ALA* 1.3 57.5 + - - +
352B ARG* 3.2 13.2 + - - +
353B GLU* 2.9 49.2 + - + +
404B PHE* 3.3 44.2 - - + +
405B ALA* 4.5 3.4 - - + -
408B LEU* 5.1 1.8 - - + -
601B 5C7 4.4 8.5 - - + -
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Residues in contact with ALA 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU 3.0 18.3 + - - +
347B THR 3.3 4.2 + - - +
349B LEU* 1.3 76.2 - - - +
351B ASP* 1.3 58.0 + - - +
353B GLU* 3.2 13.5 + - - +
354B LEU* 2.8 34.3 + - - +
387B LEU* 3.9 22.5 - - + +
540B LEU* 4.3 6.7 - - + -
601B 5C7 4.0 24.9 - - + -
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Residues in contact with ASP 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B THR 3.0 16.1 + - - +
348B ASN* 3.7 10.0 + - - +
349B LEU 3.2 0.2 - - - -
350B ALA* 1.3 76.4 - - - +
352B ARG* 1.3 66.5 + - - +
354B LEU* 3.5 20.7 - - - +
355B VAL* 3.5 14.2 - - - +
537B SER* 2.6 41.2 + - - +
539B LEU* 3.9 18.4 - - - +
540B LEU* 4.4 3.4 + - + +
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Residues in contact with ARG 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 3.7 25.7 - - + +
328B TYR 2.9 30.3 + - - +
329B SER* 3.9 12.7 - - - +
330B GLU* 4.5 3.0 - - - +
345B LEU 5.5 0.2 + - - -
348B ASN* 2.8 38.4 + - - +
349B LEU* 3.2 21.8 + - - +
351B ASP* 1.3 83.1 - - - +
353B GLU* 1.3 65.5 + - - +
354B LEU 3.2 0.2 - - - -
355B VAL* 3.2 18.4 + - + +
356B HIS* 3.3 18.1 + - + +
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Residues in contact with GLU 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 3.9 19.7 - - + -
349B LEU* 2.9 32.9 + - + +
350B ALA* 3.2 9.3 + - - +
352B ARG* 1.3 78.1 - - - +
354B LEU* 1.3 55.3 + - - +
356B HIS* 3.1 8.0 + - - +
357B MET* 2.8 29.4 + - - +
387B LEU* 3.6 17.0 - - + +
394B ARG* 3.6 20.5 + - - -
601B 5C7 2.6 41.5 + - - -
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Residues in contact with LEU 354 (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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350B ALA 2.8 19.0 + - - +
351B ASP* 3.5 11.0 - - - +
352B ARG 3.2 0.2 - - - -
353B GLU* 1.3 77.0 - - - +
355B VAL* 1.3 56.8 + - - +
357B MET* 3.2 30.3 + - + +
358B ILE* 3.0 39.9 + - + +
383B TRP* 4.0 25.1 - - + -
387B LEU* 4.7 1.8 - - + -
539B LEU* 3.8 31.6 - - + -
540B LEU* 3.5 31.0 - - + +
543B MET* 4.1 15.3 - - + -
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Residues in contact with VAL 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B ASP* 3.5 18.6 - - - +
352B ARG* 3.2 11.2 + - + +
353B GLU 3.2 0.6 - - - -
354B LEU* 1.3 77.6 - - - +
356B HIS* 1.3 65.8 - - + +
358B ILE* 3.5 8.4 + - - +
359B ASN* 2.8 37.8 + - - +
539B LEU* 4.8 9.9 - - + -
693D LEU* 5.1 11.9 - - + -
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Residues in contact with HIS 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B PRO* 4.0 18.3 - - + +
325B PRO* 3.4 33.0 - - + +
327B LEU* 3.7 29.3 - - + +
352B ARG* 3.3 20.1 + - + -
353B GLU* 3.1 8.6 + - - +
355B VAL* 1.3 79.1 - - + +
357B MET* 1.3 61.4 + - - +
359B ASN* 3.4 5.8 + - - +
360B TRP* 2.8 30.1 + - - +
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Residues in contact with MET 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B PRO* 5.2 3.1 - - - +
353B GLU 2.8 14.7 + - - +
354B LEU* 3.2 19.5 + - + +
356B HIS* 1.3 77.6 - - - +
358B ILE* 1.3 57.6 + - - +
360B TRP* 3.1 31.0 + - + -
361B ALA* 2.8 27.7 + - - +
379B LEU* 4.1 14.1 - - + -
383B TRP* 3.2 43.1 - - - +
386B ILE* 3.9 26.9 - - + -
387B LEU* 3.6 26.9 - - + -
543B MET* 6.1 0.2 - - - -
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Residues in contact with ILE 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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354B LEU* 3.0 26.0 + - + +
355B VAL* 3.8 5.8 - - - +
356B HIS 3.3 0.2 - - - -
357B MET* 1.3 76.7 - - + +
359B ASN* 1.3 65.9 + - - +
361B ALA* 3.4 10.4 + - - +
362B LYS* 3.4 17.6 + - + +
379B LEU* 4.4 11.9 - - + -
539B LEU* 4.1 14.8 - - + -
543B MET* 6.2 1.6 - - + -
690D LEU* 3.6 26.5 - - + -
693D LEU* 3.6 46.9 - - + +
694D LEU* 3.8 27.2 - - + +
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Residues in contact with ASN 359 (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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355B VAL* 2.8 33.1 + - - +
356B HIS* 3.4 7.4 + - - +
357B MET 3.3 0.2 - - - -
358B ILE* 1.3 81.1 - - - +
360B TRP* 1.3 63.5 + - - +
362B LYS* 3.6 30.9 + - + +
363B ARG* 3.4 19.8 - - - +
693D LEU* 5.2 5.1 + - - +
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Residues in contact with TRP 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 5.1 5.9 + - - +
322B ALA* 3.2 37.8 - - + +
323B GLU* 4.0 10.5 + - - -
324B PRO* 3.9 19.5 - - + -
356B HIS 2.8 19.0 + - - +
357B MET* 3.2 35.2 - - + +
359B ASN* 1.3 75.6 - - - +
361B ALA* 1.3 70.8 + - + +
363B ARG* 3.0 16.3 + - - +
364B VAL* 3.4 25.6 + - + +
386B ILE* 3.6 28.9 - - + -
446B VAL 5.4 0.9 - - - -
449B LYS* 3.8 45.9 - - + +
450B SER* 4.3 7.9 - - - -
453B LEU* 3.7 23.6 - - + -
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Residues in contact with ALA 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B MET 2.8 15.2 + - - +
358B ILE 3.6 7.2 - - - +
359B ASN 3.3 0.2 - - - -
360B TRP* 1.3 85.2 - - + +
362B LYS* 1.3 63.0 + - - +
364B VAL* 3.0 17.1 + - - +
367B PHE* 3.2 38.5 - - + +
379B LEU* 4.2 13.0 - - + -
453B LEU* 3.7 19.3 - - + -
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Residues in contact with LYS 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ILE* 3.4 17.9 - - + +
359B ASN* 3.8 28.0 + - - +
360B TRP 3.2 0.6 - - - -
361B ALA* 1.3 76.2 - - - +
363B ARG* 1.3 61.4 + - + +
364B VAL 3.3 5.0 + - - +
367B PHE* 4.2 9.0 - - + -
368B VAL* 4.3 21.6 - - + +
375B GLN* 5.4 2.7 - - - +
693D LEU 3.7 13.1 + - - +
694D LEU* 3.4 40.9 + - + +
696D ASP* 3.8 20.6 - - - +
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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