Contacts of the helix formed by residues 299 - 332 (chain A) in PDB entry 4R1Z
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 299 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LYS* 4.8 0.9 - - - +
283A LYS* 3.9 7.0 - - - +
297A GLY* 5.3 1.1 - - - -
298A LEU* 1.3 84.0 - - - +
300A GLU* 1.3 67.6 + - - +
301A ASP* 3.8 8.8 + - - +
302A HIS* 2.6 47.2 + - + +
303A VAL* 3.2 8.5 + - - +
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Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A GLN* 3.2 31.7 + - - +
260A TYR* 3.6 35.2 + - + +
264A LYS* 5.6 0.7 + - - -
283A LYS* 3.7 14.5 - - - +
299A THR* 1.3 73.3 - - - +
301A ASP* 1.3 67.4 + - - +
303A VAL* 3.1 7.6 + - - +
304A LEU* 3.0 33.4 + - + +
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Residues in contact with ASP 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ARG* 3.2 37.6 + - - +
123A LYS* 4.0 31.4 + - + -
299A THR* 3.1 7.2 + - - +
300A GLU* 1.3 85.4 - - - +
302A HIS* 1.3 57.2 + - - +
304A LEU* 3.9 3.2 - - - +
305A MET* 2.9 35.8 + - - +
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Residues in contact with HIS 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LYS* 3.4 50.3 - - + +
133A THR* 4.2 13.8 - - + +
137A HIS* 3.6 11.3 + + - +
297A GLY* 2.9 40.4 + - - +
298A LEU* 4.3 0.7 - - - -
299A THR* 2.6 40.5 + - + +
301A ASP* 1.3 76.9 - - - +
303A VAL* 1.3 61.4 + - - +
306A THR* 2.9 31.0 + - - -
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A HIS* 5.1 1.6 - - - -
260A TYR* 4.2 15.7 - - + -
276A LEU* 3.8 28.7 - - + -
279A LEU* 4.1 36.1 - - + +
280A LEU* 5.1 2.5 - - + -
283A LYS* 4.4 12.1 - - + -
298A LEU* 4.4 20.4 - - + +
299A THR 3.2 10.9 + - - +
300A GLU* 3.1 8.4 + - - +
302A HIS* 1.3 74.4 - - - +
304A LEU* 1.3 67.5 + - - +
305A MET 3.2 0.3 + - - -
306A THR* 3.2 3.7 + - - -
307A VAL* 3.1 24.9 + - - +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ARG* 3.7 27.8 - - - +
253A ASP 5.8 0.2 - - - +
256A LEU* 3.3 41.4 - - + +
257A GLN* 3.3 25.6 - - + +
260A TYR* 3.8 35.9 - - + -
276A LEU* 5.9 3.4 - - + -
300A GLU* 3.0 32.8 + - + +
301A ASP* 4.0 4.3 - - - +
303A VAL* 1.3 78.7 - - + +
305A MET* 1.3 58.7 + - - +
307A VAL* 4.1 5.1 - - + +
308A GLY* 3.0 20.5 + - - -
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Residues in contact with MET 305 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU 3.0 27.4 - - - +
119A THR* 3.5 23.1 - - + +
120A ARG* 3.7 34.5 - - + +
123A LYS* 3.5 18.2 - - + +
124A ASP* 3.6 12.7 - - + +
252A ARG* 3.4 29.2 - - - +
256A LEU* 5.1 1.3 - - - -
301A ASP 2.9 22.1 + - - +
304A LEU* 1.3 79.5 - - - +
306A THR* 1.3 60.6 + - - +
308A GLY* 3.4 2.1 + - - -
309A ASP* 3.0 34.4 + - - +
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Residues in contact with THR 306 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LYS 4.5 5.0 + - - -
124A ASP* 4.4 4.3 - - - +
125A ILE* 4.0 15.6 - - + +
137A HIS* 2.9 26.8 - - + +
141A VAL* 4.0 26.5 - - + -
275A LEU* 5.0 1.1 - - + -
279A LEU* 4.2 16.8 - - + -
302A HIS 2.9 21.0 + - - -
303A VAL 3.2 4.2 + - - -
305A MET* 1.3 75.5 - - - +
307A VAL* 1.3 66.9 + - - +
309A ASP* 3.1 16.5 + - - +
310A ILE* 3.2 13.7 + - + +
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Residues in contact with VAL 307 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A CYS* 4.0 13.7 - - + +
197A PHE* 3.3 39.5 - - + -
256A LEU* 4.8 3.4 - - + -
275A LEU* 4.5 15.7 - - + -
276A LEU* 4.3 21.8 - - + -
279A LEU* 3.6 21.8 - - + -
303A VAL 3.1 14.2 + - - +
304A LEU* 4.2 6.3 - - + +
306A THR* 1.3 76.0 - - - +
308A GLY* 1.3 59.4 + - - +
310A ILE* 3.1 2.8 + - - +
311A PHE* 2.8 27.4 + - - +
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Residues in contact with GLY 308 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ARG* 4.7 12.3 + - - -
256A LEU* 4.1 20.1 - - - +
304A LEU 3.0 17.4 + - - -
305A MET* 3.6 5.2 - - - -
307A VAL* 1.3 77.0 - - - +
309A ASP* 1.3 51.4 + - - +
311A PHE* 3.7 4.0 - - - +
312A GLY* 2.8 32.1 + - - -
601A AER 3.9 8.7 - - - +
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Residues in contact with ASP 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 5.2 1.4 - - - +
119A THR* 4.8 2.1 - - - +
124A ASP* 2.6 41.9 - - - +
125A ILE* 3.0 19.8 + - + +
126A ALA* 3.1 11.1 + - - +
252A ARG* 5.7 0.5 + - - -
305A MET* 3.0 10.9 + - - +
306A THR* 3.1 10.5 + - - +
308A GLY* 1.3 75.6 - - - +
310A ILE* 1.3 65.9 + - + +
313A ALA* 2.9 32.6 + - - +
600A HEM 4.7 5.6 - - + +
601A AER 3.8 27.7 - - + +
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Residues in contact with ILE 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ILE* 5.3 1.3 - - + -
141A VAL* 3.7 32.3 - - + -
192A VAL* 3.2 21.8 - - + +
195A LEU* 4.5 11.4 - - + -
196A CYS* 3.5 21.5 - - - -
275A LEU* 3.9 14.4 - - + -
306A THR 3.6 12.1 - - - +
307A VAL 3.1 6.3 + - - +
309A ASP* 1.3 76.8 - - + +
311A PHE* 1.3 66.5 + - - +
314A GLY* 3.0 18.4 + - - -
454A LEU* 4.2 14.6 - - + -
458A LEU* 6.1 0.9 - - + -
600A HEM 3.4 34.7 - - + +
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Residues in contact with PHE 311 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A THR* 4.3 10.5 - - + -
192A VAL* 4.1 21.1 - - + +
193A CYS* 4.5 12.3 - - + -
196A CYS* 3.9 7.3 - - - -
197A PHE* 3.9 26.2 - + + -
201A TYR* 4.0 17.5 - - - -
211A MET* 3.3 36.2 - - + +
214A TYR* 3.9 21.8 - - - -
252A ARG* 5.9 2.0 - - + -
255A LEU* 4.0 13.0 - - + -
256A LEU* 4.5 11.2 - - + -
307A VAL 2.8 21.3 + - - +
308A GLY* 3.8 5.2 - - - +
310A ILE* 1.3 76.6 - - - +
312A GLY* 1.3 64.8 + - - +
315A VAL* 3.6 19.1 + - - +
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Residues in contact with GLY 312 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A GLY 2.8 19.0 + - - -
310A ILE 3.1 0.2 - - - -
311A PHE* 1.3 78.0 - - - +
313A ALA* 1.3 64.4 + - - +
315A VAL* 3.3 4.2 + - - +
316A GLU* 3.1 24.3 + - - +
601A AER 3.8 32.6 - - - +
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Residues in contact with ALA 313 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A ASP 2.9 20.3 + - - +
312A GLY* 1.3 71.9 - - - -
314A GLY* 1.3 61.5 + - - +
315A VAL 2.9 1.7 + - - -
316A GLU 3.2 0.4 + - - +
317A THR* 2.7 34.4 + - + +
600A HEM 3.5 34.8 - - + -
601A AER 3.8 33.4 - - + +
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Residues in contact with GLY 314 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A VAL* 3.2 20.8 - - - +
192A VAL* 4.1 14.7 - - - +
310A ILE 3.0 19.1 + - - -
312A GLY 3.2 0.2 - - - -
313A ALA* 1.3 80.0 - - - +
315A VAL* 1.3 59.6 + - - +
318A THR* 3.3 12.9 + - - -
458A LEU* 6.2 0.9 - - - -
462A GLU* 4.6 3.9 - - - +
600A HEM 3.7 18.8 - - - +
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Residues in contact with VAL 315 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A THR* 4.2 17.3 - - + -
188A VAL* 3.9 3.6 - - - -
189A THR* 3.2 46.4 - - + +
192A VAL* 3.8 8.5 - - + -
211A MET* 3.9 17.0 - - + -
212A LEU* 5.8 0.9 - - + -
311A PHE 3.6 16.5 + - - +
312A GLY* 3.3 3.8 + - - +
313A ALA 2.9 1.2 + - - -
314A GLY* 1.3 77.7 - - - +
316A GLU* 1.3 72.9 + - - +
317A THR 3.4 0.2 - - - -
319A THR* 2.7 34.5 + - - +
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Residues in contact with GLU 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A SER* 4.2 19.5 + - - -
219A VAL* 4.1 25.7 - - + +
312A GLY 3.1 14.6 + - - +
313A ALA 4.4 0.4 - - - +
315A VAL* 1.3 89.3 - - - +
317A THR* 1.3 59.3 + - - +
319A THR* 4.5 1.7 - - - +
320A THR* 3.0 27.4 + - - -
493A VAL* 4.9 0.7 - - + -
494A VAL* 4.0 21.5 - - + +
496A GLN* 3.9 17.7 + - - +
601A AER 4.3 19.3 - - + +
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Residues in contact with THR 317 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ALA* 2.7 21.1 + - - +
316A GLU* 1.3 74.7 - - - +
318A THR* 1.3 73.8 + - - -
319A THR 3.1 2.3 + - - -
320A THR* 3.1 13.0 + - - -
321A VAL* 3.3 14.0 + - - +
377A VAL* 4.5 8.3 - - + -
494A VAL* 4.4 7.6 - - + -
600A HEM 3.2 36.0 - - + +
601A AER 3.2 50.3 - - + +
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Residues in contact with THR 318 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A VAL* 3.9 7.9 - - + -
314A GLY 3.3 20.5 + - - -
317A THR* 1.3 82.0 + - - +
319A THR* 1.3 64.1 + - - +
321A VAL* 3.4 3.7 + - - +
322A LEU* 3.2 22.6 + - + +
459A ALA* 4.6 5.1 - - - +
462A GLU* 3.3 43.1 + - + +
463A LEU* 4.2 16.6 - - + -
600A HEM 3.3 29.9 - - - +
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Residues in contact with THR 319 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU* 4.8 4.2 - - + +
185A THR* 3.2 38.1 - - + +
188A VAL* 3.1 28.6 - - - +
315A VAL* 2.7 27.2 + - + +
316A GLU* 4.5 2.2 - - - +
317A THR 3.1 1.0 + - - -
318A THR* 1.3 77.4 - - - +
320A THR* 1.3 63.1 + - - +
322A LEU* 3.1 15.7 + - - +
323A LYS* 3.1 31.0 + - + +
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Residues in contact with THR 320 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A GLU* 3.0 19.4 + - - -
317A THR 3.1 6.0 + - - -
319A THR* 1.3 78.9 - - - +
321A VAL* 1.3 62.9 + - - +
323A LYS* 3.0 14.8 + - - +
324A TRP* 2.9 30.9 + - - +
377A VAL* 3.4 16.6 - - + -
494A VAL* 3.6 6.9 - - - +
495A LEU 3.3 26.2 - - - +
496A GLN* 3.6 27.5 + - + +
497A PRO* 4.1 0.7 - - + -
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Residues in contact with VAL 321 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A THR 3.3 12.0 + - - +
318A THR 3.7 7.4 - - - +
319A THR 3.3 0.2 - - - -
320A THR* 1.3 74.9 - - - +
322A LEU* 1.3 58.2 + - - +
324A TRP* 3.2 11.3 + - + +
325A SER* 2.8 32.9 + - - +
368A ILE* 5.6 2.0 - - + -
371A VAL* 4.2 13.9 - - + -
372A LEU* 4.1 18.4 - - + -
375A ARG 5.7 1.8 - - - +
377A VAL* 3.7 22.9 - - + -
463A LEU* 3.6 31.0 - - + -
600A HEM 4.0 17.7 - - + -
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Residues in contact with LEU 322 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU* 4.3 27.1 - - + -
188A VAL* 3.9 24.9 - - + -
318A THR* 3.2 16.5 + - + +
319A THR* 3.1 7.4 + - - +
321A VAL* 1.3 74.4 - - - +
323A LYS* 1.3 59.2 + - - +
325A SER* 3.2 4.2 + - - -
326A ILE* 2.8 35.8 + - + +
463A LEU* 3.4 23.8 - - + -
466A PHE* 4.2 28.0 - - + -
467A LEU* 3.8 30.5 - - + -
470A ILE* 6.3 0.4 - - + -
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Residues in contact with LYS 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A GLY* 3.8 28.7 - - - -
184A LEU* 4.8 10.3 - - + -
185A THR* 3.8 12.7 + - - -
319A THR* 3.1 31.1 + - + +
320A THR* 3.0 13.1 + - - +
322A LEU* 1.3 75.1 - - - +
324A TRP* 1.3 60.8 + - - +
326A ILE* 3.4 10.0 + - - +
327A ALA* 3.2 20.8 + - - +
496A GLN* 5.3 8.0 + - + +
497A PRO* 3.8 25.1 - - + +
500A PHE* 4.6 5.5 - - + -
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Residues in contact with TRP 324 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A THR* 2.9 32.5 + - + +
321A VAL* 3.5 9.0 - - - +
322A LEU 3.2 0.2 - - - -
323A LYS* 1.3 73.6 - - - +
325A SER* 1.3 67.9 + - - +
327A ALA* 2.9 7.6 + - + +
328A TYR* 2.8 38.2 + + + -
371A VAL* 3.7 14.1 - - + -
375A ARG* 3.5 49.5 + - + +
377A VAL* 5.2 0.9 - - + -
486A ASP 5.4 0.2 - - - -
487A LEU* 3.6 43.3 - - + -
488A GLN 4.5 0.4 - - - -
489A GLY* 4.0 8.1 - - - -
495A LEU* 3.0 29.6 + - + -
496A GLN 3.7 5.2 - - - -
497A PRO* 3.4 41.5 - - + -
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Residues in contact with SER 325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A VAL* 2.8 20.5 + - - +
322A LEU* 3.5 8.7 - - - +
324A TRP* 1.3 76.0 - - - +
326A ILE* 1.3 56.7 + - - +
328A TYR* 4.5 2.5 - - - +
329A LEU* 2.7 40.9 + - - +
367A THR* 6.4 0.7 - - - -
368A ILE* 5.8 0.5 - - - +
371A VAL* 3.6 27.1 - - - +
463A LEU* 5.3 0.5 - - - +
467A LEU* 4.0 33.6 - - - +
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Residues in contact with ILE 326 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 4.3 19.3 - - + -
184A LEU* 4.2 19.7 - - + -
322A LEU* 2.8 28.1 + - + +
323A LYS* 3.7 7.9 - - - +
325A SER* 1.3 72.6 - - - +
327A ALA* 1.3 58.9 + - - +
329A LEU* 3.7 6.0 - - + +
330A VAL* 2.8 29.9 + - + +
467A LEU* 4.7 14.6 - - + -
470A ILE* 5.2 10.1 - - + -
476A LEU* 4.0 26.6 - - + +
500A PHE* 4.2 7.4 - - + -
502A VAL* 3.9 27.6 - - + -
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Residues in contact with ALA 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A LYS 3.2 10.4 + - - +
324A TRP* 2.9 16.0 + - + +
326A ILE* 1.3 79.2 - - - +
328A TYR* 1.3 58.4 + - - +
330A VAL* 3.0 6.3 + - - +
331A HIS* 2.9 34.0 + - - -
485A PRO* 4.7 6.3 - - + -
487A LEU* 3.7 24.0 - - + -
497A PRO* 5.6 1.6 - - + -
500A PHE* 3.8 23.5 - - + -
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Residues in contact with TYR 328 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A TRP* 2.8 34.9 + + + +
325A SER* 4.2 3.8 - - - +
327A ALA* 1.3 71.8 - - - +
329A LEU* 1.3 66.9 + - + +
331A HIS* 4.3 3.4 - - + -
332A ASN* 2.9 35.1 + - - +
371A VAL* 5.0 2.7 - - + -
374A ILE* 3.7 23.9 - - + +
375A ARG* 3.4 53.1 + - + -
423A PHE* 3.6 54.4 - + + -
487A LEU* 3.8 34.1 - - + +
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Residues in contact with LEU 329 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A SER* 2.7 35.1 + - - +
326A ILE* 3.7 9.2 - - + +
328A TYR* 1.3 78.9 - - + +
330A VAL* 1.3 63.7 + - - +
332A ASN* 3.1 17.8 + - - -
333A PRO 3.6 0.2 - - - -
335A VAL* 4.1 14.6 - - + -
336A GLN* 2.8 57.5 + - + +
339A ILE* 4.3 5.2 - - + -
367A THR* 5.1 6.7 - - + -
423A PHE* 6.2 1.1 - - + -
467A LEU* 4.4 12.8 - - + -
471A LEU* 4.0 28.3 - - + -
476A LEU* 5.1 7.0 - - + -
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Residues in contact with VAL 330 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ILE* 2.8 19.8 + - + +
327A ALA* 3.0 4.7 + - - +
329A LEU* 1.3 78.9 - - - +
331A HIS* 1.3 62.2 + - - +
332A ASN 3.3 0.7 + - - -
333A PRO* 3.7 11.1 - - - +
476A LEU* 3.4 37.5 - - + +
477A GLU* 4.1 2.4 - - - +
478A MET* 3.5 48.2 - - + +
484A LEU* 4.0 7.5 - - + +
485A PRO* 3.8 13.0 - - + -
500A PHE* 5.1 0.2 - - + -
502A VAL* 4.0 13.5 - - + -
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Residues in contact with HIS 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ALA 2.9 24.6 + - - +
328A TYR* 3.8 3.4 - - + +
330A VAL* 1.3 76.2 - - - +
332A ASN* 1.3 74.4 + - - +
333A PRO* 3.2 8.4 - - - +
484A LEU* 3.6 34.1 - - + +
485A PRO* 2.9 36.5 + - + +
487A LEU* 3.3 33.8 - - + +
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Residues in contact with ASN 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A TYR* 2.9 28.7 + - - +
329A LEU 3.1 7.1 + - - +
331A HIS* 1.3 91.5 - - - +
333A PRO* 1.3 58.5 - - - +
334A GLN* 2.9 28.7 + - - +
335A VAL* 2.6 38.2 + - + +
336A GLN 3.2 7.6 + - - -
423A PHE* 4.1 29.2 - - + +
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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