Contacts of the helix formed by residues 287 - 323 (chain A) in PDB entry 6TOS
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 VAL 287 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A GLU* 1.3 77.6 - - + +
288A LYS* 1.4 56.5 + - - +
290A MET* 3.5 17.3 + - + +
291A ARG* 3.0 28.3 + - + +
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Residues in contact with LYS 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLU 3.3 4.0 - - - +
287A VAL* 1.4 76.5 - - - +
289A GLN* 1.4 61.8 + - - +
291A ARG* 3.4 12.4 + - + +
292A ALA* 3.3 20.6 + - - +
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Residues in contact with GLN 289 (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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286A GLU* 3.4 24.0 + - - +
287A VAL 3.4 0.2 - - - -
288A LYS* 1.4 76.7 - - - +
290A MET* 1.4 59.1 + - - +
292A ALA* 3.2 9.2 + - + +
293A ARG* 2.9 57.3 + - + +
405A SO4 3.2 28.2 + - - +
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Residues in contact with MET 290 (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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241A LYS 5.0 4.0 - - - +
242A LEU* 3.5 39.0 - - + +
286A GLU 2.9 19.6 + - - +
287A VAL* 3.8 15.9 - - + +
289A GLN* 1.4 71.9 - - - +
291A ARG* 1.3 59.0 + - - +
293A ARG* 3.9 8.7 - - - +
294A ARG* 3.0 60.2 + - - +
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A VAL* 3.0 18.6 + - + +
288A LYS* 3.5 12.6 - - - +
289A GLN 3.2 0.2 - - - -
290A MET* 1.3 78.8 - - - +
292A ALA* 1.3 59.9 + - - +
294A ARG* 3.9 7.8 - - - +
295A LYS* 3.2 55.6 + - - +
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Residues in contact with ALA 292 (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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288A LYS 3.3 10.5 + - - +
289A GLN* 3.2 11.6 + - + +
291A ARG* 1.3 76.3 - - - +
293A ARG* 1.4 62.9 + - + +
295A LYS* 3.3 11.6 + - - +
296A THR* 3.2 25.7 + - - -
406A SO4 5.3 2.0 + - - -
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Residues in contact with ARG 293 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ARG* 4.3 10.5 - - - +
147A ALA* 3.7 22.5 + - - +
148A ILE* 4.1 22.3 + - + +
242A LEU* 3.5 23.3 - - + +
289A GLN* 2.9 46.6 + - - +
290A MET* 3.9 4.5 - - - +
292A ALA* 1.4 73.9 - - + +
294A ARG* 1.3 58.5 + - - +
296A THR* 3.5 5.6 + - - -
297A ALA* 2.9 32.4 + - - +
405A SO4 2.8 53.2 + - - +
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Residues in contact with ARG 294 (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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242A LEU* 2.8 41.1 + - + -
243A TRP* 3.4 57.3 - - + +
244A GLY 5.7 1.6 - - - -
290A MET* 3.0 45.8 + - + +
291A ARG* 3.9 7.6 - - - +
293A ARG* 1.3 74.7 - - - +
295A LYS* 1.4 59.0 + - + +
298A LYS* 3.0 31.4 + - - +
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Residues in contact with LYS 295 (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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291A ARG* 3.2 55.7 + - - +
292A ALA* 3.3 11.5 + - - +
293A ARG 3.3 0.4 - - - -
294A ARG* 1.4 78.8 - - + +
296A THR* 1.3 60.8 + - - +
298A LYS* 3.5 16.4 + - - +
299A MET* 3.2 21.8 + - - +
361A LEU 4.0 10.5 - - - +
406A SO4 3.7 26.7 - - - +
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Residues in contact with THR 296 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A THR* 4.2 20.0 - - + +
82A ASN* 6.1 0.2 - - - +
144A ARG* 4.8 10.1 - - - +
292A ALA 3.2 15.0 + - - -
293A ARG* 4.0 5.6 - - - -
295A LYS* 1.3 72.1 - - - +
297A ALA* 1.3 60.6 + - - +
299A MET* 3.3 16.0 + - + +
300A LEU* 3.0 52.9 + - + +
406A SO4 4.3 13.4 + - - -
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Residues in contact with ALA 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ARG* 5.9 3.3 - - + +
148A ILE* 5.3 2.9 - - + -
235A TYR* 5.0 3.8 - - + -
238A ILE* 4.0 8.5 - - + -
242A LEU* 3.7 20.9 - - + -
243A TRP* 4.1 1.6 - - + -
293A ARG 2.9 17.7 + - - +
294A ARG 4.0 2.7 - - - +
296A THR* 1.3 72.9 - - - +
298A LYS* 1.4 64.7 + - - +
300A LEU* 4.0 9.1 - - - +
301A MET* 3.1 49.7 + - + +
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Residues in contact with LYS 298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A TRP* 4.2 16.1 - - + -
294A ARG 3.0 19.4 + - - +
295A LYS* 3.7 14.4 - - - +
296A THR 3.3 0.2 - - - -
297A ALA* 1.4 77.7 - - - +
299A MET* 1.4 60.9 + - - +
301A MET* 3.4 8.5 + - - +
302A VAL* 3.3 31.3 + - + +
361A LEU* 3.9 27.6 - - + +
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Residues in contact with MET 299 (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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81A THR* 5.1 0.2 - - + -
82A ASN* 4.9 5.4 - - - +
85A LEU* 3.8 26.9 - - + -
295A LYS 3.2 11.1 + - - +
296A THR* 3.6 20.4 - - + +
298A LYS* 1.4 78.7 - - - +
300A LEU* 1.3 70.9 + - + +
302A VAL* 3.2 6.9 + - - +
303A VAL* 3.0 31.2 + - + +
357A ILE* 4.2 5.7 - - + +
358A TYR* 3.9 26.7 - - + -
361A LEU* 3.8 29.6 - - + +
362A SER* 3.7 30.3 - - - -
365A PHE* 5.0 2.2 - - + -
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Residues in contact with LEU 300 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A THR* 3.7 20.9 - - + -
85A LEU* 4.3 17.9 - - + -
137A LEU* 6.1 2.0 - - + -
140A ILE* 3.7 28.7 - - + -
144A ARG* 3.9 14.4 - - + -
235A TYR* 3.6 21.5 - - + +
296A THR* 3.0 40.0 + - + +
297A ALA* 4.0 3.8 - - - +
299A MET* 1.3 83.1 - - + +
301A MET* 1.3 59.6 + - - +
303A VAL* 3.4 11.2 + - + +
304A VAL* 3.1 33.8 + - + +
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Residues in contact with MET 301 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A TYR* 3.4 56.8 - - + +
238A ILE* 4.3 1.8 - - + -
239A PHE* 4.1 15.0 - - + +
243A TRP* 4.1 18.8 - - + -
297A ALA* 3.1 41.6 + - + +
298A LYS* 3.7 9.2 - - - +
300A LEU* 1.3 75.3 - - - +
302A VAL* 1.3 57.3 + - + +
304A VAL* 3.5 6.6 + - - +
305A LEU* 2.9 30.2 + - - +
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Residues in contact with VAL 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A LYS* 3.3 19.3 + - + +
299A MET 3.2 8.4 + - - +
301A MET* 1.3 74.3 - - + +
303A VAL* 1.4 58.0 + - - +
305A LEU* 3.4 12.6 + - + +
306A VAL* 2.9 47.8 + - + +
357A ILE* 3.8 14.1 - - + -
361A LEU* 3.7 26.5 - - + -
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Residues in contact with VAL 303 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 5.2 3.1 - - + -
88A LEU* 4.4 10.3 - - + -
137A LEU* 3.8 26.5 - - + -
299A MET* 3.0 20.4 + - + +
300A LEU* 3.6 14.6 - - + +
301A MET 3.4 0.2 - - - -
302A VAL* 1.4 76.6 - - - +
304A VAL* 1.3 56.4 + - - +
306A VAL* 3.5 1.7 + - - +
307A PHE* 2.9 28.3 + - + +
354A ASN* 3.8 16.3 - - - +
357A ILE* 3.8 24.5 - - + -
358A TYR* 3.7 28.5 - - + +
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Residues in contact with VAL 304 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 4.4 15.9 - - + +
228A LEU* 3.9 24.1 - - + +
231A MET* 4.1 28.5 - - + -
232A ALA* 5.3 3.1 - - + +
235A TYR* 3.8 28.0 - - + +
300A LEU 3.1 17.2 + - - +
301A MET* 3.9 5.2 - - - +
303A VAL* 1.3 70.7 - - - +
305A LEU* 1.3 61.1 + - - +
307A PHE* 3.2 7.5 + - - +
308A ALA* 2.8 30.2 + - + +
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Residues in contact with LEU 305 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A MET 2.9 18.2 + - - +
302A VAL* 3.7 14.1 - - + +
304A VAL* 1.3 76.0 - - - +
306A VAL* 1.4 56.2 + - + +
308A ALA* 3.2 9.8 + - + +
309A LEU* 2.8 61.8 + - + +
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Residues in contact with VAL 306 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A VAL* 2.9 29.8 + - + +
303A VAL 3.9 3.4 - - - +
305A LEU* 1.4 76.9 - - + +
307A PHE* 1.3 65.3 + - - +
309A LEU* 3.9 10.7 - - + +
310A CYS* 3.0 31.9 + - - -
350A ASN* 3.8 12.8 - - - +
353A ALA* 4.0 14.8 - - + -
354A ASN* 5.2 0.2 - - - +
357A ILE* 4.0 26.2 - - + -
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Residues in contact with PHE 307 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU* 5.3 2.7 - - + -
130A VAL* 4.6 4.3 - - + -
133A ALA* 3.6 26.2 - - + -
134A VAL* 4.1 33.4 - - + -
137A LEU* 3.6 26.7 - - + -
223A THR 4.8 3.8 - - - -
224A TYR* 5.3 0.9 - + - -
228A LEU* 4.0 18.2 - - + -
303A VAL* 2.9 18.6 + - + +
304A VAL* 3.6 4.7 - - - +
306A VAL* 1.3 77.1 - - - +
308A ALA* 1.4 62.4 + - - +
311A TYR* 3.0 76.2 + + + +
350A ASN* 3.6 20.1 + - - +
354A ASN* 5.7 0.7 - - - +
419A NA 4.0 1.6 - - - -
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Residues in contact with ALA 308 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A TYR* 2.7 30.8 + - - +
228A LEU* 3.9 24.2 - - + -
304A VAL* 2.8 21.6 + - + +
305A LEU* 3.4 9.9 - - + +
307A PHE* 1.4 74.2 - - - +
309A LEU* 1.3 61.4 + - + +
312A LEU* 3.1 13.6 + - - +
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Residues in contact with LEU 309 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A LEU* 2.8 50.7 + - + +
306A VAL* 4.0 10.1 - - + +
307A PHE 3.3 0.2 - - - -
308A ALA* 1.3 72.8 - - + +
310A CYS* 1.3 61.2 + - - +
312A LEU* 3.5 13.5 + - + +
313A PRO* 3.3 20.8 - - - +
346A LEU* 4.5 3.8 - - - +
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Residues in contact with CYS 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A VAL* 3.0 32.1 + - - +
307A PHE 3.9 2.9 - - - +
309A LEU* 1.3 76.4 - - - +
311A TYR* 1.3 61.1 + - + +
312A LEU 3.4 0.2 - - - -
313A PRO* 4.0 4.6 - - - +
314A ILE* 4.9 0.5 - - - +
343A SER 4.5 1.4 - - - +
346A LEU* 3.4 61.0 - - - +
347A VAL* 4.1 5.5 + - - +
349A ALA* 4.8 2.7 - - - -
350A ASN* 3.7 29.8 - - + -
353A ALA* 5.5 1.1 - - - -
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Residues in contact with TYR 311 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLN* 5.2 0.7 + - - -
129A SER* 5.4 3.1 + - - -
130A VAL* 3.8 37.0 - - + +
133A ALA* 4.8 3.3 - - - +
224A TYR* 3.7 20.2 - - + -
307A PHE* 3.0 62.6 + + + +
310A CYS* 1.3 79.6 - - + +
312A LEU* 1.3 62.3 + - - +
313A PRO 3.6 0.2 - - - -
314A ILE* 3.6 10.9 - - + +
315A SER* 2.7 34.4 + - - +
347A VAL* 3.5 39.7 + - + +
350A ASN* 4.0 14.4 - - + -
401A NRE 4.8 1.3 - - - -
419A NA 2.9 21.4 - - - -
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Residues in contact with LEU 312 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE* 5.5 3.1 - - + -
224A TYR* 3.5 26.7 - - + +
308A ALA 3.1 19.3 + - - +
309A LEU* 3.8 12.8 - - + +
310A CYS 3.4 0.2 - - - -
311A TYR* 1.3 77.9 - - - +
313A PRO* 1.4 72.3 - - + +
315A SER* 3.7 0.8 - - - -
316A VAL* 3.0 49.4 + - + +
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Residues in contact with PRO 313 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A LEU 3.3 15.7 - - - +
310A CYS 4.0 7.4 - - - +
311A TYR 3.9 1.3 - - - -
312A LEU* 1.4 89.5 - - + +
314A ILE* 1.3 56.7 + - - +
316A VAL* 3.8 4.8 - - + +
317A LEU* 2.9 35.6 + - + +
342A PHE* 5.1 6.5 - - + -
343A SER* 3.4 23.6 - - - +
346A LEU* 3.7 17.9 - - + -
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Residues in contact with ILE 314 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A CYS 4.9 0.4 - - - +
311A TYR* 3.6 17.9 + - + +
313A PRO* 1.3 74.5 - - - +
315A SER* 1.3 65.5 + - - +
317A LEU* 4.5 1.3 - - + +
318A ASN* 3.0 57.0 + - - +
340A PHE* 4.2 14.4 - - + -
343A SER* 3.8 25.0 + - - +
344A HIS* 3.5 33.0 - - + +
347A VAL* 3.6 24.2 - - + -
401A NRE 3.7 25.4 - - - +
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Residues in contact with SER 315 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A PHE* 5.9 2.8 - - - -
220A PHE* 3.7 29.3 - - - +
223A THR* 5.7 0.7 + - - -
224A TYR* 3.6 20.0 - - - +
311A TYR* 2.7 26.3 + - - +
312A LEU* 3.7 3.6 - - - -
314A ILE* 1.3 80.3 - - - +
316A VAL* 1.3 61.4 + - - +
318A ASN* 3.6 5.7 + - - +
319A VAL* 3.3 27.0 + - - +
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Residues in contact with VAL 316 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A PHE* 4.9 10.8 - - + -
312A LEU* 3.0 42.5 + - + +
313A PRO* 3.9 4.3 - - + +
315A SER* 1.3 75.3 - - - +
317A LEU* 1.4 60.9 + - + +
319A VAL* 3.1 8.5 + - - +
320A LEU* 2.9 50.7 + - + +
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Residues in contact with LEU 317 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A PRO* 2.9 21.4 + - + +
314A ILE* 3.9 4.0 - - - +
316A VAL* 1.4 71.9 - - + +
318A ASN* 1.3 57.0 + - - +
320A LEU* 3.4 9.5 + - + +
321A LYS* 2.9 31.7 + - - +
327A PHE* 3.8 27.7 - - + -
339A ALA* 3.6 21.8 - - + +
340A PHE* 3.6 29.2 - - + +
343A SER* 3.1 32.3 - - - +
415A SOG 4.1 19.1 - - + -
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Residues in contact with ASN 318 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A HIS* 4.6 15.1 - - + +
219A PHE* 5.9 3.6 - - + -
314A ILE* 3.0 33.0 + - - +
315A SER* 3.9 6.0 - - - +
317A LEU* 1.3 75.5 - - - +
319A VAL* 1.3 56.9 + - + +
321A LYS* 4.5 9.1 + - - +
322A ARG* 2.9 40.0 + - - +
340A PHE* 4.2 12.3 - - - -
401A NRE 3.0 48.4 + - + +
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Residues in contact with VAL 319 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A HIS* 4.2 9.4 - - + +
217A SER* 5.3 1.6 - - - -
220A PHE* 3.6 39.9 - - + -
315A SER 3.3 14.2 + - - +
316A VAL* 3.1 9.6 + - - +
318A ASN* 1.3 73.9 - - + +
320A LEU* 1.3 63.5 + - + +
323A VAL* 2.7 46.7 + - + +
324A PHE* 3.3 28.2 + - + -
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Residues in contact with LEU 320 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A VAL* 2.9 44.5 + - + +
317A LEU* 3.8 9.4 - - + +
319A VAL* 1.3 72.3 - - + +
321A LYS* 1.3 60.6 + - - +
324A PHE* 3.3 31.7 + - + +
325A GLY 3.3 0.2 + - - -
326A MET* 3.0 49.3 + - + +
327A PHE* 3.9 24.2 - - + -
415A SOG 5.9 2.2 - - + -
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Residues in contact with LYS 321 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ASP* 4.5 0.6 + - - -
317A LEU 2.9 19.2 + - - +
318A ASN* 3.9 8.3 + - - +
320A LEU* 1.3 75.7 - - - +
322A ARG* 1.3 90.8 + - + +
325A GLY* 3.3 12.6 + - - -
326A MET 3.8 12.1 - - - +
327A PHE* 4.0 10.2 - - + -
340A PHE* 4.1 17.6 - - + -
402A PG4 2.7 65.0 + - - +
403A CIT 3.9 0.3 - - - -
404A CIT 3.4 39.7 + - - +
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Residues in contact with ARG 322 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ASP* 3.3 18.2 + - - -
204A GLU* 3.6 40.6 + - - +
206A TRP* 4.1 3.2 - - - +
212A PRO* 4.2 0.9 - - - +
213A LYS* 3.5 12.1 - - - +
216A HIS* 3.4 44.2 + - + +
318A ASN* 2.9 27.8 + - - +
321A LYS* 1.3 107.2 - - + +
323A VAL* 1.3 60.1 + - - +
402A PG4 4.0 6.5 - - - -
403A CIT 2.6 73.3 + - - +
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Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LYS* 3.7 17.2 - - + +
216A HIS* 4.1 9.6 - - + -
217A SER* 3.4 36.8 - - - +
319A VAL* 2.7 33.2 + - + +
322A ARG* 1.3 76.1 - - - +
324A PHE* 1.3 73.3 + - + +
325A GLY 3.5 0.8 + - - -
403A CIT 4.1 4.2 - - - +
407A SOG 4.3 17.9 - - + -
412A SOG 2.8 39.7 + - + +
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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) + - + + + + + -
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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