Contacts of the helix formed by residues 359 - 392 (chain y) in PDB entry 3J45
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 GLY 359 (chain y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343y ALA* 3.7 12.7 - - - +
347y LYS* 3.7 25.1 - - - +
357y ARG 4.4 0.4 - - - -
358y PRO* 1.3 76.3 - - - +
360y GLU* 1.4 65.0 + - - -
361y GLN 3.5 2.0 - - - -
362y THR 3.5 2.8 + - - -
363y ALA* 3.3 18.5 + - - +
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Residues in contact with GLU 360 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15373 G 5.9 3.3 - - - -
357y ARG 4.9 0.2 + - - -
359y GLY* 1.4 71.4 - - - -
361y GLN* 1.4 81.9 + - + +
363y ALA* 3.4 9.9 + - - +
364y LYS* 3.0 48.0 + - - +
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Residues in contact with GLN 361 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19T LYS* 5.2 23.7 - - + +
23T ALA* 6.2 0.3 - - - +
356y ILE* 6.0 0.7 - - - -
357y ARG* 4.4 16.6 - - + +
360y GLU* 1.4 102.1 + - + +
362y THR* 1.4 61.3 + - - +
364y LYS* 3.3 21.0 + - - +
365y TYR* 2.9 34.7 + - + -
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Residues in contact with THR 362 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265y LEU* 6.2 1.8 - - + -
342y THR* 4.7 4.5 - - + -
343y ALA* 3.7 24.9 - - + +
346y LEU* 5.1 6.4 - - + +
356y ILE* 3.4 28.3 + - + +
357y ARG 3.3 19.4 + - - -
358y PRO* 4.1 4.9 - - + +
359y GLY 3.5 9.0 + - - -
360y GLU 3.4 0.4 - - - -
361y GLN* 1.4 72.7 - - - +
363y ALA* 1.3 67.4 + - - +
365y TYR* 3.0 18.9 + - - +
366y ILE* 3.1 28.7 + - + +
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Residues in contact with ALA 363 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339y PRO 3.4 8.7 - - - +
340y ARG* 4.1 26.8 + - + +
343y ALA* 3.8 14.7 - - + +
359y GLY 3.3 11.2 + - - +
360y GLU* 3.4 12.6 - - - +
362y THR* 1.3 79.8 - - - +
364y LYS* 1.4 63.9 - - + +
366y ILE* 3.2 14.0 + - - +
367y ASP* 3.3 12.0 + - - +
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Residues in contact with LYS 364 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340y ARG* 5.5 9.0 - - - +
360y GLU* 3.0 45.0 + - - +
361y GLN* 3.3 15.7 + - - +
362y THR 3.2 0.8 - - - -
363y ALA* 1.4 76.9 - - + +
365y TYR* 1.3 64.2 + - + +
367y ASP* 3.3 21.2 + - - +
368y LYS* 3.3 27.6 + - + +
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Residues in contact with TYR 365 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18T GLU* 5.3 3.1 - - - -
22T THR* 2.6 45.8 + - + +
26T LYS* 5.7 4.0 - - - -
355y GLY 6.3 0.2 - - - -
356y ILE* 4.8 24.2 - - + -
361y GLN* 2.9 35.1 + - + -
362y THR* 3.0 11.9 + - + +
364y LYS* 1.3 82.0 - - + +
366y ILE* 1.4 65.1 + - + +
368y LYS* 3.5 12.2 + - + +
369y VAL* 3.1 30.1 + - + +
372y ARG* 5.1 0.2 + - - -
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Residues in contact with ILE 366 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265y LEU* 5.7 2.5 - - + -
268y LYS* 4.2 12.5 + - + +
338y ASN* 3.5 23.3 - - - +
339y PRO 3.5 9.8 - - - +
340y ARG* 3.7 7.6 - - - +
342y THR* 3.4 43.3 - - + +
343y ALA 4.7 0.4 - - - +
362y THR* 3.1 31.5 + - + +
363y ALA* 3.2 7.1 + - - +
365y TYR* 1.4 78.7 - - + +
367y ASP* 1.3 57.6 + - - +
369y VAL* 3.3 8.9 + - + +
370y MET* 3.0 30.8 + - - +
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Residues in contact with ASP 367 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339y PRO* 3.3 28.2 + - - +
340y ARG* 3.3 23.5 + - - +
363y ALA 3.3 6.4 + - - +
364y LYS* 3.3 18.0 + - + +
365y TYR 3.2 0.2 - - - -
366y ILE* 1.3 78.0 - - - +
368y LYS* 1.4 69.0 + - - +
370y MET* 4.0 1.9 - - - +
371y THR* 3.1 28.9 + - - -
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Residues in contact with LYS 368 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364y LYS* 3.3 26.9 + - + +
365y TYR* 3.6 14.4 - - + +
367y ASP* 1.4 91.1 + - - +
369y VAL* 1.4 63.4 + - - +
371y THR* 3.5 5.3 + - - -
372y ARG* 3.4 46.4 + - - +
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Residues in contact with VAL 369 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242y ARG* 3.5 32.5 + - + +
268y LYS* 4.0 29.8 - - + +
365y TYR* 3.1 19.0 + - + +
366y ILE* 3.3 13.4 + - + +
368y LYS* 1.4 75.8 - - - +
370y MET* 1.4 56.9 + - - +
372y ARG* 3.7 23.5 - - - +
373y LEU* 3.1 29.2 + - + +
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Residues in contact with MET 370 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268y LYS* 4.0 23.3 - - - +
333y THR* 3.2 34.3 - - - +
334y ALA* 4.7 2.9 - - - +
336y VAL* 3.6 16.6 - - + +
338y ASN* 4.2 17.3 - - + -
339y PRO* 4.3 21.5 - - + -
366y ILE 3.0 17.6 + - - +
367y ASP 4.0 4.7 - - - +
368y LYS 3.4 0.2 - - - -
369y VAL* 1.4 71.2 - - - +
371y THR* 1.3 68.1 + - - +
373y LEU* 3.5 4.6 + - - +
374y THR* 3.4 43.5 + - - +
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Residues in contact with THR 371 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E VAL* 6.4 2.0 - - + -
83E ILE* 6.1 1.3 - - + -
330y PHE* 4.0 27.4 - - + -
367y ASP* 3.1 23.8 + - - -
368y LYS* 3.5 6.5 + - - +
369y VAL 3.3 0.6 - - - -
370y MET* 1.3 82.7 - - - +
372y ARG* 1.4 65.0 + - + +
374y THR* 3.6 2.6 + - - -
375y LEU* 3.3 28.1 + - + +
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Residues in contact with ARG 372 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E VAL* 4.5 19.2 - - - +
83E ILE* 4.0 28.7 - - + -
86E THR* 4.1 30.5 - - + +
242y ARG* 3.8 26.2 - - - +
365y TYR 5.1 0.2 + - - -
368y LYS* 3.4 38.4 + - - +
369y VAL* 3.7 24.5 - - - +
371y THR* 1.4 82.1 - - + +
373y LEU* 1.3 64.8 + - - +
375y LEU* 4.0 0.8 - - - +
376y VAL* 3.1 29.7 + - + +
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Residues in contact with LEU 373 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E GLU* 4.0 14.4 - - - +
237y VAL* 5.7 2.2 - - + -
242y ARG* 4.0 13.9 - - - +
268y LYS* 3.6 37.2 - - + -
270y ASN* 3.7 35.2 - - - +
271y MET 4.2 14.8 - - - +
272y ALA* 3.9 10.0 - - + +
369y VAL* 3.1 21.9 + - + +
370y MET* 3.9 5.4 - - - +
372y ARG* 1.3 81.6 - - - +
374y THR* 1.4 64.9 + - + +
376y VAL* 4.1 3.3 - - + +
377y GLY* 3.3 15.4 + - - -
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Residues in contact with THR 374 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272y ALA* 3.8 20.5 - - + +
329y CYS* 5.4 2.5 - - - +
330y PHE* 3.8 13.6 - - - -
333y THR* 3.2 44.5 + - + -
370y MET* 3.4 28.9 + - - +
371y THR* 3.6 4.3 + - - -
373y LEU* 1.4 80.4 - - + +
375y LEU* 1.4 61.0 + - - +
377y GLY* 3.4 1.0 + - - -
378y ALA* 2.9 30.1 + - - +
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Residues in contact with LEU 375 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E VAL* 3.9 16.2 - - + -
83E ILE* 3.8 24.5 - - + -
326y ILE* 4.4 20.4 - - + +
330y PHE* 4.4 26.5 - - + -
371y THR* 3.3 19.9 + - + +
372y ARG* 4.0 4.3 - - - +
373y LEU 3.3 0.2 - - - -
374y THR* 1.4 80.9 + - - +
376y VAL* 1.4 56.6 + - - +
378y ALA* 3.5 5.4 + - - +
379y LEU* 3.1 34.7 + - + +
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Residues in contact with VAL 376 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E ILE* 3.6 33.7 - - + -
86E THR* 5.5 3.6 - - - +
87E ARG* 6.0 8.7 - - + -
89E GLU* 5.1 9.9 - - - +
237y VAL* 5.0 5.8 - - + -
372y ARG* 3.1 19.2 + - + +
373y LEU* 4.3 3.8 - - - +
375y LEU* 1.4 74.6 - - - +
377y GLY* 1.3 61.0 + - - +
379y LEU* 3.4 17.6 + - + +
380y TYR* 3.4 44.7 + - + +
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Residues in contact with GLY 377 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237y VAL* 5.6 6.4 - - - +
272y ALA* 4.2 22.8 - - - +
273y GLY* 5.5 0.2 - - - -
373y LEU 3.3 14.8 + - - -
374y THR 3.4 3.1 + - - -
375y LEU 3.4 0.2 - - - -
376y VAL* 1.3 75.7 - - - +
378y ALA* 1.3 58.6 + - - +
380y TYR* 3.5 17.4 + - - +
381y ILE* 3.4 22.6 + - - +
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Residues in contact with ALA 378 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273y GLY* 5.8 0.6 - - - -
325y ILE* 4.9 1.4 - - - +
326y ILE* 4.0 35.0 - - + +
329y CYS* 4.2 22.9 - - + -
330y PHE* 5.2 2.2 - - + +
374y THR 2.9 18.9 + - - +
375y LEU* 3.6 8.1 - - + +
377y GLY* 1.3 73.5 - - - +
379y LEU* 1.4 63.0 + - - +
381y ILE* 3.6 24.0 + - - +
382y THR* 3.6 5.4 + - - -
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Residues in contact with LEU 379 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E ILE* 5.5 5.6 - - + -
326y ILE* 4.8 18.6 - - + +
375y LEU* 3.1 27.8 + - + +
376y VAL* 3.4 27.8 + - + +
378y ALA* 1.4 75.0 - - - +
380y TYR* 1.4 62.5 + - + +
382y THR* 3.2 16.0 + - - -
383y PHE* 3.1 43.6 + - + -
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Residues in contact with TYR 380 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E ARG* 5.0 14.6 + - - +
88E GLN 5.8 0.3 + - - -
89E GLU 5.6 1.6 + - - -
233y PHE* 5.3 17.5 - + + -
236y PHE* 6.5 0.9 - - + -
237y VAL* 3.6 42.4 - - + +
376y VAL* 3.4 33.2 + - + +
377y GLY* 3.8 9.6 - - - +
378y ALA 3.3 1.0 - - - -
379y LEU* 1.4 77.2 - - + +
381y ILE* 1.4 51.7 + - + +
383y PHE* 3.2 21.5 + + + +
384y ILE* 2.9 48.2 + - + +
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Residues in contact with ILE 381 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272y ALA 5.3 0.4 - - - +
273y GLY* 4.3 14.8 - - - +
277y ALA* 3.8 27.4 - - + -
325y ILE* 4.0 22.2 - - + -
329y CYS* 4.5 8.5 - - - -
377y GLY 3.4 18.2 - - - +
378y ALA* 3.6 16.8 - - - +
379y LEU 3.2 0.2 - - - -
380y TYR* 1.4 72.9 - - + +
382y THR* 1.4 62.3 + - - +
384y ILE* 3.3 19.3 + - + +
385y CYS* 3.5 19.8 + - - -
407y LEU* 4.5 26.0 - - + -
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Residues in contact with THR 382 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322y ALA* 3.7 31.2 + - + +
325y ILE* 4.3 6.7 - - - +
326y ILE* 3.6 30.6 - - + +
378y ALA 3.6 3.0 + - - -
379y LEU* 3.2 10.9 + - - -
381y ILE* 1.4 75.0 - - - +
383y PHE* 1.4 68.8 - - + +
385y CYS* 3.2 25.0 + - + +
386y LEU* 3.4 21.1 + - + +
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Residues in contact with PHE 383 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379y LEU* 3.1 50.9 + - + -
380y TYR* 3.2 24.7 + + + +
382y THR* 1.4 62.7 - - + +
384y ILE* 1.4 66.6 + - + +
386y LEU* 3.1 26.6 + - + +
387y ILE* 3.3 24.6 + - + +
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Residues in contact with ILE 384 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230y VAL* 3.7 44.9 - - + +
233y PHE* 4.5 16.2 - - + -
234y VAL* 4.7 15.5 - - + -
380y TYR* 2.9 32.3 + - + +
381y ILE* 3.6 12.1 - - + +
382y THR 3.2 0.4 - - - -
383y PHE* 1.4 77.0 - - + +
385y CYS* 1.4 58.3 + - - +
387y ILE* 3.4 8.9 + - + +
388y PRO* 2.9 28.4 - - - +
403y GLY* 4.3 21.5 - - - +
407y LEU* 4.8 15.0 - - + -
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Residues in contact with CYS 385 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318y VAL* 5.9 3.6 - - + -
321y TYR* 6.0 7.0 - - - -
325y ILE* 6.4 0.9 - - - -
381y ILE* 3.6 20.2 - - - -
382y THR* 3.2 13.4 + - + +
384y ILE* 1.4 78.4 - - - +
386y LEU* 1.4 63.6 + - + +
387y ILE 3.3 1.0 + - - -
388y PRO* 3.5 10.3 - - - +
389y GLU* 3.4 22.7 - - - +
403y GLY* 4.9 19.2 - - - -
404y THR* 5.5 4.5 - - - -
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Residues in contact with LEU 386 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318y VAL* 3.9 19.3 - - + -
319y LEU* 6.2 1.8 - - + -
382y THR* 3.4 24.4 + - + +
383y PHE* 3.1 21.9 + - + +
385y CYS* 1.4 79.0 - - + +
387y ILE* 1.4 52.0 + - + +
389y GLU* 3.1 26.8 + - + +
390y PHE* 2.8 65.2 + - + -
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Residues in contact with ILE 387 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226y LEU* 4.0 15.7 - - + +
229y ALA* 5.8 4.3 - - + -
230y VAL* 5.4 6.1 - - + -
233y PHE* 3.7 33.2 - - + -
383y PHE* 3.3 24.0 + - + +
384y ILE* 3.5 12.3 - - + +
385y CYS 3.2 0.8 - - - -
386y LEU* 1.4 73.2 - - + +
388y PRO* 1.4 71.9 - - + +
390y PHE* 3.5 11.8 + - + +
391y MET* 3.2 34.1 + - + +
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Residues in contact with PRO 388 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226y LEU* 4.2 28.0 - - + -
230y VAL* 5.8 2.9 - - + -
384y ILE* 2.9 27.4 - - + +
385y CYS 3.5 8.1 - - - +
387y ILE* 1.4 80.5 - - + +
389y GLU* 1.3 57.7 + - + +
391y MET* 3.5 0.8 + - + +
392y ARG* 3.0 47.9 + - - +
402y GLY* 4.2 12.6 - - - +
403y GLY* 4.1 23.3 - - - +
406y LEU* 5.8 2.2 - - + -
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Residues in contact with GLU 389 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315y PRO* 4.3 12.0 - - - +
318y VAL* 3.8 28.2 - - - +
385y CYS* 3.4 21.3 - - - +
386y LEU* 3.1 33.2 + - + +
388y PRO* 1.3 73.9 - - + +
390y PHE* 1.3 65.4 + - + +
392y ARG* 3.6 23.2 + - - +
393y ASP* 2.9 34.5 + - - +
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Residues in contact with PHE 390 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386y LEU* 2.8 48.7 + - + +
387y ILE* 3.8 12.3 - - + +
388y PRO 3.3 0.2 - - - -
389y GLU* 1.3 78.0 - - + +
391y MET* 1.4 69.2 + - + +
392y ARG 3.2 4.4 + - - -
393y ASP* 3.7 20.5 + - - +
394y ALA* 5.8 0.2 - - - +
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Residues in contact with MET 391 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226y LEU* 4.9 12.8 - - + -
387y ILE* 3.2 26.4 + - + +
388y PRO* 3.5 2.2 + - + +
390y PHE* 1.4 83.8 - - + +
392y ARG* 1.4 62.1 + - + +
393y ASP 3.4 0.6 + - - -
394y ALA* 4.3 2.2 + - - +
395y MET* 3.9 38.3 + - + +
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Residues in contact with ARG 392 (chain y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226y LEU* 5.4 7.4 - - + -
388y PRO* 3.0 36.2 + - + +
389y GLU* 3.9 29.7 - - - +
390y PHE 3.2 0.4 - - - -
391y MET* 1.4 79.6 - - + +
393y ASP* 1.4 57.6 - - - +
394y ALA 3.1 11.1 + - - -
395y MET 4.1 3.1 - - - +
396y LYS 2.9 25.9 - - - +
397y VAL* 4.2 24.4 + - + +
398y PRO* 3.6 49.0 + - + -
399y PHE* 5.3 7.7 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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