Contacts of the helix formed by residues 329 - 353 (chain A) in PDB entry 4OG2
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 PRO 329 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU* 3.3 39.0 - - + +
283A ASN 5.4 3.4 - - - +
284A THR* 6.0 0.9 - - - -
285A SER 6.2 0.2 - - - +
304A TYR* 4.2 1.6 - - - -
320A TYR* 3.2 27.8 - - + +
326A LYS* 4.6 8.3 - - - +
327A GLU 3.5 5.2 - - - +
328A PRO* 1.3 88.4 - - + +
330A GLN* 1.3 66.7 + - - +
331A PHE 4.3 0.4 - - - +
332A SER* 3.0 22.5 + - - +
333A ALA* 3.2 10.9 + - - +
412A PHE* 6.6 0.4 - - + -
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Residues in contact with GLN 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A THR* 6.3 0.2 - - - +
176A VAL* 5.6 1.6 - - - +
280A ASP* 2.9 28.1 + - - +
283A ASN* 3.3 21.0 + - - +
301A ALA 4.1 0.3 - - - +
302A GLN* 3.4 21.4 + - - +
303A ALA* 2.8 28.4 + - - +
304A TYR* 4.0 28.4 - - + -
328A PRO 4.0 0.6 + - - -
329A PRO* 1.3 72.1 - - - +
331A PHE* 1.3 77.6 + - + +
333A ALA* 3.1 3.3 + - - +
334A GLN* 2.9 52.0 + - - +
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Residues in contact with PHE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 3.7 29.4 - - + -
73A GLU* 3.5 30.6 + - + +
74A GLN* 3.9 21.0 - - + +
153A SER* 3.4 21.0 + - - -
280A ASP* 3.3 39.5 - - - -
283A ASN* 3.3 22.9 - - + -
329A PRO 3.2 1.2 + - - -
330A GLN* 1.3 93.8 - - - +
332A SER* 1.3 62.7 + - - +
334A GLN* 3.5 7.8 - - - +
335A ALA* 3.1 23.9 + - - +
501A LEU* 3.5 22.2 - - + -
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Residues in contact with SER 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU* 2.7 32.3 + - - +
76A ALA* 4.3 0.9 - - - +
77A GLY* 3.3 18.5 + - - -
316A PHE* 3.8 8.7 - - - -
320A TYR* 3.7 17.0 + - - -
329A PRO* 3.0 29.3 + - - +
331A PHE* 1.3 76.4 - - - +
333A ALA* 1.3 65.3 + - - +
335A ALA 3.4 0.9 + - - -
336A PHE* 3.0 20.8 + - - +
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A TYR* 3.5 49.1 - - + -
316A PHE* 3.6 19.2 - - + -
329A PRO 3.2 2.2 + - - -
330A GLN 3.1 5.4 + - - +
332A SER* 1.3 77.8 - - - +
334A GLN* 1.3 57.6 + - - +
336A PHE* 3.3 4.2 + - - +
337A ALA* 2.9 28.6 + - - +
379A PRO* 4.2 5.9 - - + +
380A LEU* 3.9 7.7 - - + +
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Residues in contact with GLN 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PRO* 3.2 21.3 - - - +
153A SER* 2.9 25.3 + - - +
155A THR* 5.5 2.4 - - - +
169A VAL* 3.6 8.6 + - - +
170A SER* 3.6 24.4 - - - +
171A ALA 4.8 0.6 + - - +
303A ALA* 3.9 24.2 - - - +
330A GLN* 2.9 38.3 + - + +
331A PHE* 3.5 5.7 - - - +
333A ALA* 1.3 75.2 - - - +
335A ALA* 1.3 65.1 + - - +
337A ALA* 3.3 3.5 + - - +
338A ALA* 3.0 19.6 + - - +
380A LEU* 3.8 26.3 - - + +
393A GLN* 5.7 0.4 + - - -
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Residues in contact with ALA 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 5.4 1.8 - - + -
74A GLN* 3.1 38.1 - - + +
78A ALA* 4.0 9.0 - - + +
127A VAL* 4.9 3.7 - - + +
152A PRO* 3.9 14.0 - - + +
331A PHE 3.1 17.4 + - - +
332A SER 3.8 3.4 - - - +
334A GLN* 1.3 73.5 - - - +
336A PHE* 1.3 64.6 + - - +
338A ALA* 3.2 3.6 + - - +
339A VAL* 3.1 26.7 + - - +
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Residues in contact with PHE 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLY 3.8 10.2 + - - +
80A ILE* 4.1 4.0 - - + -
81A ALA* 3.5 36.9 - - + +
84A TYR* 3.8 26.0 - + + -
85A PHE* 3.8 18.6 - + - -
312A ILE* 3.7 19.3 - - + -
316A PHE* 3.5 36.6 - + + -
332A SER 3.0 15.1 + - - +
333A ALA* 3.5 8.1 - - - +
334A GLN 3.3 0.2 - - - -
335A ALA* 1.3 75.9 - - - +
337A ALA* 1.3 56.3 + - - +
339A VAL* 3.2 4.5 + - - +
340A GLN* 2.9 43.2 + - - -
379A PRO* 3.5 20.6 - - + -
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A VAL* 4.4 7.0 - - + -
333A ALA 2.9 17.2 + - - +
334A GLN 3.5 5.8 - - - +
335A ALA 3.3 0.2 - - - -
336A PHE* 1.3 79.5 - - - +
338A ALA* 1.3 56.8 + - - +
340A GLN* 3.3 10.9 + - - +
341A VAL* 2.9 34.6 + - - +
378A THR* 4.0 17.3 - - + +
379A PRO* 4.6 0.7 - - + -
380A LEU* 3.7 27.1 - - + -
383A ILE* 4.7 1.3 - - + -
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Residues in contact with ALA 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 3.7 26.7 - - + -
150A VAL* 3.9 25.9 - - + +
152A PRO* 4.3 6.3 - - + -
169A VAL* 4.1 8.9 - - + +
334A GLN 3.0 13.8 + - - +
335A ALA 3.6 7.6 - - - +
336A PHE 3.2 0.4 - - - -
337A ALA* 1.3 77.2 - - - +
339A VAL* 1.3 62.8 + - - +
341A VAL* 3.3 5.9 + - - +
342A TYR* 3.3 24.8 + - - -
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Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 5.3 2.2 - - + -
59A ILE* 4.2 17.9 - - + -
78A ALA* 4.2 24.7 - - + -
81A ALA* 3.7 19.5 - - + -
82A GLU 4.7 0.7 - - - +
85A PHE* 4.4 1.8 - - + -
96A ILE* 4.2 25.1 - - + -
98A LEU* 4.4 9.9 - - + -
127A VAL* 4.4 8.7 - - + -
335A ALA 3.1 14.4 + - - +
336A PHE 3.7 6.5 - - - +
338A ALA* 1.3 74.2 - - - +
340A GLN* 1.3 64.3 + - - +
342A TYR* 3.1 7.9 + - - +
343A VAL* 2.9 24.8 + - + +
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Residues in contact with GLN 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 3.4 26.6 - - + -
312A ILE* 3.6 20.8 - - - +
336A PHE* 2.9 13.7 + - + +
337A ALA 3.3 8.7 + - - +
339A VAL* 1.3 76.7 - - - +
341A VAL* 1.3 62.8 + - - +
343A VAL* 4.4 0.4 - - - +
344A GLU* 2.9 55.6 + - - +
376A TYR* 4.6 1.3 - - + +
377A ASN 2.9 27.5 + - - +
378A THR* 3.3 32.2 - - + +
379A PRO* 3.6 6.6 - - - +
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Residues in contact with VAL 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL* 4.5 9.9 - - + -
169A VAL* 4.0 20.4 - - + -
337A ALA 2.9 17.6 + - - +
338A ALA* 3.6 9.4 - - - +
339A VAL 3.2 0.2 - - - -
340A GLN* 1.3 74.9 - - - +
342A TYR* 1.3 63.8 + - - +
345A SER* 2.8 31.0 + - - -
371A LEU* 4.0 16.4 - - + -
376A TYR* 3.8 48.0 - - + +
378A THR* 5.4 0.4 - - + -
383A ILE* 4.7 3.8 - - + -
385A PHE* 4.0 18.4 - - + -
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Residues in contact with TYR 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 4.0 27.1 - - + -
124A VAL* 5.5 0.9 - - + -
125A GLY* 3.9 8.5 - - - -
126A ILE 2.8 37.3 + - - -
127A VAL* 3.6 20.0 - - + -
148A PRO* 3.0 26.4 + - + +
150A VAL* 3.5 19.3 + - + +
338A ALA 3.3 16.2 + - - -
339A VAL* 3.1 7.9 + - - +
341A VAL* 1.3 80.0 - - - +
343A VAL* 1.3 58.6 + - - +
345A SER* 3.8 1.9 - - - -
346A LEU* 2.8 37.6 + - + +
367A LEU* 3.9 29.8 - - + -
371A LEU* 3.8 21.8 - - + -
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Residues in contact with VAL 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 4.8 2.0 - - + -
85A PHE* 3.8 41.5 - - + -
90A GLY 4.0 24.5 - - - +
91A VAL* 4.3 2.4 - - + +
96A ILE* 3.8 35.4 - - + -
339A VAL* 2.9 20.6 + - + +
340A GLN 3.9 3.1 - - - +
342A TYR* 1.3 75.5 - - - +
344A GLU* 1.3 60.3 + - + +
346A LEU* 3.3 7.5 + - - +
347A LYS* 2.9 35.3 + - + +
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Residues in contact with GLU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 4.2 14.1 - - + -
312A ILE* 5.1 1.0 - - - +
340A GLN* 2.9 48.3 + - + +
343A VAL* 1.3 78.8 - - + +
345A SER* 1.3 57.3 + - - +
347A LYS* 3.4 17.6 + - + +
348A ALA* 3.0 27.2 + - - +
375A LYS 4.5 3.1 - - - +
376A TYR* 3.5 32.5 - - + +
377A ASN 4.8 0.9 + - - -
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Residues in contact with SER 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A VAL 2.8 23.1 + - - -
342A TYR* 3.8 0.4 - - - -
344A GLU* 1.3 74.8 - - - +
346A LEU* 1.3 59.8 + - - +
348A ALA* 3.3 1.6 + - - -
349A LEU* 2.9 30.8 + - - +
367A LEU* 3.8 14.8 - - - -
370A GLN* 3.4 15.9 + - - +
371A LEU* 3.1 24.9 - - - +
376A TYR* 2.8 23.7 + - - -
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 3.9 34.1 - - + -
57A ILE* 4.0 20.6 - - + -
91A VAL* 3.6 26.6 - - + +
96A ILE* 4.8 0.2 - - + -
124A VAL* 4.4 8.7 - - + -
342A TYR* 2.8 24.3 + - + +
343A VAL* 3.6 1.1 - - - +
345A SER* 1.3 75.6 - - - +
347A LYS* 1.3 57.2 + - - +
349A LEU* 3.8 3.2 - - + +
350A ASP* 2.8 32.7 + - - +
355A VAL* 4.4 10.0 - - + +
363A LEU* 4.6 17.3 - - + -
367A LEU* 3.8 26.5 - - + -
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Residues in contact with LYS 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLY 3.8 14.1 - - - +
91A VAL* 3.9 24.7 - - - -
92A ASN* 3.3 23.7 + - - +
343A VAL* 2.9 26.1 + - + +
344A GLU* 3.6 18.4 - - + +
346A LEU* 1.3 76.8 - - - +
348A ALA* 1.3 62.0 + - - +
351A THR* 3.0 29.3 + - - -
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Residues in contact with ALA 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLU 3.0 16.6 + - - +
345A SER* 3.8 1.6 - - - +
347A LYS* 1.3 77.4 - - - +
349A LEU* 1.3 64.1 + - - +
351A THR* 3.5 5.1 + - - -
352A LYS* 3.4 30.3 + - - +
370A GLN* 3.5 26.7 - - + +
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A SER 2.9 17.9 + - - +
346A LEU* 3.8 4.9 - - + +
348A ALA* 1.3 78.1 - - - +
350A ASP* 1.3 51.4 + - - +
352A LYS* 3.0 9.1 + - + +
353A ASN* 2.7 53.5 + - + +
355A VAL* 3.9 9.9 - - + -
358A ILE* 4.5 3.4 - - + -
363A LEU* 3.6 30.3 - - + -
366A GLU* 4.0 26.9 - - + +
367A LEU* 3.9 27.8 - - + +
370A GLN* 4.1 14.9 + - + +
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Residues in contact with ASP 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 4.0 10.1 - - + +
92A ASN* 2.8 32.0 + - - +
346A LEU 2.8 22.4 + - - +
349A LEU* 1.3 73.6 - - - +
351A THR* 1.3 62.6 + - - +
352A LYS 3.4 0.2 + - - -
353A ASN 3.6 6.7 - - - -
354A LYS* 2.9 51.0 + - - +
355A VAL* 2.8 43.2 + - + +
356A SER 4.5 0.5 + - - -
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Residues in contact with THR 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASN* 3.4 14.6 + - - +
347A LYS 3.0 18.2 + - - -
348A ALA* 3.8 7.8 - - - +
349A LEU 3.2 0.4 - - - -
350A ASP* 1.3 76.5 - - - +
352A LYS* 1.3 63.5 + - + +
354A LYS* 4.8 8.3 + - - +
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Residues in contact with LYS 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ALA* 3.4 16.7 + - - +
349A LEU* 3.0 9.9 + - + +
351A THR* 1.3 82.7 - - + +
353A ASN* 1.3 63.1 + - + +
354A LYS 4.3 0.2 - - - -
370A GLN* 2.8 32.9 + - - +
373A THR* 5.6 0.6 + - - -
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Residues in contact with ASN 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 2.7 31.7 + - + +
350A ASP* 3.5 3.9 + - - -
351A THR 3.9 0.2 + - - -
352A LYS* 1.3 79.2 - - + +
354A LYS* 1.3 70.1 + - - +
355A VAL* 3.1 3.8 + - - +
358A ILE* 3.5 33.2 - - - +
362A GLU* 5.4 5.5 + - - -
366A GLU* 4.9 11.5 + - - +
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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