Contacts of the helix formed by residues 321 - 350 (chain B) in PDB entry 1AM9
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 ARG 321 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B SER* 1.3 81.1 - - - +
322B GLY* 1.3 53.1 + - - +
324B LYS* 3.2 5.4 - - - +
325B ARG* 2.8 35.4 + - - +
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Residues in contact with GLY 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B SER* 3.9 2.3 - - - +
321B ARG* 1.3 81.2 - - - +
323B GLU* 1.3 55.8 + - - +
325B ARG* 2.9 11.6 + - - +
326B THR* 2.8 32.9 + - - -
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Residues in contact with GLU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B SER* 2.7 43.9 + - - +
322B GLY* 1.3 73.8 - - - +
324B LYS* 1.3 63.7 + - - +
326B THR* 3.4 7.5 + - - -
327B ALA* 3.0 24.8 + - - +
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Residues in contact with LYS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B SER 2.7 24.6 + - - +
321B ARG* 3.2 6.1 - - - +
323B GLU* 1.3 74.7 - - - +
325B ARG* 1.3 55.1 + - - +
327B ALA* 3.3 7.3 + - - +
328B HIS* 2.8 31.1 + - - +
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Residues in contact with ARG 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ARG 2.8 17.4 + - - +
322B GLY* 3.1 13.0 - - - +
324B LYS* 1.3 75.4 - - - +
326B THR* 1.3 51.6 - - - +
328B HIS* 3.0 20.4 + - - +
329B ASN* 2.5 68.3 + - - +
332B GLU* 2.6 30.3 + - - -
30F C 2.7 85.3 + - - +
31F C 3.9 15.1 + - - +
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Residues in contact with THR 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B GLY 2.8 17.6 + - - -
323B GLU* 3.7 10.3 - - - -
325B ARG* 1.3 71.9 - - - +
327B ALA* 1.3 64.7 + - - +
329B ASN* 3.2 14.2 + - + +
330B ALA* 3.1 19.9 + - - +
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B GLU 3.0 15.3 + - - +
324B LYS* 3.5 6.1 - - - +
326B THR* 1.3 79.5 - - - +
328B HIS* 1.3 63.4 + - - +
330B ALA* 2.9 19.9 + - - +
331B ILE* 3.2 17.6 + - + +
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Residues in contact with HIS 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LYS 2.8 20.5 + - - +
325B ARG* 3.7 13.6 + - - +
327B ALA* 1.3 73.7 - - - +
329B ASN* 1.3 50.8 + - - +
331B ILE* 2.7 24.7 + - + +
332B GLU* 2.7 62.9 + - + +
31F C 4.3 0.2 + - - -
32F A 3.7 5.6 + - - -
43G A 4.1 11.2 - + - -
44G G 2.9 37.6 + - - -
45G T 2.7 29.8 - - + -
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Residues in contact with ASN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ARG* 2.5 48.1 + - - +
326B THR* 3.3 15.5 - - + +
327B ALA 3.1 0.2 - - - -
328B HIS* 1.3 72.7 - - - +
330B ALA* 1.3 61.8 + - - +
332B GLU* 3.2 14.3 + - - +
333B LYS* 3.0 23.0 + - - +
336B ARG* 4.7 0.9 + - - -
29F C 3.4 42.5 + - - +
30F C 2.9 19.8 + - - -
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B THR 3.1 9.3 + - - +
327B ALA* 2.9 13.0 + - - +
329B ASN* 1.3 77.2 - - - +
331B ILE* 1.3 62.2 + - + +
333B LYS* 3.4 7.5 + - - +
334B ARG* 3.2 34.3 + - - +
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Residues in contact with ILE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ALA* 3.2 15.9 + - + +
328B HIS* 2.7 27.6 + - + +
330B ALA* 1.3 78.4 - - + +
332B GLU* 1.3 55.1 + - - +
334B ARG* 3.2 32.9 + - - +
335B TYR* 3.0 24.8 + - - +
43G A 3.5 48.5 - - + +
44G G 3.5 41.1 + - + +
45G T 4.2 4.0 - - + -
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Residues in contact with GLU 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ARG* 2.6 28.6 + - - -
328B HIS* 2.7 33.9 + - + +
329B ASN* 3.2 15.6 + - - +
331B ILE* 1.3 71.0 - - - +
333B LYS* 1.3 59.4 + - - +
335B TYR* 3.3 10.3 + - + +
336B ARG* 2.9 44.6 + - + +
29F C 4.0 7.4 + - - -
30F C 3.1 31.0 + - - +
31F C 2.7 16.9 + - - -
45G T 4.0 9.6 - - + +
46G G 4.3 2.0 - - - +
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Residues in contact with LYS 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ASN 3.0 15.3 + - - +
330B ALA* 3.8 8.1 - - - +
331B ILE 3.3 0.2 - - - -
332B GLU* 1.3 72.8 - - - +
334B ARG* 1.3 62.6 + - - +
336B ARG* 3.3 17.5 + - + +
337B SER* 2.8 42.5 + - - +
28F C 3.5 38.9 + - - +
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Residues in contact with ARG 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ALA* 3.2 21.3 + - - +
331B ILE* 3.2 36.6 + - - +
333B LYS* 1.3 78.1 - - - +
335B TYR* 1.3 57.6 + - - +
337B SER* 3.3 7.6 + - - -
338B SER* 2.9 26.9 + - - -
43G A 3.9 6.3 + - - -
44G G 2.4 44.2 + - - +
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Residues in contact with TYR 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A LYS* 4.1 2.8 + - - +
360A SER* 5.6 1.6 - - - -
331B ILE 3.0 12.7 + - - +
332B GLU* 3.4 12.1 - - + +
334B ARG* 1.3 74.9 - - - +
336B ARG* 1.3 76.2 + - + +
338B SER* 2.4 33.5 + - - -
339B ILE* 3.4 27.0 + - + +
44G G 4.9 3.4 - - + -
45G T 3.1 67.1 - + + +
46G G 2.7 58.2 + + - +
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Residues in contact with ARG 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ASN 4.7 1.4 + - - -
332B GLU* 2.9 46.4 + - + +
333B LYS* 3.6 24.8 - - + +
335B TYR* 1.3 86.0 - - + +
337B SER* 1.3 58.7 + - - +
339B ILE* 3.1 9.0 + - - +
340B ASN* 2.8 43.6 + - - +
27F A 4.2 5.9 - - - +
28F C 3.1 85.4 + - - +
29F C 3.9 16.1 + - - +
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Residues in contact with SER 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LYS* 2.8 29.7 + - - +
334B ARG* 3.4 8.5 - - - -
336B ARG* 1.3 79.4 - - - +
338B SER* 1.3 56.3 + - - +
340B ASN* 4.2 8.6 + - - +
341B ASP* 2.9 48.9 + - - +
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Residues in contact with SER 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A SER* 3.1 22.9 + - - -
334B ARG 2.9 11.3 + - - -
335B TYR* 2.4 33.8 + - - -
337B SER* 1.3 75.5 - - - +
339B ILE* 1.3 59.4 + - - +
341B ASP* 5.3 0.4 - - - -
342B LYS* 2.7 40.6 + - - +
45G T 4.4 7.3 + - - -
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Residues in contact with ILE 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ILE* 6.1 0.4 - - + -
343A ILE* 4.6 10.1 - - + -
359A LYS* 3.8 29.8 - - + -
360A SER* 4.1 7.6 - - - +
363A LEU* 3.6 21.7 - - + +
335B TYR* 3.6 39.7 - - + +
336B ARG* 3.1 8.4 + - - +
337B SER 3.1 0.2 - - - -
338B SER* 1.3 87.2 + - - +
340B ASN* 1.3 70.3 + - - +
342B LYS* 2.9 16.8 + - - +
343B ILE* 3.1 23.8 + - + +
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Residues in contact with ASN 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ARG* 2.8 33.3 + - - +
337B SER* 4.2 6.8 + - - +
339B ILE* 1.3 80.2 - - - +
341B ASP* 1.3 63.5 + - - +
343B ILE* 3.2 11.5 + - - +
344B ILE* 3.1 31.6 + - + +
359B LYS* 3.1 28.8 + - - +
27F A 3.3 27.2 + - - +
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Residues in contact with ASP 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B SER* 2.9 37.8 + - - +
338B SER* 5.2 1.3 - - - -
340B ASN* 1.3 74.1 - - - +
342B LYS* 1.3 65.9 + - + +
344B ILE* 3.5 17.6 + - - +
345B GLU* 3.1 28.1 + - - +
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Residues in contact with LYS 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A SER* 3.4 30.0 - - - +
363A LEU* 3.5 20.6 - - + -
364A ARG* 3.7 40.6 - - - +
367A ILE* 3.5 11.6 - - + +
338B SER* 2.7 40.9 + - - +
339B ILE* 2.9 6.9 + - - +
341B ASP* 1.3 81.7 - - + +
343B ILE* 1.3 61.1 + - - +
345B GLU* 3.1 8.0 + - - +
346B LEU* 2.8 28.9 + - - +
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Residues in contact with ILE 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ILE* 5.0 5.6 - - + -
343A ILE* 5.2 0.4 - - + -
363A LEU* 3.7 13.7 - - + -
339B ILE* 3.1 28.8 + - + +
340B ASN* 3.2 11.4 + - - +
342B LYS* 1.3 76.9 - - - +
344B ILE* 1.3 54.3 + - + +
346B LEU* 3.2 6.2 + - - -
347B LYS* 2.7 35.5 + - - +
359B LYS* 4.1 44.9 - - + +
362B VAL* 3.4 26.0 - - + +
363B LEU* 4.3 20.6 - - + -
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Residues in contact with ILE 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ASN* 3.1 22.8 + - + +
341B ASP* 3.6 19.1 - - - +
342B LYS 3.1 0.2 - - - -
343B ILE* 1.3 77.9 - - + +
345B GLU* 1.3 58.0 + - + +
347B LYS* 3.2 13.3 + - + +
348B ASP* 2.9 42.0 + - - +
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Residues in contact with GLU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ARG* 3.1 37.2 + - - -
367A ILE* 3.4 20.9 - - + +
341B ASP* 3.1 20.1 + - - +
342B LYS* 3.1 13.4 + - - +
344B ILE* 1.3 76.1 - - + +
346B LEU* 1.3 66.5 + - - +
348B ASP* 3.4 9.5 + - - +
349B LEU* 3.1 24.5 + - - +
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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
----------------------------------------------------------
346A LEU* 4.2 4.5 - - + -
363A LEU* 3.9 17.9 - - + -
366A ALA* 4.0 5.4 - - + -
367A ILE* 3.7 31.2 - - + +
370A ILE* 3.7 29.6 - - + -
342B LYS 2.8 12.8 + - - +
343B ILE* 3.5 9.6 - - - +
345B GLU* 1.3 76.2 - - - +
347B LYS* 1.3 58.9 + - - +
349B LEU* 3.1 9.0 - - + +
350B VAL* 3.0 29.6 + - - +
362B VAL* 3.8 7.6 - - + -
363B LEU* 3.7 29.4 - - + -
366B ALA* 3.9 16.8 - - + -
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Residues in contact with LYS 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ILE* 2.7 18.2 + - + +
344B ILE* 3.4 13.0 - - + +
346B LEU* 1.3 73.1 - - - +
348B ASP* 1.3 66.8 + - - +
349B LEU 3.1 1.3 - - - -
350B VAL* 4.1 3.6 - - - -
351B VAL* 2.8 48.8 + - + +
352B GLY 2.9 28.7 + - - +
353B THR* 3.3 13.1 + - - +
355B ALA 2.6 32.0 + - - -
356B LYS* 4.4 1.3 - - - +
357B LEU* 4.5 12.8 - - + +
362B VAL* 3.4 30.2 - - + +
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Residues in contact with ASP 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ILE* 2.9 31.9 + - - +
345B GLU* 3.4 9.5 + - - +
347B LYS* 1.3 83.8 + - - +
349B LEU* 1.3 57.8 + - - +
352B GLY* 3.1 32.8 + - - +
353B THR* 3.4 27.0 + - - +
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ILE* 3.8 34.3 - - + +
370A ILE* 3.7 33.0 - - + -
371A ARG* 3.1 45.1 - - + +
374A GLN* 3.8 12.6 + - - +
345B GLU 3.1 11.6 + - - +
346B LEU* 3.1 12.1 - - - +
348B ASP* 1.3 80.2 - - - +
350B VAL* 1.3 64.1 + - + +
352B GLY 4.6 0.2 - - - -
369B TYR* 4.8 7.8 - - - -
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ILE* 4.7 3.4 - - + -
346B LEU 3.0 19.3 + - - +
347B LYS* 3.2 9.8 + - - +
349B LEU* 1.3 84.7 - - + +
351B VAL* 1.3 68.9 + - + +
362B VAL* 4.1 10.3 - - - +
365B LYS* 3.7 37.9 + - + +
366B ALA* 4.1 26.0 - - + +
369B TYR* 4.2 21.5 - - + -
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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