Contacts of the helix formed by residues 321 - 350 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D GLN 3.7 0.8 + - - -
320D SER* 1.3 69.7 - - - +
322D GLY* 1.3 53.0 + - - +
324D LYS* 2.6 14.1 + - - +
325D ARG* 2.6 40.6 + - + +
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Residues in contact with GLY 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D SER* 3.2 3.1 - - - -
321D ARG* 1.3 79.5 - - - +
323D GLU* 1.3 55.2 + - - +
325D ARG* 3.6 10.8 - - - +
326D THR* 2.9 35.0 + - - -
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Residues in contact with GLU 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D GLN* 3.0 26.4 + - - +
320D SER* 2.9 33.3 + - - +
322D GLY* 1.3 76.3 - - - +
324D LYS* 1.3 57.8 + - - +
326D THR* 3.5 5.4 + - - -
327D ALA* 3.1 27.2 + - - +
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Residues in contact with LYS 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D GLN* 4.8 7.2 - - - +
320D SER 2.6 17.0 + - - +
321D ARG* 2.6 13.6 + - - +
323D GLU* 1.3 72.0 - - - +
325D ARG* 1.3 61.7 + - - -
327D ALA* 3.5 5.9 + - - +
328D HIS* 3.0 24.9 + - - +
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Residues in contact with ARG 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D ARG* 2.6 21.7 + - + +
322D GLY* 3.8 9.6 - - - +
324D LYS* 1.3 71.6 - - - +
326D THR* 1.3 53.5 + - - +
328D HIS* 3.2 18.8 + - - +
329D ASN* 2.6 70.6 + - - +
332D GLU* 2.8 25.5 + - - -
68H C 3.0 73.0 + - - +
69H C 3.6 21.7 + - - +
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Residues in contact with THR 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D GLY 2.9 18.1 + - - -
323D GLU* 3.7 6.7 - - - -
325D ARG* 1.3 78.1 - - - +
327D ALA* 1.3 62.8 + - - +
329D ASN* 3.1 14.9 + - + +
330D ALA* 3.1 20.4 + - - +
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Residues in contact with ALA 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D GLU 3.1 17.6 + - - +
324D LYS* 3.8 7.2 - - - +
325D ARG 3.3 0.2 - - - -
326D THR* 1.3 76.3 - - - +
328D HIS* 1.3 62.0 + - - +
330D ALA* 3.0 18.5 + - - +
331D ILE* 3.3 17.4 + - + +
5E A 6.0 1.3 - - - +
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Residues in contact with HIS 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D LYS 3.0 17.5 + - - +
325D ARG* 3.6 14.8 + - - +
327D ALA* 1.3 73.4 - - - +
329D ASN* 1.3 61.7 + - - +
331D ILE* 2.9 23.3 + - + +
332D GLU* 2.7 64.6 + - + +
5E A 4.0 12.3 + + - +
6E G 2.8 35.0 + - - -
7E T 2.6 31.6 - - + -
69H C 4.3 0.2 + - - -
70H A 3.7 5.6 + - - -
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Residues in contact with ASN 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D ARG* 2.6 45.7 + - - +
326D THR* 3.1 18.4 + - + +
328D HIS* 1.3 72.2 - - - +
330D ALA* 1.3 55.2 + - - +
332D GLU* 3.2 15.7 + - - +
333D LYS* 3.0 28.2 + - - +
336D ARG* 4.9 0.7 + - - -
67H C 3.3 43.2 + - - +
68H C 2.9 22.5 + - - -
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Residues in contact with ALA 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D THR 3.1 8.9 + - - +
327D ALA* 3.0 13.4 + - - +
329D ASN* 1.3 77.7 - - - +
331D ILE* 1.3 59.7 + - + +
333D LYS* 3.7 7.3 + - - +
334D ARG* 3.4 26.9 + - - +
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Residues in contact with ILE 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D ALA* 3.7 14.8 - - + +
328D HIS* 2.9 26.8 + - + +
330D ALA* 1.3 75.7 - - + +
332D GLU* 1.3 62.3 + - - +
334D ARG* 3.1 25.4 - - - +
335D TYR* 2.9 25.5 + - - +
5E A 3.4 65.3 - - + +
6E G 3.8 22.4 - - + +
7E T 4.1 2.7 - - + -
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Residues in contact with GLU 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D ARG* 2.8 12.2 + - - -
328D HIS* 2.7 42.9 + - + +
329D ASN* 3.3 18.9 - - - +
331D ILE* 1.3 74.5 - - - +
333D LYS* 1.3 59.9 + - - +
335D TYR* 3.2 9.1 + - + +
336D ARG* 2.7 46.0 + - + +
7E T 4.2 8.3 - - + +
8E G 4.5 1.6 - - - +
67H C 4.1 6.4 + - - -
68H C 3.3 20.5 + - - +
69H C 2.8 29.7 + - - -
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Residues in contact with LYS 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D ASN 3.0 14.7 + - - +
330D ALA* 3.7 8.0 + - - +
331D ILE 3.3 0.2 - - - -
332D GLU* 1.3 75.7 - - - +
334D ARG* 1.3 63.0 + - - +
336D ARG* 3.3 24.8 + - + +
337D SER* 2.9 38.9 + - - +
66H C 3.4 32.0 + - - +
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Residues in contact with ARG 334 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D ALA* 3.4 16.5 + - - +
331D ILE* 3.1 26.4 + - - +
333D LYS* 1.3 77.5 - - - +
335D TYR* 1.3 66.5 + - - +
337D SER* 3.1 5.9 + - - -
338D SER* 2.9 21.5 + - - -
5E A 5.5 0.8 - - - -
6E G 2.5 40.2 + - - -
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Residues in contact with TYR 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C LYS* 4.1 3.6 + - - +
360C SER* 5.6 1.6 - - - -
331D ILE 2.9 8.6 + - - +
332D GLU* 3.4 11.0 - - + +
334D ARG* 1.3 81.5 - - - +
336D ARG* 1.3 75.8 + - + +
338D SER* 2.6 31.2 + - - -
339D ILE* 3.5 26.7 + - + +
6E G 5.0 2.0 - - + -
7E T 3.0 64.8 - + + +
8E G 2.5 65.8 + + - +
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Residues in contact with ARG 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D ASN 4.9 0.8 + - - -
332D GLU* 2.7 42.1 + - + +
333D LYS* 3.4 27.2 - - + +
335D TYR* 1.3 87.2 - - + +
337D SER* 1.3 57.5 + - - +
339D ILE* 3.2 10.6 + - - +
340D ASN* 3.0 40.6 + - - +
65H A 4.3 6.1 - - - +
66H C 3.0 84.0 + - - +
67H C 4.0 14.8 + - - +
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Residues in contact with SER 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D LYS* 2.9 30.6 + - - +
334D ARG* 3.5 5.6 - - - -
336D ARG* 1.3 72.3 - - - +
338D SER* 1.3 61.3 + - - +
339D ILE 3.0 2.5 - - - -
340D ASN* 4.1 11.3 + - - +
341D ASP* 2.9 50.5 + - - -
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Residues in contact with SER 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C SER* 3.3 22.0 + - - -
334D ARG* 2.9 11.4 + - - -
335D TYR* 2.6 29.5 + - - -
337D SER* 1.3 77.9 - - - +
339D ILE* 1.3 60.7 + - - +
341D ASP* 4.5 0.9 - - - -
342D LYS* 2.6 45.1 + - - +
7E T 4.3 5.7 + - - -
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Residues in contact with ILE 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C ILE* 6.2 0.9 - - + -
343C ILE* 4.7 9.2 - - + -
359C LYS* 3.7 22.7 - - + +
360C SER* 4.1 14.4 - - - +
363C LEU* 3.6 20.1 - - + +
335D TYR* 3.6 39.0 - - + +
336D ARG* 3.2 8.3 + - - +
337D SER 3.0 0.2 - - - -
338D SER* 1.3 89.9 - - - +
340D ASN* 1.3 69.8 + - - +
341D ASP 3.3 0.2 - - - -
342D LYS* 3.0 14.9 + - - +
343D ILE* 3.0 25.3 + - + +
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Residues in contact with ASN 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D ARG* 3.0 34.1 + - - +
337D SER* 4.2 6.7 + - - +
339D ILE* 1.3 79.0 - - - +
341D ASP* 1.3 68.2 + - - +
343D ILE* 3.0 9.0 + - - +
344D ILE* 3.0 31.4 + - + +
359D LYS* 3.2 32.0 + - - +
65H A 3.6 21.3 + - - +
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Residues in contact with ASP 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D SER* 2.9 36.6 + - - +
338D SER* 4.8 3.0 - - - +
340D ASN* 1.3 77.6 - - - +
342D LYS* 1.3 62.1 + - + +
344D ILE* 3.6 17.2 - - - +
345D GLU* 3.3 29.6 + - - +
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Residues in contact with LYS 342 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C SER* 2.9 39.1 - - - +
363C LEU* 3.7 15.5 - - + -
364C ARG* 4.0 22.7 - - - +
367C ILE* 3.6 12.3 - - + +
337D SER 5.0 0.2 + - - -
338D SER* 2.6 35.1 + - - +
339D ILE 3.0 9.9 + - - +
341D ASP* 1.3 81.7 - - + +
343D ILE* 1.3 64.3 + - - +
344D ILE 3.2 0.2 - - - -
345D GLU* 3.2 20.4 + - - +
346D LEU* 3.0 22.1 + - - +
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Residues in contact with ILE 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C ILE* 4.9 6.3 - - + -
343C ILE* 5.3 0.9 - - + -
363C LEU* 3.7 14.4 - - + -
339D ILE* 3.0 27.8 + - + +
340D ASN* 3.0 10.7 + - - +
342D LYS* 1.3 76.7 - - - +
344D ILE* 1.3 52.5 + - + +
346D LEU* 3.1 6.4 + - - -
347D LYS* 2.7 31.6 + - - +
359D LYS* 4.1 44.4 - - + +
362D VAL* 3.3 29.8 - - + +
363D LEU* 4.2 20.4 - - + -
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Residues in contact with ILE 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D ASN* 3.0 22.9 + - + +
341D ASP* 3.6 20.9 - - - +
343D ILE* 1.3 78.3 - - + +
345D GLU* 1.3 57.1 + - + +
347D LYS* 3.2 12.8 + - + +
348D ASP* 3.0 43.5 + - - +
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Residues in contact with GLU 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C ARG* 2.9 41.9 + - - -
367C ILE* 3.4 24.3 - - + +
341D ASP* 3.3 14.0 + - - +
342D LYS* 3.2 12.6 + - - +
343D ILE 3.2 0.6 - - - -
344D ILE* 1.3 76.6 - - + +
346D LEU* 1.3 64.5 + - - +
348D ASP* 3.4 9.4 + - - +
349D LEU* 3.3 23.6 + - - +
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Residues in contact with LEU 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C LEU* 4.2 5.6 - - + -
363C LEU* 4.1 18.8 - - + -
366C ALA* 4.4 4.3 - - + -
367C ILE* 3.6 29.8 - - + +
370C ILE* 3.6 31.0 - - + -
342D LYS 3.0 13.5 + - - +
343D ILE* 3.4 8.5 - - - +
345D GLU* 1.3 76.0 - - - +
347D LYS* 1.3 63.5 + - - +
349D LEU* 3.1 8.3 + - + +
350D VAL* 3.1 25.1 + - - +
362D VAL* 3.6 10.1 - - + -
363D LEU* 4.0 27.4 - - + -
366D ALA* 3.9 16.8 - - + -
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Residues in contact with LYS 347 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D ILE* 2.7 14.4 + - + +
344D ILE* 3.4 17.2 - - + +
345D GLU 3.1 0.4 - - - -
346D LEU* 1.3 75.6 - - - +
348D ASP* 1.3 75.4 + - - +
350D VAL* 2.9 4.8 + - - -
351D VAL* 2.8 40.3 + - + -
352D GLY 2.7 27.8 + - - -
353D THR 3.7 9.3 + - - -
355D ALA 3.1 34.3 + - - -
356D LYS* 4.2 6.1 - - - +
357D LEU 4.2 9.0 - - - +
362D VAL* 3.4 26.7 - - + +
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Residues in contact with ASP 348 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D ILE* 3.0 33.1 + - - +
345D GLU* 3.8 8.1 - - - +
346D LEU 3.4 0.4 - - - -
347D LYS* 1.3 93.0 + - - +
349D LEU* 1.3 59.9 + - + +
352D GLY* 3.3 25.0 + - - -
353D THR* 3.6 24.2 + - - +
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Residues in contact with LEU 349 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C ILE* 3.8 31.9 - - + +
370C ILE* 3.7 36.6 - - + -
371C ARG* 3.1 48.2 - - + +
374C GLN* 4.5 6.2 + - - +
345D GLU 3.3 13.9 + - - +
346D LEU* 3.1 12.0 + - + +
347D LYS 3.0 1.0 - - - -
348D ASP* 1.3 81.2 - - + +
350D VAL* 1.3 65.9 + - + +
352D GLY 4.6 0.2 - - - -
369D TYR* 4.5 10.8 - - + -
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Residues in contact with VAL 350 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C ILE* 5.1 2.0 - - + -
346D LEU 3.1 16.5 + - - +
347D LYS* 2.9 12.7 + - - +
349D LEU* 1.3 84.6 - - + +
351D VAL* 1.3 69.7 + - + +
352D GLY 3.7 0.2 - - - -
362D VAL* 4.3 10.8 - - - +
365D LYS* 3.9 37.9 + - + +
366D ALA* 3.9 29.8 - - + +
369D TYR* 4.3 17.9 - - + -
----------------------------------------------------------
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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