Contacts of the helix formed by residues 321 - 350 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A SER* 1.3 70.4 - - - +
322A GLY* 1.3 54.0 + - - +
324A LYS* 3.2 24.3 + - - +
325A ARG* 2.8 36.9 + - - +
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Residues in contact with GLY 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A SER* 3.0 6.3 + - - -
321A ARG* 1.3 80.7 - - - +
323A GLU* 1.3 58.4 + - - +
325A ARG* 3.5 17.5 + - - -
326A THR* 3.0 28.2 + - - -
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Residues in contact with GLU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A GLN* 3.4 19.7 + - + -
320A SER* 2.7 48.0 + - - +
322A GLY* 1.3 70.9 - - - +
324A LYS* 1.3 58.7 + - - +
325A ARG 3.1 0.2 - - - -
326A THR* 3.2 6.8 + - - -
327A ALA* 2.8 31.4 + - - +
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Residues in contact with LYS 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A GLN* 3.7 28.6 - - + +
320A SER 2.7 18.1 + - - +
321A ARG* 3.5 23.8 - - - +
323A GLU* 1.3 71.0 - - - +
325A ARG* 1.3 51.7 + - - +
327A ALA* 3.1 2.1 + - - +
328A HIS* 2.7 41.3 + - + +
22F A 6.5 0.4 - - + -
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Residues in contact with ARG 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ARG 2.8 17.7 + - - +
322A GLY* 3.5 20.6 + - - +
323A GLU 3.1 0.2 - - - -
324A LYS* 1.3 73.1 - - - +
326A THR* 1.3 92.7 + - - +
327A ALA 3.1 0.3 + - - -
328A HIS* 3.2 7.8 + - - +
329A ASN* 3.1 33.9 + - - +
50G T 3.0 42.2 + - + +
51G G 4.4 17.5 - - - +
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Residues in contact with THR 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLY 3.0 16.2 + - - -
323A GLU* 3.2 6.7 + - - -
325A ARG* 1.3 97.0 + - - +
327A ALA* 1.3 63.8 + - - +
329A ASN* 3.5 11.1 + - - +
330A ALA* 3.5 15.4 + - - +
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Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A GLN* 4.0 21.8 - - - +
323A GLU 2.8 17.3 + - - +
324A LYS 3.4 4.7 - - - +
326A THR* 1.3 76.0 - - - +
328A HIS* 1.3 65.3 + - - +
330A ALA* 2.8 19.4 + - - +
331A ILE* 2.9 18.7 + - + +
23F G 4.0 12.1 - - - +
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Residues in contact with HIS 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LYS* 2.7 25.0 + - + +
325A ARG* 3.2 7.4 + - - +
327A ALA* 1.3 73.5 - - - +
329A ASN* 1.3 53.6 + - - +
331A ILE* 3.1 16.3 + - + +
332A GLU* 2.8 35.4 + - - +
24F A 4.5 7.0 + - - -
25F T 2.7 37.0 + + + -
26F C 4.2 2.2 - - - -
50G T 3.7 26.1 - + + -
51G G 2.5 40.8 + + - -
52G A 3.7 6.1 - - - -
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Residues in contact with ASN 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ARG* 3.1 25.9 + - - +
326A THR* 3.7 8.8 - - - +
327A ALA 3.1 0.2 - - - -
328A HIS* 1.3 77.7 - - - +
330A ALA* 1.3 56.9 + - - +
332A GLU* 3.5 2.6 + - - +
333A LYS* 3.0 25.5 + - - +
336A ARG* 4.8 1.4 + - - -
49G G 3.2 50.7 + - - +
50G T 2.6 46.0 + - - +
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Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A THR 3.5 7.9 + - - +
327A ALA* 2.8 11.9 + - - +
329A ASN* 1.3 79.0 - - - +
331A ILE* 1.3 63.1 + - + +
333A LYS* 3.3 11.6 + - + +
334A ARG* 3.1 28.3 + - - +
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Residues in contact with ILE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ALA* 2.9 18.2 + - + +
328A HIS* 3.4 17.3 - - - +
330A ALA* 1.3 76.8 - - + +
332A GLU* 1.3 52.8 + - - +
333A LYS 3.1 0.2 - - - -
334A ARG* 3.0 32.4 + - - +
335A TYR* 2.8 31.5 + - - +
23F G 3.3 46.0 - - + +
24F A 3.3 45.7 + - + +
25F T 3.7 7.4 - - + -
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Residues in contact with GLU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A HIS* 2.8 19.2 + - + +
329A ASN 3.7 4.0 - - - +
331A ILE* 1.3 73.9 - - - +
333A LYS* 1.3 66.0 + - - +
335A TYR* 3.4 21.5 - - - +
336A ARG* 3.1 51.3 + - - +
25F T 3.4 14.6 - - - +
26F C 2.6 21.2 + - - -
27F A 3.2 12.8 + - - -
28F C 5.3 0.2 + - - -
49G G 4.3 3.3 - - - +
50G T 3.0 35.6 - - + +
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Residues in contact with LYS 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ASN 3.0 14.1 + - - +
330A ALA* 3.4 14.6 - - + +
331A ILE 3.1 0.4 - - - -
332A GLU* 1.3 78.4 - - - +
334A ARG* 1.3 57.4 + - - +
336A ARG* 3.5 21.3 + - - +
337A SER* 2.7 47.1 + - - -
48G G 5.3 9.5 + - - +
49G G 5.5 2.2 - - - +
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Residues in contact with ARG 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ALA* 3.1 12.9 + - - +
331A ILE* 3.0 31.6 + - - +
333A LYS* 1.3 78.4 - - - +
335A TYR* 1.3 65.2 + - - +
337A SER* 3.4 8.8 + - - -
338A SER* 3.0 23.1 + - - -
23F G 3.8 8.7 + - - -
24F A 2.5 38.9 + - - +
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Residues in contact with TYR 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ILE 2.8 16.1 + - - +
332A GLU* 3.4 37.5 - - - +
334A ARG* 1.3 73.4 - - - +
336A ARG* 1.3 68.9 + - + +
338A SER* 2.5 29.2 + - - -
339A ILE* 3.4 29.2 + - + +
359B LYS* 4.0 5.7 + - - +
360B SER* 5.6 1.6 - - - -
24F A 5.6 1.6 - - + -
25F T 3.0 55.8 - + + +
26F C 2.7 54.7 + + + +
27F A 5.7 1.3 - - - -
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Residues in contact with ARG 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ASN 4.8 0.8 + - - -
332A GLU* 3.1 39.7 + - - +
333A LYS* 3.7 29.4 - - - +
335A TYR* 1.3 85.3 - - + +
337A SER* 1.3 52.9 + - - +
339A ILE* 3.2 5.8 + - - +
340A ASN* 2.7 55.5 + - - +
47G G 5.2 5.4 - - - -
48G G 3.2 54.5 + - - +
49G G 2.7 42.4 + - - -
50G T 4.4 0.2 - - - +
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Residues in contact with SER 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LYS* 2.7 35.7 + - - -
334A ARG* 3.6 10.5 - - - -
336A ARG* 1.3 78.8 - - - +
338A SER* 1.3 56.6 + - - +
339A ILE 3.0 0.2 - - - -
340A ASN* 4.4 3.1 - - - +
341A ASP* 2.8 57.0 + - - +
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Residues in contact with SER 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ARG* 3.0 14.8 + - - -
335A TYR* 2.5 30.0 + - - -
337A SER* 1.3 75.6 - - - +
339A ILE* 1.3 59.8 + - - +
341A ASP* 4.6 1.1 - - - -
342A LYS* 2.6 43.9 + - - +
360B SER* 3.3 19.7 + - - -
25F T 4.5 5.8 + - - -
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Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A TYR* 3.7 37.7 - - + +
336A ARG* 3.2 8.0 + - - +
337A SER 3.0 0.4 - - - -
338A SER* 1.3 84.8 - - - +
340A ASN* 1.3 67.2 + - - +
341A ASP 3.2 1.1 - - - -
342A LYS* 3.0 6.1 + - - +
343A ILE* 2.9 50.4 + - + +
339B ILE* 6.1 0.7 - - + -
343B ILE* 5.0 4.5 - - + -
359B LYS* 3.5 33.2 - - + +
360B SER* 4.2 11.2 - - - +
363B LEU* 3.8 12.5 - - + +
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Residues in contact with ASN 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ARG* 2.7 42.3 + - - +
337A SER* 4.5 3.1 - - - +
339A ILE* 1.3 82.1 - - - +
341A ASP* 1.3 64.2 + - - +
343A ILE* 3.1 6.8 + - - +
344A ILE* 3.1 31.6 + - + +
359A LYS* 2.7 32.8 + - - +
47G G 3.6 18.9 + - - +
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Residues in contact with ASP 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A SER* 2.8 46.4 + - - +
338A SER* 5.0 2.0 - - - -
340A ASN* 1.3 74.5 - - - +
342A LYS* 1.3 58.7 + - + +
344A ILE* 3.2 32.6 - - + +
345A GLU* 3.3 15.8 + - - +
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Residues in contact with LYS 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A SER* 2.6 34.5 + - - +
339A ILE 3.0 9.6 + - - +
341A ASP* 1.3 78.7 - - + +
343A ILE* 1.3 64.4 + - - +
344A ILE 3.1 1.6 - - - -
345A GLU* 3.1 5.9 + - - +
346A LEU* 3.0 23.9 + - - +
360B SER* 3.2 34.9 - - - +
363B LEU* 3.7 15.0 - - + -
364B ARG* 3.6 39.9 - - - +
367B ILE* 3.4 22.0 - - + +
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Residues in contact with ILE 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ILE* 2.9 38.5 + - + +
340A ASN* 3.1 14.3 + - - +
342A LYS* 1.3 76.3 - - - +
344A ILE* 1.3 60.0 + - + +
346A LEU* 3.4 5.9 + - - -
347A LYS* 2.8 23.3 + - + +
359A LYS* 4.1 42.0 - - + +
362A VAL* 3.4 23.1 - - + +
363A LEU* 4.2 12.3 - - + -
339B ILE* 4.6 15.0 - - + -
343B ILE* 5.2 0.7 - - + -
363B LEU* 3.8 15.3 - - + -
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Residues in contact with ILE 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ASN* 3.1 18.9 + - + +
341A ASP* 3.2 30.5 - - + +
342A LYS 3.1 0.6 - - - -
343A ILE* 1.3 80.8 - - + +
345A GLU* 1.3 58.0 + - - +
347A LYS* 3.4 14.7 - - + +
348A ASP* 3.0 37.6 + - - +
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Residues in contact with GLU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ASP 3.3 16.2 + - - +
342A LYS* 3.1 6.3 + - - +
344A ILE* 1.3 76.2 - - - +
346A LEU* 1.3 62.6 + - - +
348A ASP* 3.6 8.5 + - - +
349A LEU* 3.2 28.2 + - - +
364B ARG* 3.1 24.9 + - - -
367B ILE* 3.3 22.8 - - + +
371B ARG* 2.9 42.0 + - - +
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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
----------------------------------------------------------
342A LYS 3.0 14.8 + - - +
343A ILE* 3.5 8.1 - - - +
345A GLU* 1.3 75.6 - - - +
347A LYS* 1.3 65.7 + - - +
349A LEU* 3.0 7.6 + - + +
350A VAL* 3.0 26.3 + - - +
362A VAL* 3.8 9.4 - - + -
363A LEU* 3.9 15.7 - - + -
366A ALA* 4.1 11.9 - - + -
346B LEU* 4.2 9.2 - - + -
363B LEU* 3.8 30.1 - - + -
366B ALA* 4.4 4.0 - - + -
367B ILE* 3.6 29.8 - - + +
370B ILE* 3.7 29.8 - - + -
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Residues in contact with LYS 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ILE 2.8 15.1 + - - +
344A ILE* 3.3 17.2 + - + +
346A LEU* 1.3 74.8 - - - +
348A ASP* 1.3 83.5 + - - +
349A LEU 3.1 0.5 + - - -
350A VAL* 3.1 3.3 + - - -
351A VAL* 2.8 44.7 + - + +
352A GLY 2.9 20.4 - - - -
353A THR 2.8 20.8 + - - -
355A ALA 2.9 20.9 + - - +
356A LYS* 4.4 1.3 - - - -
357A LEU 4.2 16.2 - - - +
362A VAL* 3.5 29.6 - - + +
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Residues in contact with ASP 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ILE* 3.0 22.0 + - - +
345A GLU* 3.7 8.8 - - - +
346A LEU 3.3 0.2 - - - -
347A LYS* 1.3 110.7 + - - +
349A LEU* 1.3 60.1 + - + +
352A GLY* 3.1 25.4 + - - -
353A THR* 3.2 21.3 + - - +
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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 GLU 3.2 19.7 + - - +
346A LEU* 3.0 13.6 + - + +
348A ASP* 1.3 79.9 - - + +
350A VAL* 1.3 62.5 + - + +
369A TYR* 3.7 15.0 - - - -
367B ILE* 3.8 35.2 - - + +
370B ILE* 3.7 25.4 - - + -
371B ARG* 4.2 17.0 - - + +
374B GLN* 3.3 34.3 + - - +
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Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU 3.0 18.1 + - - +
347A LYS* 3.4 10.3 - - - +
349A LEU* 1.3 82.7 - - + +
351A VAL* 1.3 69.4 + - + +
362A VAL* 4.2 10.1 - - + +
365A LYS* 3.8 33.2 - - + +
366A ALA* 3.6 33.0 - - + +
369A TYR* 3.9 20.2 - - + -
370B ILE* 5.0 1.6 - - + -
----------------------------------------------------------
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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