Contacts of the helix formed by residues 321 - 351 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C SER* 1.3 72.3 - - - +
322C GLY* 1.3 63.4 + - - +
324C LYS* 3.2 13.1 + - - +
325C ARG* 3.0 25.3 + - - +
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Residues in contact with GLY 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C SER* 3.3 4.3 + - - -
321C ARG* 1.3 79.0 - - - +
323C GLU* 1.3 57.9 + - - +
325C ARG* 3.2 30.5 + - - +
326C THR* 2.9 33.1 + - - -
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Residues in contact with GLU 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C GLN* 3.2 20.1 - - + +
320C SER* 2.5 49.2 + - - +
322C GLY* 1.3 74.5 - - - +
324C LYS* 1.3 66.4 + - - +
326C THR* 3.3 5.8 + - - +
327C ALA* 2.8 25.7 + - - +
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Residues in contact with LYS 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C GLN* 3.4 33.6 + - + +
320C SER 2.7 20.3 + - - +
321C ARG* 3.6 13.9 - - - +
323C GLU* 1.3 70.9 - - - +
325C ARG* 1.3 53.1 + - - +
327C ALA* 3.1 2.8 + - - +
328C HIS* 2.6 40.2 + - + +
60H A 5.8 0.4 - - - +
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Residues in contact with ARG 325 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C ARG* 3.0 11.1 + - - +
322C GLY* 3.2 36.5 + - - +
324C LYS* 1.3 77.6 - - - +
326C THR* 1.3 75.6 + - - +
328C HIS* 3.0 7.2 + - - +
329C ASN* 2.8 30.9 + - - +
12E T 3.3 47.7 + - + +
13E G 4.6 13.7 - - - +
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Residues in contact with THR 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C GLY 2.9 21.6 + - - -
323C GLU* 3.8 5.8 - - - -
325C ARG* 1.3 87.3 + - - +
327C ALA* 1.3 62.6 + - - +
329C ASN* 3.4 11.1 + - - +
330C ALA* 3.3 18.9 + - - +
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Residues in contact with ALA 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C GLN* 3.6 24.5 - - - +
323C GLU 2.8 19.0 + - - +
324C LYS 3.4 3.4 - - - +
326C THR* 1.3 74.1 - - - +
328C HIS* 1.3 62.2 + - - +
330C ALA* 2.9 9.9 + - - +
331C ILE* 2.8 32.8 + - + +
61H G 4.0 11.0 - - - +
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Residues in contact with HIS 328 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C LYS 2.6 22.2 + - - +
325C ARG* 3.5 6.5 - - + +
327C ALA* 1.3 74.2 - - - +
329C ASN* 1.3 57.8 + - - +
331C ILE* 3.4 18.6 - - + +
332C GLU* 2.8 31.5 + - - +
12E T 3.6 22.6 - + + +
13E G 2.6 39.4 + + - -
14E A 3.8 6.3 + - - -
62H A 4.6 7.6 + - - -
63H T 2.8 33.4 - + + -
64H C 4.3 2.5 - - - -
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Residues in contact with ASN 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C ARG* 2.8 23.1 + - - +
326C THR* 3.7 9.7 - - - +
327C ALA 3.1 0.2 - - - -
328C HIS* 1.3 79.8 - - - +
330C ALA* 1.3 58.2 + - - +
332C GLU* 3.5 6.0 + - - +
333C LYS* 3.0 26.5 + - - +
336C ARG* 4.6 0.9 + - - -
11E G 3.3 48.5 + - - +
12E T 2.6 39.1 + - + +
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Residues in contact with ALA 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C THR 3.3 9.2 + - - +
327C ALA* 2.9 11.3 + - - +
329C ASN* 1.3 77.2 - - - +
331C ILE* 1.3 67.6 + - + +
333C LYS* 3.3 12.4 + - + +
334C ARG* 3.2 26.8 + - - +
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Residues in contact with ILE 331 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C ALA* 2.8 16.2 + - + +
328C HIS* 3.4 20.2 - - - +
330C ALA* 1.3 76.0 - - + +
332C GLU* 1.3 57.7 + - - +
334C ARG* 2.9 31.6 + - - +
335C TYR* 2.9 23.5 + - + +
61H G 3.3 53.4 - - + +
62H A 3.5 41.5 + - + +
63H T 3.8 8.7 - - + -
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Residues in contact with GLU 332 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C HIS* 2.8 21.4 + - + +
329C ASN 3.8 3.6 - - - +
331C ILE* 1.3 72.5 - - - +
333C LYS* 1.3 59.0 + - - +
335C TYR* 3.3 25.3 - - - +
336C ARG* 2.9 40.4 + - - +
11E G 4.1 12.7 - - + +
12E T 3.2 27.8 - - + +
63H T 3.4 12.1 - - - +
64H C 2.5 30.1 + - - -
65H A 3.1 17.5 + - - -
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Residues in contact with LYS 333 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C ASN 3.0 14.7 + - - +
330C ALA* 3.4 15.0 - - + +
331C ILE 3.1 0.2 - - - -
332C GLU* 1.3 76.9 - - - +
334C ARG* 1.3 62.4 + - - +
336C ARG* 3.3 31.3 + - - +
337C SER* 3.0 31.6 + - - +
10E G 5.7 4.5 + - - -
11E G 5.5 1.1 - - - +
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Residues in contact with ARG 334 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C ALA* 3.2 10.9 + - - +
331C ILE* 2.9 29.2 + - - +
333C LYS* 1.3 79.0 - - - +
335C TYR* 1.3 63.1 + - - +
337C SER* 3.4 7.6 + - - -
338C SER* 3.0 24.4 + - - -
61H G 4.4 5.5 + - - -
62H A 2.8 40.4 + - - +
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Residues in contact with TYR 335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C ILE 2.9 11.6 + - - +
332C GLU* 3.2 38.3 + - - +
334C ARG* 1.3 79.1 - - - +
336C ARG* 1.3 67.3 + - + +
338C SER* 2.4 32.2 + - - -
339C ILE* 3.4 31.6 + - + +
359D LYS* 4.1 7.3 + - - +
360D SER* 5.9 1.8 - - - -
62H A 5.0 2.7 - - + -
63H T 3.3 53.1 - + + +
64H C 2.6 50.3 + + - +
65H A 5.4 2.2 - - - -
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Residues in contact with ARG 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C ASN 4.6 1.4 + - - -
332C GLU* 2.9 31.0 + - - +
333C LYS* 3.5 45.5 + - - +
335C TYR* 1.3 81.0 - - + +
337C SER* 1.3 59.1 + - - +
339C ILE* 3.0 7.5 + - - +
340C ASN* 2.7 45.6 + - - +
9E G 4.5 4.2 - - - +
10E G 3.1 80.6 + - - +
11E G 3.8 12.8 + - - -
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Residues in contact with SER 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C LYS* 3.0 22.4 + - - +
334C ARG* 3.4 7.1 + - - -
336C ARG* 1.3 76.2 - - - +
338C SER* 1.3 64.5 + - - +
340C ASN* 4.2 3.6 - - - +
341C ASP* 2.8 54.1 + - - +
----------------------------------------------------------
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Residues in contact with SER 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C ARG* 3.0 15.4 + - - -
335C TYR* 2.4 33.7 + - - -
337C SER* 1.3 77.0 - - - +
339C ILE* 1.3 60.1 + - - +
341C ASP* 5.1 0.2 - - - -
342C LYS* 2.8 42.6 + - - +
360D SER* 3.7 20.0 - - - -
63H T 4.5 6.5 + - - -
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Residues in contact with ILE 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C TYR* 3.5 38.8 - - + +
336C ARG* 3.0 7.2 + - - +
337C SER 3.0 0.4 - - - -
338C SER* 1.3 86.7 + - - +
340C ASN* 1.3 71.3 + - - +
341C ASP 3.1 1.3 - - - -
342C LYS* 2.9 15.4 + - - +
343C ILE* 3.0 24.8 + - + +
339D ILE* 6.2 0.9 - - + -
343D ILE* 4.9 6.1 - - + -
359D LYS* 3.9 24.5 - - + +
360D SER* 4.1 15.7 - - - +
363D LEU* 3.7 19.8 - - + +
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Residues in contact with ASN 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C ARG* 2.7 43.1 + - - +
337C SER* 4.5 1.3 - - - -
339C ILE* 1.3 75.8 - - - +
341C ASP* 1.3 66.8 + - - +
343C ILE* 3.2 11.5 + - - +
344C ILE* 3.1 30.4 + - + +
359C LYS* 2.7 34.1 + - - +
9E G 3.6 18.5 + - - +
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Residues in contact with ASP 341 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C SER* 2.8 43.1 + - - +
338C SER* 4.9 2.0 - - - +
340C ASN* 1.3 82.7 - - - +
342C LYS* 1.3 60.7 + - + +
344C ILE* 3.6 15.3 + - - +
345C GLU* 3.2 30.2 + - - +
----------------------------------------------------------
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Residues in contact with LYS 342 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C SER* 2.8 33.5 + - - +
339C ILE 2.9 7.5 + - - +
341C ASP* 1.3 80.3 - - + +
343C ILE* 1.3 59.6 + - - +
344C ILE 3.2 0.2 - - - -
345C GLU* 3.2 9.7 + - - +
346C LEU* 2.9 33.4 + - - +
360D SER* 3.1 34.8 + - - +
363D LEU* 3.5 16.8 - - + -
364D ARG* 3.5 35.2 - - - +
367D ILE* 3.5 15.9 - - + +
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Residues in contact with ILE 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C ILE* 3.0 32.9 + - + +
340C ASN* 3.2 11.6 + - - +
342C LYS* 1.3 78.3 - - - +
344C ILE* 1.3 51.4 + - + +
346C LEU* 3.2 8.1 + - - +
347C LYS* 2.7 32.6 + - + +
359C LYS* 3.9 48.7 - - + +
362C VAL* 3.5 18.4 - - + +
363C LEU* 4.0 26.2 - - + -
339D ILE* 4.7 7.0 - - + -
343D ILE* 5.3 0.7 - - + -
363D LEU* 4.1 9.0 - - + -
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Residues in contact with ILE 344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C ASN* 3.1 18.8 + - + +
341C ASP* 3.7 18.4 - - - +
343C ILE* 1.3 73.9 - - + +
345C GLU* 1.3 68.2 + - + +
347C LYS* 3.0 12.4 + - + +
348C ASP* 2.9 38.6 + - - +
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Residues in contact with GLU 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C ASP* 3.2 15.9 + - - +
342C LYS* 3.4 6.9 - - - +
344C ILE* 1.3 82.3 - - + +
346C LEU* 1.3 61.2 + - - +
348C ASP* 3.2 9.9 + - - +
349C LEU* 3.1 27.2 + - - +
364D ARG* 2.9 33.5 + - - -
367D ILE* 3.3 19.7 - - + +
371D ARG* 2.9 34.5 + - - +
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Residues in contact with LEU 346 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C LYS 2.9 17.6 + - - +
343C ILE 3.5 7.0 - - - +
345C GLU* 1.3 72.6 - - - +
347C LYS* 1.3 65.5 + - - +
349C LEU* 3.2 5.3 + - + +
350C VAL* 3.0 30.9 + - - +
362C VAL* 3.9 9.9 - - + -
363C LEU* 3.9 25.1 - - + -
366C ALA* 4.2 10.3 - - + -
346D LEU* 4.2 11.2 - - + -
363D LEU* 4.0 19.1 - - + +
366D ALA* 4.4 1.8 - - + -
367D ILE* 3.6 28.9 - - + +
370D ILE* 3.5 31.4 - - + -
----------------------------------------------------------
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Residues in contact with LYS 347 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C ILE* 2.7 18.5 + - + +
344C ILE* 3.3 16.2 - - + +
346C LEU* 1.3 71.5 - - - +
348C ASP* 1.3 83.9 + - - +
349C LEU 3.2 0.2 + - - -
350C VAL* 3.2 6.5 + - - -
351C VAL* 2.8 44.4 + - + +
352C GLY 2.8 31.5 + - - -
353C THR 3.1 11.5 + - - -
355C ALA 2.7 27.5 + - - +
356C LYS* 4.6 0.7 - - - -
357C LEU* 4.3 14.6 - - + +
362C VAL* 3.4 25.3 - - + +
----------------------------------------------------------
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Residues in contact with ASP 348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C ILE* 2.9 28.4 + - - +
345C GLU* 3.2 10.4 + - - +
347C LYS* 1.3 103.1 + - - +
349C LEU* 1.3 59.0 + - + +
352C GLY* 2.9 29.4 + - - -
353C THR* 3.3 23.8 + - - +
----------------------------------------------------------
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Residues in contact with LEU 349 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C GLU 3.1 17.7 + - - +
346C LEU* 3.6 17.0 - - + +
347C LYS 3.1 0.6 - - - -
348C ASP* 1.3 79.4 - - + +
350C VAL* 1.3 62.1 + - + +
352C GLY 4.6 0.4 + - - -
369C TYR* 3.6 16.3 + - - -
367D ILE* 4.0 31.2 - - + +
370D ILE* 3.8 25.1 - - + -
371D ARG* 4.1 17.9 - - + +
374D GLN* 3.4 35.0 + - - +
----------------------------------------------------------
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Residues in contact with VAL 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C LEU 3.0 19.1 - - - +
347C LYS* 3.5 9.9 - - - +
349C LEU* 1.3 83.7 - - + +
351C VAL* 1.3 72.0 + - + +
352C GLY 3.7 0.4 - - - -
362C VAL* 4.3 10.5 - - + +
365C LYS* 3.9 27.7 - - + +
366C ALA* 3.7 30.3 - - + +
369C TYR* 3.8 21.8 - - + -
370D ILE* 5.1 1.8 - - + -
----------------------------------------------------------
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Residues in contact with VAL 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C LYS* 2.8 38.6 + - + +
350C VAL* 1.3 76.9 - - + +
352C GLY* 1.3 58.2 + - - +
355C ALA* 3.1 37.7 + - + +
357C LEU* 3.5 17.7 - - + -
365C LYS* 3.5 33.7 - - + -
----------------------------------------------------------
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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