Contacts of the helix formed by residues 321 - 345 (chain C) in PDB entry 1EJI
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 THR 321 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C LYS* 3.8 12.6 - - + +
318C GLN* 2.9 26.8 + - + +
319C ALA 4.0 1.2 - - - +
320C MSE 1.3 83.0 - - - +
322C THR* 1.3 60.0 + - - +
323C GLU* 3.4 14.5 + - - +
324C PHE* 3.0 18.0 + - - +
325C LYS* 3.2 21.5 + - - +
21D MSE 3.7 16.5 - - - -
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Residues in contact with THR 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C THR* 1.3 72.2 - - - +
323C GLU* 1.3 73.8 + - - +
324C PHE 2.9 1.8 - - - -
325C LYS* 3.1 12.5 + - + +
326C ILE* 2.9 27.4 + - + +
14D LEU* 3.3 24.2 - - + -
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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
----------------------------------------------------------
321C THR* 3.3 14.8 - - - +
322C THR* 1.3 90.3 + - - +
324C PHE* 1.3 54.6 - - - +
326C ILE* 2.8 23.1 - - - +
327C TYR 3.1 8.0 + - - -
14D LEU* 3.4 12.6 - - + +
17D SER* 3.3 35.9 + - - -
18D HIS* 3.3 35.1 - - + +
21D MSE 4.2 11.7 - - - +
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Residues in contact with PHE 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C GLY* 3.9 15.3 - - - -
237C ALA* 4.6 0.7 - - + -
238C ALA* 4.2 12.1 - - + -
258C THR 4.2 5.4 - - - -
259C LEU* 4.2 23.8 - - + -
260C ARG* 3.5 28.9 - - + -
318C GLN* 3.1 21.1 - - + +
319C ALA* 2.7 46.4 - - + +
321C THR* 3.0 12.0 + - - +
323C GLU* 1.3 74.7 - - - +
325C LYS* 1.3 59.8 + - - +
326C ILE 3.0 1.6 - - - -
327C TYR* 2.8 27.8 + + - +
328C GLN* 2.9 39.0 + - - +
21D MSE 4.6 2.7 - - + +
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Residues in contact with LYS 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C ALA* 2.9 44.8 + - + +
239C GLY* 4.4 7.2 - - - -
240C VAL* 4.3 2.7 - - + +
321C THR 3.2 9.6 + - - +
322C THR* 3.1 15.8 + - + +
324C PHE* 1.3 78.6 - - - +
326C ILE* 1.3 60.9 + - - +
328C GLN* 3.8 2.6 + - - +
329C LEU* 3.2 34.2 + - + +
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Residues in contact with ILE 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C THR* 2.9 16.8 + - + +
323C GLU* 2.8 34.1 - - - +
325C LYS* 1.3 76.9 - - - +
327C TYR* 1.3 66.4 + - - +
329C LEU* 3.1 12.0 + - + +
330C GLN* 2.9 21.0 + - - +
10D ARG* 4.2 30.9 + - + +
14D LEU* 3.2 35.0 - - + +
15D TRP* 3.7 31.4 - - + +
18D HIS* 5.2 1.8 - - + -
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Residues in contact with TYR 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ASN* 3.2 14.7 + - - -
258C THR 5.4 2.0 - - - -
260C ARG* 3.4 28.3 - - + -
323C GLU 3.1 12.0 + - - +
324C PHE* 2.8 15.2 + + - +
326C ILE* 1.3 77.1 - - - +
328C GLN* 1.3 93.0 + - - +
330C GLN* 3.0 10.2 + - - +
331C VAL* 2.9 44.2 + - + +
406C PRO* 2.9 28.4 + - - +
409C THR* 3.5 8.3 - - + -
410C SER* 3.0 35.9 + - - -
15D TRP* 4.8 6.1 - + - -
18D HIS* 3.4 26.5 - + + +
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Residues in contact with GLN 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C GLY 3.9 6.1 - - - -
235C LEU* 3.0 49.2 - - + +
238C ALA* 3.5 23.1 - - + -
240C VAL* 4.0 5.8 - - + +
258C THR* 3.7 15.3 + - - +
324C PHE* 2.9 37.4 + - - +
325C LYS 4.0 1.3 - - - +
327C TYR* 1.3 100.5 + - - +
329C LEU* 1.3 62.3 + - - +
331C VAL* 3.2 14.3 - - - +
332C LEU* 3.1 25.3 + - - +
406C PRO* 5.3 0.4 - - - +
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Residues in contact with LEU 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C VAL* 3.8 23.3 - - + -
325C LYS* 3.2 28.3 + - + +
326C ILE* 3.1 15.8 + - + +
328C GLN* 1.3 74.4 - - - +
330C GLN* 1.3 66.3 + - - +
332C LEU* 3.2 10.9 + - + +
333C ALA* 3.0 22.4 + - - +
336C ARG* 4.7 6.7 + - - +
10D ARG* 5.9 4.7 - - - +
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Residues in contact with GLN 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326C ILE 2.9 11.4 + - - +
327C TYR 3.4 8.5 - - - +
329C LEU* 1.3 76.2 - - - +
331C VAL* 1.3 54.5 + - - +
333C ALA* 3.2 5.1 + - - +
334C ASN* 2.6 79.2 + - - +
409C THR* 3.7 4.0 - - + -
414C LEU* 3.3 22.8 - - + +
415C GLU* 3.2 26.9 + - - +
10D ARG* 3.7 20.4 + - - +
11D ASP* 5.3 0.5 - - - +
15D TRP* 3.6 28.7 + - + +
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Residues in contact with VAL 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C LEU* 4.6 2.2 - - + -
327C TYR* 2.9 57.4 + - + +
328C GLN* 3.2 22.4 - - - +
329C LEU 3.2 0.2 - - - -
330C GLN* 1.3 75.4 - - - +
332C LEU* 1.3 63.0 + - - +
334C ASN* 3.5 0.9 + - - +
335C CYS* 3.2 10.9 + - - +
357C HIS* 4.0 11.0 - - + -
405C THR* 2.8 32.8 + - - +
406C PRO* 3.9 23.8 - - + -
409C THR* 3.5 12.8 - - + +
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Residues in contact with LEU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C LEU* 4.3 13.0 - - + -
240C VAL* 3.4 43.7 - - + +
241C VAL* 4.4 3.1 - - + -
328C GLN 3.1 9.7 + - - +
329C LEU* 3.5 13.2 - - + +
331C VAL* 1.3 78.1 - - - +
333C ALA* 1.3 67.2 + - - +
335C CYS* 2.8 20.3 + - - +
336C ARG* 3.3 23.9 + - - +
355C ASP 3.8 8.1 - - - +
356C ASN* 3.2 42.2 - - - +
357C HIS* 4.1 0.9 - - - +
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Residues in contact with ALA 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C LEU 3.0 13.8 + - - +
330C GLN* 3.5 14.6 - - - +
332C LEU* 1.3 76.0 - - - +
334C ASN* 1.3 63.2 + - - +
336C ARG* 3.1 40.5 + - - +
337C ALA* 3.1 12.7 + - - +
415C GLU* 3.9 22.2 - - + +
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Residues in contact with ASN 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C GLN* 2.6 44.2 + - - +
331C VAL 3.7 4.9 - - - +
333C ALA* 1.3 72.1 - - - +
335C CYS* 1.3 63.1 + - - +
337C ALA* 3.4 7.7 - - - +
338C LEU* 3.1 23.2 + - - +
405C THR* 4.1 3.1 - - - -
409C THR* 2.9 28.5 + - - +
413C LEU 3.1 19.8 + - - -
414C LEU 3.3 16.6 - - - -
415C GLU* 3.3 1.6 + - - -
418C PHE* 3.2 30.4 - - + -
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Residues in contact with CYS 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C VAL 3.2 8.0 + - - +
332C LEU 2.8 12.9 + - - +
334C ASN* 1.3 76.4 - - - +
336C ARG* 1.3 67.9 + - + +
338C LEU* 3.0 6.1 + - - +
339C SER* 2.8 22.4 + - - -
354C SER* 3.6 12.6 - - - -
356C ASN 3.5 24.0 - - - +
357C HIS* 3.8 13.9 - - - -
358C LEU* 4.1 0.4 - - - -
359C ILE* 3.6 31.3 - - - +
405C THR* 3.8 16.6 - - + +
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Residues in contact with ARG 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C LEU* 4.7 6.7 + - - +
332C LEU* 3.9 20.8 + - - +
333C ALA* 3.1 38.0 + - - +
335C CYS* 1.3 75.7 - - + +
337C ALA* 1.3 66.0 + - - +
339C SER* 2.9 7.4 + - - -
340C ASP* 2.5 38.5 + - - +
354C SER* 5.4 8.1 - - - +
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Residues in contact with ALA 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C ALA 3.1 8.9 + - - +
334C ASN 3.4 11.0 - - - +
336C ARG* 1.3 78.6 - - - +
338C LEU* 1.3 56.1 + - - +
340C ASP* 3.7 5.8 - - - +
341C ALA* 3.0 31.9 + - - +
415C GLU* 3.9 39.5 - - + +
418C PHE* 4.5 2.9 - - + -
419C GLN* 4.7 8.7 - - + +
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Residues in contact with LEU 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU* 4.5 12.1 - - + -
334C ASN 3.1 9.1 + - - +
335C CYS* 3.0 9.3 + - - +
337C ALA* 1.3 77.4 - - - +
339C SER* 1.3 60.7 + - - +
341C ALA* 4.2 1.7 - - - +
342C LEU* 3.0 50.6 + - + +
359C ILE* 4.3 6.5 - - + -
403C LEU* 4.4 21.1 - - + -
405C THR* 4.5 9.2 - - + -
418C PHE* 3.8 38.6 - - + +
421C VAL* 4.9 1.8 - - + -
422C ALA* 3.8 26.0 - - + +
425C ILE* 4.5 6.5 - - + -
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Residues in contact with SER 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C CYS* 2.8 13.4 + - - -
336C ARG* 3.5 9.9 - - - -
338C LEU* 1.3 74.3 - - - +
340C ASP* 1.3 61.1 + - - +
342C LEU* 3.8 2.6 - - - +
343C THR* 2.6 37.6 + - - -
349C ILE* 3.7 25.1 - - - +
352C GLY 4.2 1.9 + - - -
353C GLY* 3.8 13.7 - - - -
354C SER* 5.2 2.2 - - - -
359C ILE* 4.0 24.6 - - - +
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Residues in contact with ASP 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C ARG* 2.5 43.2 + - - +
337C ALA* 3.7 6.3 - - - +
339C SER* 1.3 73.4 - - - +
341C ALA* 1.3 55.3 + - - +
342C LEU 3.0 1.1 - - - -
343C THR* 3.0 5.9 + - - -
344C GLU* 2.6 38.6 + - - +
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Residues in contact with ALA 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C ALA 3.0 17.7 + - - +
338C LEU 4.2 0.7 - - - +
340C ASP* 1.3 75.7 - - - +
342C LEU* 1.3 58.2 + - - +
344C GLU* 3.5 16.9 - - - +
345C LEU* 3.0 32.8 + - + +
419C GLN* 4.4 22.9 - - + +
422C ALA* 3.7 22.7 - - + -
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Residues in contact with LEU 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C LEU* 3.0 31.0 + - + +
339C SER* 3.8 4.7 - - - +
340C ASP 3.0 0.8 - - - -
341C ALA* 1.3 75.0 - - - +
343C THR* 1.3 65.2 + - - +
345C LEU* 3.3 12.9 + - + -
346C GLY 3.4 0.5 + - - -
347C TYR* 3.1 36.7 + - + +
349C ILE* 4.6 6.5 - - + -
359C ILE* 3.9 20.6 - - + -
361C MSE 4.1 20.6 - - + -
403C LEU* 3.9 14.8 - - + -
422C ALA* 3.5 41.1 - - + +
425C ILE* 4.9 7.9 - - + -
426C HIS 5.5 0.2 - - - +
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Residues in contact with THR 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C SER* 2.6 24.9 + - - -
340C ASP* 3.0 7.4 + - - -
342C LEU* 1.3 72.1 - - - +
344C GLU* 1.3 59.3 + - - +
346C GLY* 2.6 28.6 + - - -
347C TYR 3.6 14.7 + - - +
349C ILE* 3.7 16.0 - - - +
352C GLY 4.3 6.9 + - - +
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Residues in contact with GLU 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C ASP 2.6 20.9 + - - +
341C ALA* 3.5 17.6 - - - +
343C THR* 1.3 74.2 - - - +
345C LEU* 1.3 60.1 + - + +
346C GLY* 2.9 6.2 + - - -
419C GLN* 5.7 1.0 - - - +
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Residues in contact with LEU 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C ALA* 3.0 21.8 + - + +
342C LEU* 3.6 11.7 - - + +
343C THR 3.2 0.8 - - - -
344C GLU* 1.3 77.0 - - + +
346C GLY* 1.3 59.0 + - - +
347C TYR* 3.9 16.4 - - + -
422C ALA* 4.1 16.4 - - + +
423C HIS* 4.5 10.5 - - + +
426C HIS* 3.3 56.7 + - + +
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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