Contacts of the helix formed by residues 376 - 400 (chain C) in PDB entry 1SL0
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 ASP 376 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349C ALA* 5.4 3.9 + - + -
374C VAL* 3.9 4.0 - - + +
375C ASP* 1.3 78.2 - - - +
377C PRO* 1.3 75.3 - - - +
378C GLU* 3.0 24.3 + - - +
379C LYS* 3.0 29.1 + - + +
380C GLN* 3.1 12.4 + - - +
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Residues in contact with PRO 377 (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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375C ASP 3.0 10.2 - - - +
376C ASP* 1.3 86.0 - - - +
378C GLU* 1.3 67.0 + - + +
380C GLN* 3.5 5.7 + - + +
381C ALA* 3.2 22.0 + - - +
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Residues in contact with GLU 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C GLU* 5.6 0.9 - - - +
260C THR* 3.5 37.5 + - + +
376C ASP* 3.0 17.3 + - - +
377C PRO* 1.3 76.5 - - + +
379C LYS* 1.3 58.2 + - - +
381C ALA* 3.1 23.9 - - + +
382C ALA* 3.2 8.7 + - - +
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Residues in contact with LYS 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C THR* 4.4 7.9 - - + -
261C PHE* 4.7 16.2 - - + -
346C LEU* 5.3 2.4 - - + +
349C ALA* 5.2 6.7 - - + -
374C VAL* 4.1 11.0 - - + -
376C ASP* 3.0 28.2 + - + +
378C GLU* 1.3 75.5 - - - +
380C GLN* 1.3 61.3 + - - +
381C ALA 2.9 1.6 - - - -
382C ALA* 2.8 29.6 + - - +
383C ILE* 3.2 8.0 + - - +
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Residues in contact with GLN 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C VAL 5.7 1.1 - - - +
373C ARG* 5.7 2.2 - - - -
374C VAL* 3.5 31.7 - - + +
376C ASP 3.1 8.6 + - - +
377C PRO* 4.2 6.3 - - + +
379C LYS* 1.3 78.2 - - - +
381C ALA* 1.3 61.8 + - - +
383C ILE* 3.2 27.4 + - + +
384C ASP* 3.8 6.8 + - - +
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Residues in contact with ALA 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C PRO 3.2 13.3 + - - +
378C GLU* 3.1 17.0 - - - +
379C LYS 2.9 0.4 - - - -
380C GLN* 1.3 79.7 - - - +
382C ALA* 1.3 57.5 + - - +
384C ASP* 3.2 21.8 + - - +
385C LEU* 3.6 9.8 + - - +
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Residues in contact with ALA 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C LEU* 4.0 12.3 - - + -
260C THR* 4.1 9.9 - - + +
261C PHE* 3.7 26.7 - - + -
378C GLU 3.2 8.5 + - - +
379C LYS 2.8 12.8 + - - +
381C ALA* 1.3 77.3 - - - +
383C ILE* 1.3 63.4 + - - +
384C ASP 3.2 0.4 - - - -
385C LEU* 3.1 13.7 + - + +
386C ILE* 3.0 29.4 + - - +
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Residues in contact with ILE 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C LEU* 3.6 30.5 - - + -
369C LEU* 3.3 30.9 - - + +
372C VAL* 3.4 42.2 - - + +
374C VAL* 4.7 5.4 - - + -
379C LYS 3.2 4.6 + - - +
380C GLN* 3.2 23.9 + - + +
381C ALA 3.1 0.6 - - - -
382C ALA* 1.3 77.5 - - - +
384C ASP* 1.3 65.3 + - - +
386C ILE* 3.2 10.0 + - + +
387C LYS* 3.1 32.9 + - + +
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Residues in contact with ASP 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C GLN 3.8 5.6 + - - +
381C ALA* 3.2 12.3 + - - +
382C ALA 3.2 0.6 - - - -
383C ILE* 1.3 82.4 - - - +
385C LEU* 1.3 60.9 + - + +
387C LYS* 3.7 26.6 - - - +
388C GLU* 3.4 21.3 + - - +
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Residues in contact with LEU 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ARG* 5.3 2.7 - - - +
253C LEU* 3.8 18.6 - - + +
256C LYS* 4.3 18.8 - - + +
257C LEU* 3.3 31.0 - - + +
381C ALA 4.0 11.0 - - - +
382C ALA* 3.1 13.6 + - + +
383C ILE 3.1 0.6 - - - -
384C ASP* 1.3 77.9 - - + +
386C ILE* 1.3 63.1 + - - +
388C GLU* 3.6 21.4 + - - +
389C TYR* 2.8 27.9 + - - +
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Residues in contact with ILE 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C LEU* 4.0 14.6 - - + -
261C PHE* 4.4 12.3 - - + -
334C PHE* 4.1 22.4 - - + -
336C PRO* 3.8 15.5 - - + +
342C ILE* 3.3 45.1 - - + -
346C LEU* 5.2 6.1 - - + -
369C LEU* 5.5 4.5 - - + -
382C ALA 3.0 15.9 + - - +
383C ILE* 3.2 11.4 + - + +
385C LEU* 1.3 75.3 - - - +
387C LYS* 1.3 67.9 + - + +
388C GLU 3.0 1.3 - - - -
389C TYR* 2.7 5.2 + - - -
390C LEU* 2.6 30.1 + - + +
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Residues in contact with LYS 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C ASP* 2.5 51.7 + - - +
369C LEU* 3.9 21.5 - - + +
370C GLU* 3.3 27.9 - - - +
383C ILE* 3.1 28.3 + - + +
384C ASP* 3.7 29.2 - - - +
386C ILE* 1.3 81.1 - - - +
388C GLU* 1.3 58.7 + - - +
390C LEU* 3.4 10.5 + - - +
391C MET* 3.3 19.9 + - - +
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Residues in contact with GLU 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ARG* 2.9 46.1 + - - +
253C LEU* 3.3 23.8 - - + +
384C ASP 3.4 13.9 + - - +
385C LEU* 3.8 12.8 - - - +
386C ILE 3.0 0.2 - - - -
387C LYS* 1.3 78.6 - - - +
389C TYR* 1.3 59.4 + - - +
391C MET* 3.4 10.7 + - - +
392C ILE* 3.0 34.6 + - + +
447C TYR* 5.4 1.0 + - - -
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Residues in contact with TYR 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C ARG* 3.8 25.3 - - + +
253C LEU* 3.8 29.2 - - + -
254C LEU* 4.1 22.1 - - + +
257C LEU* 4.7 1.1 - - + -
335C ASN* 4.8 3.8 + - - -
336C PRO* 3.3 44.3 - - + +
337C SER* 3.4 24.2 + - - -
385C LEU 2.8 19.2 + - - +
386C ILE* 2.7 16.7 + - - +
388C GLU* 1.3 70.0 - - - +
390C LEU* 1.3 68.4 + - + +
392C ILE* 3.4 3.7 + - + +
393C GLN* 3.3 43.9 + - + +
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Residues in contact with LEU 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C PRO 3.2 25.1 - - - +
337C SER* 3.8 22.0 - - - +
339C ARG* 6.4 1.1 - - + -
342C ILE* 3.9 18.2 - - + -
364C VAL 5.2 3.8 - - - +
366C ASP 6.1 0.4 - - - +
369C LEU* 4.2 21.8 - - + -
386C ILE* 2.6 23.9 + - + +
387C LYS* 3.7 5.6 - - - +
389C TYR* 1.3 74.3 - - + +
391C MET* 1.3 62.5 + - - +
393C GLN* 3.3 10.6 + - + +
394C LYS* 3.1 18.6 + - - +
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Residues in contact with MET 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C LYS 3.3 10.9 + - - +
388C GLU* 3.8 13.2 - - - +
389C TYR 3.2 0.2 - - - -
390C LEU* 1.3 75.0 - - - +
392C ILE* 1.3 95.9 + - + +
393C GLN 2.9 1.3 - - - -
394C LYS* 2.7 20.0 + - - +
395C ARG* 3.2 44.7 + - + +
446C PRO* 3.7 27.8 - - + -
447C TYR* 3.8 14.8 - - + -
19Q C 5.2 8.3 - - - +
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Residues in contact with ILE 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C LEU* 3.8 15.7 - - + +
249C ARG* 4.2 9.9 - - + -
250C ARG* 4.0 17.9 - - + +
253C LEU* 4.2 15.0 - - + -
388C GLU* 3.0 27.1 + - + +
389C TYR* 3.8 7.9 - - + +
391C MET* 1.3 98.8 - - + +
393C GLN* 1.3 56.7 + - - +
395C ARG* 3.4 3.1 + - - +
396C ILE* 2.9 49.1 + - + +
447C TYR* 3.3 28.9 - - + +
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Residues in contact with GLN 393 (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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250C ARG* 2.6 47.4 + - - +
337C SER* 4.0 10.7 + - - +
389C TYR* 3.3 36.9 + - + +
390C LEU* 3.3 12.8 + - + +
391C MET 2.9 0.6 - - - -
392C ILE* 1.3 76.7 - - + +
394C LYS* 1.3 56.5 + - - +
395C ARG 2.9 5.4 - - - -
396C ILE* 4.2 4.2 - - - +
397C GLY* 3.0 26.3 + - - -
401C GLU* 4.3 0.8 + - - -
11U C 5.0 2.8 - - - +
12U T 4.2 29.1 + - - +
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Residues in contact with LYS 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C LEU 3.1 10.4 + - - +
391C MET* 2.7 17.4 + - - +
393C GLN* 1.3 71.4 - - - +
395C ARG* 1.3 68.3 + - - +
397C GLY 4.2 0.9 - - - -
398C GLN* 3.4 31.0 + - - +
439C GLN* 5.7 0.4 - - - +
17Q T 5.0 4.5 - - - -
18Q G 3.1 72.2 + - - +
19Q C 3.7 26.6 + - - +
10U A 5.4 2.7 + - - -
11U C 5.4 14.9 + - - +
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Residues in contact with ARG 395 (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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242C LEU* 6.0 1.3 - - + -
246C LEU* 4.1 14.4 - - + -
391C MET* 3.3 40.2 + - + +
392C ILE 3.6 7.2 - - - +
394C LYS* 1.3 96.4 - - - +
396C ILE* 1.3 65.0 + - - +
397C GLY 3.0 1.6 - - - -
398C GLN* 3.2 3.2 + - - +
399C SER* 2.8 31.4 + - - -
441C PRO* 3.6 31.2 - - - +
445C SER* 3.7 23.8 + - - -
446C PRO* 2.8 37.6 + - - +
447C TYR* 4.1 11.3 - - + +
451C CYS* 4.6 8.3 - - - -
19Q C 4.6 17.4 + - - -
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Residues in contact with ILE 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C TYR* 3.5 22.4 - - + -
246C LEU* 3.5 21.1 - - + +
247C ALA 3.7 18.8 - - - +
250C ARG* 3.4 31.9 - - - +
392C ILE* 2.9 39.6 + - + +
393C GLN* 3.4 4.2 + - - +
395C ARG* 1.3 76.0 - - - +
397C GLY* 1.3 57.1 + - - +
399C SER* 4.0 4.9 - - - -
400C ALA 3.1 6.8 + - - -
401C GLU* 2.8 51.0 + - - +
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Residues in contact with GLY 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C GLN 3.0 14.6 + - - -
394C LYS 4.8 0.4 - - - -
395C ARG 3.0 0.6 - - - -
396C ILE* 1.3 77.9 - - - +
398C GLN* 1.3 64.1 + - - +
399C SER 3.2 1.0 + - - -
401C GLU* 4.7 0.2 - - - -
402C GLY* 2.9 34.3 + - - -
405C ALA* 3.8 4.9 - - - +
11U C 3.7 25.5 - - - +
12U T 4.0 5.8 + - - -
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Residues in contact with GLN 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C LYS* 3.4 27.3 + - - +
395C ARG* 3.2 5.4 + - - +
397C GLY* 1.3 76.1 - - - +
399C SER* 1.3 58.2 + - - +
404C LYS 4.4 1.8 - - - +
405C ALA* 3.7 3.6 - - - +
406C TRP* 3.3 52.5 + - + +
436C ASN 4.9 1.0 + - - -
439C GLN* 2.5 44.8 + - - +
440C ILE* 3.7 1.8 - - - +
441C PRO* 3.3 23.0 - - - +
19Q C 4.9 6.4 - - - +
11U C 4.3 9.2 - - - -
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Residues in contact with SER 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C ILE* 4.3 11.1 + - - +
242C LEU* 4.6 8.1 - - - +
243C TYR* 5.3 2.8 - - - +
246C LEU* 4.4 9.5 - - - +
395C ARG 2.8 22.0 + - - -
396C ILE* 4.0 3.3 - - - -
398C GLN* 1.3 80.1 - - - +
400C ALA* 1.3 64.8 + - - +
405C ALA* 3.5 3.1 - - - +
406C TRP* 3.3 32.8 + - - +
407C LEU* 3.1 33.1 + - - +
451C CYS* 5.5 1.1 - - - -
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Residues in contact with ALA 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C TYR* 3.2 46.9 - - + -
396C ILE 3.1 4.1 + - - +
399C SER* 1.3 83.5 + - - +
401C GLU* 1.3 64.9 + - - +
402C GLY 4.2 0.5 - - - +
405C ALA* 3.4 14.3 - - - +
407C LEU* 3.5 21.7 - - + +
408C ARG* 5.3 2.3 + - - +
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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