Contacts of the helix formed by residues 359 - 390 (chain C) in PDB entry 6M04
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 ALA 359 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B HIS* 4.9 0.8 - - - -
333C ILE* 4.3 11.0 - - + +
334C SER 3.8 19.3 - - - +
335C PHE* 3.6 34.5 - - + -
356C HIS* 3.9 6.2 + - + +
357C ASN 3.6 4.0 + - - -
358C MET* 1.3 79.5 - - - +
360C TYR* 1.3 66.5 + - + +
361C MET 3.5 0.2 - - - -
362C LEU* 3.4 0.7 + - - +
363C LYS* 2.9 32.1 + - - +
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Residues in contact with TYR 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B HIS* 3.9 42.1 - + + +
156B LEU* 4.2 13.1 - - + +
163B LYS* 5.3 2.9 - - - +
164B TYR* 3.5 17.7 - - - +
335C PHE* 3.6 46.1 - + + +
359C ALA* 1.3 79.0 - - + +
361C MET* 1.3 62.3 + - - +
363C LYS* 3.3 19.7 + - - +
364C LYS* 2.9 45.3 + - - +
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Residues in contact with MET 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLN* 6.2 0.2 - - - +
155B HIS* 6.1 0.4 + - - -
163B LYS 5.3 0.4 - - - +
164B TYR* 3.6 42.8 + - + +
167B TYR* 3.7 33.0 - - + -
41C PHE* 5.6 2.9 - - - -
45C MET* 3.6 37.7 - - + -
49C LYS* 5.0 13.9 - - - +
357C ASN 5.8 1.3 + - - +
358C MET* 4.5 11.7 - - + -
360C TYR* 1.3 78.2 - - - +
362C LEU* 1.3 59.0 + - - +
364C LYS* 3.4 4.2 + - - +
365C LEU* 3.0 33.5 + - - +
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Residues in contact with LEU 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ALA* 6.3 4.3 - - + -
45C MET* 6.1 0.9 - - - -
46C GLN* 4.1 27.4 - - + -
161C TYR 5.3 2.7 - - - +
162C SER* 4.3 19.1 - - - +
163C LYS* 5.6 1.1 - - - -
165C PHE* 5.3 18.2 - - + -
166C PRO* 5.6 9.9 - - + -
333C ILE* 3.7 26.7 - - + -
358C MET* 3.3 33.9 + - + +
359C ALA 3.4 2.2 + - - +
360C TYR 3.3 0.2 - - - -
361C MET* 1.3 80.1 - - - +
363C LYS* 1.3 56.5 + - - +
365C LEU* 3.4 6.5 + - - +
366C LEU* 2.9 33.1 + - + +
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Residues in contact with LYS 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C VAL* 4.7 13.9 - - + +
333C ILE* 4.5 25.8 - - + +
359C ALA 2.9 20.1 + - - +
360C TYR* 3.9 19.8 - - - +
362C LEU* 1.3 79.0 - - - +
364C LYS* 1.3 74.0 + - + +
366C LEU* 3.3 8.4 + - + +
367C ILE* 3.0 45.5 + - + +
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Residues in contact with LYS 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B TRP* 5.7 8.7 - - - +
164B TYR* 3.5 38.6 - - + -
360C TYR* 2.9 28.8 + - - +
361C MET* 4.0 6.3 - - - +
363C LYS* 1.3 88.9 - - + +
365C LEU* 1.3 64.9 + - - +
367C ILE* 3.2 19.2 - - + +
368C SER* 3.0 23.2 + - - -
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Residues in contact with LEU 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C VAL* 4.1 24.8 - - + +
41C PHE* 4.0 24.7 - - + -
42C ALA* 3.7 36.1 - - + -
45C MET* 4.2 11.7 - - + -
361C MET* 3.0 21.9 + - + +
362C LEU* 3.8 6.7 - - + +
364C LYS* 1.3 77.1 - - - +
366C LEU* 1.3 57.1 + - - +
368C SER* 3.4 9.8 + - - +
369C TYR* 3.0 28.6 + - - +
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Residues in contact with LEU 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C PHE* 3.6 40.6 - - + -
326C THR* 4.9 4.7 - - - +
329C PHE* 3.9 17.0 - - + +
330C VAL* 4.4 13.9 - - + +
333C ILE* 3.8 25.8 - - + -
362C LEU* 2.9 20.8 + - + +
363C LYS* 3.4 8.1 - - + +
365C LEU* 1.3 77.2 - - - +
367C ILE* 1.3 60.2 + - + +
369C TYR* 3.3 16.9 - - + +
370C ILE* 2.9 43.0 + - + +
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Residues in contact with ILE 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C VAL* 4.8 18.6 - - + -
363C LYS* 3.0 32.7 + - + +
364C LYS* 3.2 27.6 - - + +
366C LEU* 1.3 76.6 - - + +
368C SER* 1.3 61.1 + - - +
370C ILE* 3.4 7.8 + - + +
371C SER* 3.0 28.4 + - - -
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Residues in contact with SER 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C VAL* 5.4 4.4 - - - +
364C LYS 3.0 16.7 + - - -
365C LEU* 3.7 14.6 - - - +
366C LEU 3.3 0.2 - - - -
367C ILE* 1.3 74.9 - - - +
369C TYR* 1.3 62.8 + - - +
371C SER* 2.6 23.7 + - - -
372C ILE* 3.0 24.0 + - - +
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Residues in contact with TYR 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C MET* 3.5 37.3 - - + -
38C VAL* 4.3 23.4 - - + +
39C ALA* 5.5 1.8 - - + -
165C PHE* 4.6 8.6 - + - -
168C LEU* 5.9 1.4 - - - +
169C ALA* 4.2 23.6 - - + +
172C HIS* 3.9 24.4 - - - +
322C ILE* 4.0 8.5 - - + +
326C THR* 4.4 16.0 - - + +
365C LEU 3.0 14.2 + - - +
366C LEU* 3.3 18.8 - - + +
368C SER* 1.3 76.5 - - - +
370C ILE* 1.3 77.4 + - + +
372C ILE* 3.3 8.3 + - + +
373C ILE* 3.0 43.8 + - + +
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Residues in contact with ILE 370 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C ILE* 6.2 1.1 - - + -
323C LEU* 5.6 15.3 - - + +
326C THR* 3.2 33.0 - - - +
327C ALA* 6.3 3.1 - - + -
330C VAL* 5.0 13.7 - - + -
366C LEU* 2.9 29.5 + - + +
367C ILE* 3.9 8.7 - - + +
369C TYR* 1.3 91.7 - - + +
371C SER* 1.3 61.5 + - - +
373C ILE* 3.4 6.8 + - + +
374C CYS* 2.9 31.2 + - + +
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Residues in contact with SER 371 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C ILE 3.0 11.9 + - - -
368C SER* 2.6 27.2 + - - -
370C ILE* 1.3 76.6 - - - +
372C ILE* 1.3 63.7 + - - +
374C CYS* 3.3 7.1 + - - +
375C VAL* 3.0 30.7 + - - +
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Residues in contact with ILE 372 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 3.7 30.8 - - + +
34C VAL* 3.8 29.2 - - + -
35C MET* 5.0 6.5 - - + +
38C VAL* 4.5 14.4 - - + -
368C SER* 3.0 26.3 + - - +
369C TYR* 3.7 6.3 - - - +
370C ILE 3.3 0.2 - - - -
371C SER* 1.3 84.0 + - - +
373C ILE* 1.3 63.8 + - + +
375C VAL* 3.3 8.2 + - - +
376C TYR* 3.0 25.8 + - - +
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Residues in contact with ILE 373 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 4.6 8.1 - - + -
35C MET* 3.8 33.9 - - + -
172C HIS* 5.0 3.6 - - - +
176C LEU* 5.7 2.2 - - + -
319C PHE* 3.3 22.3 - - + +
322C ILE* 3.7 26.9 - - + -
323C LEU* 5.5 4.0 - - + -
369C TYR* 3.0 36.9 + - + +
370C ILE* 4.1 7.9 - - + +
372C ILE* 1.3 82.2 - - + +
374C CYS* 1.3 56.7 + - - +
376C TYR* 3.3 13.6 - - + +
377C GLY 2.9 24.4 + - - -
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Residues in contact with CYS 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C PHE* 4.3 10.8 - - - -
323C LEU* 4.8 12.5 - - + +
370C ILE* 2.9 22.1 + - + +
371C SER* 3.6 8.5 - - - +
373C ILE* 1.3 74.7 - - - +
375C VAL* 1.3 61.1 + - + +
377C GLY* 3.5 0.5 + - - -
378C PHE* 3.0 33.6 + - - +
----------------------------------------------------------
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Residues in contact with VAL 375 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 5.0 9.0 - - + -
371C SER* 3.0 16.7 + - - +
372C ILE* 3.7 8.5 - - - +
374C CYS* 1.3 75.9 - - + +
376C TYR* 1.3 64.3 + - - +
378C PHE* 3.4 7.4 + - + +
379C ILE* 3.0 38.5 + - + +
----------------------------------------------------------
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Residues in contact with TYR 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C MET* 3.6 45.1 - - + +
31C LEU* 3.6 34.5 - - + +
172C HIS* 5.9 2.0 - + - -
176C LEU* 3.3 46.3 - - + +
315C LYS* 4.4 25.6 - - + +
319C PHE* 4.8 7.9 - + + -
372C ILE 3.0 14.3 + - - +
373C ILE* 3.3 25.8 - - + +
375C VAL* 1.3 77.4 - - - +
377C GLY* 1.3 62.2 + - - +
379C ILE* 3.9 3.2 - - - +
380C CYS* 3.0 31.1 + - + +
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Residues in contact with GLY 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C LYS* 4.2 4.1 + - - -
319C PHE* 3.5 37.7 - - - -
373C ILE 2.9 11.9 + - - -
376C TYR* 1.3 76.5 - - - +
378C PHE* 1.3 60.6 + - - +
380C CYS* 4.5 3.8 - - - -
381C LEU* 2.9 33.8 + - - +
----------------------------------------------------------
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Residues in contact with PHE 378 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C PHE* 4.5 1.4 - - - -
374C CYS* 3.0 21.9 + - - +
375C VAL* 3.7 7.0 - - + +
377C GLY* 1.3 75.8 - - - +
379C ILE* 1.3 74.0 + - + +
381C LEU* 3.9 6.5 - - + +
382C TYR* 3.0 49.5 + + + +
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Residues in contact with ILE 379 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C TRP* 4.4 28.0 - - + -
24C TRP* 5.4 0.2 - - + -
27C PHE* 5.2 9.6 - - + -
28C MET* 3.8 18.2 - - + -
375C VAL* 3.0 32.9 + - + +
376C TYR* 3.9 3.1 - - - +
378C PHE* 1.3 91.3 - - + +
380C CYS* 1.3 58.5 + - - +
382C TYR* 3.4 9.3 + - + +
383C THR* 3.0 30.0 + - - +
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Residues in contact with CYS 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C MET* 3.6 33.4 - - + -
312C THR* 5.8 0.7 - - - -
315C LYS* 3.5 41.7 - - + -
376C TYR* 3.0 18.9 + - + +
379C ILE* 1.3 77.3 - - - +
381C LEU* 1.3 57.4 + - - +
384C LEU* 2.9 57.0 + - - +
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Residues in contact with LEU 381 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C THR* 6.2 0.4 - - - -
315C LYS* 3.4 18.9 - - - +
316C THR* 5.2 9.9 - - + -
319C PHE* 5.3 10.1 - - + -
320C ILE* 6.1 2.7 - - + -
377C GLY 2.9 18.7 + - - +
378C PHE* 3.9 7.0 - - + +
380C CYS* 1.3 76.3 - - - +
382C TYR* 1.3 61.2 + - + +
384C LEU* 5.1 0.4 - - - -
385C PHE* 2.9 47.3 + - + +
----------------------------------------------------------
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Residues in contact with TYR 382 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C TRP* 6.0 1.1 - + - -
378C PHE* 3.0 38.5 + + + +
379C ILE* 3.6 10.8 - - + +
381C LEU* 1.3 80.6 - - + +
383C THR* 1.3 72.8 + - - +
385C PHE* 5.2 0.2 - - - -
386C TRP* 3.0 85.8 + + - +
----------------------------------------------------------
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Residues in contact with THR 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C TRP* 3.2 27.8 - - + -
24C TRP* 3.6 38.4 - - + -
379C ILE* 3.0 13.6 + - - +
382C TYR* 1.3 93.8 - - - +
384C LEU* 1.3 62.6 + - - +
386C TRP* 3.7 2.5 - - - -
387C LEU* 2.9 31.6 + - + +
----------------------------------------------------------
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Residues in contact with LEU 384 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C TRP* 3.5 41.5 - - + +
308C TYR* 3.4 37.8 + - + +
311C GLN* 6.1 1.8 - - + -
312C THR* 3.3 39.6 + - + +
380C CYS* 2.9 43.2 + - - +
383C THR* 1.3 82.8 - - - +
385C PHE* 1.3 56.1 + - - +
387C LEU 3.5 0.2 + - - -
388C PHE* 2.9 28.1 + - - +
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Residues in contact with PHE 385 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C THR* 5.0 5.5 - - + +
381C LEU* 2.9 31.4 + - + +
382C TYR 4.2 0.2 - - - +
384C LEU* 1.3 78.5 - - - +
386C TRP* 1.3 75.8 + + + +
388C PHE* 3.2 28.3 + + + +
389C ARG* 2.9 68.1 + - - +
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Residues in contact with TRP 386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C TYR* 3.0 70.8 + + + +
383C THR* 3.7 2.7 - - - +
385C PHE* 1.3 101.3 - + + +
387C LEU* 1.3 60.2 + - - +
388C PHE 3.5 0.2 - - - -
389C ARG* 4.1 11.3 - - - +
390C ILE* 3.4 28.9 - - + +
----------------------------------------------------------
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Residues in contact with LEU 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C TRP* 3.6 34.1 - - + -
308C TYR* 3.3 23.4 + - + +
383C THR* 2.9 17.9 + - + +
386C TRP* 1.3 77.3 - - - +
388C PHE* 1.3 64.0 + - - +
389C ARG 3.4 0.2 - - - -
390C ILE* 6.0 0.9 - - + -
391C PRO* 3.3 30.4 - - + +
418C PHE* 4.0 22.2 - - + -
421C HIS* 6.1 5.4 - - + -
422C MET* 6.0 5.8 - - + -
425C GLN* 5.1 19.5 - - + +
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Residues in contact with PHE 388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C TYR* 3.2 37.9 + + - -
308C TYR* 3.9 9.8 + + + -
309C VAL* 4.3 25.1 - - + -
312C THR* 6.0 3.1 - - + +
384C LEU 2.9 19.2 + - - +
385C PHE* 3.2 31.4 + + + +
387C LEU* 1.3 80.3 - - - +
389C ARG* 1.3 72.7 + - + +
391C PRO* 4.4 2.9 - - - +
392C LEU* 4.5 6.8 + - - +
----------------------------------------------------------
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Residues in contact with ARG 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C PHE* 2.9 52.9 + - + +
386C TRP* 4.1 9.4 - - - +
387C LEU 3.4 0.4 - - - -
388C PHE* 1.3 91.6 - - + +
390C ILE* 1.3 84.7 + - + +
392C LEU* 4.2 13.3 + - - +
----------------------------------------------------------
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Residues in contact with ILE 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C TRP* 3.4 22.8 + - + +
387C LEU* 6.0 0.9 - - + -
389C ARG* 1.3 98.2 - - + +
391C PRO* 1.3 73.4 - - + +
392C LEU* 3.3 14.0 - - - +
----------------------------------------------------------
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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