Contacts of the helix formed by residues 276 - 307 (chain C) in PDB entry 3OX4
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 PRO 276 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LYS* 5.3 3.1 - - - +
70C PRO* 5.7 6.5 - - + -
71C ASN* 4.6 4.3 - - - +
274C ASN 4.1 1.5 - - - +
275C LEU* 1.3 92.1 - - + +
277C HIS* 1.3 66.4 + - - +
278C GLY 3.4 2.7 - - - +
279C VAL* 3.2 32.0 - - + +
280C CYS* 3.2 15.9 - - - -
343C LEU* 5.7 2.0 - - + -
1385C NAD 6.0 2.5 - - - +
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Residues in contact with HIS 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ASN* 4.5 2.6 + - - -
160C LYS* 4.3 11.9 - - - +
194C ASP* 4.7 1.5 + - - -
263C HIS* 3.0 15.6 - + - -
266C ALA* 4.3 7.2 - - + -
267C HIS* 3.4 27.5 + + - -
270C GLY* 5.4 1.6 - - - -
275C LEU 3.2 6.2 + - - -
276C PRO* 1.3 72.5 - - - +
278C GLY* 1.3 67.6 + - - +
280C CYS* 3.3 4.4 + - - +
281C ASN* 2.6 45.2 + - - +
501C FE2 3.0 19.9 - - - -
1385C NAD 3.3 59.4 + + + -
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Residues in contact with GLY 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C ALA* 3.7 25.5 - - - +
191C THR* 5.0 2.0 - - - -
194C ASP* 4.1 16.5 + - - +
276C PRO* 3.4 2.6 - - - +
277C HIS* 1.3 80.1 - - - +
279C VAL* 1.3 60.9 + - - +
281C ASN* 3.5 4.5 + - - +
282C ALA* 3.1 19.9 + - - +
1385C NAD 4.8 11.9 + - - -
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Residues in contact with VAL 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C GLY 5.5 0.4 - - - +
190C ALA* 3.5 23.3 - - + -
276C PRO* 3.2 37.1 - - + +
278C GLY* 1.3 71.0 - - - +
280C CYS* 1.3 73.0 + - - +
282C ALA* 3.1 7.9 + - - +
283C VAL* 3.0 28.0 + - - +
336C ILE* 5.0 3.6 - - + +
337C PRO* 5.1 15.5 - - + -
343C LEU* 4.2 21.5 - - + -
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Residues in contact with CYS 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C ALA* 4.0 20.6 - - + +
269C LEU* 4.1 20.9 - - + -
270C GLY 4.6 1.3 - - - -
275C LEU* 3.6 28.3 - - - -
276C PRO 3.2 21.3 - - - -
277C HIS* 3.3 7.5 + - - +
279C VAL* 1.3 81.9 - - - +
281C ASN* 1.3 60.7 + - - +
283C VAL* 3.0 24.5 - - - +
284C LEU* 3.1 15.8 + - - +
340C LEU* 4.5 1.0 - - - +
343C LEU* 4.1 16.8 - - + -
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Residues in contact with ASN 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C ASP* 3.3 10.3 - - - +
197C THR* 4.2 8.5 - - - +
262C VAL* 3.0 33.3 + - + +
263C HIS* 2.8 20.8 + - - +
266C ALA* 2.9 25.3 - - - +
277C HIS* 2.6 34.2 + - - +
278C GLY 3.7 7.9 - - - +
279C VAL 3.2 0.4 - - - -
280C CYS* 1.3 77.3 - - - +
282C ALA* 1.3 60.3 + - - +
284C LEU* 3.2 1.1 + - - -
285C LEU* 2.8 34.1 + - - +
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Residues in contact with ALA 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C ALA 4.7 1.1 - - - +
193C MET* 3.4 42.4 + - + +
197C THR* 4.5 4.5 + - - -
278C GLY 3.1 9.8 + - - +
279C VAL* 3.1 12.5 + - - +
281C ASN* 1.3 81.9 - - - +
283C VAL* 1.3 61.5 + - - +
285C LEU* 3.5 3.3 - - - +
286C PRO* 3.5 17.3 - - - +
331C ALA* 5.0 2.1 - - - +
336C ILE* 3.9 23.0 - - + +
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Residues in contact with VAL 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C VAL* 3.0 11.4 - - + +
280C CYS* 3.0 25.1 - - - +
282C ALA* 1.3 77.5 - - - +
284C LEU* 1.3 59.9 + - - +
285C LEU 3.5 0.5 + - - -
286C PRO* 3.7 14.9 - - - +
287C HIS* 3.8 11.6 + - + +
331C ALA* 6.2 0.2 - - - -
336C ILE* 4.0 16.3 - - + +
337C PRO* 4.2 12.6 - - + +
338C ALA* 3.9 29.8 - - - +
339C ASN* 4.0 11.2 - - - +
340C LEU* 3.9 17.3 - - + +
343C LEU* 4.1 8.5 - - + -
382C ALA* 4.9 4.3 - - + +
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Residues in contact with LEU 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C VAL* 4.1 10.3 - - + +
265C MET* 3.6 42.2 - - + -
266C ALA* 4.0 13.2 - - - +
269C LEU* 4.7 4.3 - - + -
280C CYS 3.1 20.6 + - - +
281C ASN* 3.5 3.6 - - - +
283C VAL* 1.3 77.7 - - + +
285C LEU* 1.3 63.8 + - - +
286C PRO 3.8 0.2 - - - -
287C HIS* 3.7 8.5 + - + +
288C VAL* 3.4 28.3 + - + +
340C LEU* 4.1 16.6 - - + -
378C LEU* 5.3 4.3 - - + +
379C PHE* 4.7 4.0 - - + -
382C ALA* 3.5 27.6 - - + -
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Residues in contact with LEU 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C MET* 4.4 12.6 - - + +
196C LEU* 4.6 4.3 - - + -
197C THR* 3.6 37.2 - - + +
200C PHE* 4.4 15.7 - - + -
201C GLU* 5.4 0.9 - - + -
262C VAL* 4.1 18.8 - - + -
281C ASN 2.8 16.8 + - - +
282C ALA 3.5 3.1 - - - +
284C LEU* 1.3 72.7 - - - +
286C PRO* 1.3 72.8 - - + +
287C HIS 2.9 6.8 + - - -
288C VAL* 3.0 12.5 + - - +
289C LEU* 3.1 36.6 + - + +
327C VAL* 3.7 21.3 - - + -
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Residues in contact with PRO 286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C MET* 5.7 0.4 - - + -
282C ALA 3.5 11.9 - - - +
283C VAL* 3.7 12.1 - - - +
285C LEU* 1.3 98.8 - - + +
287C HIS* 1.3 69.3 + - + +
289C LEU* 3.9 10.3 - - + +
290C ALA* 3.5 18.2 + - - +
324C ILE* 3.8 14.7 - - + +
327C VAL* 4.3 15.9 - - + -
328C ARG* 3.9 36.5 + - + +
331C ALA* 5.9 4.0 - - + -
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Residues in contact with HIS 287 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C VAL* 3.8 23.3 + - + +
284C LEU* 3.7 12.1 + - + +
285C LEU 3.0 0.8 - - - -
286C PRO* 1.3 83.1 - - + +
288C VAL* 1.3 65.2 + - - +
289C LEU 3.2 0.2 - - - -
290C ALA* 3.6 6.1 + - - +
291C TYR* 3.3 18.9 + - - +
328C ARG* 5.4 11.7 + - - -
338C ALA 5.0 7.5 + - - -
378C LEU* 3.9 13.2 - - + +
381C SER* 3.1 43.8 + - - +
382C ALA* 3.8 17.1 - - + -
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Residues in contact with VAL 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C GLU* 4.9 0.4 - - - +
261C TYR* 3.6 26.0 - - + +
262C VAL* 3.4 37.0 - - + +
265C MET* 4.1 8.3 - - - -
284C LEU* 3.4 18.2 - - + +
285C LEU 3.0 2.1 + - - +
287C HIS* 1.3 74.3 - - - +
289C LEU* 1.3 65.4 + - + +
291C TYR* 3.2 8.0 + - + +
292C ASN* 3.0 37.2 + - - +
366C ASN* 4.6 0.4 - - - +
378C LEU* 3.9 23.1 - - + -
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Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C PHE* 3.4 46.2 - - + -
201C GLU* 6.3 1.3 - - + -
204C SER* 5.2 2.7 - - - +
285C LEU* 3.1 41.1 + - + +
286C PRO* 3.9 7.9 - - + +
287C HIS 3.2 0.2 - - - -
288C VAL* 1.3 75.4 - - + +
290C ALA* 1.3 66.4 + - - +
291C TYR 3.1 0.3 + - - -
292C ASN* 3.1 8.5 + - - +
293C ALA* 2.9 23.2 + - - +
300C LEU* 3.6 20.2 - - + +
324C ILE* 3.7 22.2 - - + -
327C VAL* 4.1 17.9 - - + -
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Residues in contact with ALA 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C PRO 3.5 11.2 + - - +
287C HIS* 3.8 9.0 - - - +
288C VAL 3.4 0.4 - - - -
289C LEU* 1.3 78.6 - - - +
291C TYR* 1.3 62.6 + - - +
293C ALA* 3.4 14.8 - - - +
294C SER* 4.4 1.2 + - - -
321C GLU* 5.2 5.5 - - - +
324C ILE* 3.3 19.6 - - + +
328C ARG* 4.6 11.0 - - - +
368C ARG* 5.1 0.5 + - - -
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Residues in contact with TYR 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C TYR* 3.6 32.7 - + - -
287C HIS 3.3 10.8 + - - +
288C VAL* 3.2 9.8 + - + +
289C LEU 3.0 0.4 - - - -
290C ALA* 1.3 80.4 - - - +
292C ASN* 1.3 79.5 + - - +
293C ALA 3.3 0.7 + - - -
294C SER* 3.4 3.1 + - - -
368C ARG* 2.8 77.7 + - + +
369C GLN 4.2 0.2 + - - -
370C GLY* 3.6 19.6 - - - -
374C GLU* 2.6 33.3 + - + +
375C VAL* 5.7 2.4 - - + +
377C GLU* 6.0 1.3 - - - -
378C LEU* 3.8 26.2 - - + -
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Residues in contact with ASN 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C GLU* 5.6 1.0 + - - -
204C SER* 5.1 5.2 + - - +
288C VAL* 3.0 28.7 + - - +
289C LEU* 3.6 8.7 - - - +
291C TYR* 1.3 81.6 - - - +
293C ALA* 1.3 57.7 + - - +
294C SER 3.0 3.8 - - - -
295C VAL* 2.9 7.7 + - - +
296C VAL* 2.9 35.1 + - + +
300C LEU* 5.4 1.8 - - + -
366C ASN* 3.1 37.3 + - - -
367C PRO* 3.6 25.5 - - + +
368C ARG* 3.3 10.9 - - - +
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Residues in contact with ALA 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C LEU 2.9 11.9 + - - +
290C ALA* 3.4 19.7 - - - +
291C TYR 3.2 1.2 - - - -
292C ASN* 1.3 77.7 - - - +
294C SER* 1.3 59.0 + - - +
295C VAL 3.2 0.2 - - - -
297C ALA* 2.9 33.4 + - - +
300C LEU* 3.6 21.1 - - + -
317C LYS* 5.7 2.3 - - - -
320C ALA* 4.4 12.1 - - + -
321C GLU* 4.5 9.9 - - - +
324C ILE* 4.6 0.7 - - + -
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Residues in contact with SER 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C ALA 4.4 1.0 + - - -
291C TYR 3.4 4.2 + - - -
293C ALA* 1.3 79.3 - - - +
295C VAL* 1.3 65.7 + - - +
297C ALA* 5.5 0.5 - - - +
317C LYS* 6.0 5.4 - - - +
368C ARG* 3.1 36.3 + - - -
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Residues in contact with VAL 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C ASN 2.9 4.6 + - - +
294C SER* 1.3 93.6 - - - +
296C VAL* 1.3 69.8 + - + +
297C ALA 3.7 1.5 + - - -
367C PRO* 3.7 20.0 - - + +
368C ARG* 3.8 26.9 - - + -
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Residues in contact with VAL 296 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C SER* 4.1 18.2 - - - +
292C ASN* 2.9 34.9 + - + +
295C VAL* 1.3 84.9 - - + +
297C ALA* 1.3 66.0 + - - +
298C GLY 3.1 3.1 - - - -
299C ARG* 2.9 38.7 + - + +
300C LEU* 3.0 18.2 + - + +
367C PRO* 3.6 27.8 - - + -
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Residues in contact with ALA 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C ALA* 2.9 26.2 + - + +
294C SER 5.3 0.7 - - - -
295C VAL 3.7 1.8 + - - -
296C VAL* 1.3 75.7 - - - +
298C GLY* 1.3 63.3 + - - +
300C LEU* 3.2 5.0 + - - +
301C LYS* 3.1 20.3 + - - +
316C ASP* 3.9 25.9 - - + +
317C LYS* 4.3 9.6 - - + +
320C ALA* 3.7 18.3 - - + +
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Residues in contact with GLY 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C VAL* 3.1 1.2 + - - +
297C ALA* 1.3 80.9 - - - +
299C ARG* 1.3 60.2 + - - +
301C LYS* 3.3 5.8 + - - +
302C ASP* 3.2 26.6 + - - +
316C ASP* 3.5 31.5 + - - +
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Residues in contact with ARG 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C TYR* 2.8 70.2 + - + +
204C SER* 4.5 7.2 + - - +
205C SER 5.2 1.8 + - - -
208C ALA* 4.1 7.8 - - - +
213C ASP* 3.0 38.0 + - - -
296C VAL* 2.9 33.3 + - + +
298C GLY* 1.3 74.6 - - - +
300C LEU* 1.3 65.2 + - - +
302C ASP* 3.3 11.7 + - - +
303C VAL* 3.3 13.3 + - - +
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Residues in contact with LEU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C PHE* 4.2 11.2 - - + -
204C SER* 3.8 22.2 - - - +
289C LEU* 3.6 48.0 - - + +
292C ASN* 4.7 2.5 - - + -
293C ALA* 3.6 25.8 - - + +
296C VAL* 3.0 20.9 + - + +
297C ALA 3.2 6.0 + - - +
299C ARG* 1.3 78.7 - - - +
301C LYS* 1.3 62.5 + - - +
303C VAL* 3.0 10.9 + - + +
304C GLY 2.9 16.5 + - - -
320C ALA* 4.0 16.2 - - + +
323C THR* 3.4 11.5 + - + +
324C ILE* 4.5 8.1 - - + -
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Residues in contact with LYS 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ALA 3.1 12.6 + - - +
298C GLY* 3.5 10.3 - - - +
299C ARG 3.2 0.2 - - - -
300C LEU* 1.3 76.1 - - - +
302C ASP* 1.3 59.5 + - - +
304C GLY* 2.8 4.0 + - - -
305C VAL* 2.7 39.1 + - + +
311C ILE* 3.2 28.3 - - + +
312C ALA* 3.3 21.3 + - - +
314C LEU 3.1 22.7 + - - +
315C GLY 4.3 1.1 - - - +
316C ASP* 2.9 26.7 + - - +
319C GLY* 3.7 27.4 - - - -
320C ALA* 4.5 0.4 - - - +
323C THR* 3.7 8.3 - - - -
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Residues in contact with ASP 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C TYR* 3.3 28.2 + - + +
217C LEU* 4.5 8.2 - - + +
298C GLY 3.2 17.0 + - - +
299C ARG* 3.5 17.8 + - - +
300C LEU 3.3 0.8 - - - -
301C LYS* 1.3 83.2 - - - +
303C VAL* 1.3 55.7 + - - +
305C VAL* 3.3 12.2 + - - +
306C ALA* 3.0 26.2 + - - +
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Residues in contact with VAL 303 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C ALA 5.5 0.7 - - - +
200C PHE* 3.3 48.5 - - + -
203C TYR* 3.5 28.9 - - + -
204C SER* 6.1 0.2 - - - +
217C LEU* 4.1 10.8 - - + -
220C ALA* 3.9 20.9 - - + -
299C ARG 3.3 15.0 - - - +
300C LEU* 3.0 9.8 + - + +
302C ASP* 1.3 73.4 - - - +
304C GLY* 1.3 68.0 + - - +
306C ALA* 3.1 3.8 + - - +
307C MET* 2.9 28.4 + - - +
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Residues in contact with GLY 304 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C LEU 2.9 7.3 + - - -
301C LYS 2.8 4.7 + - - -
303C VAL* 1.3 76.7 - - - +
305C VAL* 1.3 61.8 + - - +
307C MET* 3.0 17.4 + - - +
309C LEU* 3.3 25.7 + - - +
311C ILE* 4.1 3.6 - - - -
323C THR* 3.0 33.6 - - - +
----------------------------------------------------------
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Residues in contact with VAL 305 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C LYS* 2.7 26.2 + - + +
302C ASP* 3.4 12.8 - - - +
304C GLY* 1.3 72.6 - - - +
306C ALA* 1.3 63.2 + - - +
308C GLY* 2.9 16.1 + - - -
309C LEU 3.6 12.3 - - - +
311C ILE* 4.1 6.2 - - + +
312C ALA* 3.9 39.3 - - + +
----------------------------------------------------------
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Residues in contact with ALA 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C LEU* 3.5 39.5 - - + +
220C ALA* 4.8 2.0 - - + -
221C SER* 3.2 30.3 + - - +
225C LYS* 5.0 2.4 - - - -
302C ASP 3.0 13.4 + - - +
303C VAL* 3.4 10.5 - - - +
305C VAL* 1.3 78.4 - - - +
307C MET* 1.3 58.0 + - - +
308C GLY* 3.1 4.6 + - - -
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Residues in contact with MET 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C LEU* 3.9 33.4 - - + -
200C PHE* 3.9 26.5 - - + -
220C ALA* 3.6 17.7 - - + +
221C SER 5.6 0.4 - - - -
224C ALA* 3.3 36.3 - - + +
225C LYS* 5.5 3.8 - - - +
303C VAL* 2.9 18.5 + - - +
304C GLY* 3.0 9.8 + - - +
306C ALA* 1.3 77.1 - - - +
308C GLY* 1.3 57.1 + - - +
309C LEU* 3.5 14.1 + - + +
323C THR* 4.5 10.1 - - - +
326C ALA* 5.3 8.7 - - + +
327C VAL* 4.7 9.9 - - + -
330C LEU* 4.5 11.7 - - + -
----------------------------------------------------------
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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