Contacts of the helix formed by residues 293 - 317 (chain A) in PDB entry 3R29
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 293 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU 3.9 4.7 - - - +
292A LEU* 1.3 91.7 - - + +
294A LEU* 1.3 65.5 + - - +
295A ASP* 3.1 5.2 - - + +
296A ASP* 3.0 27.2 + - - +
297A GLN 3.2 8.0 + - - -
384A SER* 4.0 19.1 - - - +
385A ASN* 6.2 0.7 - - + -
388A GLU* 3.7 17.5 - - - +
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU 3.1 4.5 + - - -
293A PRO* 1.3 73.0 - - - +
295A ASP* 1.3 68.0 + - - +
296A ASP 3.3 0.7 + - - -
297A GLN* 3.4 23.9 + - - +
298A VAL* 3.4 22.7 + - + +
2346C ARG* 3.6 38.1 - - + +
2349C LEU* 4.8 13.7 - - + -
2350C MET* 4.5 22.2 - - + -
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Residues in contact with ASP 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PRO* 3.1 4.3 - - + +
294A LEU* 1.3 84.3 - - - +
296A ASP* 1.3 65.1 + - - +
298A VAL* 3.8 11.6 + - - +
299A ILE* 3.6 19.2 + - - +
384A SER* 6.3 0.9 - - - -
2342C GLU* 6.0 0.6 - - - -
2346C ARG* 3.2 35.2 + - - -
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Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 4.4 19.6 - - + +
293A PRO* 3.0 24.3 + - - +
295A ASP* 1.3 77.3 - - - +
297A GLN* 1.3 69.6 + - - +
298A VAL 3.0 1.1 - - - -
299A ILE* 2.7 18.9 + - - +
300A LEU* 3.0 17.1 + - + +
382A GLY 5.0 0.7 - - - +
383A LEU* 4.2 19.1 - - + +
384A SER* 3.1 46.3 + - - -
385A ASN* 3.9 10.2 + - - +
388A GLU* 5.3 0.5 - - - +
389A VAL* 4.9 2.1 - - + +
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Residues in contact with GLN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LYS* 5.7 1.0 + - - +
289A PHE* 3.5 44.1 - - + +
290A SER* 2.8 30.1 + - - +
292A LEU* 2.7 32.4 + - + +
293A PRO 3.6 1.3 - - - +
294A LEU* 3.4 22.7 - - - +
296A ASP* 1.3 77.2 - - - +
298A VAL* 1.3 65.4 + - - +
300A LEU* 3.4 3.2 + - - +
301A LEU* 3.3 26.8 + - - +
2349C LEU* 3.2 29.5 - - + +
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LEU* 3.4 16.0 + - + +
295A ASP* 3.9 10.5 - - - +
296A ASP 2.9 2.6 + - - -
297A GLN* 1.3 76.9 - - + +
299A ILE* 1.3 59.5 + - + +
301A LEU* 3.4 2.3 + - - +
302A ARG* 2.8 40.0 + - + +
2342C GLU* 4.3 27.6 - - + -
2345C ILE* 4.2 33.8 - - + +
2346C ARG* 4.3 28.9 - - + +
2349C LEU* 5.2 3.6 - - + -
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Residues in contact with ILE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ASP 3.6 16.8 - - - +
296A ASP* 2.7 13.3 + - - +
298A VAL* 1.3 70.1 - - + +
300A LEU* 1.3 67.6 + - - +
302A ARG* 3.0 23.3 + - - +
303A ALA* 2.7 27.3 + - + +
380A SER* 3.4 30.5 - - - -
381A LYS 3.5 13.5 - - - +
382A GLY* 3.4 36.1 - - - +
383A LEU* 3.7 13.9 - - + +
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Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PHE* 4.1 13.2 - - + -
292A LEU* 3.7 29.6 - - + -
296A ASP* 3.0 15.2 + - + +
297A GLN 4.0 4.3 - - - +
299A ILE* 1.3 74.7 - - - +
301A LEU* 1.3 59.2 + - - +
303A ALA* 3.0 5.2 + - - +
304A GLY* 2.8 27.5 + - - -
375A LEU* 3.7 35.5 - - + +
376A PHE* 4.2 10.5 - - + -
377A ASN* 3.5 27.1 - - - +
380A SER* 3.7 6.1 - - - +
383A LEU* 4.0 16.4 - - + -
389A VAL* 4.2 10.5 - - + -
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 4.3 21.6 - - + +
280A VAL* 3.7 27.8 - - + -
282A TRP* 5.6 0.2 - - + -
283A ALA* 3.7 26.7 - - + -
289A PHE* 4.1 12.1 - - + -
297A GLN 3.3 16.7 + - - +
298A VAL 3.7 3.1 - - - +
299A ILE 3.2 0.6 - - - -
300A LEU* 1.3 74.0 - - - +
302A ARG* 1.3 67.8 + - - +
304A GLY* 4.4 0.9 - - - +
305A TRP* 2.9 36.7 + - + +
308A LEU* 5.1 6.5 - - + +
375A LEU* 4.3 10.7 - - + +
2345C ILE* 4.0 23.3 - - + -
2349C LEU* 4.7 8.3 - - + -
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Residues in contact with ARG 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A VAL* 2.8 39.5 + - + +
299A ILE* 3.4 22.8 - - - +
301A LEU* 1.3 75.0 - - - +
303A ALA* 1.3 62.7 - - - +
305A TRP* 3.7 15.4 + - - +
2337C THR* 3.2 35.3 + - - +
2339C MET* 4.8 7.5 - - - +
2341C LEU* 5.0 13.9 - - + +
2342C GLU* 4.6 16.4 + - - +
2345C ILE* 4.7 16.5 - - + +
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ILE* 2.7 22.4 + - + +
300A LEU* 3.2 4.3 - - - +
302A ARG* 1.3 77.2 - - - +
304A GLY* 1.3 60.1 + - - +
305A TRP 3.6 0.3 + - - -
306A ASN* 4.9 3.1 + - - +
307A GLU* 5.4 3.3 - - - +
377A ASN* 5.3 9.6 - - + +
380A SER* 3.8 27.6 - - - +
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Residues in contact with GLY 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LEU 2.8 17.8 + - - -
301A LEU 3.7 0.7 - - - -
303A ALA* 1.3 72.0 - - - +
305A TRP* 1.3 68.8 + - - +
306A ASN 2.9 4.0 + - - -
307A GLU* 3.1 8.2 + - - +
308A LEU* 3.0 35.4 + - - +
374A VAL* 4.8 15.9 - - - -
375A LEU* 5.7 0.9 - - - -
377A ASN* 6.3 1.6 - - - -
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Residues in contact with TRP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ALA* 4.4 12.3 - - + -
275A GLN* 4.4 6.1 - - + -
276A LEU* 3.6 49.8 - - + -
279A LEU* 3.3 29.7 - - + +
280A VAL* 5.9 1.8 - - + -
301A LEU* 2.9 23.7 + - + +
302A ARG* 3.7 12.3 - - - +
303A ALA 3.3 1.8 - - - -
304A GLY* 1.3 77.6 - - - +
306A ASN* 1.3 70.0 - - - +
308A LEU* 3.7 2.5 - - - +
309A LEU* 3.0 49.9 + - + +
2341C LEU* 5.9 5.6 - - + -
2345C ILE* 4.8 17.3 - - + -
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Residues in contact with ASN 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA 4.9 3.0 + - - +
304A GLY 2.9 3.6 + - - -
305A TRP* 1.3 82.2 - - - +
307A GLU* 1.3 71.3 + - + +
309A LEU* 3.0 8.5 + - - +
310A ILE* 3.0 29.7 + - - +
429A GLY* 2.8 40.8 + - - -
432A CYS* 4.2 9.3 - - - +
433A LEU* 4.2 21.5 - - - +
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA 5.4 3.5 - - - +
304A GLY* 3.1 6.6 + - - +
306A ASN* 1.3 82.4 - - + +
308A LEU* 1.3 54.0 + - - +
310A ILE* 3.3 9.6 + - - +
311A ALA* 2.7 36.7 + - - +
374A VAL* 3.5 31.5 - - + +
377A ASN* 5.3 2.9 + - - -
422A LEU* 4.9 1.9 - - - +
425A LEU* 3.6 35.6 - - + +
426A ARG* 2.9 53.6 + - - +
429A GLY* 5.0 4.3 - - - -
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 3.6 25.6 - - + -
282A TRP* 3.5 31.0 - - + -
301A LEU* 5.1 7.4 - - + +
304A GLY* 3.0 32.1 + - - +
305A TRP 3.7 0.7 - - - +
307A GLU* 1.3 78.1 - - - +
309A LEU* 1.3 61.9 + - - +
311A ALA* 3.4 4.1 + - + +
312A SER* 3.3 17.7 + - - -
371A ARG* 3.4 55.9 + - + +
374A VAL* 4.5 9.6 - - + -
375A LEU* 4.6 15.9 - - + +
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLN* 3.4 48.2 - - + +
278A THR* 6.0 0.2 - - + -
279A LEU* 4.0 19.5 - - + -
305A TRP* 3.0 48.2 + - + +
306A ASN* 3.0 8.9 + - - +
308A LEU* 1.3 76.1 - - - +
310A ILE* 1.3 66.7 + - + +
312A SER* 3.0 16.6 + - - -
313A PHE* 3.2 22.9 + - + +
316A ARG* 5.0 0.7 + - - -
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Residues in contact with ILE 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ASN* 3.0 24.1 + - - +
307A GLU* 3.5 8.3 - - - +
309A LEU* 1.3 73.6 - - + +
311A ALA* 1.3 60.0 + - - +
313A PHE* 3.7 27.4 - - + -
314A SER* 2.3 42.5 + - - +
349A VAL* 5.1 0.7 - - + -
353A LEU* 4.0 9.9 - - + -
425A LEU* 3.7 17.3 - - + +
428A ILE* 4.0 16.2 - - + -
429A GLY* 3.6 35.0 - - - +
432A CYS* 4.2 14.1 - - - -
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLU 2.7 17.5 + - - +
308A LEU* 3.7 7.0 - - + +
309A LEU 3.2 0.2 - - - -
310A ILE* 1.3 77.5 - - - +
312A SER* 1.3 63.5 + - - +
314A SER* 3.8 5.4 - - - -
315A HIS* 3.4 12.5 + - - +
357A MET* 4.5 5.4 - - + +
367A LEU* 3.6 21.1 - - + +
371A ARG* 4.0 21.8 - - + -
374A VAL* 6.1 0.9 - - + -
425A LEU* 4.1 19.5 - - + -
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Residues in contact with SER 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLU* 5.0 2.9 + - - -
242A VAL* 6.1 0.7 - - - +
278A THR* 6.1 1.2 - - - +
308A LEU 3.3 3.0 + - - -
309A LEU* 3.0 12.9 + - - -
311A ALA* 1.3 76.6 - - - +
313A PHE* 1.3 67.6 + - - +
315A HIS* 3.1 7.4 + - - +
316A ARG* 2.9 39.1 + - - +
367A LEU* 5.2 3.4 - - - -
371A ARG* 3.3 34.8 + - - +
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Residues in contact with PHE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ILE* 5.8 7.4 - - + -
309A LEU* 3.2 20.8 + - + -
310A ILE* 3.7 34.8 - - + -
312A SER* 1.3 79.4 - - - +
314A SER* 1.3 67.2 + - - +
316A ARG* 3.5 19.1 - - - +
317A SER* 2.8 28.1 + - - -
324A ILE* 3.7 21.1 - - + -
325A LEU 3.3 17.0 - - - +
326A LEU* 4.1 19.1 - - + -
327A ALA 5.0 0.7 - - - +
345A ILE* 6.4 0.7 - - + -
349A VAL* 3.8 29.4 - - + -
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Residues in contact with SER 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ILE* 2.3 30.3 + - - +
311A ALA* 3.8 1.1 - - - -
313A PHE* 1.3 89.8 - - - +
315A HIS* 1.3 64.4 + - - +
317A SER* 3.3 9.0 + - - -
318A ILE* 3.7 10.0 + - - +
349A VAL* 4.1 1.4 - - - +
353A LEU* 3.8 17.0 - - - +
354A VAL* 3.9 26.7 - - - +
357A MET* 3.8 24.7 - - - -
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Residues in contact with HIS 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ALA 3.4 5.6 + - - +
312A SER 3.1 8.1 + - - +
314A SER* 1.3 79.3 - - - +
316A ARG* 1.3 68.3 + - - +
318A ILE* 2.9 48.7 + - + +
357A MET* 3.9 9.6 - - - -
362A MET* 3.3 39.3 + - + -
363A ASP* 4.3 4.0 - - - -
364A LYS* 4.3 29.6 - - + -
367A LEU* 3.6 36.6 - - + +
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Residues in contact with ARG 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A GLU* 6.6 0.4 - - + -
244A PRO* 3.8 28.5 - - - +
275A GLN* 5.7 1.2 - - - +
309A LEU 5.0 0.6 + - - -
312A SER* 2.9 24.1 + - - +
313A PHE* 3.5 28.5 - - - +
314A SER 3.1 0.2 - - - -
315A HIS* 1.3 82.6 - - - +
317A SER* 1.3 54.9 + - - +
318A ILE* 3.1 4.5 + - - +
319A ALA* 3.6 16.6 + - - +
325A LEU* 3.0 47.3 + - + +
326A LEU 3.1 1.9 - - - -
327A ALA* 2.9 45.4 - - - +
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Residues in contact with SER 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A PHE 2.8 17.0 + - - -
314A SER 3.8 6.3 - - - -
315A HIS 3.1 0.8 - - - -
316A ARG* 1.3 72.9 - - - +
318A ILE* 1.3 59.9 + - - +
319A ALA 3.0 6.1 - - - +
320A VAL* 3.2 30.5 + - - +
323A GLY 3.8 7.3 - - - +
324A ILE* 3.3 14.9 - - - +
325A LEU* 2.6 31.5 + - - +
354A VAL* 3.7 16.2 - - - +
358A ARG* 4.0 0.5 + - - -
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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