Contacts of the helix formed by residues 296 - 319 (chain A) in PDB entry 5I4V
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 GLY 296 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A GLN 4.1 0.4 + - - -
295A LEU* 1.3 77.6 - - - +
297A ARG* 1.3 60.9 + - - -
298A GLU 3.3 2.9 - - - -
299A ASP* 3.3 11.3 + - - +
300A GLN* 3.1 23.9 + - - +
388A GLU* 4.8 9.2 + - - -
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Residues in contact with ARG 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A LEU* 4.4 13.1 + - - +
295A LEU 3.8 0.6 + - - -
296A GLY* 1.3 69.8 - - - -
298A GLU* 1.3 66.1 + - + +
300A GLN* 3.3 34.4 + - - +
301A ILE* 3.2 28.9 + - + +
472A HIS* 3.2 42.0 - - + +
475A LEU* 4.1 22.1 + - + +
476A GLN* 3.1 36.9 + - - +
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLY 3.3 0.8 - - - -
297A ARG* 1.3 80.0 - - + +
299A ASP* 1.3 59.6 + - - +
301A ILE* 3.5 12.7 + - + +
302A ALA* 3.0 26.3 + - - +
385A ASN 4.9 2.4 - - - +
387A GLN* 2.9 41.4 + - - +
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Residues in contact with ASP 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 4.7 16.8 - - + +
296A GLY* 3.3 12.5 + - - +
298A GLU* 1.3 77.2 - - - +
300A GLN* 1.3 59.5 + - - +
301A ILE 3.2 0.4 - - - -
302A ALA* 3.7 4.2 - - - +
303A LEU* 2.8 40.0 + - + +
385A ASN 3.7 5.7 - - - +
386A VAL* 3.8 11.7 - - + +
387A GLN* 3.0 33.4 + - - +
388A GLU* 3.0 37.0 + - - +
392A VAL* 4.8 2.2 - - + +
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Residues in contact with GLN 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A PHE* 3.1 51.4 + - + +
293A LEU* 3.5 20.7 + - - +
295A LEU* 3.0 25.4 + - + +
296A GLY 3.1 14.7 + - - +
297A ARG* 3.3 39.0 + - - +
298A GLU 3.5 0.2 - - - -
299A ASP* 1.3 75.4 - - - +
301A ILE* 1.3 62.7 + - - +
303A LEU* 3.5 1.2 + - - +
304A LEU* 3.1 31.4 + - - +
475A LEU* 3.6 18.3 - - + +
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Residues in contact with ILE 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A ARG* 3.2 29.9 + - + +
298A GLU* 3.5 13.2 - - + +
300A GLN* 1.3 77.6 - - - +
302A ALA* 1.3 58.6 + - - +
304A LEU* 3.3 2.3 + - - +
305A LYS* 2.9 44.6 + - + +
469A LYS* 6.4 1.1 - - + -
471A LEU* 4.1 26.1 - - + +
472A HIS* 4.3 22.0 - - + +
475A LEU* 3.9 16.6 - - + -
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Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A GLU 3.0 18.5 + - - +
299A ASP* 3.1 6.9 + - - +
301A ILE* 1.3 77.3 - - - +
303A LEU* 1.3 63.5 + - - +
305A LYS* 3.6 9.4 + - - +
306A ALA* 3.4 21.7 + - - +
383A ARG* 4.3 4.7 - - - +
384A PRO* 3.6 23.5 - - - +
385A ASN* 3.9 19.1 - - + +
386A VAL* 4.3 6.1 - - + -
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A PHE* 4.5 3.6 - - + -
295A LEU* 3.7 30.5 - - + -
299A ASP* 2.8 23.3 + - + +
300A GLN 3.9 3.1 - - - +
302A ALA* 1.3 75.2 - - - +
304A LEU* 1.3 62.1 + - + +
306A ALA* 4.1 2.3 - - - +
307A SER* 3.0 28.5 + - - -
378A ILE* 3.4 31.2 - - + +
379A PHE* 4.4 7.0 - - + -
380A SER 3.4 25.1 - - - +
383A ARG* 4.0 11.0 - - + +
386A VAL* 4.0 15.0 - - + -
392A VAL* 4.3 20.0 - - + -
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ILE* 4.8 11.7 - - + -
283A VAL* 3.8 35.0 - - + -
286A ALA* 4.1 10.5 - - + -
292A PHE* 3.3 38.1 - - + -
300A GLN 3.1 11.6 + - - +
301A ILE 3.3 3.3 + - - +
303A LEU* 1.3 77.7 - - + +
305A LYS* 1.3 64.6 + - - +
307A SER* 3.8 5.8 - - - +
308A THR* 2.8 36.8 + - - +
378A ILE* 4.7 8.1 - - + -
456A ILE* 4.7 1.3 - - + -
471A LEU* 4.3 17.0 - - + -
475A LEU* 4.4 14.1 - - + -
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Residues in contact with LYS 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A ILE* 2.9 37.9 + - + +
302A ALA* 3.8 8.7 - - - +
304A LEU* 1.3 75.8 - - - +
306A ALA* 1.3 62.5 + - - +
308A THR* 4.0 5.0 + - - -
309A ILE* 5.0 1.4 + - - +
385A ASN* 5.7 4.3 - - - -
455A GLU* 3.4 17.2 + - + +
456A ILE* 3.8 42.9 - - + +
457A TRP* 4.6 7.8 + - - -
458A ASP* 3.0 31.0 + - - -
464A GLY 5.0 1.4 + - - -
465A SER 6.2 0.6 - - - -
466A GLY* 5.9 3.4 - - - -
471A LEU* 4.4 6.2 - - + +
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Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A ALA 3.4 9.2 + - - +
303A LEU 4.1 0.4 - - - +
304A LEU 3.2 0.4 - - - -
305A LYS* 1.3 80.7 - - + +
307A SER* 1.3 61.3 + - - +
308A THR 3.5 0.2 - - - -
309A ILE* 4.0 13.2 - - - +
310A GLU* 3.9 13.5 - - - +
383A ARG* 3.4 43.4 + - + +
384A PRO* 4.6 9.2 - - + -
432A SER* 4.7 3.6 + - - -
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Residues in contact with SER 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ILE* 5.3 0.2 - - - +
303A LEU 3.0 21.8 + - - -
304A LEU* 3.3 7.8 + - - +
306A ALA* 1.3 74.3 - - - +
308A THR* 1.3 69.1 + - - +
309A ILE 3.3 2.5 - - - -
310A GLU* 3.0 4.8 + - - +
311A ILE* 2.8 41.2 + - - +
377A ASN* 3.4 27.6 - - - -
378A ILE* 4.1 8.9 - - - +
383A ARG* 3.8 10.5 - - - +
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Residues in contact with THR 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A VAL* 4.1 15.9 - - + +
282A ILE* 3.6 27.0 - - + +
304A LEU* 2.8 25.1 + - - +
305A LYS 4.2 2.9 - - - -
306A ALA 3.5 1.0 - - - -
307A SER* 1.3 78.1 + - - +
309A ILE* 1.3 60.0 + - - +
311A ILE* 3.3 1.5 + - - -
312A MET* 2.8 48.1 + - - +
456A ILE* 3.1 29.9 - - + +
457A TRP* 4.4 7.6 - - + -
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Residues in contact with ILE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A LYS 5.0 0.9 + - - +
306A ALA 4.0 12.5 - - - +
308A THR* 1.3 82.3 - - - +
310A GLU* 1.3 62.3 + - + +
312A MET* 3.3 27.7 + - + +
313A LEU* 2.9 41.8 + - + +
349A PHE* 4.6 9.0 - - + -
432A SER* 3.7 31.6 - - - +
435A HIS* 3.7 48.2 - - + +
457A TRP* 4.2 14.9 - - + +
501A 67S 4.9 2.9 - - + +
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Residues in contact with GLU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ALA 3.9 6.8 - - - +
307A SER 3.0 6.8 + - - +
309A ILE* 1.3 87.7 - - + +
311A ILE* 1.3 58.8 + - - +
313A LEU* 3.1 7.4 + - - +
314A LEU* 3.0 30.5 + - - +
377A ASN* 2.7 37.8 + - - +
383A ARG* 2.8 36.8 + - - -
425A LEU 4.8 0.7 - - - +
428A LEU* 3.7 42.7 - - + +
429A ARG* 3.4 16.8 + - - -
432A SER* 4.1 7.5 + - - +
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Residues in contact with ILE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ILE* 3.8 34.5 - - + -
285A PHE* 6.3 0.4 - - + -
307A SER* 2.8 37.9 + - - +
308A THR 3.8 2.9 - - - +
310A GLU* 1.3 73.7 - - - +
312A MET* 1.3 60.6 + - - +
314A LEU* 3.0 8.8 + - + +
315A GLU* 2.8 41.6 + - + +
374A ILE* 4.1 30.5 - - + +
377A ASN* 4.1 11.2 - - - +
378A ILE* 3.7 25.8 - - + -
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Residues in contact with MET 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ALA* 4.7 4.0 - - + +
278A SER* 3.1 31.2 - - - +
279A VAL* 4.7 5.8 - - - -
282A ILE* 4.2 3.6 - - + +
308A THR* 2.8 43.4 + - - +
309A ILE* 3.3 15.9 - - + +
311A ILE* 1.3 74.2 - - - +
313A LEU* 1.3 52.0 + - - +
315A GLU* 3.5 3.4 + - - +
316A THR* 2.6 38.0 + - - -
457A TRP* 3.7 24.2 - - + -
501A 67S 3.4 54.3 - - + +
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Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A ILE* 2.9 29.3 + - + +
310A GLU* 3.4 8.7 - - - +
311A ILE 3.1 0.2 - - - -
312A MET* 1.3 74.6 - - - +
314A LEU* 1.3 64.0 + - - +
316A THR* 3.2 4.2 + - - -
317A ALA* 3.0 23.9 + - - +
349A PHE* 4.9 7.4 - - + -
353A ILE* 3.8 35.9 - - + -
356A PHE* 3.8 12.2 - - + -
428A LEU* 4.0 12.3 - - + -
431A LEU* 3.4 45.1 - - + +
432A SER 4.9 0.9 - - - +
501A 67S 4.0 16.6 - - + -
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A GLU 3.0 15.0 + - - +
311A ILE* 3.4 11.2 - - - +
313A LEU* 1.3 76.2 - - - +
315A GLU* 1.3 62.6 + - - +
316A THR 3.2 0.3 + - - -
317A ALA* 3.2 4.2 + - - +
318A ARG* 3.1 23.3 + - - +
356A PHE* 4.1 21.8 - - + -
360A MET* 4.2 21.1 - - + -
370A TYR* 3.8 18.1 - - + +
373A LEU* 4.5 21.3 - - + +
374A ILE* 3.9 34.5 - - + -
377A ASN* 5.0 5.4 - - + +
424A LYS* 5.7 0.4 - - + -
428A LEU* 4.0 22.2 - - + -
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Residues in contact with GLU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A GLN* 2.6 32.0 + - - -
239A ASN* 5.0 1.3 + - - -
278A SER* 5.8 0.4 - - - +
281A GLU* 4.8 7.0 - - - +
282A ILE* 5.9 2.5 - - + -
311A ILE* 2.8 32.3 + - + +
312A MET* 3.8 4.0 - - - +
314A LEU* 1.3 73.7 - - - +
316A THR* 1.3 63.3 + - - +
318A ARG* 2.9 30.3 + - - +
319A ARG* 2.4 61.9 + - - +
370A TYR* 6.1 0.2 - - - -
374A ILE* 3.2 9.3 - - + +
501A 67S 4.0 21.3 - - + +
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Residues in contact with THR 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A MET 2.6 24.8 + - - -
313A LEU* 3.4 10.3 - - - +
314A LEU 3.1 0.4 - - - -
315A GLU* 1.3 74.5 - - - +
317A ALA* 1.3 66.9 + - - +
319A ARG* 2.9 18.2 + - - +
320A TYR* 3.4 8.3 + - - +
327A ILE* 3.7 36.2 - - + +
329A PHE* 4.2 6.9 - - + -
340A PHE* 5.2 0.9 - - + -
353A ILE* 4.0 18.8 - - + -
357A SER* 4.6 1.3 - - - +
501A 67S 3.4 30.5 - - + +
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Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A LEU 3.0 13.3 + - - +
314A LEU 3.6 7.6 - - - +
316A THR* 1.3 76.4 - - - +
318A ARG* 1.3 63.8 + - - +
320A TYR* 3.0 20.8 + - - +
356A PHE* 4.2 8.3 - - + -
357A SER* 3.5 36.1 + - - +
360A MET* 3.8 23.9 - - + +
361A ARG* 5.9 1.4 + - - +
370A TYR* 4.3 2.9 + - - -
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Residues in contact with ARG 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLN* 3.0 30.7 + - - +
239A ASN* 6.0 1.8 - - - -
314A LEU 3.1 13.4 + - - +
315A GLU* 2.9 47.1 + - - +
317A ALA* 1.3 76.7 - - - +
319A ARG* 1.3 64.0 + - - +
320A TYR 3.4 3.5 + - - +
367A ASP* 3.3 46.6 + - - +
370A TYR* 3.6 47.0 + - + +
374A ILE* 4.2 1.4 - - - +
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Residues in contact with ARG 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ASN* 3.3 32.5 + - - +
281A GLU* 4.1 1.0 + - - -
315A GLU* 2.4 50.7 + - - +
316A THR 2.9 10.6 + - - +
318A ARG* 1.3 84.3 - - - +
320A TYR* 1.3 61.1 + - - +
321A ASN* 3.8 1.4 + - - +
326A CYS 3.8 0.3 - - - +
327A ILE* 3.4 5.5 - - + -
328A THR* 3.0 53.9 + - - +
329A PHE* 4.5 9.4 - - - -
330A LEU* 4.9 5.9 + - - +
501A 67S 3.7 29.8 + - - -
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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