Contacts of the helix formed by residues 285 - 311 (chain A) in PDB entry 4IKV
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 THR 285 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LYS 5.8 0.2 - - - +
284A THR* 1.3 75.5 - - - +
286A ALA* 1.3 64.7 + - - +
287A GLU* 3.4 17.3 + - - +
288A GLU* 3.0 37.0 + - - +
289A ARG* 3.0 29.3 + - - +
291A ARG* 4.9 0.5 + - - -
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A THR* 1.3 74.1 - - - +
287A GLU* 1.3 71.2 + - - +
289A ARG* 3.2 17.2 + - - +
290A SER* 3.1 25.3 + - - -
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A THR* 3.4 21.3 + - - +
286A ALA* 1.3 86.1 + - - +
288A GLU* 1.3 60.5 + - - +
290A SER* 3.4 8.8 + - - -
291A ARG* 3.2 42.4 + - - +
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Residues in contact with GLU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LYS 4.2 2.8 - - - +
284A THR* 3.3 13.4 - - - -
285A THR* 3.0 43.0 + - - +
287A GLU* 1.3 76.8 - - - +
289A ARG* 1.3 61.9 + - - +
291A ARG* 3.1 32.4 + - - +
292A VAL* 3.0 26.1 + - - +
427A LEU 4.5 0.9 - - - +
428A ALA 4.9 1.7 - - - +
429A PRO* 3.7 20.9 - - + +
430A ALA* 2.8 38.8 + - - +
431A ALA 5.2 0.2 + - - -
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Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A MET 5.2 0.4 - - - +
279A TYR* 3.6 48.5 + - + +
280A ARG* 4.7 4.3 + - - -
281A SER 3.1 22.6 + - - -
282A PRO* 4.2 6.9 + - - +
284A THR* 3.0 28.8 + - - +
285A THR 3.0 14.2 + - - +
286A ALA* 3.2 15.8 + - - +
288A GLU* 1.3 78.1 - - - +
290A SER* 1.3 61.5 + - - +
292A VAL* 3.2 15.5 + - - +
293A ILE* 3.3 17.5 + - - +
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Residues in contact with SER 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR* 5.6 0.2 - - - -
286A ALA 3.1 14.0 + - - -
287A GLU* 3.7 10.0 - - - -
288A GLU 3.3 0.2 - - - -
289A ARG* 1.3 76.7 - - - +
291A ARG* 1.3 57.5 + - - +
293A ILE* 3.3 11.1 + - - +
294A ALA* 3.0 26.6 + - - +
487A ARG* 5.8 2.2 - - - -
491A LEU* 4.4 19.4 - - - +
605A OLA 4.9 3.0 - - - +
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A THR* 4.9 0.4 + - - -
287A GLU* 3.2 29.2 + - - +
288A GLU* 3.1 38.8 + - - +
290A SER* 1.3 75.8 - - - +
292A VAL* 1.3 59.0 + - - +
294A ALA* 3.2 8.8 + - - +
295A TYR* 2.9 25.5 + - - +
426A LYS 3.8 20.9 + - - -
427A LEU* 3.5 28.8 + - + +
428A ALA 5.5 2.8 + - - -
491A LEU* 3.2 35.3 + - + +
493A LYS* 4.5 15.8 - - - +
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A PHE* 3.8 35.8 - - + +
278A MET* 4.2 19.3 - - + +
279A TYR* 4.3 13.9 - - + +
288A GLU 3.0 18.1 + - - +
289A ARG* 3.2 12.3 + - - +
291A ARG* 1.3 74.6 - - - +
293A ILE* 1.3 66.1 + - + +
295A TYR* 3.2 15.5 + - - +
296A ILE* 3.4 13.0 + - - +
427A LEU 4.0 4.3 - - - +
428A ALA* 5.2 0.2 - - - -
429A PRO* 3.7 33.2 - - + -
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Residues in contact with ILE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR* 3.6 33.7 - - + +
289A ARG 3.3 13.6 + - - +
290A SER* 3.4 10.1 - - - +
292A VAL* 1.3 81.0 - - + +
294A ALA* 1.3 61.5 + - - +
296A ILE* 3.1 38.2 + - + +
297A PRO* 3.4 5.0 - - - +
605A OLA 4.0 31.1 - - + +
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A SER 3.0 14.0 + - - +
291A ARG* 3.2 11.9 + - - +
293A ILE* 1.3 76.3 - - - +
295A TYR* 1.3 60.8 + - - +
297A PRO* 3.3 17.0 - - - +
298A LEU* 4.1 2.6 - - - +
427A LEU* 4.1 12.6 - - + -
488A ILE* 3.9 23.8 - - + +
491A LEU* 3.8 24.0 - - + -
605A OLA 4.3 13.4 - - + +
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Residues in contact with TYR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A PHE* 3.4 30.1 - + + -
278A MET* 5.3 1.6 - - + -
291A ARG 2.9 12.6 + - - +
292A VAL* 3.4 11.9 - - - +
293A ILE 3.1 0.4 - - - -
294A ALA* 1.3 77.6 - - - +
296A ILE* 1.3 65.0 + - - +
298A LEU* 2.9 18.2 + - + +
299A PHE* 2.8 40.7 + + + -
302A SER* 6.1 0.3 - - - -
371A PHE* 5.5 2.8 - + - -
423A ALA* 4.2 5.6 - - + -
424A THR* 2.7 46.5 + - + +
427A LEU* 3.8 30.5 - - + +
428A ALA* 6.5 0.4 - - + -
439A LEU* 3.8 27.1 - - + +
440A TRP* 4.1 15.2 - - - -
443A SER* 5.3 0.7 + - - -
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Residues in contact with ILE 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A PHE* 3.7 31.2 - - + -
292A VAL* 3.6 7.9 - - + +
293A ILE* 3.1 39.6 + - + +
295A TYR* 1.3 77.2 - - - +
297A PRO* 1.3 71.2 - - + +
299A PHE* 3.2 3.1 + - - +
300A VAL* 3.0 33.3 + - + +
605A OLA 4.3 16.4 - - + -
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Residues in contact with PRO 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ILE 3.4 6.7 - - - +
294A ALA 3.3 16.4 - - - +
296A ILE* 1.3 96.1 - - + +
298A LEU* 1.3 56.8 + - - +
300A VAL* 3.9 7.3 - - + +
301A ALA* 3.0 28.2 + - - +
477A LEU* 5.9 1.0 - - - +
481A LEU* 4.2 10.4 - - + +
484A ILE* 4.0 17.5 - - + -
488A ILE* 3.7 14.6 - - + -
605A OLA 3.7 28.5 - - + -
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ALA 4.1 10.3 - - - +
295A TYR* 2.9 17.7 + - + +
297A PRO* 1.3 74.4 - - - +
299A PHE* 1.3 62.0 + - - +
301A ALA* 4.4 0.2 - - - -
302A SER* 2.9 24.9 + - - -
368A PRO* 4.2 12.8 - - + -
371A PHE* 3.3 41.8 - - + -
423A ALA* 4.0 14.6 - - + -
427A LEU* 3.9 13.0 - - + -
481A LEU* 4.0 24.7 - - + -
488A ILE* 4.2 7.0 - - + -
492A MET* 3.5 32.5 - - + -
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Residues in contact with PHE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PRO* 3.7 34.8 - - + -
275A PHE* 3.6 31.2 - + + -
295A TYR* 2.8 28.8 + + + +
296A ILE* 3.6 7.4 - - - +
298A LEU* 1.3 78.0 - - - +
300A VAL* 1.3 65.1 + - + +
302A SER* 3.4 6.1 + - - -
303A ALA* 2.9 33.0 + - + +
439A LEU* 3.8 16.4 - - + -
442A LEU* 3.8 16.4 - - + -
443A SER* 3.5 40.0 - - - -
446A ALA* 4.8 2.9 - - + -
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Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE* 3.0 29.3 + - + +
297A PRO* 3.9 6.7 - - + +
299A PHE* 1.3 84.8 - - + +
301A ALA* 1.3 57.1 + - - +
303A ALA* 3.3 7.1 + - - +
304A MET* 2.9 30.6 + - + +
477A LEU* 3.9 25.4 - - + -
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A PRO 3.0 19.5 + - - +
298A LEU 3.7 3.6 - - - +
299A PHE 3.3 0.2 - - - -
300A VAL* 1.3 74.0 - - - +
302A SER* 1.3 62.3 + - - +
304A MET* 3.4 2.5 + - - +
305A PHE* 2.8 30.7 + - - +
371A PHE* 4.3 9.9 - - + +
375A LEU* 3.8 24.5 - - + +
416A LEU* 4.3 1.9 - - - +
477A LEU* 5.4 2.9 - - + +
481A LEU* 3.6 27.1 - - + -
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Residues in contact with SER 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A TYR* 6.1 0.4 - - - -
298A LEU 2.9 17.7 + - - -
299A PHE* 3.5 4.9 - - - -
301A ALA* 1.3 73.3 - - - +
303A ALA* 1.3 59.1 + - - +
305A PHE* 3.1 1.2 + - - +
306A TRP* 2.8 53.4 + - - -
371A PHE* 4.1 6.4 - - - -
416A LEU* 4.2 12.1 - - - -
440A TRP* 3.2 16.6 - - - -
443A SER* 2.6 26.2 + - - -
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A PHE* 2.9 28.1 + - + +
300A VAL* 3.3 8.0 + - - +
302A SER* 1.3 72.7 + - - +
304A MET* 1.3 57.7 + - - +
307A ALA* 2.8 27.4 + - - +
443A SER* 3.5 24.3 - - - +
446A ALA* 5.2 4.0 - - + -
447A ALA* 3.1 16.2 - - + +
450A ILE* 5.8 5.2 - - + -
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Residues in contact with MET 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A VAL* 2.9 19.9 + - + +
301A ALA* 3.8 4.3 - - - +
303A ALA* 1.3 76.3 - - - +
305A PHE* 1.3 64.3 + - - +
307A ALA* 3.3 17.1 + - - +
308A ILE* 3.3 14.0 + - - +
375A LEU* 3.4 24.7 - - + -
470A ILE* 4.7 15.0 - - - +
473A ALA* 3.9 19.5 - - + -
474A ALA* 4.1 15.9 - - + -
477A LEU* 3.5 30.7 - - + -
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Residues in contact with PHE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ALA 2.8 18.4 + - - +
302A SER 3.5 2.9 - - - +
304A MET* 1.3 77.8 - - - +
306A TRP* 1.3 107.4 + + - +
308A ILE* 3.1 5.7 + - - +
309A GLN* 3.0 32.5 + - + +
374A GLY* 3.4 31.6 - - - -
375A LEU* 3.6 11.8 - - + +
378A ALA* 3.6 16.8 - - + -
409A VAL* 4.0 10.1 - - + -
412A GLY 3.7 2.7 - - - -
413A GLU* 3.4 40.6 - - + -
416A LEU* 3.7 20.4 - - + -
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Residues in contact with TRP 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A SER* 2.8 50.5 + - - +
305A PHE* 1.3 95.0 - + - +
307A ALA* 1.3 66.4 + - - +
309A GLN* 3.4 30.1 - - - -
310A GLU* 2.8 29.2 + - - +
413A GLU* 3.8 17.5 - - - -
416A LEU* 4.2 2.6 - - + +
417A SER* 3.7 36.8 - - - -
440A TRP* 3.6 21.2 + + - -
443A SER* 4.4 0.2 + - - -
444A ASN* 3.5 44.4 - - + +
447A ALA* 3.8 14.8 - - + -
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Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA 2.8 15.6 + - - +
304A MET* 3.4 17.7 - - - +
305A PHE 3.2 0.4 - - - -
306A TRP* 1.3 75.8 - - - +
308A ILE* 1.3 64.1 + - + +
311A GLN* 3.2 17.3 + - - +
447A ALA* 3.4 11.6 - - + +
450A ILE* 5.9 3.6 - - + -
451A ASN* 3.1 39.4 + - - +
454A LEU* 5.7 4.7 - - + -
470A ILE* 6.0 2.2 - - + -
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Residues in contact with ILE 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A MET* 3.3 9.8 + - - +
305A PHE 3.1 8.1 + - - +
307A ALA* 1.3 76.0 - - + +
309A GLN* 1.3 66.7 + - - +
311A GLN* 3.1 19.4 + - - +
312A GLY* 3.6 3.6 + - - -
316A LEU* 5.9 0.9 - - - +
378A ALA* 3.7 36.3 - - + +
379A GLY* 4.1 1.8 - - - +
381A SER* 3.8 11.4 - - - +
382A PHE* 3.9 25.3 - - + -
409A VAL* 4.4 7.9 - - + +
470A ILE* 3.9 30.3 - - + +
474A ALA* 3.7 31.0 - - + -
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Residues in contact with GLN 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A PHE* 3.0 29.9 + - + +
306A TRP* 3.4 29.2 - - + -
308A ILE* 1.3 77.1 - - - +
310A GLU* 1.3 76.4 + - - +
312A GLY* 3.0 20.4 + - - -
313A SER 4.6 0.3 + - - -
342A ASN* 3.4 23.6 + - - +
378A ALA* 5.7 0.2 - - - +
409A VAL* 3.5 31.3 - - + +
413A GLU* 3.6 16.6 - - - +
----------------------------------------------------------
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Residues in contact with GLU 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 4.8 5.0 + - - -
306A TRP* 2.8 25.5 + - - +
309A GLN* 1.3 81.1 + - - +
311A GLN* 1.3 59.6 + - - +
312A GLY 3.0 6.3 + - - -
313A SER* 3.2 28.1 + - - -
314A THR* 3.8 7.3 + - - +
444A ASN* 3.0 30.3 + - - +
448A GLN* 3.5 35.4 + - + +
451A ASN* 3.7 15.3 - - - +
----------------------------------------------------------
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Residues in contact with GLN 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ALA* 3.2 16.6 + - - +
308A ILE* 3.1 12.4 + - - +
310A GLU* 1.3 72.4 - - - +
312A GLY* 1.3 61.3 + - - +
313A SER 3.0 2.7 - - - -
314A THR* 3.1 20.0 + - - +
315A ILE* 3.2 14.7 + - + +
316A LEU* 2.9 28.8 + - - +
382A PHE* 3.4 26.7 - - + -
451A ASN* 2.7 34.1 + - + +
454A LEU* 4.4 7.1 - - - +
466A TYR* 2.6 30.1 + - - -
470A ILE* 4.4 12.3 - - - +
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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