Contacts of the helix formed by residues 290 - 318 (chain A) in PDB entry 1ZDT
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 GLU 290 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLU 4.3 8.7 - - - +
289A LEU* 1.3 77.5 - - - +
291A VAL* 1.3 67.8 + - - +
292A ALA* 3.1 7.3 + - + +
293A ASP* 3.2 10.0 + - + +
294A GLN* 3.1 17.3 + - - +
385A ASN* 5.8 4.7 - - - +
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Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLU* 1.3 76.6 + - - +
292A ALA* 1.3 56.6 + - - +
294A GLN* 3.2 20.4 + - - +
295A MET* 2.9 53.7 + - + +
746P ARG* 4.1 26.2 - - + +
749P LEU* 4.7 11.2 - - + +
750P ASP* 3.6 20.0 - - - +
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLU* 3.1 4.5 + - + +
291A VAL* 1.3 77.2 - - - +
293A ASP* 1.3 61.9 + - - +
295A MET* 3.2 20.0 + - + +
296A THR* 3.0 27.3 + - - -
385A ASN* 4.5 14.4 - - - +
746P ARG* 5.8 1.1 - - - +
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Residues in contact with ASP 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 4.1 19.2 - - + +
290A GLU* 3.2 13.3 + - - +
292A ALA* 1.3 76.2 - - - +
294A GLN* 1.3 64.7 - - - +
296A THR* 3.3 3.2 + - - -
297A LEU* 3.0 30.4 + - - +
383A PHE 4.9 0.3 - - - +
384A LEU* 3.5 21.6 - - + +
385A ASN* 3.1 34.6 + - - +
386A ASN* 3.1 35.2 + - - +
390A VAL* 5.6 0.2 - - - +
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Residues in contact with GLN 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ARG* 5.3 3.4 + - - +
286A PHE* 2.7 74.3 + - + +
287A LYS* 3.9 7.9 + - - +
289A LEU* 3.4 20.1 + - + +
290A GLU 3.1 10.6 + - - +
291A VAL* 3.4 29.1 - - - +
293A ASP* 1.3 75.7 - - - +
295A MET* 1.3 62.5 + - - +
297A LEU* 3.6 0.8 + - - -
298A LEU* 3.2 21.5 + - - +
749P LEU* 3.9 19.1 - - + +
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Residues in contact with MET 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A VAL* 2.9 17.4 + - + +
292A ALA* 3.5 26.2 - - + +
293A ASP 3.1 0.2 - - - -
294A GLN* 1.3 75.8 - - - +
296A THR* 1.3 55.5 + - - +
298A LEU 3.3 0.3 + - - -
299A GLN* 2.7 38.5 + - - +
741P GLU* 4.2 12.6 - - + +
742P ASN* 3.9 15.0 - - + +
745P LEU* 3.5 19.6 - - + +
746P ARG* 3.4 52.0 - - - +
749P LEU* 3.6 19.1 - - + -
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Residues in contact with THR 296 (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 ALA 3.0 16.9 + - - -
293A ASP* 3.7 6.8 + - - -
295A MET* 1.3 76.2 - - - +
297A LEU* 1.3 57.2 + - - +
299A GLN* 3.3 6.7 + - + +
300A ASN* 2.9 28.9 + - - +
379A LEU* 3.8 21.1 - - + -
383A PHE* 3.9 21.6 + - + +
384A LEU* 3.7 8.9 - - - +
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A PHE* 3.6 31.9 - - + -
289A LEU* 3.7 23.8 - - + -
293A ASP 3.0 18.4 + - - +
294A GLN 3.8 3.6 - - - +
296A THR* 1.3 75.1 - - - +
298A LEU* 1.3 62.6 + - - +
300A ASN* 3.3 6.2 + - - +
301A CYS* 3.2 27.4 + - - +
376A LEU* 3.7 21.1 - - + +
377A PHE* 4.0 20.9 - - + -
379A LEU* 4.0 19.5 - - + -
384A LEU* 3.7 28.5 - - + -
390A VAL* 5.1 0.9 - - + -
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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
----------------------------------------------------------
273A PHE* 5.7 1.6 - - + -
276A ILE* 5.3 2.0 - - + +
277A VAL* 4.1 34.3 - - + -
280A ALA* 4.1 12.3 - - + -
286A PHE* 3.8 24.0 - - + -
294A GLN 3.2 13.1 + - - +
295A MET 3.9 2.2 - - - +
297A LEU* 1.3 76.9 - - - +
299A GLN* 1.3 59.3 + - - +
301A CYS* 4.1 8.1 - - - -
302A TRP* 3.0 40.3 + - + +
305A LEU* 4.4 8.7 - - + -
376A LEU* 4.0 20.4 - - + -
455A MET* 5.0 0.4 - - - -
745P LEU* 4.1 21.8 - - + -
749P LEU* 4.1 10.1 - - + -
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Residues in contact with GLN 299 (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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295A MET 2.7 23.9 + - - +
296A THR* 3.5 8.1 - - + +
298A LEU* 1.3 71.4 - - - +
300A ASN* 1.3 60.6 + - - +
302A TRP* 3.3 17.0 + - - -
434A LYS* 5.5 0.3 + - - -
455A MET* 3.0 17.2 + - - +
458A ALA 3.0 24.6 + - - +
459A LYS 4.1 7.9 - - - +
460A GLN* 2.8 50.4 + - + +
742P ASN* 2.7 37.7 + - - +
745P LEU* 3.8 5.2 - - + +
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Residues in contact with ASN 300 (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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296A THR 2.9 16.8 + - - +
297A LEU* 3.5 7.8 + - - +
298A LEU 3.2 0.4 - - - -
299A GLN* 1.3 77.9 - - - +
301A CYS* 1.3 61.6 + - - +
302A TRP* 3.8 0.7 - - - -
304A GLU* 3.3 16.3 - - - +
375A ILE 5.1 0.2 + - - -
376A LEU 5.6 0.6 + - - -
378A SER* 2.9 34.4 + - - -
379A LEU* 3.6 31.0 - - + +
460A GLN* 5.5 2.2 - - - -
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Residues in contact with CYS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU 3.2 21.5 + - - +
298A LEU* 3.3 6.9 + - - -
300A ASN* 1.3 83.1 - - - +
302A TRP* 1.3 66.6 + - - +
304A GLU* 3.1 14.0 + - + +
305A LEU* 2.9 45.8 + - - +
375A ILE* 3.6 24.5 - - + +
376A LEU* 3.8 25.6 - - - +
378A SER* 4.7 0.9 - - - +
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Residues in contact with TRP 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A PHE* 3.5 26.1 - + + -
276A ILE* 5.3 0.6 - - - +
298A LEU* 3.0 17.2 + - + +
299A GLN 3.3 21.6 + - - -
300A ASN 3.8 0.9 - - - -
301A CYS* 1.3 80.2 - - - +
303A SER* 1.3 86.9 + - - +
304A GLU* 5.7 0.2 - - - -
305A LEU* 3.5 7.4 + - - +
306A LEU* 3.2 35.7 + - + +
434A LYS* 3.9 19.6 - - + +
437A LEU* 4.5 7.6 - - + -
452A LEU* 3.7 37.2 - - + -
455A MET* 3.7 26.9 + - + -
456A LEU* 3.8 26.0 - - + -
460A GLN* 2.7 28.1 + - - -
1001A PEF 4.2 11.7 - - + -
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TRP* 1.3 93.4 + - - +
304A GLU* 1.3 72.2 + - - +
306A LEU* 3.4 2.9 + - - +
307A VAL* 2.9 33.3 + - - +
430A SER* 3.3 21.0 + - - -
434A LYS* 3.5 24.5 - - - -
1001A PEF 3.7 23.2 - - - +
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ASN 3.3 15.2 - - - +
301A CYS* 3.2 22.9 - - - +
302A TRP* 5.7 0.2 - - - -
303A SER* 1.3 85.0 + - - +
305A LEU* 1.3 56.7 + - - +
307A VAL* 3.5 0.6 + - - -
308A PHE* 2.9 33.0 + - - +
375A ILE* 3.7 19.3 - - + -
426A VAL* 3.8 13.4 - - + +
427A ARG* 4.1 34.3 + - + +
430A SER* 3.4 25.6 + - - +
434A LYS* 5.6 0.7 - - - -
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Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ILE* 3.7 33.0 - - + +
279A TRP* 4.1 17.5 - - + -
298A LEU* 4.4 11.7 - - + -
301A CYS* 2.9 41.1 + - - +
302A TRP* 3.8 5.6 - - - +
304A GLU* 1.3 78.5 - - - +
306A LEU* 1.3 56.3 + - - +
308A PHE* 3.8 3.5 - - + +
309A ASP* 2.8 29.5 + - - +
372A LYS* 3.7 39.0 - - + +
375A ILE* 3.8 15.0 - - + -
376A LEU* 4.4 2.5 - - + +
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ALA* 3.8 19.1 - - + +
272A THR* 3.9 24.2 - - + -
273A PHE* 4.0 11.4 - - + +
276A ILE* 3.9 14.6 - - + -
302A TRP* 3.2 28.3 + - + +
303A SER 3.7 4.3 - - - +
304A GLU 3.3 0.2 - - - -
305A LEU* 1.3 74.6 - - - +
307A VAL* 1.3 59.9 + - - +
309A ASP* 3.3 3.1 + - - +
310A HIS* 3.0 28.2 + - - +
452A LEU* 3.6 30.3 - - + -
1001A PEF 3.8 41.8 - - + +
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Residues in contact with VAL 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A SER 2.9 20.5 + - - +
304A GLU* 3.9 3.6 - - - +
306A LEU* 1.3 76.1 - - - +
308A PHE* 1.3 58.2 + - - +
310A HIS* 3.1 7.6 + - - +
311A ILE* 2.8 45.9 + - + +
426A VAL* 4.2 12.1 - - + +
429A LEU* 4.1 26.5 - - + -
430A SER* 3.8 25.6 - - - +
433A ALA* 4.4 4.7 - - + -
1001A PEF 4.3 34.1 - - + -
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Residues in contact with PHE 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU 2.9 19.7 + - - +
305A LEU* 4.0 4.9 - - + +
307A VAL* 1.3 78.1 - - - +
309A ASP* 1.3 62.4 + - - +
311A ILE* 4.1 10.5 - - + -
312A TYR* 3.0 25.5 + - + +
358A LEU* 4.6 19.1 - - + -
363A LEU* 5.1 6.5 - - + -
368A PHE* 3.6 42.4 - + - -
371A LEU* 3.7 33.2 - - + -
372A LYS* 3.9 14.6 - - + -
375A ILE* 3.7 21.3 - - + -
422A CYS* 6.6 0.2 - - + -
423A LEU* 4.7 8.5 - - + -
426A VAL* 4.0 20.4 - - + -
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Residues in contact with ASP 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A THR* 3.5 20.7 - - + +
276A ILE* 4.2 11.4 - - + +
305A LEU 2.8 20.2 + - - +
306A LEU* 3.4 10.0 - - - +
308A PHE* 1.3 78.2 - - - +
310A HIS* 1.3 62.7 + - - +
312A TYR* 4.2 3.4 - - - +
313A ARG* 2.9 60.0 + - - +
368A PHE* 5.1 13.9 - - - -
372A LYS* 5.7 2.6 + - - -
1001A PEF 6.0 0.7 - - - +
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Residues in contact with HIS 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LEU 3.0 12.2 + - - +
307A VAL 3.1 8.0 + - - +
309A ASP* 1.3 77.6 + - - +
311A ILE* 1.3 64.8 - - + +
313A ARG* 3.1 19.6 + - - +
314A GLN* 3.0 63.2 + - + +
323A ILE* 3.6 22.4 - - + +
324A LEU 4.4 2.6 + - - -
325A LEU* 5.7 0.4 - - - +
348A VAL* 5.7 2.6 + - - +
351A ALA* 4.5 11.9 - - + +
352A GLN* 4.6 3.0 + - - -
1001A PEF 3.1 71.9 - - + +
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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
----------------------------------------------------------
307A VAL* 2.8 35.7 + - + +
308A PHE* 3.6 13.2 - - + +
309A ASP 3.4 0.2 - - - -
310A HIS* 1.3 76.3 - - + +
312A TYR* 1.3 58.5 + - - +
314A GLN* 2.9 20.8 + - - +
315A VAL* 3.1 12.5 + - + +
351A ALA* 3.4 44.4 - - + +
354A LEU* 4.1 19.3 - - + -
355A VAL* 3.9 14.3 - - + +
358A LEU* 3.5 32.5 - - + -
426A VAL* 5.1 0.9 - - + -
429A LEU* 4.4 2.9 - - + -
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Residues in contact with TYR 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A PHE* 3.0 15.3 + - + +
309A ASP 4.2 2.0 - - - +
311A ILE* 1.3 77.1 - - - +
313A ARG* 1.3 62.5 + - - +
315A VAL* 3.1 23.5 + - + -
316A GLN* 3.0 54.8 + - + +
363A LEU* 3.4 30.7 + - + -
364A ASP* 3.9 5.3 - - - -
365A ARG* 3.4 34.7 + - - +
368A PHE* 3.3 61.7 - + + -
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Residues in contact with ARG 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A VAL* 5.3 3.4 - - - +
272A THR* 5.0 2.0 - - - +
309A ASP* 2.9 50.0 + - - +
310A HIS* 3.1 25.8 + - - +
312A TYR* 1.3 78.7 - - - +
314A GLN* 1.3 55.5 + - - +
316A GLN* 3.4 18.2 + - - +
317A HIS* 3.1 25.1 + - - +
324A LEU* 3.4 42.8 + - + +
325A LEU* 3.6 17.6 - - - +
326A VAL* 3.5 38.9 - - - +
1001A PEF 5.9 3.2 - - - +
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Residues in contact with GLN 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A HIS* 3.0 48.3 + - + +
311A ILE 2.9 9.9 + - - +
313A ARG* 1.3 79.8 - - - +
315A VAL* 1.3 61.9 + - - +
317A HIS* 3.5 10.2 - - + +
318A GLY* 3.3 18.2 + - - -
319A LYS 4.8 1.6 + - - +
322A SER 4.1 0.7 - - - +
323A ILE* 3.5 10.2 - - - +
324A LEU* 2.9 44.5 + - - -
352A GLN* 3.4 20.5 + - - +
355A VAL* 3.4 29.2 - - + +
359A LEU* 4.8 0.7 - - - +
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Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ILE* 3.1 17.0 + - + +
312A TYR* 3.1 37.0 + - + -
314A GLN* 1.3 77.2 - - - +
316A GLN* 1.3 67.1 + - + +
317A HIS 3.3 0.5 + - - -
318A GLY* 3.6 7.8 + - - -
355A VAL* 4.1 16.4 - - + +
358A LEU* 4.1 24.5 - - + -
359A LEU* 3.7 33.2 - - + +
363A LEU* 4.1 17.5 - - + +
----------------------------------------------------------
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Residues in contact with GLN 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ASP* 4.7 11.1 + - - +
312A TYR* 3.0 48.1 + - + +
313A ARG* 3.4 25.9 + - - +
315A VAL* 1.3 78.5 - - + +
317A HIS* 1.3 59.7 + - - +
324A LEU* 6.3 0.9 - - + -
365A ARG* 4.0 12.7 - - - +
----------------------------------------------------------
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Residues in contact with HIS 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ARG 3.1 16.2 + - - +
314A GLN* 3.5 12.3 - - - +
315A VAL 3.2 0.2 - - - -
316A GLN* 1.3 79.5 - - - +
318A GLY* 1.3 62.6 + - - +
319A LYS* 3.2 54.6 + - + +
322A SER* 3.0 43.8 + - - -
323A ILE 4.1 0.2 - - - -
324A LEU* 3.8 31.3 + - + +
330A GLU* 3.6 20.3 + - + -
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Residues in contact with GLY 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLN 3.3 9.7 + - - -
315A VAL 3.6 9.2 + - - -
316A GLN 3.6 1.2 - - - -
317A HIS* 1.3 80.5 - - - +
319A LYS* 1.3 61.5 + - - +
320A GLU 4.3 0.4 + - - -
359A LEU* 4.9 13.5 - - - -
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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).
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