Contacts of the helix formed by residues 290 - 318 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLU 3.7 2.0 + - - -
289B LEU* 1.3 77.5 - - - +
291B VAL* 1.3 69.0 + - - +
292B ALA* 3.0 15.8 + - + +
293B ASP* 3.0 22.4 + - - +
294B GLN* 3.2 7.4 + - - +
385B ASN* 4.2 17.9 + - - +
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Residues in contact with VAL 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU 4.0 0.6 + - - -
290B GLU* 1.3 74.8 - - - +
292B ALA* 1.3 63.6 + - - +
294B GLN* 3.3 18.4 + - - +
295B MET* 3.0 45.4 + - + +
746Q ARG* 4.0 23.6 - - + +
749Q LEU* 4.3 13.2 - - + +
750Q ASP* 3.4 22.7 - - - +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLU* 3.0 9.8 + - + +
291B VAL* 1.3 80.0 - - - +
293B ASP* 1.3 62.3 + - - +
295B MET* 3.3 9.9 + - - +
296B THR* 3.1 25.9 + - - -
385B ASN* 4.4 15.5 - - - +
746Q ARG* 5.4 7.3 - - - +
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Residues in contact with ASP 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU* 3.9 23.1 - - + +
290B GLU* 3.0 16.6 + - + +
292B ALA* 1.3 76.2 - - - +
294B GLN* 1.3 66.4 + - - +
296B THR* 3.2 5.9 + - - -
297B LEU* 3.1 27.5 + - - +
384B LEU* 3.2 22.0 - - + +
385B ASN* 3.1 33.6 + - - +
386B ASN* 3.2 32.4 + - - +
390B VAL* 5.7 0.2 - - - -
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Residues in contact with GLN 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ARG* 4.9 5.5 + - - +
286B PHE* 2.8 72.7 + - + +
287B LYS* 4.0 8.7 + - - +
289B LEU* 3.4 17.8 + - + +
290B GLU 3.2 9.8 + - - +
291B VAL* 3.4 18.7 - - - +
293B ASP* 1.3 78.5 - - - +
295B MET* 1.3 60.8 + - - +
297B LEU 3.7 0.2 + - - -
298B LEU* 3.3 21.1 + - - +
749Q LEU* 3.4 33.0 - - + +
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Residues in contact with MET 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B VAL* 3.0 36.7 + - + +
292B ALA* 3.6 7.0 - - - +
293B ASP 3.2 0.2 - - - -
294B GLN* 1.3 74.3 - - - +
296B THR* 1.3 56.5 + - - +
298B LEU* 3.5 1.0 + - - +
299B GLN* 2.8 47.3 + - - +
741Q GLU* 3.6 18.8 - - - +
742Q ASN* 3.2 35.4 - - + +
745Q LEU* 3.9 15.9 - - + +
746Q ARG* 3.7 33.4 - - - +
749Q LEU* 3.5 18.2 - - + -
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Residues in contact with THR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA 3.1 12.7 + - - -
293B ASP* 3.2 10.7 + - - -
295B MET* 1.3 78.9 - - - +
297B LEU* 1.3 62.2 + - - +
299B GLN* 3.3 15.4 + - - +
300B ASN* 3.1 22.0 + - - +
379B LEU* 3.7 16.3 - - + +
383B PHE* 3.6 28.3 - - + +
384B LEU* 4.0 7.9 - - + -
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PHE* 3.7 22.4 - - + -
289B LEU* 3.6 29.4 - - + -
293B ASP 3.1 15.5 + - - +
294B GLN 3.9 3.4 - - - +
296B THR* 1.3 77.0 - - - +
298B LEU* 1.3 57.4 + - - +
300B ASN* 3.0 19.8 + - - +
301B CYS* 3.2 18.8 + - - +
376B LEU* 3.7 21.1 - - + +
377B PHE* 3.8 25.4 - - + +
379B LEU* 4.0 25.6 - - + -
384B LEU* 3.9 22.0 - - + -
390B VAL* 5.0 0.9 - - + -
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B PHE* 5.0 8.1 - - + -
276B ILE* 5.1 1.8 - - + -
277B VAL* 4.4 19.7 - - + -
280B ALA* 4.3 12.1 - - + -
286B PHE* 3.7 19.3 - - + -
294B GLN 3.3 17.5 + - - +
295B MET 3.9 2.9 - - - +
297B LEU* 1.3 79.4 - - - +
299B GLN* 1.3 61.3 + - - +
301B CYS* 4.0 2.9 - - - -
302B TRP* 3.1 29.9 + - - +
305B LEU* 4.7 14.1 - - + -
376B LEU* 4.1 17.9 - - + -
455B MET* 3.7 4.6 - - + +
745Q LEU* 4.0 23.6 - - + -
749Q LEU* 3.8 20.0 - - + -
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Residues in contact with GLN 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B MET* 2.8 30.9 + - - +
296B THR* 3.6 16.3 + - - +
297B LEU 3.2 0.2 - - - -
298B LEU* 1.3 74.0 - - - +
300B ASN* 1.3 56.5 + - - +
302B TRP* 3.1 21.0 + - - -
434B LYS* 5.5 1.9 + - - -
455B MET* 3.9 15.2 - - + +
458B ALA* 4.3 18.3 - - + +
459B LYS* 5.6 4.2 - - - +
741Q GLU* 4.8 2.1 - - - +
742Q ASN* 3.0 36.1 + - - +
745Q LEU* 4.4 3.8 - - + +
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Residues in contact with ASN 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B THR 3.1 11.3 + - - +
297B LEU 3.0 9.8 + - - +
299B GLN* 1.3 79.8 - - - +
301B CYS* 1.3 66.8 + - - +
302B TRP* 3.8 1.3 - - - -
304B GLU* 3.4 16.2 - - - +
375B ILE 4.7 0.6 + - - -
376B LEU 5.3 0.8 + - - -
378B SER* 3.0 28.7 + - - -
379B LEU* 3.4 33.4 - - + +
427B ARG* 5.8 1.7 + - - -
434B LYS* 5.2 6.3 + - - -
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Residues in contact with CYS 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LEU 3.2 24.3 + - - +
298B LEU* 4.0 9.2 - - - -
299B GLN 3.5 0.2 - - - -
300B ASN* 1.3 83.4 - - - +
302B TRP* 1.3 67.5 + - - +
303B SER 3.3 2.7 - - - -
304B GLU* 3.2 10.9 + - + -
305B LEU* 3.1 42.4 + - - +
375B ILE* 3.6 26.9 - - + +
376B LEU* 3.9 20.0 - - - -
378B SER* 4.9 0.7 - - - +
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Residues in contact with TRP 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B PHE* 3.4 31.5 - + + -
298B LEU* 3.1 15.1 + - - +
299B GLN 3.1 27.8 + - - -
300B ASN 4.9 0.7 - - - -
301B CYS* 1.3 78.2 - - - +
303B SER* 1.3 87.8 + - - +
305B LEU* 3.5 5.5 + - - +
306B LEU* 3.3 38.7 + - + +
434B LYS* 3.9 26.2 - - + +
437B LEU* 3.8 22.2 - - + -
452B LEU* 3.6 39.0 - - + -
455B MET* 3.5 34.0 + - + -
456B LEU* 3.7 25.8 - - + -
1002B PEF 4.5 2.0 - - + -
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Residues in contact with SER 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B TRP* 1.3 104.8 + - - +
304B GLU* 1.3 72.0 + - - +
306B LEU* 3.5 1.6 + - - +
307B VAL* 3.0 34.8 + - - +
430B SER* 3.4 25.8 - - - -
434B LYS* 3.6 19.4 + - - -
1002B PEF 4.3 12.1 - - - +
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ASN* 3.4 13.9 - - - +
301B CYS* 3.2 21.7 + - - +
303B SER* 1.3 88.5 + - - +
305B LEU* 1.3 56.5 + - - +
307B VAL 3.5 0.3 + - - -
308B PHE* 3.0 31.9 + - - +
375B ILE* 3.7 20.9 - - + -
426B VAL* 3.6 13.3 - - + +
427B ARG* 3.5 28.4 + - + +
430B SER* 3.2 18.2 - - - +
431B MET* 3.3 22.9 - - - +
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ILE* 4.0 36.3 - - + +
279B TRP* 4.5 13.2 - - + -
298B LEU* 4.7 9.4 - - + -
301B CYS* 3.1 38.6 + - - +
302B TRP* 3.8 6.5 - - - +
303B SER 3.3 0.2 - - - -
304B GLU* 1.3 76.9 - - - +
306B LEU* 1.3 58.4 + - - +
308B PHE* 3.9 2.8 - - - +
309B ASP* 2.9 30.3 + - - +
372B LYS* 3.6 34.8 - - + +
375B ILE* 3.3 29.4 - - + -
376B LEU* 4.8 2.7 - - + -
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ALA 3.8 19.7 - - - +
272B THR* 4.0 23.6 - - + -
273B PHE* 3.9 19.5 - - + +
276B ILE* 4.1 4.3 - - + -
302B TRP* 3.3 22.9 + - + +
303B SER 3.8 1.8 - - - +
305B LEU* 1.3 75.2 - - - +
307B VAL* 1.3 65.8 + - - +
309B ASP* 3.4 5.5 + - - +
310B HIS* 3.0 22.5 + - - +
452B LEU* 3.7 30.1 - - + -
1002B PEF 3.8 44.4 - - + +
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Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B SER 3.0 24.1 + - - +
304B GLU 3.8 3.1 - - - +
306B LEU* 1.3 75.7 - - - +
308B PHE* 1.3 52.6 + - - +
310B HIS* 3.1 8.7 + - - +
311B ILE* 2.8 50.1 + - + +
426B VAL* 4.0 11.4 - - + -
429B LEU* 4.0 27.6 - - + -
430B SER* 3.5 22.7 - - - +
433B ALA* 4.7 3.8 - - + -
1002B PEF 4.2 34.5 - - + -
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Residues in contact with PHE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLU 3.0 18.5 + - - +
305B LEU* 3.9 3.1 - - - +
307B VAL* 1.3 74.3 - - - +
309B ASP* 1.3 61.1 + - - +
311B ILE* 3.5 10.7 - - + +
312B TYR* 2.8 31.4 + - + +
358B LEU* 4.5 20.9 - - + -
363B LEU* 4.9 6.3 - - + -
368B PHE* 3.4 49.6 - + - -
371B LEU* 3.7 34.8 - - + -
372B LYS* 3.9 11.9 - - + -
375B ILE* 3.9 19.5 - - + -
422B CYS* 6.1 0.9 - - + -
423B LEU* 4.4 10.8 - - + -
426B VAL* 4.0 20.4 - - + -
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Residues in contact with ASP 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B GLU* 5.1 1.0 - - - +
272B THR* 3.4 24.0 - - - +
276B ILE* 4.4 10.7 - - + +
305B LEU 2.9 19.9 + - - +
306B LEU* 3.4 9.7 - - - +
308B PHE* 1.3 77.6 - - - +
310B HIS* 1.3 61.6 + - - +
312B TYR* 3.4 4.2 + - - +
313B ARG* 2.9 60.2 + - - +
368B PHE* 4.9 11.5 - - + -
372B LYS* 5.9 3.2 + - + +
1002B PEF 5.9 1.4 - - - +
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Residues in contact with HIS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LEU 3.0 13.8 + - - +
307B VAL* 3.3 9.9 - - - +
309B ASP* 1.3 72.2 + - - +
311B ILE* 1.3 71.6 + - + +
313B ARG* 3.3 14.5 + - - +
314B GLN* 3.2 61.5 + - + +
323B ILE* 4.4 23.6 - - + +
324B LEU 4.6 4.3 + - - -
325B LEU* 5.2 1.5 - - + +
348B VAL* 5.6 2.4 + - - +
351B ALA* 4.4 9.1 - - + +
352B GLN* 4.4 6.1 + - - -
1002B PEF 3.4 66.2 - - + +
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Residues in contact with ILE 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B VAL* 2.8 39.4 + - + +
308B PHE* 3.3 13.9 + - + +
310B HIS* 1.3 74.5 - - + +
312B TYR* 1.3 64.3 + - - +
314B GLN* 3.1 7.3 + - - +
315B VAL* 3.1 20.2 + - + +
351B ALA* 3.4 43.1 - - + +
354B LEU* 3.9 20.4 - - + -
355B VAL* 3.7 13.6 - - + +
358B LEU* 3.4 33.2 - - + -
426B VAL* 5.1 0.2 - - + -
429B LEU* 4.3 2.5 - - + -
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Residues in contact with TYR 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PHE* 2.8 12.0 + - + +
309B ASP 4.0 2.0 - - - +
311B ILE* 1.3 78.4 - - + +
313B ARG* 1.3 64.7 + - - +
315B VAL* 3.2 16.4 + - + +
316B GLN* 3.0 56.5 + - + +
363B LEU* 3.6 33.8 + - + -
364B ASP* 4.0 3.0 - - - -
365B ARG* 3.4 34.3 + - - +
368B PHE* 3.4 66.6 - + + -
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Residues in contact with ARG 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B GLU* 2.8 33.0 + - - +
240B VAL* 5.7 0.6 - - - +
272B THR* 4.8 2.0 - - - +
309B ASP* 2.9 48.3 + - - +
310B HIS* 3.5 17.4 + - - +
312B TYR* 1.3 75.5 - - - +
314B GLN* 1.3 58.9 + - - +
316B GLN* 3.5 14.5 - - - +
317B HIS* 3.0 24.9 + - - +
324B LEU* 3.3 40.4 + - + +
325B LEU* 3.6 16.5 - - - +
326B VAL* 3.4 34.8 - - - +
1002B PEF 6.1 2.4 - - - +
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Residues in contact with GLN 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B HIS* 3.2 44.8 + - - +
311B ILE 3.1 8.2 + - - +
312B TYR 3.1 0.2 - - - -
313B ARG* 1.3 79.8 - - - +
315B VAL* 1.3 58.6 + - - +
317B HIS* 3.5 11.5 - - + +
318B GLY* 3.0 25.5 + - - -
319B LYS 4.7 1.4 + - - +
322B SER 4.1 0.9 - - - +
323B ILE* 3.2 12.2 - - - +
324B LEU* 2.8 48.5 + - - +
352B GLN* 3.5 21.4 + - - +
355B VAL* 3.5 25.0 - - + +
----------------------------------------------------------
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ILE* 3.1 18.7 + - + +
312B TYR* 3.2 30.3 + - + +
314B GLN* 1.3 79.1 - - - +
316B GLN* 1.3 61.4 + - + +
317B HIS 3.5 0.2 + - - -
318B GLY* 3.6 6.8 + - - -
355B VAL* 4.1 17.9 - - + +
358B LEU* 4.0 24.2 - - + -
359B LEU* 3.6 30.6 - - + +
363B LEU* 4.5 19.7 - - + +
----------------------------------------------------------
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Residues in contact with GLN 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B GLU* 4.6 22.5 - - - +
312B TYR* 3.0 47.7 + - + +
313B ARG* 3.5 20.2 - - - +
315B VAL* 1.3 78.0 - - + +
317B HIS* 1.3 61.1 + - - +
318B GLY* 3.7 0.5 + - - -
324B LEU* 6.2 0.7 - - + -
365B ARG* 4.0 13.7 - - - +
----------------------------------------------------------
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Residues in contact with HIS 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ARG 3.0 17.9 + - - +
314B GLN* 3.3 20.4 + - + +
316B GLN* 1.3 75.6 - - - +
318B GLY* 1.3 66.8 + - - +
319B LYS* 3.3 43.0 + - + +
322B SER* 3.1 43.4 + - - -
324B LEU* 3.7 27.7 + - + +
330B GLU* 3.5 30.4 + - + -
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Residues in contact with GLY 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLN 3.0 14.2 + - - -
315B VAL 3.6 8.0 + - - -
316B GLN 3.4 1.9 - - - -
317B HIS* 1.3 77.3 - - - +
319B LYS* 1.3 61.3 + - - +
359B LEU* 4.9 15.0 - - - -
----------------------------------------------------------
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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