Contacts of the helix formed by residues 289 - 318 (chain B) in PDB entry 3TKL
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 ASP 289 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LYS* 2.8 23.3 + - - -
286B HIS* 2.9 21.5 + - + +
287B LYS 3.7 0.2 + - - -
288B GLY* 1.3 74.8 - - - +
290B GLU* 1.3 62.9 + - - +
291B LYS* 3.3 9.2 + - - +
292B THR* 2.8 41.3 + - - +
293B VAL* 3.0 22.4 + - - +
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Residues in contact with GLU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLY* 3.4 24.1 + - - +
289B ASP* 1.3 74.8 + - - +
291B LYS* 1.3 58.7 + - + +
293B VAL* 4.1 19.5 - - - +
294B GLN* 2.8 56.3 + - + +
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Residues in contact with LYS 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LYS* 6.3 0.2 - - - +
289B ASP* 3.1 7.6 + - - +
290B GLU* 1.3 77.4 - - + +
292B THR* 1.3 68.5 + - + +
294B GLN* 3.3 31.8 + - - +
295B SER* 3.1 22.0 + - - -
298B ARG* 5.2 0.5 + - - -
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Residues in contact with THR 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LYS* 3.7 8.7 - - - +
104A GLN* 4.4 8.5 - - - +
107A GLN* 3.2 37.2 - - - +
286B HIS* 3.3 27.5 - - - +
289B ASP* 2.8 31.6 + - - +
291B LYS* 1.3 75.6 - - + +
293B VAL* 1.3 67.1 + - - +
295B SER* 3.0 10.0 + - - -
296B LEU* 2.8 29.0 + - - +
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B MET* 4.0 16.6 - - + +
286B HIS* 3.4 36.1 - - + +
287B LYS* 4.0 11.0 - - + +
288B GLY 4.5 1.8 - - - +
289B ASP 3.0 12.8 + - - +
290B GLU* 4.1 19.3 - - - +
292B THR* 1.3 80.9 + - - +
294B GLN* 1.3 58.4 + - + +
296B LEU* 3.3 8.8 + - - +
297B GLN* 3.0 53.6 + - + +
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Residues in contact with GLN 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLU* 2.8 54.5 + - + +
291B LYS* 3.6 27.0 - - - +
293B VAL* 1.3 76.0 - - + +
295B SER* 1.3 62.1 + - - +
297B GLN* 3.5 16.4 + - - +
298B ARG* 3.1 44.0 + - - +
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Residues in contact with SER 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLN* 6.1 1.4 - - - +
107A GLN* 4.9 3.5 + - - -
291B LYS 3.1 9.2 + - - -
292B THR* 3.0 23.9 + - - -
294B GLN* 1.3 73.6 - - - +
296B LEU* 1.3 68.4 + - - +
298B ARG* 3.2 26.6 + - - +
299B GLU* 3.0 26.9 + - - +
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLN* 5.1 13.7 - - + +
111A ARG* 5.9 2.5 - - + -
279B LEU* 4.0 24.4 - - + +
282B LEU* 3.8 45.1 - - + +
283B MET* 3.8 19.3 - - + +
286B HIS* 4.3 7.0 - - + -
292B THR* 2.8 38.7 + - - +
293B VAL* 3.7 6.5 - - - +
295B SER* 1.3 74.5 + - - +
297B GLN* 1.3 57.5 + - - +
299B GLU* 3.3 9.3 + - + +
300B HIS* 2.9 29.2 + - - +
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Residues in contact with GLN 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B MET* 3.8 20.3 - - - +
293B VAL* 3.0 39.1 + - + +
294B GLN* 3.6 18.2 - - - +
295B SER 3.2 0.2 - - - -
296B LEU* 1.3 72.9 - - - +
298B ARG* 1.3 61.3 + - - +
300B HIS* 3.7 6.4 - - - +
301B HIS* 2.9 31.0 + - - +
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LYS 5.2 0.8 + - - -
294B GLN* 3.1 43.7 + - - +
295B SER* 3.4 32.0 - - - +
297B GLN* 1.3 77.3 - - - +
299B GLU* 1.3 63.6 + - + +
301B HIS* 3.5 6.0 + - - +
302B ASP* 3.1 33.0 + - - +
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ARG* 3.4 32.7 + - - +
279B LEU* 4.0 17.3 - - + -
295B SER* 3.0 18.9 + - - +
296B LEU* 3.3 11.6 + - + +
298B ARG* 1.3 75.2 - - - +
300B HIS* 1.3 58.8 + - - +
302B ASP* 3.1 14.5 + - - +
303B ILE* 2.9 34.1 + - - +
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Residues in contact with HIS 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B SER* 3.0 45.8 + - - -
279B LEU* 3.7 9.8 - - + +
280B THR* 3.8 12.5 + - - -
283B MET* 3.5 25.4 - - + +
296B LEU 2.9 16.3 + - - +
297B GLN* 3.3 5.8 + - - +
299B GLU* 1.3 77.5 - - - +
301B HIS* 1.3 59.3 + - - +
303B ILE* 3.3 2.8 + - - +
304B LYS* 2.9 43.9 + - + +
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Residues in contact with HIS 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLN 2.9 17.9 + - - +
298B ARG* 3.7 7.9 - - - +
300B HIS* 1.3 79.1 + - - +
302B ASP* 1.3 69.8 + - - +
304B LYS* 3.4 30.5 + - - +
305B ALA* 3.1 27.8 + - + +
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Residues in contact with ASP 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ARG* 3.1 20.8 + - - +
299B GLU* 3.1 20.7 + - - +
301B HIS* 1.3 87.0 + - - +
303B ILE* 1.3 63.7 + - + +
305B ALA* 3.2 6.7 + - - +
306B LYS* 3.1 35.6 + - - +
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Residues in contact with ILE 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ARG* 3.9 12.6 - - - +
272B PHE* 3.4 58.5 - - + +
275B ASP* 3.4 23.6 - - - +
276B SER* 4.2 13.2 - - - +
279B LEU* 4.1 6.7 - - + -
299B GLU* 2.9 22.1 + - - +
300B HIS* 3.8 6.1 - - - +
302B ASP* 1.3 77.0 - - + +
304B LYS* 1.3 57.4 + - - +
306B LYS* 3.2 12.1 + - + +
307B LEU* 2.9 29.0 + - + +
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B SER* 5.8 2.0 - - - +
300B HIS* 2.9 33.1 + - + +
301B HIS* 3.7 32.3 + - - +
302B ASP 3.3 0.2 - - - -
303B ILE* 1.3 76.9 - - - +
305B ALA* 1.3 56.1 + - - +
307B LEU* 3.4 12.7 + - + +
308B ALA* 3.0 28.3 + - + +
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B HIS* 3.1 22.7 + - + +
302B ASP* 3.2 9.8 + - - +
304B LYS* 1.3 77.0 - - - +
306B LYS* 1.3 58.7 + - + +
308B ALA* 3.4 6.8 + - - +
309B ASN* 3.0 37.6 + - - +
392B GLU* 5.9 0.7 - - - +
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Residues in contact with LYS 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 4.0 32.7 - - + -
302B ASP* 3.1 26.5 + - - +
303B ILE* 3.2 12.5 + - + +
305B ALA* 1.3 73.2 - - + +
307B LEU* 1.3 60.8 + - - +
309B ASN* 3.2 2.9 + - - +
310B LEU* 2.9 35.6 + - - +
392B GLU* 3.8 36.0 + - - +
395B ILE* 5.4 5.7 - - - +
396B HIS* 4.4 17.4 + - + +
442B GLN* 5.1 13.9 + - - +
445B LEU* 5.3 3.3 - - - +
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B MET* 3.6 49.9 - - + +
272B PHE* 3.6 32.5 - - + +
273B SER* 3.8 14.8 - - - +
276B SER* 4.7 6.5 - - - -
303B ILE* 2.9 16.1 + - + +
304B LYS* 3.4 14.6 - - + +
306B LYS* 1.3 76.3 - - - +
308B ALA* 1.3 57.0 + - - +
310B LEU* 3.2 8.1 + - - +
311B GLN* 2.9 28.3 + - - +
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LYS* 3.0 18.4 + - + +
305B ALA* 3.7 8.1 - - - +
307B LEU* 1.3 75.2 - - - +
309B ASN* 1.3 65.1 + - - +
311B GLN* 3.4 9.8 + - - +
312B VAL* 3.2 25.2 + - - +
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Residues in contact with ASN 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ALA* 3.0 25.6 + - - +
306B LYS 3.2 3.6 + - - +
308B ALA* 1.3 76.6 - - - +
310B LEU* 1.3 65.6 + - + +
312B VAL* 3.3 12.8 + - - +
313B LEU* 3.5 15.5 + - - +
385B ASP* 5.0 6.5 - - - +
388B THR* 3.8 15.1 - - - +
389B ILE* 3.5 32.9 - - + +
392B GLU* 2.7 37.0 + - + +
396B HIS* 6.3 0.2 - - - +
----------------------------------------------------------
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU* 4.3 15.7 - - + -
265B ILE* 3.8 17.8 - - + +
268B LYS* 3.7 22.0 - - + -
269B MET* 3.5 24.7 - - + -
272B PHE* 3.4 38.8 - - + -
306B LYS 2.9 13.5 + - - +
307B LEU* 3.5 5.6 - - - +
309B ASN* 1.3 76.1 - - + +
311B GLN* 1.3 56.9 + - - +
313B LEU* 3.2 14.2 + - + +
314B HIS* 2.9 26.0 + - - +
396B HIS* 3.9 24.2 - - + +
----------------------------------------------------------
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Residues in contact with GLN 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B MET* 3.5 21.5 - - + +
307B LEU 2.9 13.6 + - - +
308B ALA* 3.6 13.7 - - - +
309B ASN 3.3 0.2 - - - -
310B LEU* 1.3 76.2 - - - +
312B VAL* 1.3 57.7 + - + +
314B HIS* 3.2 21.0 + - - +
315B ASP* 2.8 65.8 + - - +
320B LYS* 5.8 1.2 - - - +
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Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ALA 3.2 16.8 + - - +
309B ASN* 3.5 8.7 - - - +
310B LEU 3.2 0.8 - - - -
311B GLN* 1.3 76.8 - - + +
313B LEU* 1.3 60.7 + - + +
315B ASP* 3.3 10.5 + - - +
316B ALA* 2.9 26.3 + - + +
321B LYS* 4.0 28.9 - - + +
323B TYR* 6.0 0.4 - - + -
340B ALA* 4.2 15.7 - - + -
386B LEU* 5.1 3.6 - - + -
389B ILE* 3.8 27.1 - - + -
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Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B GLU* 6.0 0.2 - - - +
260B LEU* 4.0 28.7 - - + -
265B ILE* 3.7 15.5 - - + -
309B ASN 3.5 4.7 + - - +
310B LEU* 3.2 15.1 + - + +
312B VAL* 1.3 77.3 - - + +
314B HIS* 1.3 59.6 + - - +
316B ALA* 3.3 3.2 + - - +
317B HIS* 2.7 41.3 + - + +
323B TYR* 3.7 21.3 - - + +
334B LEU* 4.1 18.2 - - + -
386B LEU* 5.6 0.4 - - + -
389B ILE* 3.4 35.0 - - + -
393B ALA* 4.2 11.2 - - + -
----------------------------------------------------------
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Residues in contact with HIS 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LEU* 3.8 15.7 - - + +
265B ILE* 4.2 14.5 - - + +
266B ASN* 3.3 28.6 + - - -
269B MET* 4.3 9.0 - - - -
310B LEU 2.9 12.2 + - - +
311B GLN* 3.3 28.7 + - - +
312B VAL 3.2 0.2 - - - -
313B LEU* 1.3 74.2 - - - +
315B ASP* 1.3 66.8 + - - +
317B HIS* 3.0 7.3 + - - +
318B THR* 2.9 49.0 + - + +
320B LYS* 5.7 3.4 - - - -
----------------------------------------------------------
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Residues in contact with ASP 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B GLN* 2.8 51.7 + - - +
312B VAL* 3.3 7.0 + - - +
314B HIS* 1.3 71.8 + - - +
316B ALA* 1.3 57.9 + - - +
318B THR* 3.2 7.4 + - - -
319B GLY 2.9 9.4 + - - -
320B LYS* 2.9 57.1 + - + +
321B LYS* 3.2 29.3 + - + -
----------------------------------------------------------
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Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B VAL 2.9 16.3 + - - +
313B LEU* 3.6 4.7 - - - +
314B HIS 3.1 0.2 - - - -
315B ASP* 1.3 75.8 - - - +
317B HIS* 1.3 63.9 + - - +
318B THR 3.4 0.3 + - - -
319B GLY* 3.5 8.1 + - - -
321B LYS* 3.6 24.0 - - + +
322B SER* 5.8 0.2 - - - -
323B TYR* 3.4 44.9 - - + +
340B ALA* 5.3 1.8 - - + -
----------------------------------------------------------
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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
----------------------------------------------------------
259B GLU* 4.0 19.9 + - - +
260B LEU* 3.3 20.4 + - + -
261B SER* 4.6 1.0 - - - -
262B LEU* 4.2 37.5 - - + -
265B ILE* 3.7 17.0 - - + +
313B LEU* 2.7 33.5 + - + +
314B HIS* 3.6 4.9 - - - +
316B ALA* 1.3 80.0 - - - +
318B THR* 1.3 60.9 + - + +
319B GLY 3.5 0.4 + - - -
323B TYR* 4.4 10.1 - + - -
----------------------------------------------------------
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Residues in contact with THR 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LEU* 5.2 7.2 - - + -
314B HIS* 2.9 42.1 + - + +
315B ASP* 3.2 11.6 + - - -
317B HIS* 1.3 82.7 - - + +
319B GLY* 1.3 57.9 + - - +
320B LYS* 3.3 28.1 + - - +
----------------------------------------------------------
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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