Contacts of the helix formed by residues 298 - 322 (chain A) in PDB entry 1DKF
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 PRO 298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLU 3.8 0.6 - - - +
297A LEU* 1.3 98.3 - - + +
299A LEU* 1.3 65.6 + - - +
300A ASP* 4.7 3.4 - - + +
301A ASP* 3.1 36.0 + - + +
302A GLN* 3.1 20.4 + - - +
389A SER* 3.7 15.7 - - - +
390A ASN* 5.6 0.4 - - + -
393A GLU* 4.0 9.9 - - - +
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU 3.4 2.4 + - - -
298A PRO* 1.3 66.4 - - - +
300A ASP* 1.3 79.1 + - - +
301A ASP 2.7 6.6 + - - -
302A GLN* 2.6 38.7 + - - +
303A VAL* 3.1 14.7 + - + +
457A MET* 5.6 1.6 - - + -
460A LEU* 4.2 30.7 - - + +
461A GLU* 4.0 35.7 - - + +
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Residues in contact with ASP 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A PRO* 3.5 3.7 - - + +
299A LEU* 1.3 91.2 - - - +
301A ASP* 1.3 62.5 + - - +
303A VAL* 3.9 8.9 + - - +
304A ILE* 3.2 28.5 + - + +
389A SER* 6.2 1.6 - - - -
457A MET* 4.5 15.9 - - - +
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Residues in contact with ASP 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU* 4.9 5.5 - - + +
298A PRO* 3.1 37.9 + - + +
299A LEU 2.7 4.9 + - - -
300A ASP* 1.3 76.4 - - - +
302A GLN* 1.3 59.2 + - - +
303A VAL 3.1 2.0 - - - -
304A ILE* 2.8 19.6 + - - +
305A LEU* 2.9 21.9 + - + +
387A GLY 4.2 2.3 - - - +
388A LEU* 3.6 20.3 - - + +
389A SER* 2.7 30.4 + - - -
390A ASN* 3.4 21.8 + - - +
394A VAL* 4.7 4.3 - - - +
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Residues in contact with GLN 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LYS* 5.6 1.8 - - - +
294A PHE* 3.1 53.8 - - + +
295A SER* 3.1 20.2 + - - +
297A LEU* 3.1 22.7 - - + +
298A PRO 3.1 15.1 + - - +
299A LEU* 2.6 22.7 + - - +
301A ASP* 1.3 71.1 - - - +
303A VAL* 1.3 59.3 + - - +
305A LEU* 3.5 2.5 + - - +
306A LEU* 3.3 28.9 + - - +
460A LEU* 3.6 25.0 - - + +
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 3.1 12.8 + - + +
300A ASP* 4.0 11.7 - - - +
301A ASP 3.1 0.8 - - - -
302A GLN* 1.3 80.0 - - - +
304A ILE* 1.3 64.3 + - + +
306A LEU* 3.6 3.9 + - - +
307A ARG* 3.1 35.6 + - - +
453A ASP* 4.4 20.6 - - + +
456A LEU* 4.2 6.6 - - + +
457A MET* 3.8 39.7 - - + +
460A LEU* 3.5 23.3 - - + -
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ASP* 3.2 22.0 - - + +
301A ASP* 2.8 13.0 + - - +
303A VAL* 1.3 78.6 - - + +
305A LEU* 1.3 64.2 + - - +
307A ARG* 3.8 23.0 + - - +
308A ALA* 3.3 22.3 + - - +
385A SER* 3.6 14.6 - - - -
386A LYS 3.5 19.7 - - - +
387A GLY* 2.9 33.4 - - - +
388A LEU* 3.4 20.2 - - + +
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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
----------------------------------------------------------
294A PHE* 4.0 13.9 - - + -
297A LEU* 3.9 27.8 - - + -
301A ASP* 2.9 18.6 + - + +
302A GLN* 3.9 5.2 - - - +
304A ILE* 1.3 77.3 - - - +
306A LEU* 1.3 61.9 + - - +
308A ALA* 3.4 3.8 + - - +
309A GLY* 3.3 17.3 + - - -
379A VAL 5.1 1.0 - - - +
380A LEU* 3.4 38.3 - - + +
381A PHE* 4.1 10.3 - - + -
382A ASN* 3.4 30.5 - - - +
385A SER* 3.8 8.2 + - - +
388A LEU* 4.1 11.0 - - + -
394A VAL* 4.0 13.2 - - + -
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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
----------------------------------------------------------
284A LEU* 4.1 26.9 - - + -
285A VAL* 4.0 19.3 - - + +
288A ALA* 4.2 15.0 - - + -
294A PHE* 4.4 7.4 - - + -
302A GLN 3.3 16.8 + - - +
303A VAL 4.1 0.9 - - - +
305A LEU* 1.3 76.0 - - - +
307A ARG* 1.3 63.8 + - - +
308A ALA 2.9 6.9 + - - -
309A GLY 3.0 0.4 + - - +
310A TRP* 2.9 29.8 + - + +
313A LEU* 4.2 6.5 - - + -
380A LEU* 3.6 24.7 - - + -
456A LEU* 3.5 35.9 - - + -
460A LEU* 4.8 6.7 - - + -
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Residues in contact with ARG 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A VAL* 3.1 20.0 + - - +
304A ILE* 4.1 29.5 + - - +
306A LEU* 1.3 77.8 - - - +
308A ALA* 1.3 59.1 + - - +
310A TRP* 3.3 20.4 + - - +
386A LYS 5.4 2.6 + - - -
452A ILE* 3.9 19.1 - - + -
453A ASP* 3.1 39.5 + - + +
456A LEU* 3.4 13.6 - - + +
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ILE 3.3 18.4 + - - +
305A LEU 3.6 4.9 - - - +
306A LEU 2.9 0.6 - - - -
307A ARG* 1.3 84.6 - - - +
309A GLY* 1.3 57.2 + - - +
310A TRP 3.8 0.4 - - - -
311A ASN* 3.9 8.1 - - - +
312A GLU* 4.5 7.1 - - - +
382A ASN* 4.9 11.0 + - + +
385A SER* 3.7 22.7 - - - +
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Residues in contact with GLY 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU 3.3 8.8 + - - -
306A LEU 3.0 3.0 + - - -
308A ALA* 1.3 80.6 - - - +
310A TRP* 1.3 58.7 + - - +
311A ASN* 3.3 6.7 - - - -
312A GLU* 3.3 6.2 + - - +
313A LEU* 2.8 43.5 + - - +
379A VAL* 4.1 17.2 - - - +
380A LEU* 6.1 0.2 - - - -
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Residues in contact with TRP 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU* 3.8 26.5 - - + -
284A LEU* 3.6 19.3 - - + -
306A LEU 2.9 15.0 + - - +
307A ARG* 3.3 32.1 + - - +
309A GLY* 1.3 76.5 - - - +
311A ASN* 1.3 93.9 + - + +
313A LEU* 3.6 9.6 - - - +
314A LEU* 2.9 40.6 + - + +
438A LEU* 4.7 5.1 - - + +
441A LEU* 4.3 25.4 - - + -
446A LEU* 3.5 33.4 - - + -
452A ILE* 4.0 29.6 - - + +
456A LEU* 5.5 3.1 - - + -
700A OLA 4.3 15.3 - - + -
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Residues in contact with ASN 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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308A ALA 3.9 10.7 - - - +
309A GLY* 3.8 8.0 - - - -
310A TRP* 1.3 110.6 + - + +
312A GLU* 1.3 79.6 + - - +
315A ILE* 3.1 34.6 + - + +
434A GLY* 2.9 37.8 + - - +
435A LEU* 6.0 0.4 - - - +
437A CYS* 5.6 1.8 - - + -
438A LEU* 3.4 22.0 - - + +
700A OLA 3.6 10.8 - - + +
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Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ALA 4.5 8.0 - - - +
309A GLY* 3.3 8.7 + - - +
310A TRP 3.3 0.2 - - - -
311A ASN* 1.3 89.9 + - - +
313A LEU* 1.3 61.4 + - - +
315A ILE* 3.4 1.5 + - - -
316A ALA* 2.9 30.8 + - - +
379A VAL* 4.1 21.1 - - + +
427A LEU* 4.9 1.4 - - - +
430A LEU* 3.5 48.1 - - + +
431A ARG* 3.0 47.8 + - - +
434A GLY* 4.4 6.7 - - - -
382B THR* 5.9 0.3 - - - +
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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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284A LEU* 4.0 20.2 - - + -
287A TRP* 3.8 21.5 - - + -
306A LEU* 4.2 14.6 - - + -
309A GLY* 2.8 35.4 + - - +
310A TRP* 3.6 11.4 - - - +
311A ASN 3.3 0.2 - - - -
312A GLU* 1.3 78.5 - - - +
314A LEU* 1.3 60.7 + - + +
316A ALA* 3.4 3.5 + - - +
317A SER 3.3 16.3 + - - -
376A ARG* 3.3 61.7 + - + +
379A VAL* 4.0 11.7 - - + -
380A LEU* 4.6 7.6 - - + +
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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
----------------------------------------------------------
277A ALA* 3.6 38.8 - - + +
280A GLN* 3.7 26.7 - - + +
281A LEU* 4.4 8.1 - - + +
284A LEU* 4.1 24.2 - - + -
310A TRP* 2.9 29.9 + - + +
313A LEU* 1.3 77.8 - - - +
315A ILE* 1.3 65.8 + - - +
316A ALA 3.3 0.2 + - - -
317A SER* 3.3 5.6 + - - -
318A ALA* 3.0 24.8 + - - +
376A ARG* 4.7 5.6 - - - +
700A OLA 3.8 33.1 + - + -
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Residues in contact with ILE 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ASN* 3.1 20.5 + - + +
312A GLU* 3.4 5.1 + - - +
314A LEU* 1.3 76.4 - - - +
316A ALA* 1.3 56.2 + - - +
318A ALA* 3.9 4.8 - - - +
319A SER* 2.9 37.9 + - - +
354A VAL* 4.4 8.7 - - + -
358A LEU* 3.8 17.9 - - + -
430A LEU* 3.7 15.5 - - + -
433A ILE* 4.2 10.1 - - + -
434A GLY* 3.8 22.4 - - - -
437A CYS* 3.7 30.1 - - + -
700A OLA 3.7 27.4 - - + -
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Residues in contact with ALA 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU 2.9 17.7 + - - +
313A LEU* 3.6 6.7 - - - +
314A LEU 3.1 0.2 - - - -
315A ILE* 1.3 78.0 - - - +
317A SER* 1.3 61.3 + - - +
319A SER* 3.3 6.0 + - - -
320A HIS 3.2 17.3 + - - -
358A LEU* 6.0 0.9 - - - -
362A MET* 4.0 5.4 - - + +
372A LEU* 3.4 19.9 - - + +
375A LEU* 6.5 0.9 - - + -
376A ARG* 4.1 20.6 - - + +
379A VAL* 6.4 0.2 - - + -
430A LEU* 4.2 17.7 - - + +
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Residues in contact with SER 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLU* 3.6 4.9 + - - -
247A VAL* 5.9 0.5 - - - +
280A GLN* 4.7 9.8 + - - -
313A LEU 3.3 5.3 + - - -
314A LEU* 3.9 7.0 - - - -
316A ALA* 1.3 78.4 - - - +
318A ALA* 1.3 58.6 + - - +
319A SER 3.3 0.2 + - - -
320A HIS* 3.3 2.9 + - - +
321A ARG* 2.9 44.3 + - - +
372A LEU* 4.3 9.5 - - - +
376A ARG* 3.0 39.7 + - - +
700A OLA 5.3 0.7 - - - -
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Residues in contact with ALA 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LEU 3.0 16.7 + - - +
315A ILE* 4.1 2.7 - - - +
317A SER* 1.3 76.6 - - - +
319A SER* 1.3 57.3 + - - +
321A ARG* 3.3 29.8 + - - +
322A SER* 2.6 33.8 + - - -
329A ILE* 4.4 16.3 - - + +
330A LEU 4.3 0.3 - - - +
700A OLA 3.7 21.5 - - + +
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Residues in contact with SER 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ILE 2.9 22.2 + - - -
316A ALA* 3.5 6.3 - - - -
317A SER 3.2 0.2 - - - -
318A ALA* 1.3 74.9 - - - +
320A HIS* 1.3 65.3 + - - +
322A SER 3.1 8.7 + - - -
323A ILE* 3.6 4.3 + - - +
329A ILE* 5.7 0.4 - - - -
354A VAL* 3.4 25.9 - - - +
358A LEU* 3.4 19.8 - - - +
359A VAL* 3.2 27.3 - - - +
362A MET* 3.8 17.0 - - - -
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Residues in contact with HIS 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ALA 3.2 8.5 + - - +
317A SER 3.7 1.6 - - - +
319A SER* 1.3 78.4 - - - +
321A ARG* 1.3 63.7 + - - +
323A ILE* 3.0 47.9 + - + +
362A MET* 3.6 8.7 - - - -
367A MET* 2.6 40.0 + - + -
368A ASP* 3.8 1.6 + - - -
369A LYS* 3.9 40.1 - - + +
372A LEU* 3.7 39.4 - - + +
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Residues in contact with ARG 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PRO* 3.5 33.6 - - - +
280A GLN* 4.0 9.7 - - - +
317A SER* 2.9 33.0 + - - +
318A ALA* 3.3 18.6 - - - +
319A SER 3.3 0.2 - - - -
320A HIS* 1.3 77.7 + - - +
322A SER* 1.3 57.9 - - - +
323A ILE 3.4 1.4 + - - -
324A ALA* 4.3 9.0 + - - +
330A LEU* 3.1 43.2 + - + +
331A LEU 3.8 5.5 + - - -
332A ALA* 3.1 11.3 - - - +
700A OLA 2.5 43.2 + - - -
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Residues in contact with SER 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ALA 2.6 22.0 + - - -
319A SER 3.1 7.1 + - - -
320A HIS 3.0 1.0 - - - -
321A ARG* 1.3 76.0 - - - +
323A ILE* 1.3 64.6 + - - +
324A ALA 3.1 2.2 - - - -
325A VAL* 3.0 38.3 - - - +
328A GLY 3.9 9.1 - - - +
329A ILE* 3.4 6.7 - - - +
330A LEU* 3.0 22.3 + - - +
359A VAL* 3.7 19.3 - - - +
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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