Contacts of the helix formed by residues 298 - 324 (chain A) in PDB entry 4CEJ
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 298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A GLY* 3.1 23.0 + - - +
297A PHE* 1.3 83.3 - - - +
299A PRO* 1.3 61.8 - - - +
300A ALA* 3.4 17.2 + - - +
301A LEU* 2.9 20.2 + - + +
302A LEU* 2.5 36.4 + - - -
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Residues in contact with PRO 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 ASP* 5.3 9.6 - - - +
297A PHE* 4.2 4.0 - - + +
298A ASP* 1.3 90.2 - - - +
300A ALA* 1.3 55.6 + - - +
302A LEU* 3.7 13.7 - - + +
303A ASP* 3.0 32.2 + - - +
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ASP* 3.0 12.3 + - - +
299A PRO* 1.3 81.0 - - - +
301A LEU* 1.3 58.3 + - - +
303A ASP* 3.7 3.4 - - - +
304A GLU* 3.0 33.6 + - - +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.6 49.4 - - + +
246A ALA* 4.2 13.2 - - + -
248A GLY* 4.3 4.5 - - - +
249A GLY* 3.8 19.5 - - - +
250A PRO* 3.7 13.0 - - + -
298A ASP* 2.9 21.9 + - + +
300A ALA* 1.3 75.7 - - - +
302A LEU* 1.3 66.0 + - - +
304A GLU* 3.5 10.6 - - - +
305A ALA* 3.0 22.9 + - + +
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A GLY 5.5 0.2 + - - -
250A PRO* 4.7 13.3 - - + +
253A ARG* 3.6 21.0 + - - +
292A VAL* 3.6 38.6 - - + +
294A GLY 5.6 1.8 - - - +
297A PHE* 4.4 15.9 - - + -
298A ASP 2.5 21.7 + - - +
299A PRO* 3.7 14.4 - - + +
301A LEU* 1.3 75.2 - - - +
303A ASP* 1.3 64.4 + - + +
305A ALA* 3.8 2.9 + - - +
306A THR* 3.5 21.1 + - + +
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Residues in contact with ASP 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A PRO 3.0 19.3 + - - +
300A ALA* 3.7 4.0 - - - +
302A LEU* 1.3 80.0 - - + +
304A GLU* 1.3 57.2 + - - +
306A THR* 2.8 23.9 + - - -
307A ASP* 2.8 24.8 - - - +
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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
----------------------------------------------------------
239A ARG* 5.3 6.8 + - - -
243A LEU* 4.8 11.8 - - + +
300A ALA* 3.0 19.6 + - - +
301A LEU* 3.1 13.2 + - - +
303A ASP* 1.3 77.9 - - - +
305A ALA* 1.3 65.6 + - - +
306A THR 3.2 1.1 - - - -
307A ASP* 3.0 28.2 + - + +
308A LEU* 3.2 19.6 + - + +
896A ALA* 5.3 9.2 - - - +
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ALA* 4.5 2.8 - - + +
243A LEU* 4.3 22.3 - - + +
250A PRO* 4.5 15.9 - - + -
253A ARG* 5.7 2.0 - - - -
257A PHE* 4.1 25.7 - - + -
301A LEU 3.0 15.2 + - - +
302A LEU 4.2 4.0 - - - +
304A GLU* 1.3 75.3 - - - +
306A THR* 1.3 63.9 + - + +
308A LEU* 3.1 8.2 + - - +
309A ARG* 3.0 21.7 + - - +
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Residues in contact with THR 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ARG* 3.5 40.6 - - - +
257A PHE* 5.8 0.7 - - - -
289A ALA* 5.4 4.0 - - + -
302A LEU* 3.5 10.1 + - + +
303A ASP* 2.8 31.7 + - - -
305A ALA* 1.3 75.6 - - + +
307A ASP* 1.3 58.1 + - - +
309A ARG* 3.7 9.3 - - - +
310A ASN* 2.9 44.0 + - - -
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Residues in contact with ASP 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LYS* 5.6 0.2 - - - -
303A ASP* 2.8 27.1 - - - +
304A GLU* 3.0 19.4 + - + +
306A THR* 1.3 84.3 + - - +
308A LEU* 1.3 59.2 + - + +
310A ASN* 3.4 10.2 + - - +
311A GLY* 2.9 24.9 + - - -
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LYS* 3.4 49.0 - - + +
237A LEU* 4.9 1.1 - - - +
239A ARG* 3.6 22.0 - - + +
240A ALA* 3.5 25.1 - - + +
243A LEU* 4.3 11.4 - - + -
304A GLU* 3.2 24.7 + - + +
305A ALA 3.1 9.5 + - - +
307A ASP* 1.3 83.1 - - + +
309A ARG* 1.3 61.9 + - - +
311A GLY* 3.0 11.7 + - - -
312A ALA* 3.0 12.0 + - - +
896A ALA* 6.2 4.7 - - + -
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Residues in contact with ARG 309 (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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237A LEU* 4.2 13.2 - - + +
240A ALA* 5.2 0.6 - - - +
253A ARG* 6.1 1.8 - - - +
256A ASN* 3.9 17.4 + - - +
257A PHE* 3.7 26.0 - - + -
260A ASP* 2.8 40.8 + - - +
286A PHE* 3.5 25.3 + - + +
287A LYS* 2.7 33.1 + - - +
289A ALA* 4.0 20.3 - - - +
305A ALA 3.0 12.1 + - - +
306A THR* 3.7 11.4 - - - +
308A LEU* 1.3 76.5 - - - +
310A ASN* 1.3 59.5 + - - +
312A ALA* 3.1 7.3 + - - +
313A LYS* 3.0 28.6 + - + +
41X C 4.2 7.7 + - - -
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Residues in contact with ASN 310 (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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306A THR* 2.9 32.1 + - - +
307A ASP* 3.7 10.9 + - - +
309A ARG* 1.3 75.6 - - - +
311A GLY* 1.3 60.1 + - - +
313A LYS* 3.3 25.5 + - + +
314A LYS* 2.9 29.3 + - - +
41X C 4.6 12.2 + - - -
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Residues in contact with GLY 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LYS* 4.1 22.9 - - - -
307A ASP 2.9 14.6 + - - -
308A LEU 3.0 6.2 + - - -
310A ASN* 1.3 75.1 - - - +
312A ALA* 1.3 62.0 - - - +
314A LYS* 3.3 6.3 + - - +
315A LEU* 3.0 30.0 + - - +
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Residues in contact with ALA 312 (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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233A ALA* 4.1 24.6 - - + +
236A LYS* 4.3 2.3 - - + +
237A LEU* 3.8 30.7 - - + -
264A ILE* 4.6 0.4 - - + -
286A PHE* 3.9 13.7 - - + -
308A LEU 3.0 7.8 + - - +
309A ARG 3.1 10.3 + - - +
311A GLY* 1.3 75.5 - - - +
313A LYS* 1.3 63.1 + - - +
315A LEU* 3.4 3.0 + - - +
316A LEU* 3.0 27.7 + - - +
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Residues in contact with LYS 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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286A PHE* 3.4 39.3 - - + +
309A ARG* 3.0 17.9 + - + +
310A ASN* 3.3 26.2 - - - +
311A GLY 3.2 0.2 - - - -
312A ALA* 1.3 76.1 - - - +
314A LYS* 1.3 58.1 + - - +
316A LEU* 3.1 7.3 + - - +
317A GLU* 2.9 30.1 + - - +
41X C 4.1 11.1 + - - +
42X G 2.4 40.6 + - - +
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Residues in contact with LYS 314 (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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310A ASN 2.9 14.9 + - - +
311A GLY* 3.8 7.2 - - - +
313A LYS* 1.3 76.9 - - - +
315A LEU* 1.3 65.2 + - + +
317A GLU* 3.4 9.0 + - + +
318A LYS* 2.9 34.5 + - + +
9X T 5.4 3.4 + - - +
10X A 3.9 20.5 + - - -
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Residues in contact with LEU 315 (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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229A VAL* 3.5 34.1 - - + +
232A GLY* 3.6 8.5 - - - +
233A ALA* 3.6 23.6 - - + +
236A LYS* 4.1 13.7 - - + +
311A GLY* 3.0 25.7 + - - +
312A ALA 3.6 4.7 - - - +
314A LYS* 1.3 86.4 - - + +
316A LEU* 1.3 58.0 + - + +
318A LYS* 3.3 7.1 + - - +
319A LEU* 3.0 28.6 + - - +
908A PHE* 3.5 42.6 - - + -
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Residues in contact with LEU 316 (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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229A VAL 5.9 0.7 - - - +
230A LEU* 3.9 28.3 - - + -
233A ALA* 4.8 4.9 - - + -
264A ILE* 4.4 16.8 - - + -
267A LEU* 4.3 9.9 - - + -
281A VAL* 4.4 11.1 - - + +
284A VAL* 3.6 41.3 - - + +
286A PHE* 4.4 15.0 - - + -
312A ALA 3.0 14.9 + - - +
313A LYS* 3.1 8.9 + - - +
315A LEU* 1.3 74.6 - - + +
317A GLU* 1.3 60.3 + - - +
319A LEU* 3.1 8.5 + - + +
320A LYS* 2.8 30.0 + - - +
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Residues in contact with GLU 317 (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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313A LYS 2.9 16.8 + - - +
314A LYS* 3.8 10.3 - - + +
316A LEU* 1.3 75.8 - - - +
318A LYS* 1.3 59.4 + - + +
320A LYS* 3.5 22.5 - - - +
321A THR* 2.9 48.3 + - + +
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Residues in contact with LYS 318 (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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229A VAL* 6.5 0.7 - - + -
314A LYS* 2.9 24.4 + - + +
315A LEU* 3.5 7.4 - - - +
316A LEU 3.2 0.2 - - - -
317A GLU* 1.3 77.2 - - - +
319A LEU* 1.3 59.5 + - - +
321A THR* 3.1 8.0 + - - +
322A ASP* 2.7 73.2 + - - +
853A LYS* 3.4 18.4 - - - +
9X T 5.4 9.0 - - - +
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Residues in contact with LEU 319 (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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225A ASP* 5.0 1.3 - - - +
226A ILE* 3.9 18.2 - - + -
229A VAL* 3.7 26.5 - - + -
230A LEU* 3.7 33.0 - - + -
281A VAL* 4.3 18.6 - - + -
315A LEU 3.0 15.5 + - - +
316A LEU* 3.4 11.2 - - + +
318A LYS* 1.3 75.5 - - - +
320A LYS* 1.3 62.9 + - - +
322A ASP* 3.4 3.5 + - - -
323A TYR* 3.1 52.7 + - + -
324A PHE* 3.7 15.3 - - + -
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Residues in contact with LYS 320 (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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281A VAL* 4.0 9.4 - - + +
282A PRO* 3.7 41.1 - - + +
316A LEU 2.8 16.6 + - - +
317A GLU* 3.5 24.9 - - - +
319A LEU* 1.3 75.1 - - - +
321A THR* 1.3 69.9 + - - +
324A PHE* 2.7 51.4 + - + +
325A THR* 3.5 17.8 + - - +
1020B LEU* 5.6 5.7 - - - +
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Residues in contact with THR 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A GLU* 2.9 41.7 + - - +
318A LYS* 3.1 14.7 + - - +
320A LYS* 1.3 85.3 - - - +
322A ASP* 1.3 64.1 + - - +
325A THR* 3.6 15.8 + - + -
1019B ASN* 2.4 42.1 + - + +
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Residues in contact with ASP 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ASP* 4.5 0.2 - - - +
318A LYS* 2.7 58.2 + - - +
319A LEU* 3.6 6.3 - - - +
321A THR* 1.3 83.3 + - - +
323A TYR* 1.3 78.0 + - + +
325A THR* 5.2 1.0 + - - -
331A HIS* 4.7 6.4 + - - -
849A ILE* 3.1 32.1 - - + +
853A LYS* 3.1 22.2 + - - -
1019B ASN* 4.7 3.7 + - - +
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Residues in contact with TYR 323 (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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221A TYR 4.9 0.2 + - - -
222A VAL* 3.5 35.9 - - + +
225A ASP* 2.5 39.4 + - + +
226A ILE* 4.2 8.7 - - + -
274A PHE* 3.8 10.9 - + + -
319A LEU* 3.1 36.4 + - + -
322A ASP* 1.3 90.2 - - + +
324A PHE* 1.3 85.9 + + + +
325A THR* 3.7 2.2 - - - -
326A ARG 3.7 2.1 - - - +
331A HIS* 3.1 29.5 + - - -
846A LEU* 4.1 15.5 - - + -
849A ILE* 3.7 25.5 + - + +
850A ALA* 5.5 0.2 - - - -
853A LYS* 3.6 9.4 - - - +
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Residues in contact with PHE 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ILE* 4.3 5.2 - - + -
274A PHE* 3.4 34.3 - + - -
277A LEU* 3.6 22.0 - - + -
278A TYR* 3.6 52.3 - - + -
281A VAL* 3.6 34.1 - - + -
282A PRO* 4.2 21.3 - - + +
319A LEU* 3.7 26.5 - - + -
320A LYS* 2.7 27.6 + - - +
323A TYR* 1.3 90.3 - - + +
325A THR* 1.3 59.5 + - - +
326A ARG 3.4 1.1 - - - +
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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