Contacts of the helix formed by residues 246 - 268 (chain A) in PDB entry 4JYH
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 THR 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A LEU* 1.3 77.0 - - - +
247A ILE* 1.3 55.4 + - - +
248A ALA 4.3 0.2 - - - -
249A ASP* 3.1 24.2 + - - +
250A GLN* 2.7 35.7 + - - +
336A GLU* 2.7 30.6 + - + +
337A GLU* 2.8 33.1 + - + +
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Residues in contact with ILE 247 (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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245A LEU 5.1 0.7 - - - +
246A THR* 1.3 73.4 - - - +
248A ALA* 1.3 65.7 + - - +
250A GLN* 4.1 16.2 - - - +
251A ILE* 2.9 31.5 + - - +
634G HIS* 4.1 26.0 - - + +
637G LEU* 4.3 12.8 - - + -
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Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A THR* 4.3 0.4 - - - -
247A ILE* 1.3 78.6 - - - +
249A ASP* 1.3 51.3 + - - +
251A ILE* 3.6 4.9 - - - +
252A THR* 2.7 43.0 + - - +
334A ASP 5.9 1.3 - - - +
336A GLU* 3.4 31.0 - - + +
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Residues in contact with ASP 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 4.3 10.8 - - + +
246A THR* 3.1 27.9 + - - +
248A ALA* 1.3 76.6 - - - +
250A GLN* 1.3 59.6 + - - +
252A THR* 3.6 4.6 - - - -
253A LEU* 2.8 38.6 + - - +
334A ASP 4.2 2.1 - - - +
335A LEU* 3.5 16.6 - - + +
336A GLU* 2.6 30.4 + - - +
337A GLU* 2.8 36.6 + - - +
341A VAL* 4.5 3.9 - - + +
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Residues in contact with GLN 250 (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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242A PHE* 3.3 56.6 - - + +
243A THR* 3.5 26.7 + - - +
245A LEU* 3.1 25.2 + - + +
246A THR 2.7 28.5 + - - +
247A ILE* 4.0 16.9 - - - +
249A ASP* 1.3 72.3 - - - +
251A ILE* 1.3 64.2 + - - +
253A LEU* 3.8 1.2 - - - +
254A LEU* 3.1 30.5 + - - +
637G LEU* 4.0 18.4 - - + +
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Residues in contact with ILE 251 (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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247A ILE 2.9 25.9 + - - +
248A ALA* 3.6 6.1 - - - +
250A GLN* 1.3 75.0 - - - +
252A THR* 1.3 65.6 + - - +
254A LEU* 3.3 6.6 + - + +
255A LYS* 3.0 50.8 + - + +
405A GLU* 5.5 0.7 - - - +
633G LEU* 3.6 26.9 - - + +
634G HIS* 3.4 36.8 - - + +
637G LEU* 3.4 25.1 - - + -
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Residues in contact with THR 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ALA* 2.7 28.1 + - - +
249A ASP* 3.6 8.1 - - - -
251A ILE* 1.3 75.6 - - - +
253A LEU* 1.3 63.7 + - - +
255A LYS* 3.4 7.4 + - - +
256A ALA* 3.1 23.5 + - + +
332A ARG* 5.0 5.2 - - + -
333A GLN 3.5 24.7 - - - +
334A ASP* 4.0 13.3 + - + +
335A LEU* 3.7 15.7 - - + -
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Residues in contact with LEU 253 (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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242A PHE* 4.1 12.6 - - + -
245A LEU* 3.5 31.9 - - + -
249A ASP 2.8 21.6 + - - +
250A GLN 3.8 3.4 - - - +
252A THR* 1.3 69.3 - - - +
254A LEU* 1.3 65.4 + - - +
256A ALA* 3.3 3.8 + - - +
257A ALA* 3.0 28.4 + - - +
327A LEU* 3.3 28.0 - - + +
328A ILE* 4.5 3.8 - - + -
329A CYS 3.5 25.6 - - - +
332A ARG* 4.1 13.2 + - + +
335A LEU* 4.0 15.7 - - + -
341A VAL* 4.1 14.1 - - + -
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Residues in contact with LEU 254 (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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232A ILE* 4.6 9.9 - - + +
233A VAL* 4.2 23.1 - - + -
236A ALA* 3.9 24.0 - - + -
242A PHE* 4.1 13.2 - - + -
250A GLN 3.1 21.7 + - - +
251A ILE* 3.6 9.4 - - - +
253A LEU* 1.3 75.9 - - - +
255A LYS* 1.3 58.1 + - - +
258A CYS* 2.8 36.1 + - - +
327A LEU* 4.1 13.2 - - + +
406A MET* 3.3 13.4 - - + +
633G LEU* 4.2 20.6 - - + -
637G LEU* 4.3 19.5 - - + -
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Residues in contact with LYS 255 (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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251A ILE* 3.0 41.5 + - + +
252A THR* 3.8 7.0 - - - +
253A LEU 3.3 0.2 - - - -
254A LEU* 1.3 77.4 - - - +
256A ALA* 1.3 59.3 + - - +
257A ALA 3.8 0.2 + - - -
258A CYS* 4.2 5.5 + - - +
259A LEU* 5.1 1.9 + - - +
405A GLU* 3.5 44.7 + - - +
406A MET* 3.3 36.9 - - - +
407A MET* 6.0 0.2 - - - +
408A GLU* 4.0 25.3 + - + +
633G LEU* 4.2 3.6 - - + -
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Residues in contact with ALA 256 (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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252A THR* 3.1 18.5 + - + +
253A LEU 4.0 0.7 - - - +
254A LEU 3.2 0.2 - - - -
255A LYS* 1.3 77.6 - - - +
257A ALA* 1.3 60.0 + - - +
259A LEU* 5.2 2.2 + - - +
260A ASP* 3.5 14.7 + - - +
332A ARG* 3.4 41.3 + - + +
381A SER* 5.1 2.1 + - - -
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Residues in contact with ALA 257 (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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253A LEU 3.0 16.4 + - - +
254A LEU 3.8 0.2 - - - -
256A ALA* 1.3 77.0 - - - +
258A CYS* 1.3 66.5 + - - +
259A LEU 3.2 2.9 - - - -
260A ASP* 3.2 10.7 + - - +
261A ILE* 3.0 27.2 + - + +
326A CYS* 3.5 31.0 - - + +
327A LEU* 3.6 18.8 - - + +
332A ARG* 3.8 2.7 - - - +
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Residues in contact with CYS 258 (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 ILE* 3.7 35.7 - - - -
232A ILE* 4.0 16.9 - - + +
254A LEU 2.8 19.2 + - - +
255A LYS 4.3 4.3 - - - +
256A ALA 3.6 1.2 - - - -
257A ALA* 1.3 78.9 - - - +
259A LEU* 1.3 58.1 + - - +
261A ILE* 3.5 1.5 + - - -
262A LEU* 2.9 39.5 + - - +
406A MET* 3.4 34.3 - - + -
407A MET* 4.5 4.0 - - + -
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Residues in contact with LEU 259 (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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255A LYS 5.1 2.5 + - - +
256A ALA 5.2 1.5 + - - +
257A ALA 3.2 0.8 - - - -
258A CYS* 1.3 77.5 - - - +
260A ASP* 1.3 67.3 + - - +
262A LEU* 4.0 10.1 - - + -
263A ILE* 3.0 36.1 + - + +
381A SER* 3.6 20.2 - - - +
384A GLY* 3.8 8.1 - - - +
385A ALA* 3.5 34.8 - - + +
388A VAL* 4.8 1.1 - - + -
407A MET* 4.4 19.7 - - + -
501A JYH 3.8 47.6 - - + -
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Residues in contact with ASP 260 (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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256A ALA 3.5 11.1 - - - +
257A ALA* 3.4 8.8 - - - +
259A LEU* 1.3 77.4 - - - +
261A ILE* 1.3 58.0 + - - +
263A ILE* 3.4 3.0 + - - +
264A LEU* 3.0 22.8 + - - +
326A CYS* 4.2 21.4 - - + +
332A ARG* 3.0 29.3 + - - -
377A LEU* 3.4 24.3 - - + +
378A ARG* 3.9 14.9 - - - -
381A SER* 2.7 38.8 + - - -
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Residues in contact with ILE 261 (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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232A ILE* 3.8 33.7 - - + -
235A PHE* 4.9 5.2 - - + -
257A ALA* 3.0 17.4 + - + +
260A ASP* 1.3 74.8 - - - +
262A LEU* 1.3 56.5 + - - +
264A LEU* 4.2 5.8 - - + -
265A ARG* 2.7 58.2 + - + +
323A SER* 3.6 45.8 - - - +
326A CYS* 4.5 9.4 - - + -
327A LEU* 4.4 20.9 - - + -
377A LEU* 5.8 0.2 - - - -
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Residues in contact with LEU 262 (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 ALA* 4.2 3.6 - - + +
228A CYS* 3.9 24.5 - - + -
229A ILE* 4.1 18.8 - - + -
232A ILE* 3.9 10.0 - - + +
258A CYS* 2.9 41.0 + - - +
259A LEU* 3.4 22.0 + - + +
261A ILE* 1.3 75.2 - - - +
263A ILE* 1.3 63.6 + - - +
265A ARG* 4.7 0.7 - - - -
266A ILE* 3.1 19.2 + - - +
407A MET* 4.4 5.6 - - + -
501A JYH 3.3 61.5 + - + +
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Residues in contact with ILE 263 (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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259A LEU* 3.0 21.4 + - + +
260A ASP* 3.4 7.0 - - - +
262A LEU* 1.3 75.7 - - - +
264A LEU* 1.3 63.8 + - - +
266A ILE* 3.0 5.5 - - - +
267A CYS* 3.0 27.7 + - - +
302A VAL* 4.9 5.4 - - + -
305A PHE* 4.1 17.5 - - + -
377A LEU* 3.9 16.4 - - + +
380A ILE* 3.6 24.7 - - + +
381A SER* 3.5 37.7 - - - +
501A JYH 3.7 29.6 - - + -
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Residues in contact with LEU 264 (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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260A ASP 3.0 14.2 + - - +
261A ILE* 3.7 7.2 - - + +
263A ILE* 1.3 79.3 - - - +
265A ARG* 1.3 64.2 + - + +
267A CYS* 3.3 12.2 + - - -
268A THR* 3.3 26.1 + - + +
305A PHE* 4.7 6.7 - - + -
309A LEU* 4.3 21.8 - - + -
314A MET* 5.5 2.0 - - + -
319A THR* 4.0 21.5 - - + +
322A LEU* 4.4 21.1 - - + -
323A SER* 3.2 36.1 - - - +
373A LYS* 6.5 0.2 - - + -
377A LEU* 3.8 25.8 - - + +
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Residues in contact with ARG 265 (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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188A HIS* 4.5 15.3 + - - +
191A THR* 2.9 48.7 + - - -
192A PHE* 3.2 54.2 - - + +
228A CYS* 3.7 19.5 - - - -
231A LYS* 3.7 16.8 + - - +
232A ILE* 4.1 9.9 - - - +
235A PHE* 4.2 18.6 - - - +
261A ILE* 2.7 41.1 + - + +
262A LEU 3.9 2.9 - - - +
264A LEU* 1.3 75.2 - - + +
266A ILE* 1.3 60.0 + - - +
268A THR* 2.7 22.6 + - - -
269A ARG* 3.5 3.1 - - - +
319A THR* 5.9 2.0 - - + -
323A SER* 5.5 2.0 + - - +
501A JYH 4.3 6.1 - - + -
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Residues in contact with ILE 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PHE* 6.4 0.2 - - + -
262A LEU 3.1 10.5 + - - +
263A ILE* 3.0 20.0 - - - +
265A ARG* 1.3 78.9 - - - +
267A CYS* 1.3 65.0 + - - +
268A THR 3.1 0.4 - - - -
269A ARG* 3.0 26.6 + - + +
270A TYR 3.8 0.3 + - - -
277A MET* 3.8 36.5 - - + +
278A THR 4.3 16.2 - - - +
279A PHE* 4.2 19.5 - - + -
290A MET* 4.4 9.0 - - + -
295A PHE* 4.9 0.7 - - + -
302A VAL* 4.7 3.8 - - + -
501A JYH 3.5 49.1 - - + +
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Residues in contact with CYS 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ILE* 3.0 19.6 + - - +
264A LEU 3.8 4.3 - - - +
265A ARG 3.2 0.4 - - - -
266A ILE* 1.3 77.9 - - - +
268A THR* 1.3 57.5 + - - +
269A ARG 3.2 1.3 - - - -
270A TYR* 3.7 15.0 - - - +
277A MET* 4.5 3.1 - - - -
302A VAL* 3.4 41.1 - - - -
305A PHE* 3.4 31.9 - - + -
306A ALA* 3.9 23.5 - - + +
309A LEU* 4.0 11.5 - - + +
310A LEU* 5.1 3.6 - - - +
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Residues in contact with THR 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A PHE* 3.7 15.6 - - - -
195A LEU* 4.1 14.7 + - - +
264A LEU* 3.3 18.8 - - + +
265A ARG* 2.7 21.5 + - - -
267A CYS* 1.3 76.0 - - - +
269A ARG* 1.3 58.4 + - - +
270A TYR 3.3 5.0 + - - +
309A LEU* 3.9 19.3 - - + -
310A LEU* 6.2 2.5 - - - -
314A MET* 6.0 2.2 - - + -
319A THR* 4.2 24.3 - - + +
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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