Contacts of the helix formed by residues 281 - 308 (chain A) in PDB entry 5TIN
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 LYS 281 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 3.3 38.4 - - + +
143A LYS 3.2 6.5 - - - -
145A PHE* 4.2 9.4 - - + +
271A ARG* 3.9 23.0 - - - +
274A LEU* 3.8 30.1 - - + -
275A PRO 5.4 0.6 + - - -
277A VAL* 3.6 27.5 + - + +
279A TYR* 3.7 13.6 + - + +
280A VAL* 1.3 82.2 - - - +
282A ALA* 1.3 65.9 + - - +
283A ILE* 3.3 6.7 - - + +
284A ASP* 3.0 41.3 + - - +
285A ILE* 3.2 12.0 + - - +
345A TYR* 4.9 0.7 - - - -
222B TYR* 6.1 0.2 - - - -
225B ILE* 5.4 1.8 - - - +
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LYS 2.9 7.3 + - - -
144A ASN 3.7 13.0 - - - +
145A PHE 3.3 12.1 + - - +
147A MET* 4.0 5.6 - - + -
281A LYS* 1.3 74.5 - - - +
283A ILE* 1.3 61.6 + - - +
285A ILE* 3.3 2.9 + - - +
286A TRP 3.3 12.8 + - - -
341A TYR* 2.8 25.7 + - - +
345A TYR* 3.5 42.6 - - + -
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PHE* 3.0 35.7 + - + +
146A PRO* 4.1 6.9 - - + +
227A MET* 4.0 24.9 - - + -
228A TYR* 3.6 36.3 - - + +
270A SER* 3.9 29.8 - - - +
281A LYS* 4.3 10.3 - - + -
282A ALA* 1.3 76.1 - - - +
284A ASP* 1.3 70.0 + - - +
286A TRP* 3.5 2.3 + - + +
287A MET* 3.0 37.9 + - + +
341A TYR* 3.9 3.1 + - - -
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Residues in contact with ASP 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A SER* 4.5 1.2 + - - -
271A ARG* 3.0 37.5 + - - +
279A TYR 4.0 0.5 - - - +
280A VAL* 3.9 12.7 - - + -
281A LYS* 3.0 51.6 + - - +
283A ILE* 1.3 79.5 - - - +
285A ILE* 1.3 60.6 + - - +
287A MET* 3.4 4.8 + - - +
288A ALA* 2.9 33.0 + - - +
225B ILE* 4.5 11.7 - - + +
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Residues in contact with ILE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A VAL* 3.5 20.9 - - + -
281A LYS 3.2 13.1 + - - +
282A ALA 3.3 7.4 + - - +
284A ASP* 1.3 76.8 - - - +
286A TRP* 1.3 58.3 + - - +
288A ALA* 3.3 5.0 + - + +
289A VAL* 3.0 41.0 + - + +
337A PHE* 4.7 4.0 - - + -
341A TYR* 4.3 17.0 - - + -
345A TYR* 4.0 16.6 - - + +
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Residues in contact with TRP 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A TYR* 3.5 43.4 - + + +
231A SER* 2.8 23.6 + - - -
232A LEU* 4.8 9.9 - - + -
282A ALA 3.3 2.6 + - - -
283A ILE* 3.6 7.6 - - + +
285A ILE* 1.3 80.7 - - - +
287A MET* 1.3 74.5 + - + +
289A VAL* 3.4 2.3 + - - +
290A CYS* 2.9 47.3 + - - +
334A PHE* 4.3 7.0 - + - -
337A PHE* 3.7 30.1 - + - -
338A ASN* 3.7 34.3 - - - -
341A TYR* 3.7 38.3 - + + +
342A TRP* 4.1 14.1 - + - -
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Residues in contact with MET 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A MET* 3.7 45.5 - - + +
231A SER* 4.1 0.4 - - - -
263A MET* 3.4 27.1 - - - +
266A GLN* 4.0 24.2 - - + +
267A SER* 4.0 23.9 - - - +
270A SER* 4.0 16.4 - - - +
271A ARG* 5.8 0.2 - - - +
283A ILE* 3.0 26.0 + - + +
284A ASP* 3.9 5.2 - - - +
286A TRP* 1.3 90.4 - - + +
288A ALA* 1.3 58.7 + - - +
290A CYS* 3.7 3.2 - - - +
291A LEU* 2.9 30.0 + - - +
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ASP 2.9 19.9 + - - +
285A ILE* 3.6 7.0 - - + +
287A MET* 1.3 76.2 - - - +
289A VAL* 1.3 58.5 + - + +
291A LEU* 3.2 11.3 + - - +
292A LEU* 2.9 29.9 + - - +
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ILE* 3.0 24.6 + - + +
286A TRP 3.9 0.4 - - - +
288A ALA* 1.3 73.3 - - + +
290A CYS* 1.3 66.6 + - - +
292A LEU* 3.1 15.2 + - + +
293A PHE* 2.9 43.1 + - + -
334A PHE* 5.1 0.4 - - + -
337A PHE* 3.5 54.5 - - + -
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Residues in contact with CYS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A SER* 4.3 8.1 - - - -
235A VAL* 3.8 25.8 - - + +
263A MET* 3.7 23.1 - - + -
286A TRP* 2.9 53.8 + - - +
287A MET* 3.7 0.9 - - - +
289A VAL* 1.3 76.3 - - - +
291A LEU* 1.3 62.9 + - - +
293A PHE* 3.4 4.5 + - - +
294A VAL* 3.1 28.1 + - - +
334A PHE* 4.1 11.2 - - - -
337A PHE* 5.5 0.7 - - - -
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A VAL* 3.8 24.7 - - + +
263A MET* 3.7 30.0 - - + +
264A THR* 4.1 20.2 - - + +
267A SER* 5.6 6.3 - - - +
287A MET 2.9 19.0 + - - +
288A ALA* 3.4 9.6 - - - +
290A CYS* 1.3 76.9 - - - +
292A LEU* 1.3 56.4 + - - +
294A VAL* 3.4 1.5 + - + -
295A PHE* 2.9 34.6 + - + +
229B ILE* 6.2 0.2 - - + -
230B PRO* 6.1 1.1 - - + -
233B LEU* 3.4 32.8 - - + -
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ALA 2.9 14.9 + - - +
289A VAL* 3.1 18.6 + - + +
291A LEU* 1.3 76.6 - - - +
293A PHE* 1.3 59.1 + - + +
295A PHE* 3.3 6.9 + - + +
296A SER* 2.8 44.8 + - - +
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Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A VAL* 4.5 12.6 - - + -
238A SER* 4.6 1.8 + - - -
239A TRP* 4.8 4.9 - - - +
289A VAL* 2.9 45.5 + - + +
290A CYS* 3.7 6.7 - - - +
292A LEU* 1.3 77.9 - - + +
294A VAL* 1.3 58.8 + - - +
296A SER* 3.5 4.6 + - - -
297A ALA* 3.1 24.1 + - - +
330A PHE* 3.5 40.0 - + - -
333A ALA* 3.6 17.9 - - + -
334A PHE* 3.5 53.4 - + + -
337A PHE* 4.7 4.0 - - + -
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Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE* 3.9 19.3 - - + +
235A VAL* 3.9 12.6 - - + -
238A SER* 3.7 26.6 - - - +
256A GLY* 4.8 1.0 - - - +
259A THR* 3.3 16.9 + - - +
260A VAL* 3.2 43.2 - - + +
263A MET* 4.6 5.2 - - + -
290A CYS 3.1 16.1 + - - +
291A LEU* 3.9 4.7 - - + +
293A PHE* 1.3 77.4 - - - +
295A PHE* 1.3 66.2 + - - +
297A ALA* 3.5 4.3 + - - +
298A LEU* 3.5 14.7 + - - +
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Residues in contact with PHE 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A VAL* 3.8 26.0 - - + -
291A LEU* 2.9 22.4 + - + +
292A LEU* 3.7 9.2 - - + +
294A VAL* 1.3 75.9 - - - +
296A SER* 1.3 59.4 + - - +
298A LEU* 3.2 8.0 + - + +
299A LEU* 3.0 53.6 + - + +
233B LEU* 3.8 37.9 - - + -
236B ILE* 3.7 31.6 - - + -
237B LEU* 4.0 25.1 - - + -
240B VAL* 5.0 3.8 - - + -
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Residues in contact with SER 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 2.8 34.8 + - - +
293A PHE* 3.6 7.9 - - - -
295A PHE* 1.3 77.4 - - - +
297A ALA* 1.3 52.4 + - - +
299A LEU* 3.3 13.5 + - - +
300A GLU* 2.8 33.4 + - - +
330A PHE* 3.7 18.4 - - - -
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A SER* 4.0 26.5 - - - +
241A SER* 5.2 5.2 + - - -
242A PHE* 3.8 22.7 - - + -
256A GLY* 5.9 1.3 - - - -
293A PHE 3.1 14.0 + - - +
294A VAL 3.7 9.4 - - - +
295A PHE 3.2 0.4 - - - -
296A SER* 1.3 72.9 - - - +
298A LEU* 1.3 65.1 + - - +
300A GLU* 3.3 8.8 - - - +
301A TYR* 3.2 18.5 + - - +
330A PHE* 3.6 10.5 - - + -
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ARG 4.7 3.4 - - - +
253A VAL* 4.4 27.4 - - + +
256A GLY* 4.0 38.3 - - - +
257A ILE 4.4 1.3 - - - +
260A VAL* 4.6 5.2 - - + -
294A VAL 3.5 6.6 + - - +
295A PHE* 3.2 14.4 + - + +
297A ALA* 1.3 76.7 - - - +
299A LEU* 1.3 65.3 + - + +
301A TYR* 3.0 9.2 + - + -
302A ALA* 3.0 19.8 + - + +
237B LEU* 3.5 34.8 - - + -
240B VAL* 4.5 22.9 - - + -
244B ILE* 6.2 1.1 - - + -
255B LEU* 4.9 1.1 - - + -
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A PHE* 3.0 40.9 + - + +
296A SER* 3.6 15.3 - - - +
298A LEU* 1.3 73.1 - - + +
300A GLU* 1.3 66.4 + - - +
302A ALA* 3.2 10.4 + - + +
303A ALA* 3.0 22.7 + - - +
236B ILE* 6.0 1.6 - - + -
240B VAL* 4.0 26.0 - - + -
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Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 3.6 16.8 - - + -
252A ARG* 3.9 4.7 + - - -
296A SER 2.8 14.7 + - - +
297A ALA* 3.3 14.2 - - - +
298A LEU 3.2 0.2 - - - -
299A LEU* 1.3 76.3 - - - +
301A TYR* 1.3 63.0 + - - +
303A ALA* 3.3 9.6 + - - +
304A VAL* 3.0 25.1 + - - +
322A ILE* 3.5 20.0 - - + +
323A ASP* 2.8 28.0 - - - +
326A SER* 3.0 31.5 + - - +
330A PHE* 4.4 7.4 - - + -
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Residues in contact with TYR 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A SER* 4.9 1.3 - - - +
246A MET* 2.9 25.7 + - - -
249A ALA* 3.1 28.2 - - + +
252A ARG* 3.0 55.9 - - + +
253A VAL* 3.9 31.0 - - + -
297A ALA 3.2 6.5 + - - +
298A LEU* 3.0 13.2 + - + +
300A GLU* 1.3 79.9 + - - +
302A ALA* 1.3 61.8 + - - +
304A VAL* 4.0 17.5 - - + -
305A ASN* 2.8 59.2 + - + +
244B ILE* 4.5 4.0 - - + -
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Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 3.0 12.4 + - + +
299A LEU* 3.4 16.8 - - + +
301A TYR* 1.3 75.4 - - - +
303A ALA* 1.3 58.4 + - - +
305A ASN* 3.8 1.7 - - - +
306A PHE* 2.9 31.1 + - - +
240B VAL* 4.7 17.7 - - + -
243B TRP* 4.3 15.0 - - + +
244B ILE* 4.1 21.7 - - + +
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU 3.0 12.1 + - - +
300A GLU* 3.4 11.2 - - - +
301A TYR 3.1 0.2 - - - -
302A ALA* 1.3 74.7 - - - +
304A VAL* 1.3 59.5 + - - +
306A PHE* 4.4 4.5 - - - -
307A VAL* 2.8 42.2 + - + +
322A ILE* 4.6 15.7 - - + -
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Residues in contact with VAL 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A MET* 3.8 29.6 - - + -
300A GLU* 3.0 20.5 + - - +
301A TYR* 3.6 19.3 - - + +
303A ALA* 1.3 76.5 - - - +
305A ASN* 1.3 55.1 + - - +
307A VAL* 4.3 6.1 - - - -
308A SER* 2.7 35.0 + - - +
319A ALA* 3.7 22.1 - - + +
322A ILE* 3.7 23.3 - - + -
323A ASP* 3.7 22.4 - - - +
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Residues in contact with ASN 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A MET 4.8 2.9 + - - -
249A ALA* 4.1 11.3 - - - +
301A TYR* 2.8 52.4 + - + +
302A ALA 3.8 3.8 - - - +
304A VAL* 1.3 76.9 - - - +
306A PHE* 1.3 61.5 + - - +
308A SER* 3.5 12.1 + - - -
309A ARG* 3.6 13.5 + - - +
243B TRP 3.9 1.2 - - - +
244B ILE* 3.6 15.3 - - + +
245B ASN* 2.9 42.8 + - - +
----------------------------------------------------------
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Residues in contact with PHE 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ALA 2.9 20.2 + - - +
303A ALA* 3.7 4.7 - - - +
305A ASN* 1.3 73.8 - - - +
307A VAL* 1.3 74.7 + - + +
308A SER 3.2 2.1 + - - -
309A ARG* 3.0 76.1 + - - -
243B TRP* 3.7 44.2 - + + +
327B ARG* 3.8 27.4 - - - -
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Residues in contact with VAL 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA* 2.8 31.0 + - + +
304A VAL 3.8 0.2 - - - +
306A PHE* 1.3 81.3 - - + +
308A SER* 1.3 60.3 + - - +
309A ARG* 3.4 1.8 + - - +
310A ALA 5.0 1.0 + - - -
315A PHE* 3.4 36.3 - - + +
318A ARG* 4.5 11.7 - - + -
319A ALA* 3.6 35.7 - - + +
322A ILE* 4.2 15.7 - - + -
----------------------------------------------------------
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Residues in contact with SER 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A MET* 4.3 9.7 + - - +
304A VAL* 2.7 22.3 + - - +
305A ASN* 3.5 8.6 + - - -
306A PHE 3.2 0.6 - - - -
307A VAL* 1.3 78.9 - - - +
309A ARG* 1.3 63.8 + - - +
310A ALA 3.4 13.1 + - - +
311A GLY* 4.2 1.2 + - - -
315A PHE 4.2 4.9 - - - -
316A ILE* 4.1 24.4 - - - +
319A ALA* 3.8 17.0 - - - -
----------------------------------------------------------
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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