Contacts of the helix formed by residues 276 - 299 (chain B) in PDB entry 3P3W
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 276 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASN* 4.1 25.1 + - - -
17B VAL* 5.6 1.8 - - - +
18B GLN* 3.0 34.4 + - - +
19B GLU* 4.2 17.7 + - - +
226B ASP* 3.5 22.0 - - - +
269B GLU* 5.0 7.5 + - - +
273B ALA* 5.1 9.4 - - - -
274B PRO 4.0 6.7 - - - +
275B LEU* 1.3 76.8 - - - +
277B TYR* 1.3 62.4 + - + +
278B THR* 4.0 9.4 - - - +
279B SER* 2.9 24.2 + - - +
280B ALA 3.2 8.1 + - - -
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Residues in contact with TYR 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG* 3.1 44.7 + - - -
195B VAL* 4.2 11.5 - - + +
221B ASN* 4.1 13.4 + - - -
222B LEU* 3.6 37.6 + - + +
223B GLY* 3.4 33.0 - - - -
225B THR* 5.7 0.8 + - - -
226B ASP* 4.0 5.5 + - - -
244B ILE* 4.3 14.3 - - + +
245B VAL* 4.8 5.4 - - + -
275B LEU* 3.9 9.2 + - - -
276B LYS* 1.3 72.5 - - + +
278B THR* 1.3 75.8 + - + +
280B ALA* 3.3 6.9 + - - +
281B LEU* 3.1 41.8 + - + +
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Residues in contact with THR 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU* 2.7 32.0 + - - +
76B PHE* 4.7 10.8 - - + -
99B PRO* 4.2 11.4 - - + +
114B ARG* 3.7 16.6 - - - +
276B LYS* 4.0 9.2 - - - +
277B TYR* 1.3 105.4 - - + +
279B SER* 1.3 54.1 + - - +
281B LEU* 3.3 10.1 + - - +
282B THR* 2.7 36.2 + - - -
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLN* 2.8 26.0 + - - -
19B GLU* 3.4 27.4 + - - +
22B ALA* 3.3 31.3 - - - +
275B LEU* 3.8 10.8 - - - -
276B LYS* 2.9 11.6 + - - +
278B THR* 1.3 77.3 + - - +
280B ALA* 1.3 61.4 + - - +
282B THR* 3.3 7.6 - - - -
283B HIS* 3.3 13.5 + - - +
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Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B VAL* 4.2 16.8 - - + -
255B PHE* 6.3 0.9 - - - -
275B LEU* 3.7 27.3 - - + +
276B LYS 3.2 3.4 + - - -
277B TYR 3.5 9.6 - - - +
279B SER* 1.3 78.5 - - - +
281B LEU* 1.3 58.2 + - + +
283B HIS* 3.4 8.3 + - - +
284B ASP* 2.9 35.4 + - - +
338B MET* 4.2 18.8 - - + +
339B THR* 5.1 2.2 - - - +
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PRO* 3.8 31.2 - - + +
113B MET* 3.6 33.5 - - + +
114B ARG* 4.4 9.9 - - + -
115B PRO* 4.5 0.9 - - + -
244B ILE* 3.4 31.0 - - + -
277B TYR* 3.1 37.7 + - + +
278B THR* 3.6 8.1 - - - +
279B SER 3.3 0.2 - - - -
280B ALA* 1.3 74.3 - - - +
282B THR* 1.3 55.4 + - - +
284B ASP* 3.6 4.3 - - - -
285B ALA* 2.8 35.5 + - - +
339B THR* 3.7 16.6 - - + +
350B ARG* 4.5 1.1 - - - +
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Residues in contact with THR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU* 3.4 34.1 - - - +
22B ALA* 4.2 0.2 - - - -
23B PHE* 3.8 21.1 - - + +
74B PHE* 3.6 36.0 - - + -
76B PHE* 4.2 2.9 - - - -
99B PRO* 4.2 0.6 - - - +
278B THR 2.7 22.2 + - - -
279B SER* 3.3 13.0 - - - -
280B ALA 3.3 0.2 - - - -
281B LEU* 1.3 77.0 - - - +
283B HIS* 1.3 61.2 + - - +
285B ALA* 3.3 15.2 + - - +
286B ILE* 3.4 12.7 - - - +
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Residues in contact with HIS 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA* 4.4 6.2 + - + +
26B ALA* 4.1 26.9 - - + -
29B LEU* 5.0 13.0 - - + +
251B MET* 6.3 1.8 - - + -
255B PHE* 4.1 28.7 - + + -
279B SER 3.3 8.7 + - - +
280B ALA* 3.6 7.2 - - - +
282B THR* 1.3 79.9 - - - +
284B ASP* 1.3 68.5 + - - +
286B ILE* 3.1 17.2 + - + +
287B LEU* 3.3 44.1 + - + +
338B MET* 3.3 35.6 - - + -
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Residues in contact with ASP 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B MET* 3.6 16.8 - - + +
280B ALA* 2.9 17.3 + - - +
281B LEU* 3.8 1.3 - - - +
283B HIS* 1.3 80.9 + - - +
285B ALA* 1.3 64.4 + - - +
287B LEU* 3.3 24.3 + - - +
288B VAL* 3.3 24.8 + - - +
337B GLY* 3.6 2.4 - - - -
338B MET* 3.1 26.1 + - - +
339B THR* 2.7 38.4 + - - +
342B ILE* 4.0 8.9 - - + +
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PHE* 3.5 27.1 - - + -
97B VAL* 3.8 15.6 - - + +
113B MET* 3.8 15.7 - - + -
281B LEU 2.8 17.5 + - - +
282B THR 3.4 7.6 - - - +
283B HIS 3.2 0.2 - - - -
284B ASP* 1.3 75.8 - - - +
286B ILE* 1.3 64.0 + - + +
288B VAL* 3.4 4.9 + - - +
289B ILE* 3.2 28.5 + - - +
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Residues in contact with ILE 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 5.0 3.6 - - + -
23B PHE* 3.7 36.1 - - + +
26B ALA* 3.4 42.8 - - + +
27B VAL* 4.9 7.4 - - + -
30B TYR* 5.6 4.0 - - + -
43B LEU* 5.0 16.1 - - + +
74B PHE* 5.4 2.2 - - + -
282B THR 3.4 19.6 + - - +
283B HIS* 3.1 10.4 + - + +
285B ALA* 1.3 78.1 - - + +
287B LEU* 1.3 60.1 + - + +
289B ILE* 3.2 15.3 + - + +
290B ALA* 2.8 38.9 + - + +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 5.9 6.7 - - + -
251B MET* 5.7 4.0 - - - -
283B HIS* 3.3 32.8 + - + +
284B ASP* 3.3 32.8 - - + +
285B ALA 3.3 0.2 - - - -
286B ILE* 1.3 83.4 - - + +
288B VAL* 1.3 58.7 + - - +
290B ALA* 4.1 6.6 - - + +
291B GLU* 3.2 24.3 + - - +
294B ARG* 4.9 1.2 + - - -
335B VAL* 4.3 23.7 - - + +
336B GLN 5.4 0.7 - - - +
337B GLY* 4.1 16.4 - - - -
342B ILE* 5.0 0.4 - - + -
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Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL* 5.9 2.5 - - + -
111B ILE* 5.2 4.9 - - + -
113B MET* 4.2 5.4 - - - -
284B ASP 3.3 14.7 + - - +
285B ALA* 3.6 7.4 - - - +
286B ILE 3.2 0.4 - - - -
287B LEU* 1.3 74.9 - - - +
289B ILE* 1.3 61.3 + - + +
291B GLU* 3.3 3.0 + - - +
292B ALA* 2.9 29.3 + - - +
330B LEU* 3.7 33.9 - - + +
333B VAL* 3.7 14.4 - - + +
335B VAL* 5.8 3.6 - - + -
342B ILE* 3.8 30.7 - - + -
344B PHE* 3.8 18.2 - - + -
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Residues in contact with ILE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 5.9 0.4 - - + -
8B ILE* 4.3 35.2 - - + -
41B PHE* 5.8 0.2 - - - -
43B LEU* 5.3 9.2 - - + -
72B ALA* 4.7 9.4 - - + -
74B PHE* 4.9 9.0 - - + +
97B VAL* 4.0 30.3 - - + -
285B ALA* 3.3 20.6 - - + +
286B ILE* 3.2 12.5 + - + +
288B VAL* 1.3 76.6 - - + +
290B ALA* 1.3 62.3 + - - +
292B ALA* 3.5 0.3 + - - +
293B PHE* 3.2 52.2 + - + +
330B LEU* 4.2 13.7 - - + -
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 4.7 20.2 - - + -
41B PHE* 4.2 9.1 - - - -
43B LEU* 5.9 4.9 - - + +
286B ILE* 2.8 26.7 + - + +
287B LEU* 4.1 8.3 - - + +
289B ILE* 1.3 74.9 - - - +
291B GLU* 1.3 61.0 + - - +
293B PHE* 3.5 1.7 + - - +
294B ARG* 3.2 45.9 + - - +
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B LEU 3.2 17.6 + - - +
288B VAL 3.8 3.1 - - - +
290B ALA* 1.3 76.4 - - - +
292B ALA* 1.3 63.9 + - - +
293B PHE 3.4 0.2 - - - -
294B ARG* 2.4 33.8 + - - +
295B TYR* 3.3 21.7 + - - +
298B ARG* 3.6 24.8 + - - -
333B VAL* 3.8 21.2 - - + +
334B GLN 5.4 1.3 - - - +
335B VAL* 3.8 26.6 - - + +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B VAL 2.9 16.7 + - - +
289B ILE 3.8 2.7 - - - +
290B ALA 3.3 0.2 - - - -
291B GLU* 1.3 77.8 - - - +
293B PHE* 1.3 59.7 + - + +
295B TYR* 3.4 5.9 + - - +
296B LEU* 3.0 32.6 + - + +
329B ALA* 3.7 25.9 - - + +
330B LEU* 3.7 29.2 - - + -
333B VAL* 4.0 4.0 - - + +
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Residues in contact with PHE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 3.7 43.1 - - + -
41B PHE* 3.4 29.5 - + + -
71B TYR* 3.8 31.6 - + + -
72B ALA* 4.7 7.6 - - + -
289B ILE* 3.2 42.7 + - + +
292B ALA* 1.3 79.6 - - + +
294B ARG* 1.3 60.3 + - - +
295B TYR 3.2 1.3 - - - -
296B LEU* 3.3 31.5 + - + +
297B ARG* 3.2 23.9 + - - +
303B VAL* 4.6 7.0 - - + -
326B ILE* 4.5 9.9 - - + -
330B LEU* 5.2 11.0 - - + -
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Residues in contact with ARG 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 4.1 8.5 - - - +
37B THR 4.4 7.0 - - - -
38B GLU* 3.1 34.9 + - - +
40B PRO* 4.0 15.7 - - + +
41B PHE* 4.0 15.5 - - + -
287B LEU 4.9 1.0 + - - -
290B ALA* 3.2 42.6 + - - +
291B GLU* 2.4 46.7 + - - +
292B ALA 3.4 0.2 - - - -
293B PHE* 1.3 72.6 - - - +
295B TYR* 1.3 59.4 + - - +
296B LEU 3.2 0.2 - - - -
297B ARG* 3.5 3.4 + - - +
298B ARG* 3.0 43.1 + - - +
335B VAL* 5.3 0.8 - - - +
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Residues in contact with TYR 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLU* 3.3 13.7 + - - +
292B ALA* 3.4 11.4 - - - +
293B PHE 3.2 0.4 - - - -
294B ARG* 1.3 78.3 - - - +
296B LEU* 1.3 59.3 + - + +
298B ARG* 3.2 30.6 + - - +
299B GLN* 3.0 61.0 + - + +
329B ALA* 3.9 17.7 - - + +
332B MET* 3.2 48.6 - - + +
333B VAL* 5.7 2.0 - - + -
322C GLN* 3.7 18.1 + - - +
324C ILE* 5.1 0.3 - - - +
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA* 3.0 19.2 + - + +
293B PHE* 3.3 44.6 - - + +
294B ARG 3.2 0.4 - - - -
295B TYR* 1.3 80.7 - - + +
297B ARG* 1.3 57.4 + - - +
299B GLN* 3.5 6.4 + - + +
300B ARG 3.0 18.0 + - - -
301B VAL* 3.2 25.0 + - + +
303B VAL* 3.8 25.6 - - + -
325B ASP 4.9 7.0 - - - +
326B ILE* 3.8 16.2 - - + -
329B ALA* 3.4 27.8 - - + -
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Residues in contact with ARG 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PHE* 4.3 25.8 - - + +
40B PRO* 3.5 42.4 + - + +
41B PHE* 5.4 4.7 - - + -
293B PHE 3.2 14.0 + - - +
294B ARG* 3.5 6.5 + - - +
296B LEU* 1.3 73.3 - - - +
298B ARG* 1.3 63.4 + - - +
299B GLN 3.3 0.9 - - - -
300B ARG* 3.3 43.3 + - - +
301B VAL 5.1 0.2 - - - +
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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 GLU* 3.6 22.6 + - - -
294B ARG* 3.0 36.1 + - - +
295B TYR* 3.3 31.9 - - - +
297B ARG* 1.3 78.8 - - - +
299B GLN* 1.3 70.1 + - - +
300B ARG* 4.2 9.2 + - - +
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Residues in contact with GLN 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B TYR* 3.0 59.1 + - + +
296B LEU* 3.9 4.3 - - + +
298B ARG* 1.3 87.9 + - - +
300B ARG* 1.3 71.5 + - - +
301B VAL* 3.6 21.4 + - + +
322C GLN* 5.4 7.6 + - - +
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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