Contacts of the helix formed by residues 280 - 305 (chain B) in PDB entry 3N1Z
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 GLY 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B LYS 3.6 0.6 + - - -
279B GLU* 1.3 74.1 - - - +
281B ASN* 1.3 59.0 + - - +
282B ARG 3.4 2.0 - - - +
283B GLU* 3.1 29.5 + - - +
284B VAL* 2.9 31.5 + - - +
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Residues in contact with ASN 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PRO 3.6 8.7 - - - +
67B LEU* 3.6 15.2 - - + +
68B LYS* 2.7 48.4 + - - +
275B ALA* 2.8 40.1 + - + +
276B LEU* 5.0 0.2 - - + -
278B LYS* 3.3 16.8 + - - +
279B GLU 3.1 6.6 + - - +
280B GLY* 1.3 75.8 - - - +
282B ARG* 1.3 58.7 + - - +
284B VAL* 2.7 6.1 + - - +
285B LEU* 2.6 39.1 + - - +
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Residues in contact with ARG 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 3.5 50.7 - - + +
278B LYS 4.9 0.8 + - - -
280B GLY* 3.4 0.8 - - - +
281B ASN* 1.3 76.6 - - - +
283B GLU* 1.3 73.2 + - - +
285B LEU* 3.3 5.7 + - - +
286B GLN* 2.9 59.0 + - + +
329B GLY* 3.7 30.5 - - - -
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B GLY* 3.1 33.7 + - - +
281B ASN 3.0 0.4 - - - -
282B ARG* 1.3 100.0 + - - +
284B VAL* 1.3 61.5 + - + +
286B GLN* 3.8 10.6 - - - +
287B LYS* 3.1 37.2 + - + +
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PRO* 3.9 34.8 - - + +
67B LEU* 4.1 8.3 - - + +
280B GLY 2.9 20.9 + - - +
281B ASN* 2.7 16.9 + - - +
283B GLU* 1.3 74.9 - - + +
285B LEU* 1.3 62.2 + - - +
287B LYS* 3.4 8.2 + - + +
288B TRP* 3.3 55.4 + - + -
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.7 31.4 - - + -
219B PHE* 5.0 5.2 - - + -
220B THR* 3.4 25.3 - - - +
224B LEU* 4.4 11.4 - - + -
272B VAL* 4.2 30.1 - - + -
275B ALA* 4.4 11.0 - - + -
276B LEU* 4.5 11.2 - - + -
281B ASN 2.6 19.3 + - - +
282B ARG* 3.7 4.7 - - - +
284B VAL* 1.3 74.3 - - - +
286B GLN* 1.3 58.2 + - + +
288B TRP* 3.5 9.4 + - + +
289B VAL* 3.0 34.6 + - + +
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Residues in contact with GLN 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ARG* 2.9 53.2 + - + +
283B GLU* 3.3 10.8 + - - +
284B VAL 3.3 0.2 - - - -
285B LEU* 1.3 77.2 - - + +
287B LYS* 1.3 62.3 + - + +
288B TRP 3.2 0.2 - - - -
289B VAL* 3.8 7.2 - - + +
290B ALA* 2.8 31.2 + - - +
329B GLY 4.5 16.6 + - - +
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Residues in contact with LYS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B GLU* 3.1 29.7 + - + +
284B VAL* 3.9 7.4 - - + +
285B LEU 3.4 0.2 - - - -
286B GLN* 1.3 78.1 - - + +
288B TRP* 1.3 59.8 + - + +
290B ALA* 3.5 7.7 + - - +
291B LYS* 3.0 26.3 + - - +
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Residues in contact with TRP 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B SER* 3.9 3.4 - - - -
66B PRO* 3.4 33.4 - - + +
67B LEU* 3.9 9.2 - - + -
214B ASP* 3.5 18.8 - - - -
216B GLY* 3.4 21.5 - - - -
217B GLU* 3.4 48.7 + - + +
220B THR* 3.6 27.4 - - + -
284B VAL* 3.3 29.5 + - + -
285B LEU* 3.7 14.8 - - + +
286B GLN 3.2 0.4 - - - -
287B LYS* 1.3 79.8 - - + +
289B VAL* 1.3 66.1 + - - +
291B LYS* 3.1 15.0 + - + +
292B TRP* 3.0 25.8 - - + -
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B THR* 3.6 17.5 - - + -
224B LEU* 4.9 4.9 - - + -
225B VAL* 4.2 13.7 - - + -
285B LEU* 3.0 20.3 + - + +
286B GLN* 3.9 7.2 - - + +
288B TRP* 1.3 72.9 - - - +
290B ALA* 1.3 60.8 + - - +
291B LYS 3.1 0.2 + - - -
292B TRP 3.1 0.5 + - - -
293B GLU* 2.7 47.6 + - + +
325B ARG* 3.4 41.1 - - - +
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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
----------------------------------------------------------
286B GLN 2.8 20.6 + - - +
287B LYS* 3.5 9.0 - - - +
289B VAL* 1.3 77.7 - - - +
291B LYS* 1.3 56.9 + - - +
293B GLU* 4.7 8.3 - - - -
294B PRO* 3.0 25.8 - - - +
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Residues in contact with LYS 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLU* 2.9 30.8 + - - -
287B LYS 3.0 13.7 + - - +
288B TRP* 3.2 16.4 - - + +
289B VAL 3.0 0.8 - - - -
290B ALA* 1.3 79.5 - - - +
292B TRP* 1.3 81.6 + - + +
294B PRO* 3.4 14.6 - - - +
295B LEU* 4.8 5.2 + - - +
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Residues in contact with TRP 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 3.9 21.7 - - + +
208B LYS* 3.6 20.4 - - + -
209B ALA* 3.3 39.9 - - + -
212B ALA* 4.1 15.3 - - + -
217B GLU* 3.2 29.6 + - - +
221B ALA* 3.8 24.9 - - + +
225B VAL* 3.9 25.8 - - + +
288B TRP* 3.0 32.8 + - + +
289B VAL* 5.1 0.2 - - - -
291B LYS* 1.3 94.9 - - + +
293B GLU* 1.3 67.0 + - - +
294B PRO* 3.1 3.1 - - - -
295B LEU* 2.9 30.2 + - + +
296B ALA 3.1 8.1 + - - -
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Residues in contact with GLU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B VAL* 4.1 9.1 - - + +
289B VAL* 2.7 31.2 + - + +
290B ALA* 4.4 6.4 - - - +
292B TRP* 1.3 69.4 - - - +
294B PRO* 1.3 70.5 - - + +
296B ALA* 2.9 13.8 + - + +
297B ASP* 3.0 29.0 + - - +
322B ARG* 3.9 22.3 + - - +
325B ARG* 3.2 32.4 + - - +
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Residues in contact with PRO 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ALA 3.0 23.8 - - - +
291B LYS 3.4 8.7 - - - +
292B TRP 3.2 4.0 - - - -
293B GLU* 1.3 94.4 - - + +
295B LEU* 1.3 61.2 + - + +
297B ASP* 3.5 10.3 + - + +
298B LYS* 3.2 24.2 + - - +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B GLY 4.3 2.0 - - - +
204B GLU* 3.7 19.7 - - + +
205B LEU* 3.7 25.3 - - + +
208B LYS* 3.8 27.8 - - + +
291B LYS 4.8 4.2 + - - +
292B TRP* 2.9 35.4 + - + +
294B PRO* 1.3 80.7 - - + +
296B ALA* 1.3 60.6 + - - +
298B LYS* 3.6 35.0 - - + +
299B ALA* 3.2 19.8 + - - +
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Residues in contact with ALA 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 3.9 15.7 - - + +
225B VAL* 3.6 28.7 - - + +
229B ALA* 4.4 13.9 - - + +
292B TRP 3.1 3.2 + - - -
293B GLU* 2.9 12.7 + - + +
295B LEU* 1.3 74.9 - - - +
297B ASP* 1.3 68.9 + - - +
299B ALA* 2.9 13.3 + - - +
300B ILE* 3.0 20.0 + - + +
325B ARG* 5.9 1.3 - - - +
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Residues in contact with ASP 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B GLU* 3.0 26.7 + - - +
294B PRO* 3.9 9.3 - - + +
296B ALA* 1.3 77.2 - - - +
298B LYS* 1.3 57.4 + - - +
300B ILE* 3.3 8.8 + - - +
301B GLU* 2.9 50.6 + - - +
318B LYS* 3.8 15.4 - - - +
322B ARG* 2.9 34.3 + - - -
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Residues in contact with LYS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B GLN 6.1 0.2 - - - -
201B GLY* 3.9 13.4 + - - +
204B GLU* 2.4 41.2 + - - +
294B PRO 3.2 11.9 + - - +
295B LEU* 3.6 24.5 - - + +
296B ALA 3.1 0.2 - - - -
297B ASP* 1.3 80.6 - - - +
299B ALA* 1.3 59.6 - - - +
301B GLU* 3.6 13.7 + - - +
302B ALA* 3.1 24.6 + - - +
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ALA 4.7 0.2 - - - +
201B GLY* 3.5 15.5 - - - +
202B PHE* 3.4 49.3 + - + +
205B LEU* 4.4 5.2 - - + -
295B LEU 3.2 10.0 + - - +
296B ALA 2.9 10.1 + - - +
298B LYS* 1.3 77.4 - - - +
300B ILE* 1.3 62.5 + - - +
302B ALA* 3.3 2.3 + - - +
303B TYR* 3.1 26.0 + - - +
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Residues in contact with ILE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B PHE* 4.7 5.4 - - + -
229B ALA* 4.0 33.4 - - + +
233B ALA* 4.9 1.1 - - + -
296B ALA* 3.0 15.3 + - + +
297B ASP* 3.8 9.4 - - - +
299B ALA* 1.3 75.3 - - - +
301B GLU* 1.3 57.4 + - - +
303B TYR* 4.8 1.8 - - - -
304B CYS* 3.0 35.2 + - - +
314B ILE* 3.9 26.1 - - + +
317B ALA* 3.9 45.3 - - + +
318B LYS* 4.1 12.1 - - + +
321B SER* 4.1 7.0 - - - +
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Residues in contact with GLU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ASP* 2.9 30.1 + - - +
298B LYS* 3.9 13.1 + - - +
300B ILE* 1.3 75.0 - - - +
302B ALA* 1.3 55.5 + - - +
305B SER* 2.6 38.6 + - - -
314B ILE* 3.6 18.2 - - + -
318B LYS* 2.6 33.3 + - - +
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B PRO 3.6 21.2 - - - +
198B ALA* 3.1 22.3 - - - +
201B GLY* 4.1 12.1 - - - +
298B LYS 3.1 17.9 + - - +
299B ALA 3.9 3.1 - - - +
301B GLU* 1.3 78.7 - - - +
303B TYR* 1.3 64.5 + - - +
305B SER* 3.6 8.2 + - - -
306B ALA* 4.0 3.1 - - - +
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Residues in contact with TYR 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B PHE* 2.8 57.6 + + - +
198B ALA* 3.3 19.5 + - - +
199B TRP* 3.7 30.5 - + - -
202B PHE* 3.9 16.6 - + + -
233B ALA* 3.7 27.4 - - + -
234B LEU* 3.5 24.8 - - + +
238B LEU* 3.9 10.9 - - + +
299B ALA 3.1 17.1 + - - +
300B ILE 4.3 1.6 - - - +
302B ALA* 1.3 78.2 - - - +
304B CYS* 1.3 74.0 + - - +
306B ALA* 3.0 20.1 + - - +
307B LEU* 3.7 14.0 + - + +
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Residues in contact with CYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ALA* 4.2 13.5 - - - -
237B GLN* 4.3 9.2 - - - -
300B ILE* 3.0 32.0 + - - +
303B TYR* 1.3 89.9 - - - +
305B SER* 1.3 64.5 + - - +
307B LEU* 3.0 25.1 + - - +
310B GLY* 3.1 14.9 - - - -
313B ALA* 3.5 31.4 - - + +
314B ILE* 3.6 11.4 - - + -
317B ALA* 4.6 0.7 - - - -
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Residues in contact with SER 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B GLU* 2.6 26.2 + - - -
302B ALA* 3.6 7.4 + - - -
303B TYR 3.3 0.2 - - - -
304B CYS* 1.3 78.3 - - - +
306B ALA* 1.3 63.0 + - - +
307B LEU 3.2 6.9 + - - +
310B GLY* 4.0 9.6 - - - -
311B GLU* 4.3 11.5 - - - +
314B ILE* 3.5 17.6 - - - +
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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