Contacts of the helix formed by residues 260 - 282 (chain C) in PDB entry 3PK1
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 ASN 260 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C VAL* 4.1 14.3 - - + +
259C THR* 1.3 76.1 - - - +
261C TRP* 1.3 63.6 + - - +
262C GLY* 3.1 2.9 + - - -
263C ARG* 2.7 41.9 + - - +
264C ILE* 3.1 21.7 + - - +
305C TRP* 3.8 12.6 - - - -
67D GLY 4.0 0.5 - - - +
68D ASP* 3.1 24.4 + - - +
71D ASP* 3.3 38.0 + - - +
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Residues in contact with TRP 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ASN* 1.3 72.3 - - - +
262C GLY* 1.3 56.2 + - - +
264C ILE* 3.7 31.6 - - + +
265C VAL* 2.7 37.9 + - - +
305C TRP* 3.6 21.5 - + - -
306C LEU* 3.7 21.1 - - + -
309C GLN* 4.0 19.1 + - + +
311C GLY* 3.4 25.8 - - - -
312C TRP* 5.1 11.2 - + - -
314C GLY* 4.1 4.0 - - - -
315C PHE* 3.5 48.7 - + + +
318C PHE* 3.7 45.5 - + + +
319C PHE* 3.8 9.2 - - + -
71D ASP* 3.9 2.0 + - - -
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Residues in contact with GLY 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ASN* 3.1 4.1 + - - -
261C TRP* 1.3 78.8 - - - +
263C ARG* 1.3 52.1 + - - +
265C VAL* 3.5 2.6 - - - +
266C THR* 2.5 36.9 + - - -
319C PHE* 4.6 2.5 - - - -
67D GLY* 3.1 24.2 - - - -
70D LEU* 4.1 13.4 - - - +
71D ASP* 3.6 15.3 + - - -
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Residues in contact with ARG 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C VAL* 3.1 36.2 + - + -
254C PHE* 3.8 12.6 - - + -
256C ASP* 2.9 32.5 + - - -
258C VAL* 3.0 42.0 + - - +
260C ASN* 2.7 28.8 + - - +
262C GLY* 1.3 70.0 - - - +
264C ILE* 1.3 68.5 + - - +
266C THR* 3.1 3.8 + - - -
267C LEU* 2.9 28.8 + - - +
63D LEU 5.0 1.3 - - - -
64D LYS* 3.5 18.8 - - - +
67D GLY* 3.7 11.4 - - - -
68D ASP* 2.8 38.8 + - - +
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Residues in contact with ILE 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C PHE* 3.9 21.5 - - + -
259C THR* 3.9 7.0 - - + -
260C ASN 3.1 14.1 + - - +
261C TRP* 3.7 28.7 - - + +
263C ARG* 1.3 79.2 - - - +
265C VAL* 1.3 62.4 + - - +
267C LEU* 3.2 6.2 + - - +
268C ILE* 3.2 29.0 + - + +
298C LEU* 3.4 31.0 - - + -
302C LYS* 5.5 2.0 - - + -
305C TRP* 3.3 35.9 - - + -
306C LEU* 3.9 11.2 - - + -
312C TRP* 5.6 2.0 - - + -
315C PHE* 5.8 1.3 - - + -
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Residues in contact with VAL 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C LEU* 3.7 28.9 - - + -
216C VAL* 4.1 19.7 - - + -
217C GLY 5.0 3.1 - - - +
220C VAL* 4.4 4.9 - - + -
261C TRP 2.7 18.9 + - - +
262C GLY 3.5 2.7 - - - +
264C ILE* 1.3 75.6 - - - +
266C THR* 1.3 59.7 - - - +
268C ILE* 3.4 5.4 + - + +
269C SER* 3.0 33.2 + - - +
315C PHE* 3.8 19.1 - - + -
319C PHE* 4.6 4.0 - - + -
70D LEU* 3.2 34.8 - - + -
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Residues in contact with THR 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C VAL* 4.7 3.7 - - + +
228C PHE* 4.2 6.7 - - + -
262C GLY 2.5 21.9 + - - -
263C ARG* 3.4 5.8 - - - -
265C VAL* 1.3 81.8 - - - +
267C LEU* 1.3 57.6 + - + +
269C SER* 3.4 6.6 + - - -
270C PHE* 3.1 27.4 + - - +
63D LEU* 3.6 38.8 - - + +
66D ILE* 3.8 22.7 + - + +
67D GLY* 3.1 16.9 + - - -
70D LEU* 4.5 3.1 - - - +
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Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C LEU* 6.1 0.2 - - - +
250C MET* 3.8 45.8 - - + +
253C VAL* 4.0 25.1 - - + -
254C PHE* 3.6 31.9 - - + -
263C ARG 2.9 15.3 + - - +
264C ILE* 3.4 9.4 - - - +
266C THR* 1.3 78.1 - - - +
268C ILE* 1.3 60.2 + - + +
270C PHE* 3.5 4.9 + - + +
271C GLY* 3.0 21.8 + - - -
294C ILE* 4.2 10.0 - - + +
297C VAL* 5.1 0.7 - - + -
298C LEU* 4.4 10.3 - - + -
63D LEU* 4.1 20.9 - - + -
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Residues in contact with ILE 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C ILE* 3.9 27.8 - - + -
185C TYR* 3.8 24.7 - - + -
186C LEU* 3.7 12.0 - - + +
213C LEU* 4.2 22.4 - - + -
264C ILE* 3.2 20.7 + - + +
265C VAL* 3.9 6.7 - - + +
266C THR 3.3 0.2 - - - -
267C LEU* 1.3 74.3 - - - +
269C SER* 1.3 61.5 + - - +
271C GLY* 3.2 3.2 + - - +
272C ALA* 2.8 23.7 + - - +
294C ILE* 4.0 23.6 - - + -
298C LEU* 4.2 9.2 - - + -
312C TRP* 4.1 17.0 - - + -
315C PHE* 6.0 0.4 - - + -
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Residues in contact with SER 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C TYR* 4.6 3.2 - - - -
213C LEU* 6.0 0.3 - - - +
217C GLY* 3.0 42.1 + - - -
220C VAL* 3.5 18.4 - - - +
221C GLN* 3.5 9.5 - - - -
228C PHE* 4.0 2.5 - - - -
265C VAL* 3.0 17.8 + - - +
266C THR 3.8 4.9 - - - -
267C LEU 3.3 0.2 - - - -
268C ILE* 1.3 74.3 - - - +
270C PHE* 1.3 59.6 + - - +
272C ALA* 3.2 8.8 + - - +
273C PHE* 2.8 27.7 + - - +
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Residues in contact with PHE 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C PHE* 3.5 53.8 - + + -
231C MET* 3.9 15.9 - - + -
232C LEU* 3.9 12.3 - - - -
235C LEU* 3.2 37.2 - - + -
246C LEU* 3.6 18.4 - - + -
249C VAL* 6.0 0.4 - - + -
266C THR 3.1 17.0 + - - +
267C LEU* 3.8 6.3 - - + +
269C SER* 1.3 72.9 - - - +
271C GLY* 1.3 56.7 + - - +
273C PHE* 3.4 4.1 - + - +
274C VAL* 2.7 56.1 + - + +
59D LEU* 5.7 0.7 - - + -
63D LEU* 4.0 24.7 - - + -
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Residues in contact with GLY 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C LEU* 3.9 7.0 - - - -
246C LEU* 5.0 4.5 - - - +
267C LEU 3.0 11.7 + - - -
268C ILE 3.2 5.3 + - - -
270C PHE* 1.3 78.0 - - - +
272C ALA* 1.3 54.8 + - - +
274C VAL* 3.3 5.4 + - - -
275C ALA* 2.8 25.3 + - - +
290C LEU* 3.3 12.6 - - - +
294C ILE* 3.6 24.7 - - - -
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Residues in contact with ALA 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C TYR* 3.7 15.9 - - + -
186C LEU* 3.6 12.0 - - + +
189C GLN* 3.5 24.9 - - + +
221C GLN* 3.3 23.6 - - - +
268C ILE 2.8 9.8 + - - +
269C SER 3.2 4.7 + - - +
271C GLY* 1.3 71.7 - - - +
273C PHE* 1.3 56.2 + - - +
275C ALA* 3.1 4.1 + - - +
276C LYS* 2.9 34.8 + - - +
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Residues in contact with PHE 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C GLN* 3.4 23.5 - - + +
225C GLU* 3.8 24.7 - - + -
228C PHE* 3.4 52.7 - + + -
229C GLN* 3.3 38.1 - - - -
232C LEU* 3.8 18.8 - - + -
269C SER 2.8 16.4 + - - +
270C PHE* 3.4 9.4 - + - +
272C ALA* 1.3 76.5 - - - +
274C VAL* 1.3 62.9 + - - +
276C LYS* 3.5 8.3 + - + +
277C HIS* 3.3 17.9 + - + +
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Residues in contact with VAL 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C LEU* 4.3 16.6 - - + -
235C LEU* 4.2 7.0 - - + -
237C ILE* 3.5 32.5 - - + -
246C LEU* 4.7 4.3 - - + -
270C PHE* 2.7 59.2 + - + +
271C GLY* 3.7 5.8 - - - +
273C PHE* 1.3 73.1 - - + +
275C ALA* 1.3 64.8 + - - +
277C HIS* 3.1 12.2 + - - +
278C LEU* 3.1 14.6 + - + +
290C LEU* 4.2 16.8 - - + -
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Residues in contact with ALA 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C LEU* 3.9 24.7 - - + +
190C ALA* 3.5 12.0 - - + +
271C GLY 2.8 20.2 + - - +
272C ALA* 3.1 7.8 + - - +
274C VAL* 1.3 73.0 - - - +
276C LYS* 1.3 63.7 + - - +
278C LEU* 3.5 13.8 + - - +
279C LYS* 3.6 8.7 + - - +
287C ILE* 3.9 16.2 - - + +
290C LEU* 3.7 16.7 - - + +
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Residues in contact with LYS 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C GLN* 3.0 62.2 - - - +
190C ALA* 4.2 8.7 - - - +
221C GLN* 3.2 25.2 - - - +
272C ALA 2.9 14.9 + - - +
273C PHE* 3.8 7.7 - - + +
274C VAL 3.2 0.2 - - - -
275C ALA* 1.3 74.1 - - - +
277C HIS* 1.3 66.9 + - - +
278C LEU 3.4 0.3 + - - -
279C LYS* 3.4 12.0 + - - +
280C THR* 3.4 12.2 + - - -
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Residues in contact with HIS 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A CD 2.3 34.9 - - - -
222A ARG 5.8 3.6 - - - -
225A GLU* 3.5 10.7 + - - -
232C LEU* 3.8 34.5 - - + +
237C ILE* 5.2 6.5 - - + -
273C PHE* 3.3 9.7 + - + +
274C VAL 3.1 9.4 + - - +
276C LYS* 1.3 80.1 - - - +
278C LEU* 1.3 65.9 + - + +
280C THR* 2.9 32.7 + - + -
281C ILE* 3.1 37.4 + - + +
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Residues in contact with LEU 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C ILE* 3.9 42.6 - - + +
238C LYS 5.4 0.2 - - - -
239C ASN* 4.5 12.1 - - - -
240C GLU* 3.9 28.0 - - + +
274C VAL* 3.1 16.8 + - + +
275C ALA* 3.8 8.5 - - - +
276C LYS 3.3 0.2 - - - -
277C HIS* 1.3 82.4 - - + +
279C LYS* 1.3 51.9 + - + +
281C ILE* 3.0 13.8 + - + +
282C ASN* 2.8 32.6 + - - +
285C SER* 3.6 14.2 + - - +
286C CYS 5.0 5.8 - - - +
287C ILE* 6.4 1.1 - - + -
290C LEU* 4.9 13.7 - - + -
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Residues in contact with LYS 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C ALA* 3.9 26.6 - - + +
191C THR* 4.6 22.0 - - - +
275C ALA 3.6 12.5 + - - +
276C LYS 3.4 7.0 + - - +
277C HIS 3.2 0.6 - - - -
278C LEU* 1.3 71.6 - - + +
280C THR* 1.3 65.9 + - - +
281C ILE 2.9 2.0 + - - -
282C ASN 3.1 13.4 + - - +
283C GLN* 3.0 67.8 + - - +
284C GLU 3.9 2.4 + - - -
285C SER* 2.9 29.5 + - - +
286C CYS* 5.0 3.8 - - - +
287C ILE* 6.0 3.3 - - + +
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Residues in contact with THR 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ARG* 3.7 36.1 + - + -
225A GLU* 5.2 7.8 + - - +
276C LYS 3.4 8.5 + - - -
277C HIS* 2.9 25.9 + - + +
279C LYS* 1.3 77.4 - - - +
281C ILE* 1.3 71.8 + - + +
283C GLN* 4.3 5.7 + - - +
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Residues in contact with ILE 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ARG* 4.8 7.4 - - + -
238C LYS 5.1 9.9 - - - +
239C ASN* 6.4 0.9 - - - -
277C HIS* 3.4 39.7 - - + +
278C LEU* 3.0 17.0 + - + +
279C LYS 2.9 0.6 - - - -
280C THR* 1.3 100.2 - - + +
282C ASN* 1.3 63.2 + - + +
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Residues in contact with ASN 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C GLU* 5.7 0.2 + - - -
278C LEU 2.8 7.0 + - - +
279C LYS* 3.1 6.9 + - - +
281C ILE* 1.3 85.1 - - + +
283C GLN* 1.3 59.2 + - - +
284C GLU* 2.8 35.0 + - - +
285C SER* 2.8 54.1 + - - +
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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