Contacts of the helix formed by residues 260 - 285 (chain E) in PDB entry 2GPV
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 SER 260 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257E VAL* 5.4 1.0 - - - +
258E PRO 3.6 7.8 + - - -
259E ASP* 1.3 78.1 - - - +
261E ASP* 1.3 72.7 + - - +
262E ILE* 3.6 8.3 + - - +
263E LYS* 3.5 18.9 + - - +
264E ALA* 3.4 21.7 + - - +
339E LEU* 4.4 10.5 - - - +
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Residues in contact with ASP 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E SER* 1.3 75.5 - - - +
262E ILE* 1.3 99.2 + - + +
264E ALA* 3.5 2.3 + - - +
265E LEU* 3.1 30.9 + - + +
339E LEU* 3.4 24.1 + - - +
340E ALA* 4.3 11.4 - - - +
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Residues in contact with ILE 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E SER* 3.3 7.7 + - - +
261E ASP* 1.3 96.9 + - - +
263E LYS* 1.3 52.3 + - - +
265E LEU* 3.1 12.4 + - + +
266E THR* 2.6 48.2 + - - +
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Residues in contact with LYS 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253E PRO* 4.2 19.2 - - - +
254E ASP 3.2 27.1 + - - +
255E PRO* 4.6 5.3 + - - +
257E VAL* 3.0 42.7 + - + +
258E PRO 3.7 8.5 - - - +
259E ASP* 3.4 24.3 + - - -
260E SER* 3.5 17.6 + - - +
261E ASP 3.5 0.2 - - - -
262E ILE* 1.3 79.3 - - - +
264E ALA* 1.3 52.2 + - - +
266E THR* 3.1 9.2 + - + -
267E THR* 2.6 48.2 + - - +
330E TYR* 6.3 1.8 - - - -
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Residues in contact with ALA 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E SER 3.4 12.4 + - - +
261E ASP 3.7 7.9 - - - +
262E ILE 3.3 0.6 - - - -
263E LYS* 1.3 77.6 - - - +
265E LEU* 1.3 59.3 + - - +
267E THR* 3.3 2.3 + - - -
268E LEU* 3.0 37.5 + - + +
330E TYR* 3.5 24.2 - - - +
332E MET* 4.9 4.0 - - + -
336E GLN 5.7 0.4 - - - +
340E ALA* 3.9 25.6 - - + +
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Residues in contact with LEU 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261E ASP* 3.2 20.9 - - + +
262E ILE* 3.1 13.7 + - + +
264E ALA* 1.3 78.1 - - - +
266E THR* 1.3 57.8 + - - +
268E LEU* 3.9 4.2 - - - +
269E CYS* 2.9 39.7 + - - -
340E ALA* 3.8 23.8 - - + +
342E LEU* 4.0 24.7 - - + -
434E HIS* 6.2 0.4 - - - +
438E ILE* 3.9 32.3 - - + -
504E OHT 4.0 18.1 - - + -
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Residues in contact with THR 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E ILE* 2.6 40.2 + - - +
263E LYS* 3.3 12.9 - - + -
265E LEU* 1.3 73.9 - - - +
267E THR* 1.3 63.8 + - - +
269E CYS* 3.4 7.0 + - - +
270E ASP* 3.1 24.0 + - + +
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Residues in contact with THR 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E ALA* 3.7 38.8 - - + +
253E PRO* 4.1 21.9 - - + +
254E ASP 5.4 0.2 + - - -
263E LYS* 2.6 40.2 + - - +
264E ALA* 3.7 6.0 - - - -
266E THR* 1.3 74.9 - - - +
268E LEU* 1.3 57.1 + - - +
270E ASP* 3.5 6.4 + - - +
271E LEU* 3.1 26.2 + - - +
330E TYR* 4.6 15.6 - - + -
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Residues in contact with LEU 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264E ALA 3.0 23.8 + - - +
265E LEU* 3.9 4.5 - - - +
266E THR 3.3 0.2 - - - -
267E THR* 1.3 74.1 - - - +
269E CYS* 1.3 61.1 + - - +
271E LEU* 3.8 5.8 - - + +
272E ALA* 3.0 29.8 + - - +
326E TYR* 3.8 36.8 - - + -
330E TYR* 3.9 17.3 - - + -
332E MET* 4.2 13.5 - - - -
342E LEU* 3.9 28.3 - - + -
504E OHT 3.6 42.8 - - + -
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Residues in contact with CYS 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E LEU* 2.9 31.1 + - - +
266E THR* 3.6 7.0 - - - +
267E THR 3.4 0.2 - - - -
268E LEU* 1.3 74.6 - - - +
270E ASP* 1.3 63.9 + - - +
272E ALA* 4.0 0.9 - - - +
273E ASP* 3.1 34.7 + - - +
435E PHE* 4.3 17.7 - - - -
504E OHT 4.0 35.6 - - - +
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Residues in contact with ASP 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E ALA 4.7 4.5 - - - +
266E THR* 3.1 18.6 + - + +
267E THR* 3.7 7.9 - - - +
269E CYS* 1.3 77.1 - - - +
271E LEU* 1.3 60.5 + - - +
273E ASP* 3.8 9.1 - - - +
274E ARG* 3.3 50.8 + - - +
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Residues in contact with LEU 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249E ILE* 3.8 33.0 - - + +
250E TYR 3.9 20.2 - - - +
251E ALA* 4.1 10.3 - - + +
267E THR 3.1 17.1 + - - +
268E LEU* 3.8 9.6 - - + +
269E CYS 3.2 0.2 - - - -
270E ASP* 1.3 75.8 - - - +
272E ALA* 1.3 55.5 + - - +
274E ARG* 3.2 8.2 + - - +
275E GLU* 2.8 49.3 + - + +
326E TYR* 3.5 41.1 - - + +
327E ALA* 4.5 2.7 - - + -
504E OHT 3.9 13.2 - - + -
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Residues in contact with ALA 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E LEU 3.0 15.7 + - - +
271E LEU* 1.3 75.0 - - - +
273E ASP* 1.3 54.5 + - - +
275E GLU* 3.1 7.4 + - - +
276E LEU* 2.6 42.1 + - + +
309E LEU* 4.0 11.4 - - + -
504E OHT 3.3 52.6 - - + -
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Residues in contact with ASP 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E CYS* 3.1 27.6 + - - +
270E ASP* 3.8 10.9 - - - +
272E ALA* 1.3 77.7 - - - +
274E ARG* 1.3 63.0 + - + +
276E LEU* 3.3 16.0 + - - +
277E VAL* 3.3 18.9 + - - +
504E OHT 3.1 34.7 + - - -
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Residues in contact with ARG 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249E ILE* 3.4 32.5 - - + +
250E TYR 2.9 30.5 + - - +
251E ALA* 3.9 10.7 + - - +
252E MET* 4.5 15.1 - - - +
270E ASP* 3.3 43.6 + - - +
271E LEU* 3.2 15.0 + - - +
273E ASP* 1.3 79.3 - - + +
275E GLU* 1.3 65.6 + - - +
277E VAL* 3.5 15.6 + - + +
278E VAL* 3.6 13.3 + - - +
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Residues in contact with GLU 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249E ILE* 4.3 15.7 - - + -
271E LEU* 2.8 34.3 + - + +
272E ALA 3.5 3.8 - - - +
274E ARG* 1.3 76.3 - - - +
276E LEU* 1.3 54.2 + - - +
278E VAL* 2.8 13.7 - - + +
279E ILE* 2.7 41.0 + - + +
309E LEU* 3.7 17.8 - - + +
312E GLY* 5.7 0.5 - - - -
316E ARG* 3.8 23.9 + - - -
326E TYR 5.2 0.7 - - - -
504E OHT 2.7 36.8 + - - -
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Residues in contact with LEU 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A MET* 4.3 17.0 - - + -
450A PHE* 4.8 11.4 - - + -
453A MET* 4.8 0.9 - - + -
272E ALA 2.6 24.5 + - - +
273E ASP* 3.5 10.5 - - - +
275E GLU* 1.3 73.4 - - - +
277E VAL* 1.3 55.6 + - + +
279E ILE* 3.6 14.0 - - + +
280E ILE* 2.9 43.0 + - + +
305E TRP* 3.8 50.9 - - + -
309E LEU* 4.1 15.0 - - + -
504E OHT 4.7 9.4 - - - -
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Residues in contact with VAL 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A MET* 3.8 37.4 - - + +
273E ASP 3.3 15.4 + - - +
274E ARG* 3.8 11.7 - - + +
275E GLU 3.2 0.4 - - - -
276E LEU* 1.3 79.2 - - + +
278E VAL* 1.3 63.1 + - + +
280E ILE* 3.5 3.1 + - - +
281E GLY* 3.2 17.5 + - - -
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Residues in contact with VAL 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E PRO* 4.1 27.6 - - + +
247E GLU 5.7 0.2 - - - +
249E ILE* 3.6 35.0 - - + -
274E ARG 3.6 3.8 + - - +
275E GLU* 2.8 25.3 + - + +
277E VAL* 1.3 76.8 - - + +
279E ILE* 1.3 63.1 + - + +
281E GLY* 3.4 3.1 + - - +
282E TRP* 2.9 27.9 + - - +
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Residues in contact with ILE 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E PRO* 5.4 3.1 - - + -
275E GLU* 2.7 24.5 + - + +
276E LEU* 3.6 17.0 - - + +
277E VAL 3.3 0.2 - - - -
278E VAL* 1.3 79.4 - - + +
280E ILE* 1.3 68.9 + - + +
282E TRP* 3.0 25.8 + - + +
283E ALA* 3.1 11.6 + - - +
301E LEU* 4.7 14.6 - - + -
305E TRP* 4.9 3.8 - - + +
308E ILE* 3.6 39.0 - - + +
309E LEU* 3.5 34.8 - - + +
370E LYS* 6.3 0.2 - - - +
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Residues in contact with ILE 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A PHE* 3.4 37.2 - - + -
453A MET* 3.0 56.8 - - + -
454A LEU* 4.0 24.5 - - + +
276E LEU* 2.9 22.9 + - + +
277E VAL 3.8 3.8 - - - +
279E ILE* 1.3 80.5 - - + +
281E GLY* 1.3 62.0 + - - +
282E TRP 3.2 0.5 + - - -
283E ALA* 3.3 12.2 + - - +
284E LYS* 3.6 13.0 + - - +
301E LEU* 4.3 19.3 - - + -
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Residues in contact with GLY 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A MET* 5.4 1.7 - - - +
277E VAL 3.2 11.6 + - - -
278E VAL* 3.4 4.5 + - - -
280E ILE* 1.3 80.4 - - - +
282E TRP* 1.3 61.2 + - - +
284E LYS* 3.6 21.2 + - - +
285E HIS* 3.6 18.8 + - - -
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Residues in contact with TRP 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E LEU* 4.7 10.5 + - + +
244E ALA* 3.5 36.0 - - + +
245E GLU* 4.2 10.3 + - - -
246E PRO* 4.0 16.6 - - + -
278E VAL 2.9 14.4 + - - +
279E ILE* 3.0 26.2 + - + +
281E GLY* 1.3 74.7 - - - +
283E ALA* 1.3 71.4 + - + +
285E HIS* 2.8 32.1 + - - +
286E ILE* 3.5 32.9 + - + +
308E ILE* 4.0 26.5 - - + -
367E VAL* 4.4 6.0 - - + +
370E LYS* 3.8 50.0 - - + -
371E ALA* 4.1 5.6 - - + -
374E LEU* 4.0 6.3 - - + -
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Residues in contact with ALA 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279E ILE 3.1 10.3 + - - +
280E ILE 3.3 8.2 + - - +
282E TRP* 1.3 83.1 - - + +
284E LYS* 1.3 64.1 + - - +
286E ILE* 3.0 18.5 + - - +
289E PHE* 3.2 43.3 - - + +
301E LEU* 4.1 10.3 - - + -
374E LEU* 3.6 21.1 - - + -
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Residues in contact with LYS 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A MET* 3.4 28.1 + - - -
454A LEU* 3.8 38.3 - - + +
455A GLU 6.0 0.6 + - - -
280E ILE* 3.6 7.2 + - - +
281E GLY* 3.6 16.0 - - - +
282E TRP 3.2 0.8 - - - -
283E ALA* 1.3 78.1 - - - +
285E HIS* 1.3 64.9 + - + +
286E ILE 3.3 6.3 + - - +
289E PHE* 3.9 3.8 - - + -
290E SER* 2.9 31.8 + - - +
297E GLN* 5.1 2.2 - - - +
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Residues in contact with HIS 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E HIS* 3.2 34.0 + - - +
241E LEU* 5.0 1.3 - - - +
244E ALA* 3.8 29.1 - - + +
281E GLY 3.6 19.9 + - - -
282E TRP* 2.8 17.9 + - - +
284E LYS* 1.3 75.5 + - + +
286E ILE* 1.3 65.0 + - - +
287E PRO* 3.6 0.3 - - - +
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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
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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