Contacts of the helix formed by residues 249 - 273 (chain G) in PDB entry 3FKS
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 249 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LYS* 5.5 4.0 - - - +
245G GLY* 3.3 16.0 + - - +
247G MET 3.1 0.2 - - - -
248G ILE* 1.3 96.8 + - - +
250G ARG* 1.3 63.7 + - - +
251G TYR 3.5 0.2 - - - -
252G SER* 3.4 9.0 + - - -
253G ILE* 3.2 27.4 + - - +
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Residues in contact with ARG 250 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245G GLY 4.3 0.4 + - - -
246G ASP* 3.0 54.0 + - - +
247G MET* 3.3 7.7 + - - +
249G ASN* 1.3 81.3 - - - +
251G TYR* 1.3 77.9 + - + +
253G ILE* 3.4 13.4 + - - +
254G LEU* 3.5 10.4 + - + +
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Residues in contact with TYR 251 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F ASP* 4.5 6.2 + - - -
6G VAL* 4.9 12.1 - - + +
9G ARG* 3.0 51.8 + - + -
10G LEU* 3.8 18.4 - - + +
13G ILE* 6.1 1.3 - - + -
247G MET* 2.9 44.3 + - + +
250G ARG* 1.3 92.5 - - + +
252G SER* 1.3 58.8 + - - +
253G ILE 3.3 0.2 - - - -
254G LEU* 3.2 27.4 + - + +
255G TYR* 2.8 28.1 + - - +
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Residues in contact with SER 252 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G LEU* 3.5 15.4 - - - +
248G ILE 2.8 24.8 + - - -
249G ASN* 3.4 16.8 + - - -
250G ARG 3.1 0.2 - - - -
251G TYR* 1.3 78.3 - - - +
253G ILE* 1.3 65.7 + - - +
255G TYR* 3.2 13.5 + - - +
256G ASN* 3.3 21.5 + - - -
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Residues in contact with ILE 253 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B GLN 4.8 10.1 - - - +
333B GLY* 4.4 26.0 - - - +
335B ASP* 5.0 9.4 - - + -
318E THR* 5.1 13.2 - - + +
249G ASN 3.2 17.2 + - - +
250G ARG* 3.7 8.1 - - - +
251G TYR 3.3 0.4 - - - -
252G SER* 1.3 79.7 - - - +
254G LEU* 1.3 56.6 + - - +
256G ASN* 3.3 12.2 + - + +
257G ARG* 2.9 28.9 + - + +
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Residues in contact with LEU 254 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ALA 5.0 4.3 - - - +
6G VAL* 3.7 28.3 - - + -
250G ARG* 3.5 6.5 + - + +
251G TYR* 3.2 37.8 + - + +
253G ILE* 1.3 76.6 - - - +
255G TYR* 1.3 63.0 + - - +
257G ARG* 3.7 16.9 + - - +
258G THR* 2.8 34.3 + - - +
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Residues in contact with TYR 255 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ASP* 5.6 1.7 + - - -
337A SER* 5.9 3.3 - - - -
314E ALA* 6.3 1.1 - - + -
3G LEU 5.0 5.8 - - - -
6G VAL* 4.4 16.1 - - + +
7G GLU* 3.8 52.1 + - + -
10G LEU* 4.1 15.5 - - + -
251G TYR 2.8 12.3 + - - +
252G SER 3.2 9.6 + - - +
254G LEU* 1.3 78.0 - - - +
256G ASN* 1.3 75.2 + - - +
258G THR* 3.1 8.8 + - - -
259G ARG* 2.8 49.7 + - + +
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Residues in contact with ASN 256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314E ALA* 4.8 4.0 + - - +
315E ASP 4.7 4.0 + - - -
316E ASP* 3.2 50.0 + - - +
318E THR* 4.1 6.7 - - - +
252G SER* 3.3 19.9 + - - -
253G ILE* 3.3 14.5 + - + +
255G TYR* 1.3 90.5 - - - +
257G ARG* 1.3 56.7 + - - +
258G THR 2.9 5.2 - - - -
259G ARG* 3.8 13.7 + - - +
260G GLN* 2.9 37.8 + - - +
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Residues in contact with ARG 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ARG* 5.5 1.8 - - - +
335B ASP* 3.1 39.1 + - - +
337B SER* 2.8 30.6 + - - -
338B ALA* 4.7 2.6 - - - +
318E THR* 5.4 0.8 + - - -
314F ALA* 3.6 19.4 + - - +
316F ASP* 5.9 1.2 - - - +
253G ILE* 2.9 19.1 + - + +
254G LEU* 3.8 19.1 - - - +
255G TYR 3.4 0.2 - - - -
256G ASN* 1.3 75.1 - - - +
258G THR* 1.3 58.9 + - - +
260G GLN* 4.5 6.3 - - - +
261G ALA* 3.5 20.3 + - - +
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Residues in contact with THR 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ALA* 4.1 16.6 + - - +
2G THR 4.1 20.6 - - - +
3G LEU* 4.8 3.4 - - - +
6G VAL* 4.2 11.5 - - + +
254G LEU* 2.8 27.8 + - - +
255G TYR 3.1 9.3 + - - -
256G ASN 2.9 0.6 - - - -
257G ARG* 1.3 83.0 + - - +
259G ARG* 1.3 58.3 + - - +
260G GLN 3.4 0.4 - - - -
261G ALA* 3.5 4.3 + - - +
262G VAL* 2.9 46.0 + - + +
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Residues in contact with ARG 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 4.3 10.7 - - - +
337A SER* 5.4 8.8 + - - -
279E VAL* 5.1 1.0 - - - +
313E PRO* 4.5 6.0 + - - +
314E ALA* 4.6 18.1 - - - +
316E ASP* 3.4 24.7 + - - +
319E ASP* 3.4 25.3 + - - -
255G TYR* 2.8 42.4 + - + +
256G ASN* 2.9 16.6 + - - +
258G THR* 1.3 76.2 - - - +
260G GLN* 1.3 73.4 + - - +
262G VAL* 3.2 7.0 + - + +
263G ILE* 3.1 59.8 + - + +
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Residues in contact with GLN 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E VAL* 3.8 24.7 - - + +
316E ASP* 3.0 21.8 + - - +
318E THR* 3.1 39.7 + - - +
319E ASP* 3.2 7.6 - - - +
320E PRO* 4.3 6.1 - - - +
256G ASN 2.9 18.6 + - - +
257G ARG* 4.9 4.7 - - - +
259G ARG* 1.3 90.6 - - - +
261G ALA* 1.3 62.3 + - - +
263G ILE* 3.6 5.8 + - - +
264G THR* 3.2 27.7 + - - -
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Residues in contact with ALA 261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257G ARG 3.5 18.7 + - - +
258G THR* 3.5 7.9 + - + +
259G ARG 3.2 0.6 - - - -
260G GLN* 1.3 78.2 - - - +
262G VAL* 1.3 59.0 + - - +
264G THR* 4.1 5.2 - - - -
265G ASN* 3.1 42.2 + - - +
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Residues in contact with VAL 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G LEU* 3.6 36.8 - - + -
258G THR* 2.9 34.8 + - + +
259G ARG* 3.2 10.3 + - + +
261G ALA* 1.3 76.9 - - - +
263G ILE* 1.3 63.6 + - + +
265G ASN* 4.3 2.1 - - - +
266G GLU* 2.9 45.5 + - + +
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Residues in contact with ILE 263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 3.3 62.1 - - + +
294A GLU* 5.4 3.7 + - + +
279E VAL* 3.9 28.7 - - + +
280E GLY* 5.4 0.4 - - - -
259G ARG* 3.1 44.1 + - + +
260G GLN 4.1 3.8 - - - +
262G VAL* 1.3 81.5 - - + +
264G THR* 1.3 61.2 + - - +
266G GLU* 3.9 10.7 - - - +
267G LEU* 3.2 23.1 + - + +
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Residues in contact with THR 264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B GLY 5.0 1.6 - - - +
294B GLU* 4.9 8.1 - - - +
295B ALA* 4.4 26.5 - - + +
277E SER 4.9 3.8 - - - +
278E ALA* 3.7 3.6 - - - +
279E VAL* 2.8 31.2 + - - +
280E GLY 5.5 0.7 - - - +
260G GLN 3.2 14.3 + - - -
261G ALA* 4.3 5.2 - - - -
263G ILE* 1.3 76.7 - - - +
265G ASN* 1.3 70.1 + - - +
267G LEU* 2.9 7.4 + - - +
268G VAL* 2.8 38.1 + - + +
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Residues in contact with ASN 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B GLY 5.4 2.9 - - - +
293B ARG* 5.8 2.3 - - - -
294B GLU 5.7 2.1 + - - -
279F VAL* 5.6 13.4 - - - +
261G ALA* 3.1 26.1 + - - +
262G VAL* 4.3 2.2 - - - +
264G THR* 1.3 84.0 - - - +
266G GLU* 1.3 61.1 + - - +
267G LEU 3.3 0.3 + - - -
268G VAL* 3.5 16.0 + - - +
269G ASP* 3.6 19.8 + - - +
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Residues in contact with GLU 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLU* 3.7 41.9 + - + +
278D ALA* 4.1 16.2 - - - +
279D VAL* 4.3 22.2 - - - +
262G VAL* 2.9 32.7 + - + +
263G ILE* 3.9 8.9 - - - +
264G THR 3.2 0.2 - - - -
265G ASN* 1.3 78.2 - - - +
267G LEU* 1.3 56.3 + - - +
269G ASP* 4.4 5.0 + - - +
270G ILE* 3.3 23.0 + - - +
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Residues in contact with LEU 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLY* 3.0 28.5 - - - +
293A ARG* 4.2 16.6 - - + +
294A GLU 4.5 3.6 - - - +
276E PRO* 3.7 33.9 - - + +
277E SER 5.0 2.5 - - - +
279E VAL 5.3 0.2 - - - -
280E GLY* 3.9 20.9 - - - +
263G ILE 3.2 16.9 + - - +
264G THR* 2.9 7.4 + - - +
266G GLU* 1.3 79.9 - - - +
268G VAL* 1.3 63.0 + - - +
269G ASP 3.4 0.7 - - - -
270G ILE* 3.2 11.8 + - + -
271G ILE* 3.1 42.2 + - + +
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Residues in contact with VAL 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B PRO* 4.5 36.3 - - + +
292B GLY 5.0 4.5 - - - +
276F PRO* 6.5 0.4 - - + -
277F SER 5.6 5.8 - - - +
279F VAL* 5.8 4.7 - - - +
280F GLY* 5.7 4.5 - - - +
264G THR* 2.8 32.7 + - + +
265G ASN* 3.5 11.8 + - - +
267G LEU* 1.3 74.5 - - - +
269G ASP* 1.3 64.2 + - - +
271G ILE* 3.2 6.7 + - - +
272G THR* 2.7 48.8 + - - +
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Residues in contact with ASP 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C PRO* 5.2 1.4 - - - +
292C GLY 4.1 15.5 - - - +
293C ARG* 3.7 8.4 - - - +
294C GLU* 2.7 37.7 + - - +
295C ALA* 4.0 9.0 + - - +
276D PRO* 4.2 5.6 - - - +
280D GLY* 6.3 2.5 - - - +
277F SER 5.7 0.7 - - - +
265G ASN 3.6 14.6 + - - +
266G GLU* 4.6 6.6 - - - +
267G LEU 3.4 0.4 - - - -
268G VAL* 1.3 83.8 - - - +
270G ILE* 1.3 61.9 + - + +
272G THR* 4.0 5.5 - - - -
273G GLY* 3.1 24.1 + - - -
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Residues in contact with ILE 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PRO* 3.5 34.1 - - + -
294A GLU* 5.6 0.4 - - - -
295A ALA* 4.6 13.5 - - + +
275D ILE* 4.3 1.5 - - + +
276D PRO* 3.7 28.6 - - + +
277D SER 3.2 31.6 - - - +
278D ALA* 4.2 4.5 - - - +
279D VAL 5.2 0.2 - - - +
280D GLY* 5.0 3.4 - - - +
266G GLU 3.3 22.7 - - - +
267G LEU* 3.4 15.9 - - + +
268G VAL 3.1 0.6 - - - -
269G ASP* 1.3 79.7 - - + +
271G ILE* 1.3 65.1 + - - +
273G GLY 3.5 2.3 + - - -
274G ALA* 3.2 24.9 + - - +
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Residues in contact with ILE 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PRO* 4.2 22.9 - - + +
288B ARG* 5.7 0.2 - - - +
291B PRO* 5.6 6.7 - - + -
275E ILE* 3.8 37.9 - - + -
276E PRO* 3.8 33.0 - - + -
267G LEU* 3.1 27.9 + - + +
268G VAL* 3.8 7.0 - - - +
270G ILE* 1.3 76.7 - - - +
272G THR* 1.3 63.4 + - - +
274G ALA* 3.3 14.8 + - + +
275G SER* 3.6 11.3 + - - -
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Residues in contact with THR 272 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B PRO* 5.6 3.6 - - - +
291C PRO* 4.2 15.1 - - + +
295C ALA* 6.0 2.5 - - + -
275F ILE* 3.8 27.1 - - + +
276F PRO* 3.8 30.0 - - + +
277F SER 5.6 2.0 + - - +
268G VAL* 2.7 38.1 + - - +
269G ASP* 4.0 6.1 - - - -
271G ILE* 1.3 77.8 - - - +
273G GLY* 1.3 57.1 + - - +
274G ALA 3.1 0.4 + - - -
275G SER* 2.8 24.3 + - - +
276G SER 4.4 0.7 + - - -
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Residues in contact with GLY 273 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C PRO* 5.0 6.8 - - - +
291C PRO* 3.6 26.3 - - - +
274D ARG 4.4 2.6 - - - +
275D ILE* 4.4 2.4 - - - +
276D PRO* 3.4 25.9 - - - +
269G ASP 3.1 17.6 + - - -
270G ILE 3.7 2.7 - - - -
271G ILE 3.3 0.2 - - - -
272G THR* 1.3 76.6 - - - +
274G ALA* 1.3 58.1 + - - +
275G SER 3.5 0.4 - - - -
276G SER* 4.4 7.7 + - - -
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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