Contacts of the helix formed by residues 251 - 275 (chain B) in PDB entry 4FDI
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 ARG 251 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLY 3.7 19.6 + - - +
446A ARG* 3.5 14.8 + - - +
45B ASP* 2.9 47.9 + - - +
51B GLU* 3.4 33.3 + - - +
53B SER* 4.2 6.7 - - - +
55B GLU* 3.9 12.3 - - - +
249B SER* 2.9 12.5 + - - +
250B GLN* 1.3 79.2 - - - +
252B GLY* 1.3 63.1 + - - +
254B TYR* 4.0 17.8 + - + +
255B GLY* 3.7 15.1 + - - +
258B VAL* 4.7 9.2 - - - +
297B PRO 3.9 13.3 - - - +
298B GLU 4.5 0.3 - - - +
300B GLY 4.7 1.2 + - - -
301B GLY* 3.7 10.3 - - - -
302B SER* 3.6 22.0 - - - +
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Residues in contact with GLY 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ARG* 3.6 11.7 - - - +
249B SER* 3.7 7.5 + - - -
250B GLN 3.4 4.0 - - - -
251B ARG* 1.3 78.5 - - - +
253B ARG* 1.3 60.7 + - - -
255B GLY* 2.8 18.4 + - - -
256B ASP* 3.0 18.2 + - - +
298B GLU* 3.4 14.8 - - - -
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Residues in contact with ARG 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 3.1 21.6 + - - +
199B LYS 3.1 24.2 + - - -
200B THR* 3.3 22.4 + - - +
201B GLY* 3.7 12.7 - - - -
239B VAL* 3.3 34.5 + - + +
240B TYR* 4.9 1.8 - - - +
241B ALA* 5.3 0.2 - - - +
246B LEU* 4.7 8.5 - - + +
252B GLY* 1.3 69.9 - - - -
254B TYR* 1.3 62.9 + - - +
256B ASP* 3.1 16.6 + - + +
257B ALA 3.1 18.0 + - - -
298B GLU* 3.3 23.2 + - + +
299B GLN* 3.5 25.7 - - - +
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Residues in contact with TYR 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASP* 3.1 17.1 + - + -
41B MET* 3.5 10.6 - - - +
45B ASP* 2.8 29.8 + - - -
235B THR* 3.2 40.2 - - + -
239B VAL* 3.7 11.8 - - + +
251B ARG* 4.0 15.7 - - + +
252B GLY 3.2 0.6 + - - -
253B ARG* 1.3 75.2 - - - +
255B GLY* 1.3 63.1 + - - +
257B ALA* 3.4 4.2 + - - +
258B VAL* 3.1 35.3 + - + +
297B PRO 5.1 0.2 - - - +
298B GLU 3.0 22.1 + - - +
299B GLN 3.8 3.8 - - - -
300B GLY* 3.8 24.9 - - - +
301B GLY* 3.2 31.5 - - - -
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Residues in contact with GLY 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLU* 4.3 1.2 - - - +
249B SER* 3.1 22.7 - - - -
251B ARG* 3.7 19.0 + - - -
252B GLY 2.8 5.3 + - - -
254B TYR* 1.3 78.8 - - - +
256B ASP* 1.3 57.9 + - - +
258B VAL* 3.3 8.9 + - - +
259B ARG* 2.9 34.1 + - - +
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Residues in contact with ASP 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ALA* 4.0 14.8 - - + -
245B PHE* 3.2 24.2 - - - +
246B LEU* 3.5 9.9 - - + +
247B GLY* 2.8 19.3 + - - -
248B THR 3.1 5.2 + - - -
249B SER* 2.9 32.7 + - - +
252B GLY 3.0 13.8 + - - +
253B ARG* 3.1 21.0 + - - +
255B GLY* 1.3 74.7 - - - +
257B ALA* 1.3 61.9 + - - +
259B ARG* 3.2 7.3 + - - +
260B GLU* 3.1 22.5 + - - +
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Residues in contact with ALA 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ALA* 3.8 14.3 - - + +
235B THR* 4.1 8.7 - - + -
239B VAL* 3.6 17.7 - - + -
240B TYR 3.4 25.1 - - - +
241B ALA* 4.1 4.6 - - - +
253B ARG 3.1 3.0 + - - -
254B TYR 3.5 9.2 - - - +
256B ASP* 1.3 79.1 - - - +
258B VAL* 1.3 56.8 + - - +
260B GLU* 3.3 4.3 + - - +
261B ILE* 3.0 35.3 + - - +
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Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B MET* 3.9 23.8 - - + -
45B ASP 4.5 5.8 - - - +
55B GLU* 5.1 3.4 - - + +
56B THR* 3.6 28.0 - - + -
59B LEU* 5.9 0.7 - - + -
235B THR* 3.7 20.9 - - + -
251B ARG* 4.7 7.4 - - - +
254B TYR* 3.1 34.4 + - + +
255B GLY* 3.3 10.1 + - - +
257B ALA* 1.3 75.0 - - - +
259B ARG* 1.3 58.1 + - + +
261B ILE* 3.3 5.6 + - - +
262B ASP* 2.9 28.6 + - + +
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Residues in contact with ARG 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLU* 3.9 49.4 + - + +
244B PRO 5.0 0.6 + - - -
245B PHE* 3.7 27.1 - - + -
248B THR* 2.9 47.7 + - - +
249B SER* 4.5 0.4 - - - +
255B GLY 2.9 19.6 + - - +
256B ASP 3.2 8.0 + - - +
258B VAL* 1.3 77.0 - - + +
260B GLU* 1.3 57.0 + - - +
262B ASP* 3.5 3.3 + - - +
263B ASP* 2.9 29.5 + - - +
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Residues in contact with GLU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B THR* 3.8 27.2 + - + -
207B GLN* 2.7 29.1 + - - +
240B TYR 4.7 0.3 - - - +
241B ALA* 3.2 12.5 - - - +
242B SER* 2.6 51.6 + - - -
245B PHE* 3.6 24.6 - - + -
256B ASP 3.1 10.2 + - - +
257B ALA* 3.7 7.4 - - - +
259B ARG* 1.3 74.5 - - - +
261B ILE* 1.3 59.7 + - - +
263B ASP* 3.2 3.5 + - - +
264B SER* 2.8 32.7 + - - -
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Residues in contact with ILE 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B MET* 3.5 30.7 - - + -
41B MET* 4.9 3.4 - - - -
59B LEU* 5.7 1.8 - - + -
206B THR* 4.2 16.6 - - + -
230B TRP* 4.4 3.6 - - + -
232B VAL* 4.1 21.1 - - + -
234B ALA* 4.2 15.9 - - + +
235B THR* 3.8 30.1 - - + +
257B ALA 3.0 21.0 + - - +
258B VAL* 3.7 5.2 - - - +
260B GLU* 1.3 74.3 - - - +
262B ASP* 1.3 57.8 + - - +
264B SER* 3.2 7.5 + - - -
265B ILE* 2.9 41.7 + - + +
285B PHE* 5.3 0.2 - - + -
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Residues in contact with ASP 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR* 3.3 27.1 - - + -
57B PRO* 3.2 10.4 - - - +
58B ASN* 2.8 43.6 + - - +
59B LEU* 2.8 41.9 + - + +
258B VAL 2.9 17.5 + - - +
259B ARG* 3.6 7.6 - - - +
261B ILE* 1.3 76.5 - - - +
263B ASP* 1.3 56.7 + - - +
265B ILE* 3.3 6.3 + - - +
266B GLY 3.0 24.1 + - - -
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Residues in contact with ASP 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASN* 3.6 13.7 + - - +
207B GLN* 5.4 2.4 + - - -
210B LEU* 5.7 0.9 - - - +
245B PHE* 3.6 27.8 - - + -
259B ARG 2.9 18.7 + - - +
260B GLU 3.2 5.5 + - - +
262B ASP* 1.3 75.9 + - - +
264B SER* 1.3 64.1 + - - +
266B GLY* 3.3 2.8 + - - -
267B LYS* 2.9 52.4 + - - +
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Residues in contact with SER 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B THR* 3.8 12.9 - - - +
207B GLN* 4.4 4.3 + - - -
210B LEU* 3.5 34.5 - - - +
230B TRP* 3.9 20.2 - - - -
260B GLU* 2.8 30.9 + - - +
261B ILE* 3.2 6.3 + - - -
263B ASP* 1.3 73.7 + - - +
265B ILE* 1.3 64.1 + - - +
267B LYS* 3.2 2.3 + - - -
268B ILE* 3.0 27.5 + - - +
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Residues in contact with ILE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.9 25.4 - - + -
38B MET* 4.2 5.8 - - + -
58B ASN* 5.4 2.5 - - + -
59B LEU* 3.9 22.4 - - + +
62B MET* 4.8 1.3 - - - -
230B TRP* 3.8 15.7 - - + -
261B ILE* 2.9 37.6 + - + +
262B ASP* 3.3 5.8 + - - +
264B SER* 1.3 76.6 - - - +
266B GLY* 1.3 61.9 + - - +
268B ILE* 3.1 9.1 + - + +
269B LEU* 3.0 36.9 + - + +
285B PHE* 3.8 31.0 - - + -
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Residues in contact with GLY 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASN* 3.4 30.5 - - - +
262B ASP 3.0 11.5 + - - -
263B ASP 3.3 2.2 + - - -
265B ILE* 1.3 76.7 - - - +
267B LYS* 1.3 56.4 + - - +
269B LEU* 3.5 8.1 + - - +
270B GLU* 2.9 40.0 + - - +
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Residues in contact with LYS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 3.8 30.1 - - + -
214B LEU* 4.1 11.2 - - + +
263B ASP* 2.9 41.4 + - - +
264B SER 3.2 8.3 + - - +
266B GLY* 1.3 73.4 - - - +
268B ILE* 1.3 61.1 + - - +
270B GLU* 3.7 15.3 - - - +
271B LEU* 3.0 27.7 + - - +
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Residues in contact with ILE 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 3.6 32.1 - - + -
36B LEU* 4.4 11.7 - - + -
210B LEU* 3.8 12.1 - - + -
213B ALA* 4.0 14.4 - - + -
214B LEU* 4.1 11.9 - - + -
217B ILE* 4.0 11.8 - - + +
230B TRP* 3.9 42.2 - - + -
264B SER 3.0 19.2 + - - +
265B ILE* 3.1 8.7 + - + +
267B LYS* 1.3 76.1 - - - +
269B LEU* 1.3 65.5 + - + +
271B LEU* 3.1 13.0 + - - +
272B LEU* 3.1 15.7 + - + +
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 5.7 0.2 - - + -
36B LEU* 5.5 1.1 - - + -
58B ASN 4.8 4.7 - - - +
62B MET* 4.0 33.7 - - + -
65B GLU* 5.4 1.6 - - - +
265B ILE* 3.0 28.7 + - + +
266B GLY* 3.9 5.8 - - - +
268B ILE* 1.3 80.2 - - + +
270B GLU* 1.3 62.3 + - + +
272B LEU* 3.2 12.6 + - + +
273B GLN* 3.1 29.1 + - - +
283B VAL* 4.0 22.0 - - + -
325B TRP* 3.7 45.5 - - + +
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Residues in contact with GLU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASN* 4.6 4.9 - - - +
61B ARG* 4.3 16.4 + - - +
266B GLY* 2.9 25.4 + - - +
267B LYS* 3.7 17.9 - - - +
269B LEU* 1.3 77.6 - - + +
271B LEU* 1.3 56.7 + - - +
273B GLN* 3.4 15.3 + - - +
274B ASP* 2.8 42.6 + - - +
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 3.6 49.6 - - + +
217B ILE* 3.9 19.5 - - + -
218B LYS* 3.8 24.9 - - + -
267B LYS 3.0 14.1 + - - +
268B ILE 3.1 8.5 + - - +
270B GLU* 1.3 76.0 - - - +
272B LEU* 1.3 57.9 + - - +
274B ASP* 3.1 9.8 + - + +
275B LEU* 2.8 52.0 + - + +
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.0 17.3 - - + -
217B ILE* 3.9 17.0 - - + -
226B PHE* 3.8 25.6 - - + -
268B ILE* 3.1 15.1 + - + +
269B LEU* 3.2 12.7 + - + +
271B LEU* 1.3 75.6 - - - +
273B GLN* 1.3 59.5 + - - +
275B LEU* 4.8 0.4 - - - -
276B HIS 3.3 2.3 + - - -
277B VAL* 2.8 51.7 + - + +
278B ALA* 3.0 17.1 + - + -
281B THR* 3.8 21.3 - - + +
283B VAL* 4.1 4.3 - - + -
325B TRP* 4.1 19.1 - - + -
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Residues in contact with GLN 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLU* 4.3 13.7 + - - -
269B LEU* 3.1 15.9 + - - +
270B GLU* 3.6 22.5 + - - +
272B LEU* 1.3 77.4 - - - +
274B ASP* 1.3 61.0 + - - +
276B HIS* 3.0 29.7 + - - +
278B ALA* 3.9 18.8 - - + -
325B TRP* 3.8 20.6 - - + -
327B PRO* 5.5 2.0 - - - +
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Residues in contact with ASP 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLU* 2.8 34.5 + - - +
271B LEU* 3.1 12.8 + - + +
273B GLN* 1.3 77.5 - - - +
275B LEU* 1.3 62.7 + - + +
276B HIS* 3.2 16.7 + - - -
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ILE* 3.7 32.8 - - + +
218B LYS* 4.3 12.6 - - + +
221B ALA* 4.0 20.8 - - + +
222B ARG* 5.6 6.6 - - - +
271B LEU* 2.8 39.2 + - + +
272B LEU 4.1 3.4 - - - +
274B ASP* 1.3 78.1 - - - +
276B HIS* 1.3 71.2 + - - +
277B VAL* 3.5 11.4 + - + +
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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