Contacts of the helix formed by residues 252 - 275 (chain B) in PDB entry 3GUC
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 ALA 252 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 5.2 7.0 - - + -
95A CYS* 4.0 25.0 - - + +
270A LEU* 3.8 29.2 - - + +
274A LEU* 4.8 11.7 - - + -
251B ALA* 1.3 79.1 - - - +
253B SER* 1.3 61.7 + - - +
254B LEU 3.3 0.2 - - - -
255B PRO* 3.1 11.1 - - - +
256B THR* 3.0 19.6 + - - -
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Residues in contact with SER 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLN* 2.8 24.3 + - - -
270A LEU* 4.0 4.7 - - - +
276A PHE* 4.4 21.6 - - - -
210B ASN 5.2 1.6 - - - -
211B ALA* 3.7 22.5 + - - -
212B VAL* 5.4 1.3 - - - +
251B ALA 4.1 4.0 - - - +
252B ALA* 1.3 81.6 - - - +
254B LEU* 1.3 56.8 + - - +
256B THR* 3.1 3.3 + - - -
257B THR* 2.8 32.1 + - - -
287B ALA* 5.1 1.7 - - - +
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Residues in contact with LEU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B VAL* 3.9 7.0 - - + -
208B SER 3.8 22.0 - - - +
209B GLU* 4.4 10.5 - - - +
211B ALA* 3.3 18.8 - - + +
251B ALA* 4.3 13.1 - - - +
253B SER* 1.3 78.8 - - - +
255B PRO* 1.4 68.2 - - + +
257B THR* 3.5 1.0 + - - -
258B MET* 3.0 59.2 + - + +
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Residues in contact with PRO 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET* 4.8 3.8 - - - +
94A ARG* 6.4 1.6 - - + -
95A CYS* 5.8 4.9 - - - -
87B VAL* 5.9 1.0 - - - +
251B ALA 3.3 18.6 - - - +
252B ALA* 3.1 15.5 - - - +
254B LEU* 1.4 99.2 - - + +
256B THR* 1.3 55.9 + - - +
258B MET* 3.6 13.9 + - + +
259B GLY* 3.0 21.8 + - - -
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Residues in contact with THR 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET* 3.9 21.2 - - + +
95A CYS* 4.2 5.0 - - - -
263A GLY 3.3 27.1 - - - +
266A VAL* 3.9 9.8 - - + +
267A GLN* 3.7 29.2 - - - +
270A LEU* 3.7 8.4 - - - +
252B ALA 3.0 15.7 + - - -
253B SER* 3.1 8.8 + - - -
255B PRO* 1.3 77.1 - - - +
257B THR* 1.3 65.2 + - - +
259B GLY* 3.0 3.6 + - - -
260B VAL* 3.0 22.7 + - - +
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Residues in contact with THR 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLN* 2.9 22.5 + - - +
207B VAL* 4.0 20.6 - - + -
211B ALA* 2.7 29.9 + - - +
213B SER 4.0 14.6 - - - +
253B SER 2.8 14.5 + - - -
254B LEU 3.9 3.8 - - - -
256B THR* 1.3 71.6 - - - +
258B MET* 1.3 62.8 + - - +
260B VAL* 3.3 1.7 + - - +
261B VAL* 3.0 24.4 + - + +
285B TYR* 3.8 23.6 - - + -
287B ALA* 3.9 0.9 - - + +
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Residues in contact with MET 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLY* 3.6 31.9 - - - +
84B VAL* 4.0 19.4 - - + +
87B VAL* 5.1 6.1 - - + -
207B VAL* 4.1 25.5 - - + +
254B LEU* 3.0 51.9 + - + +
255B PRO* 3.7 10.1 - - + +
257B THR* 1.3 76.1 - - - +
259B GLY* 1.3 57.2 + - - +
261B VAL* 3.9 1.2 - - - +
262B ALA* 2.9 32.7 + - - +
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Residues in contact with GLY 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET* 5.1 8.5 - - - -
259A GLY 5.0 8.3 - - - +
263A GLY* 5.5 1.6 - - - -
87B VAL* 4.7 13.0 - - - +
91B MET* 5.2 0.9 - - - +
255B PRO 3.0 12.2 + - - -
256B THR* 3.0 8.1 + - - -
258B MET* 1.3 73.8 - - - +
260B VAL* 1.3 58.7 + - - +
262B ALA* 3.5 5.0 + - - +
263B GLY* 2.9 26.2 + - - -
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A VAL* 4.6 10.1 - - + +
263A GLY* 3.6 32.3 - - - +
264A ILE* 3.7 17.9 - - + +
267A GLN* 4.9 0.2 - - - +
256B THR 3.0 13.5 + - - +
257B THR 3.8 1.3 - - - +
259B GLY* 1.3 74.6 - - - +
261B VAL* 1.3 63.8 + - - +
263B GLY* 3.2 2.5 + - - -
264B ILE* 3.0 45.0 + - + +
285B TYR* 3.7 44.0 - - + +
292B PHE* 4.7 0.2 - - + -
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B VAL* 4.2 13.5 - - + -
205B SER* 4.4 2.5 - - - -
206B GLY 3.9 9.0 - - - +
207B VAL* 3.9 20.0 - - + -
214B GLY* 3.9 19.3 - - - -
215B HIS* 3.8 24.5 - - - +
216B ILE* 3.8 9.9 - - + +
257B THR* 3.0 20.3 + - + +
258B MET 4.0 1.3 - - - +
260B VAL* 1.3 75.5 - - - +
262B ALA* 1.3 57.0 + - - +
264B ILE* 3.8 6.1 - - + +
265B LEU* 2.9 27.9 + - - +
285B TYR* 4.2 16.6 - - + -
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Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B VAL* 3.9 10.3 - - + +
87B VAL* 3.5 34.1 - - + -
88B THR* 3.6 20.0 - - - +
91B MET* 4.2 2.0 - - - -
258B MET 2.9 19.9 + - - +
259B GLY 3.8 0.9 - - - +
261B VAL* 1.3 78.3 - - - +
263B GLY* 1.3 57.4 + - - +
265B LEU* 3.3 3.0 + - - +
266B VAL* 2.9 34.1 + - - +
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Residues in contact with GLY 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A THR* 3.6 5.1 + - - -
259A GLY 5.6 0.7 - - - -
260A VAL* 3.7 18.6 - - - -
91B MET* 3.8 24.3 - - - -
259B GLY 2.9 15.5 + - - -
260B VAL 3.7 2.2 - - - -
262B ALA* 1.3 72.9 - - - +
264B ILE* 1.3 59.2 + - - +
266B VAL* 3.3 0.7 + - - -
267B GLN* 2.9 30.1 + - - +
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Residues in contact with ILE 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A VAL* 3.8 12.5 - - + +
285A TYR* 5.0 3.6 - - + +
290A ASP* 4.8 1.3 - - - +
292A PHE* 3.8 30.7 - - + -
216B ILE* 3.6 16.2 - - + -
260B VAL* 3.0 39.0 + - + +
261B VAL* 3.8 6.3 - - - +
263B GLY* 1.3 74.4 - - - +
265B LEU* 1.3 63.3 + - - +
267B GLN* 3.4 6.1 + - - +
268B ASN* 3.1 27.3 + - - +
283B LEU* 3.1 36.3 - - + +
285B TYR* 5.3 5.2 - - + -
292B PHE* 4.3 7.6 - - + -
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Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B VAL* 4.7 1.8 - - + -
88B THR* 3.6 31.6 - - + +
179B LEU* 4.3 12.8 - - + -
180B SER 5.5 0.2 - - - +
181B CYS* 4.0 19.1 - - - -
203B MET* 3.9 36.8 - - + +
205B SER* 4.1 14.6 - - - +
216B ILE* 3.8 27.3 - - + +
261B VAL 2.9 15.1 + - - +
262B ALA 3.3 8.9 + - - +
264B ILE* 1.3 77.2 - - - +
266B VAL* 1.3 58.2 + - - +
268B ASN* 3.2 3.3 + - - +
269B VAL* 2.8 31.4 + - - +
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Residues in contact with VAL 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A THR* 4.1 18.8 - - + -
88B THR* 3.8 27.4 - - + +
91B MET* 3.8 36.8 - - + -
92B LEU* 3.7 22.4 - - + -
95B CYS* 4.7 3.8 - - - -
262B ALA 2.9 23.1 + - - +
263B GLY 3.8 3.4 - - - +
265B LEU* 1.3 72.5 - - - +
267B GLN* 1.3 59.0 + - - +
269B VAL* 3.0 9.3 + - - +
270B LEU* 2.8 32.2 + - + +
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Residues in contact with GLN 267 (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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253A SER* 3.1 29.5 + - - -
256A THR* 3.5 18.1 + - - +
257A THR* 2.9 29.1 + - - +
260A VAL* 4.8 0.2 - - - +
285A TYR* 2.8 29.5 + - - +
287A ALA* 3.4 22.8 - - - +
290A ASP* 5.0 1.6 - - - +
263B GLY 2.9 17.0 + - - +
264B ILE* 3.6 6.1 - - - +
266B VAL* 1.3 77.7 - - - +
268B ASN* 1.3 58.1 + - - +
270B LEU* 3.3 8.9 + - - +
271B LYS* 2.9 35.0 + - + +
276B PHE* 4.7 2.7 - - - -
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Residues in contact with ASN 268 (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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290A ASP* 2.7 32.3 + - - +
203B MET* 3.6 14.8 - - + +
216B ILE* 3.7 21.1 - - + +
264B ILE* 3.1 26.7 + - - +
265B LEU 3.7 3.4 - - - +
267B GLN* 1.3 74.9 - - - +
269B VAL* 1.3 59.8 + - - +
271B LYS* 3.3 10.0 + - - +
272B PHE* 2.8 31.2 + - - +
279B VAL* 3.5 11.5 - - + +
280B SER* 2.8 32.8 + - - +
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 4.4 8.1 - - + -
92B LEU* 4.0 20.2 - - + -
177B LEU* 3.7 13.2 - - + -
179B LEU* 3.6 38.6 - - + -
203B MET* 3.9 10.0 - - - +
265B LEU* 2.8 23.8 + - + +
266B VAL* 3.3 11.0 - - - +
268B ASN* 1.3 72.2 - - - +
270B LEU* 1.3 58.2 + - + +
272B PHE* 3.3 1.6 + - - +
273B LEU* 2.8 51.7 + - + +
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ALA* 3.5 43.5 - - + +
253A SER* 4.1 6.7 - - - +
256A THR* 3.6 18.8 - - + -
71B ILE* 3.9 31.4 - - + -
92B LEU* 4.7 8.7 - - + -
95B CYS* 4.3 9.2 - - - -
266B VAL* 2.8 22.5 + - + +
267B GLN* 3.6 11.0 - - - +
269B VAL* 1.3 73.6 - - + +
271B LYS* 1.3 58.0 + - - +
273B LEU* 4.8 3.4 - - + -
274B LEU* 2.9 42.9 + - + +
276B PHE* 3.8 12.6 - - + -
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Residues in contact with LYS 271 (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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287A ALA 3.0 29.0 + - - +
288A MET* 3.3 18.8 + - - +
290A ASP* 3.2 25.0 + - - -
267B GLN* 2.9 21.8 + - + +
268B ASN* 3.7 23.1 - - - +
270B LEU* 1.3 75.5 - - - +
272B PHE* 1.3 56.4 + - - +
275B ASN* 3.0 28.2 + - - -
276B PHE* 3.3 47.4 + - + +
277B GLY* 4.3 0.7 - - - -
278B THR 2.8 24.3 + - - +
279B VAL* 4.0 11.2 - - + +
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Residues in contact with PHE 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ASP* 3.7 21.8 - - + -
177B LEU* 3.7 13.2 - - + -
201B THR* 3.7 35.4 - - + -
203B MET* 3.9 12.1 - - + -
218B LEU* 4.6 13.0 - - + -
220B ILE* 5.8 4.3 - - + -
268B ASN 2.8 17.6 + - - +
269B VAL 3.6 2.9 - - - +
271B LYS* 1.3 77.3 - - - +
273B LEU* 1.3 79.9 + - + +
275B ASN* 3.8 6.1 + - - +
279B VAL* 3.6 18.7 - - + +
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LYS* 4.9 1.2 - - - +
71B ILE* 5.3 3.1 - - + -
74B PHE* 3.4 45.5 - - + -
76B VAL* 4.1 5.4 - - + -
92B LEU* 5.9 0.2 - - + -
97B ILE* 3.8 26.9 - - + -
176B ASP* 3.8 28.0 - - + -
177B LEU* 4.5 6.7 - - + -
269B VAL* 2.8 42.7 + - + +
270B LEU* 4.3 4.7 - - + +
272B PHE* 1.3 94.2 - - + +
274B LEU* 1.3 65.4 + - + +
275B ASN* 3.8 1.4 + - - +
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ARG* 5.3 4.5 - - - +
248A GLY 4.3 19.3 - - - +
249A VAL* 4.5 10.8 - - + +
252A ALA* 4.4 13.9 - - + -
70B LYS* 4.0 31.7 + - + -
71B ILE* 4.1 21.3 - - + +
74B PHE* 4.0 18.8 - - + -
270B LEU* 2.9 25.5 + - + +
273B LEU* 1.3 82.4 - - + +
275B ASN* 1.3 72.8 + - - +
276B PHE* 3.6 27.7 - - + +
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Residues in contact with ASN 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LYS* 6.0 1.1 - - - +
271B LYS 3.0 12.2 + - - -
272B PHE 3.8 5.3 + - - +
273B LEU 3.5 3.2 - - - +
274B LEU* 1.3 83.6 - - - +
276B PHE* 1.3 59.6 + - - +
277B GLY 5.3 0.2 - - - -
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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