Contacts of the helix formed by residues 247 - 273 (chain A) in PDB entry 1UU1
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 HIS 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.4 30.6 - - + +
40A GLU* 2.7 41.3 + - - -
243A VAL 3.0 21.8 + - - +
244A ALA 3.0 5.8 + - - +
246A ASP* 1.3 86.5 + - + +
248A ARG* 1.3 63.7 + - - +
249A GLU 2.9 5.7 + - - -
250A ILE* 3.0 33.0 + - + +
251A PHE* 3.4 8.1 - - - -
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Residues in contact with ARG 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LYS* 3.8 12.5 + - - +
67A SER* 3.6 34.2 + - - -
68A TYR* 3.7 40.6 - - + +
204A PHE* 4.8 9.3 - - + -
244A ALA 3.0 9.0 + - - +
245A LEU* 3.1 31.5 + - - +
246A ASP* 3.5 1.0 + - - -
247A HIS* 1.3 74.9 - - - +
249A GLU* 1.3 66.5 + - + +
250A ILE 3.3 0.2 - - - -
251A PHE* 3.3 11.0 + - - +
252A GLU* 2.9 39.8 + - + +
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Residues in contact with GLU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A HIS 2.9 2.6 + - - -
248A ARG* 1.3 81.3 - - + +
250A ILE* 1.3 69.9 + - + +
251A PHE 3.3 0.2 + - - -
252A GLU* 3.4 17.2 + - - +
253A GLU* 3.3 20.6 + - - +
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Residues in contact with ILE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PRO* 4.3 23.8 - - + -
36A ASP* 6.0 1.3 - - - +
37A LEU* 5.1 4.9 - - + -
247A HIS* 3.0 44.8 + - + +
249A GLU* 1.3 82.9 - - + +
251A PHE* 1.3 64.9 + - + +
253A GLU* 3.6 16.8 - - - +
254A ARG* 3.3 29.9 + - - +
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Residues in contact with PHE 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PHE* 3.8 14.1 - + - -
34A PRO* 3.9 20.4 - - + -
37A LEU* 3.6 24.9 - - + -
203A ALA* 3.4 23.6 - - + +
204A PHE* 3.6 42.0 - + + -
244A ALA* 3.4 30.3 - - + -
247A HIS 3.4 16.8 - - - -
248A ARG* 3.3 6.7 + - - +
249A GLU 3.1 0.6 - - - -
250A ILE* 1.3 77.2 - - + +
252A GLU* 1.3 60.3 + - + +
253A GLU 3.1 2.0 - - - -
254A ARG* 3.3 19.8 + - - +
255A THR* 2.8 32.9 + - - -
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Residues in contact with GLU 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 5.1 7.2 - - + -
248A ARG* 2.9 37.2 - - + +
249A GLU* 3.4 17.5 + - - +
251A PHE* 1.3 78.0 - - + +
253A GLU* 1.3 58.0 + - - +
255A THR* 3.7 6.9 - - - -
256A LYS* 2.8 29.5 + - - +
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Residues in contact with GLU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A GLU 3.3 10.0 + - - +
250A ILE* 3.6 25.2 - - - +
251A PHE 3.1 0.4 - - - -
252A GLU* 1.3 76.8 - - - +
254A ARG* 1.3 72.7 + - - +
256A LYS* 3.2 11.8 + - - +
257A PHE* 3.1 20.6 + - - +
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Residues in contact with ARG 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASN* 4.9 10.8 - - - +
31A PHE* 3.5 40.4 - - + +
32A PRO* 2.7 34.5 + - - +
34A PRO* 3.7 29.1 - - - +
203A ALA 5.5 0.4 - - - +
205A SER* 3.5 20.0 + - - -
250A ILE* 3.3 23.5 + - - +
251A PHE* 3.3 22.3 + - - +
253A GLU* 1.3 83.6 + - - +
255A THR* 1.3 58.8 + - - +
257A PHE* 3.2 10.1 + - - +
258A ILE* 2.8 32.4 + - - +
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Residues in contact with THR 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASN* 5.3 1.1 + - - +
178A GLU* 3.4 28.5 - - + +
179A PHE* 3.6 29.1 - - + -
203A ALA* 4.0 17.7 + - - +
251A PHE 2.8 20.3 + - - -
252A GLU* 3.8 7.8 - - - -
254A ARG* 1.3 75.9 - - - +
256A LYS* 1.3 65.4 + - - +
258A ILE* 3.1 9.3 + - - +
259A VAL* 2.9 25.2 + - + +
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Residues in contact with LYS 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A GLU 2.8 19.1 + - - +
253A GLU* 3.2 10.7 + - - +
255A THR* 1.3 78.0 - - - +
257A PHE* 1.3 61.0 + - - +
259A VAL* 2.9 29.7 - - + +
260A GLU* 3.1 50.1 + - + +
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Residues in contact with PHE 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 3.4 37.9 - + + -
253A GLU* 3.1 12.6 + - + +
254A ARG* 3.3 9.4 - - - +
256A LYS* 1.3 78.6 - - - +
258A ILE* 1.3 71.2 - - + +
260A GLU* 3.2 16.8 + - + +
261A GLU* 3.0 48.1 + - + +
319A GLY 4.0 15.3 - - - -
320A LYS* 4.7 0.2 - - - -
321A ARG* 3.4 46.7 - - + -
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Residues in contact with ILE 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASN* 4.8 5.2 - - - +
30A PRO* 3.3 41.7 - - + -
31A PHE* 4.3 1.6 - - + -
179A PHE* 3.9 13.7 - - + -
254A ARG 2.8 20.9 + - - +
255A THR* 3.1 11.4 + - - +
257A PHE* 1.3 90.2 - - + +
259A VAL* 1.3 58.5 + - - +
261A GLU* 3.4 5.0 + - - +
262A ARG 2.9 21.8 + - - -
281A GLY 5.1 0.4 - - - +
282A ASN* 3.8 23.8 - - + -
318A ILE* 3.5 33.1 - - + +
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Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A PHE* 3.8 35.9 - - + +
255A THR* 2.9 18.1 + - + +
256A LYS* 2.9 29.4 - - + +
258A ILE* 1.3 73.8 - - + +
260A GLU* 1.3 70.1 + - + +
262A ARG* 3.1 24.7 + - - +
263A GLU* 2.9 29.7 + - + +
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Residues in contact with GLU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LYS* 3.1 49.9 + - + +
257A PHE* 3.4 20.6 - - + +
259A VAL* 1.3 84.2 - - + +
261A GLU* 1.3 55.5 + - - +
263A GLU* 3.2 5.2 + - - +
264A ARG* 2.8 36.9 + - - +
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Residues in contact with GLU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A PHE* 3.0 31.2 + - + +
258A ILE* 3.4 5.4 - - - +
260A GLU* 1.3 82.4 - - - +
262A ARG* 1.3 57.1 + - - +
264A ARG* 3.3 33.9 + - - +
265A MET* 2.9 34.9 + - - +
318A ILE* 3.6 12.1 - - + -
321A ARG* 3.0 28.3 + - - +
324A ASN* 2.8 38.3 + - + +
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Residues in contact with ARG 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A PHE 3.5 15.0 + - - -
258A ILE 2.9 10.2 + - - +
259A VAL* 3.1 23.4 + - - +
261A GLU* 1.3 75.8 - - - +
263A GLU* 1.3 90.0 + - - +
265A MET* 3.3 5.2 + - - +
266A LYS* 2.8 36.7 + - + +
279A SER 3.1 21.4 + - - -
280A ARG* 3.0 31.3 + - - +
281A GLY 2.8 35.6 + - - -
283A PHE 3.9 7.9 - - - +
284A VAL* 4.0 15.9 - - + +
318A ILE* 3.2 25.5 - - + +
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Residues in contact with GLU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A VAL* 2.9 21.3 + - + +
260A GLU* 3.8 4.7 - - - +
262A ARG* 1.3 111.1 + - - +
264A ARG* 1.3 62.5 + - - +
266A LYS* 2.8 34.9 + - - +
267A SER* 3.0 28.0 + - - -
270A ARG* 4.3 4.9 + - - -
280A ARG* 4.7 2.4 + - - -
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Residues in contact with ARG 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A GLU 2.8 19.2 + - - +
261A GLU* 3.3 40.5 + - - +
263A GLU* 1.3 77.0 - - - +
265A MET* 1.3 63.8 + - - +
267A SER* 3.3 7.1 + - - -
268A ALA* 3.2 21.5 + - + +
321A ARG* 4.2 10.2 + - - +
324A ASN* 4.5 6.1 - - - +
325A ASP* 2.5 31.1 + - - -
328A LEU* 4.2 21.3 - - + +
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Residues in contact with MET 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A GLU* 2.9 19.6 + - + +
262A ARG 3.8 3.4 - - - +
264A ARG* 1.3 79.0 - - + +
266A LYS* 1.3 58.9 + - - +
268A ALA* 3.3 0.9 + - - +
269A LEU* 2.9 43.5 + - + +
284A VAL* 4.6 14.4 - - + -
316A ILE* 4.9 8.1 - - + -
317A THR 5.7 0.7 - - - +
318A ILE* 4.8 13.9 - - - -
324A ASN* 3.5 49.8 - - + +
327A ILE* 3.4 35.4 - - + -
328A LEU* 4.1 25.4 - - + -
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Residues in contact with LYS 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ARG* 2.8 25.5 + - + +
263A GLU* 2.8 38.6 + - - +
265A MET* 1.3 78.2 - - - +
267A SER* 1.3 59.3 + - - +
269A LEU* 3.5 1.7 + - - -
270A ARG* 2.9 51.9 + - - +
276A ILE* 3.5 14.9 - - + +
277A THR 3.9 17.7 - - - +
278A ASP* 3.0 23.8 + - - -
279A SER* 2.7 34.1 + - - +
280A ARG* 4.5 0.8 - - - +
284A VAL* 3.5 20.6 - - + -
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Residues in contact with SER 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLU 3.0 14.8 + - - -
264A ARG* 3.7 8.6 - - - -
266A LYS* 1.3 75.9 - - - +
268A ALA* 1.3 58.8 + - - +
270A ARG* 3.1 20.2 + - - +
271A GLU* 2.9 35.3 + - - +
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ARG* 3.2 11.3 + - + +
265A MET 3.7 6.7 - - - +
267A SER* 1.3 81.4 - - - +
269A LEU* 1.3 57.7 + - - +
271A GLU* 3.3 7.5 - - - +
272A MET* 2.8 37.9 + - + +
328A LEU* 3.8 28.0 - - + -
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Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A MET* 2.9 30.9 + - + +
266A LYS* 4.0 5.8 - - - +
268A ALA* 1.3 72.9 - - - +
270A ARG* 1.3 65.8 + - - +
272A MET* 3.0 17.5 + - - +
273A GLY 3.1 0.2 + - - -
274A TYR* 3.0 35.4 + - + +
276A ILE* 4.2 19.5 - - + -
284A VAL* 4.3 18.8 - - + -
286A VAL* 4.3 20.2 - - + -
316A ILE* 5.9 0.2 - - + -
327A ILE* 6.2 0.4 - - + -
328A LEU* 3.6 17.7 - - + -
331A LEU* 3.5 33.4 - - + -
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Residues in contact with ARG 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A GLU* 4.3 4.9 + - - -
266A LYS* 2.9 54.8 + - - +
267A SER* 3.1 41.9 + - - +
269A LEU* 1.3 73.4 - - - +
271A GLU* 1.3 55.8 + - - +
273A GLY* 2.8 25.8 + - - -
274A TYR 3.8 10.7 + - - +
276A ILE* 3.8 19.8 - - + +
278A ASP* 5.1 5.1 + - - +
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Residues in contact with GLU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A SER* 2.9 22.4 + - - +
268A ALA* 3.3 9.4 - - - +
270A ARG* 1.3 77.5 - - + +
272A MET* 1.3 62.0 + - + +
273A GLY* 3.1 1.7 + - - -
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Residues in contact with MET 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ALA* 2.8 27.1 + - + +
269A LEU* 3.0 15.4 + - - +
271A GLU* 1.3 76.2 - - + +
273A GLY* 1.3 58.4 + - - +
274A TYR* 3.4 20.3 - - + -
328A LEU* 3.9 16.8 - - - +
331A LEU* 3.1 15.7 - - + +
332A GLU* 3.0 49.1 - - + +
334A PHE 5.3 0.4 - - - +
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Residues in contact with GLY 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ARG 2.8 14.4 + - - -
271A GLU 3.0 1.9 - - - -
272A MET* 1.3 80.0 - - - +
274A TYR* 1.3 63.9 + - - +
275A ARG* 3.7 1.4 + - - +
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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