Contacts of the helix formed by residues 258 - 286 (chain A) in PDB entry 1GEY
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 258 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN* 4.4 6.5 - - - +
254A ALA 3.4 10.3 + - - -
255A GLN* 2.8 22.0 + - - -
256A ALA 3.4 0.4 - - - -
257A LEU* 1.3 80.6 - - - +
259A PRO* 1.3 67.2 - - - +
260A GLN* 3.1 25.0 + - - -
261A GLY 2.8 25.6 + - - -
262A ILE* 3.0 11.1 + - - +
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Residues in contact with PRO 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN* 5.9 1.8 - - - +
257A LEU 4.6 0.4 - - - +
258A SER* 1.3 86.6 - - - +
260A GLN* 1.3 79.1 + - + +
262A ILE* 3.5 12.8 + - + +
263A VAL* 3.1 27.8 + - - +
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Residues in contact with GLN 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A SER* 3.1 21.2 + - - -
259A PRO* 1.3 100.8 - - + +
261A GLY* 1.3 63.5 + - - +
263A VAL* 3.3 9.9 + - - +
264A ALA* 3.1 22.0 + - - +
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Residues in contact with GLY 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 6.3 0.9 - - - -
255A GLN 4.3 2.7 - - - -
256A ALA* 3.5 24.0 - - - +
258A SER* 2.8 15.5 + - - -
260A GLN* 1.3 81.5 - - - +
262A ILE* 1.3 56.0 + - - +
264A ALA* 3.5 6.1 + - - +
265A MET* 3.0 26.9 + - - +
268A ARG* 4.6 4.0 + - - -
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Residues in contact with ILE 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN 4.9 1.1 - - - +
70A TYR* 3.7 51.6 - - + -
216A PHE* 4.7 5.4 - - + -
256A ALA 4.5 3.4 - - - +
257A LEU* 3.5 27.4 - - + +
258A SER 3.0 11.3 + - - +
259A PRO* 3.9 11.2 - - + +
260A GLN 3.3 0.2 - - - -
261A GLY* 1.3 74.8 - - - +
263A VAL* 1.3 65.1 + - + +
265A MET* 3.6 8.7 + - + +
266A ARG* 3.2 48.4 + - - +
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Residues in contact with VAL 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PRO 3.1 17.6 + - - +
260A GLN* 3.5 11.0 - - - +
261A GLY 3.2 0.4 - - - -
262A ILE* 1.3 76.7 - - + +
264A ALA* 1.3 64.6 + - - +
266A ARG* 3.3 13.4 + - - +
267A GLU* 3.0 37.4 + - + +
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Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 6.4 0.2 - - + -
260A GLN 3.1 16.5 + - - +
261A GLY* 3.8 7.0 - - - +
263A VAL* 1.3 74.2 - - - +
265A MET* 1.3 65.5 + - - +
267A GLU* 3.2 22.4 + - - +
268A ARG* 3.2 30.1 + - - +
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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
----------------------------------------------------------
70A TYR* 3.4 41.3 - - + +
189A GLU* 3.8 14.1 - - + +
215A ALA* 4.1 10.3 - - - +
216A PHE* 3.8 32.5 - - + -
261A GLY 3.0 18.6 + - - +
262A ILE* 3.6 7.2 - - + +
263A VAL 3.2 0.4 - - - -
264A ALA* 1.3 76.5 - - - +
266A ARG* 1.3 75.1 + - + +
268A ARG* 2.9 36.4 + - - +
269A VAL* 3.0 31.9 + - - +
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Residues in contact with ARG 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 4.4 16.2 + - - -
192A PRO* 6.3 0.4 - - - +
262A ILE* 3.2 37.2 + - - +
263A VAL* 3.3 14.2 + - - +
265A MET* 1.3 88.7 - - + +
267A GLU* 1.3 68.9 + - - +
269A VAL* 3.3 7.2 + - + +
270A ALA* 3.0 24.1 + - - +
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Residues in contact with GLU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A VAL* 3.0 34.1 + - + +
264A ALA* 3.3 16.4 - - - +
265A MET 3.1 0.2 - - - -
266A ARG* 1.3 80.2 - - - +
268A ARG* 1.3 58.8 + - + +
270A ALA* 3.3 7.5 + - - +
271A GLN* 3.0 42.6 + - - +
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Residues in contact with ARG 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 3.6 43.5 - - + +
43A VAL* 3.7 28.6 - - - +
45A PHE* 5.9 4.4 - - - -
190A PHE* 5.6 0.2 - - - -
215A ALA* 3.0 23.3 + - - +
216A PHE* 2.9 38.2 + - - +
217A ALA* 3.7 3.6 - - - +
218A LEU* 5.6 0.6 - - - +
256A ALA* 5.8 1.4 + - - +
261A GLY 4.6 2.8 + - - -
264A ALA* 3.3 32.0 + - - +
265A MET* 2.9 27.7 + - - +
267A GLU* 1.3 75.7 - - + +
269A VAL* 1.3 65.4 + - - +
271A GLN* 3.4 13.4 + - - +
272A ILE* 3.1 29.7 + - - +
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU* 3.4 27.8 - - + +
190A PHE* 4.0 16.8 - - + +
192A PRO* 5.9 0.9 - - + -
215A ALA* 3.8 18.2 - - + -
265A MET* 3.0 35.6 + - - +
266A ARG* 3.6 10.3 - - + +
268A ARG* 1.3 74.1 - - - +
270A ALA* 1.3 65.0 + - - +
272A ILE* 3.2 3.5 + - - +
273A ILE* 2.9 43.1 + - + +
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Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ARG 3.0 13.9 + - - +
267A GLU* 3.4 12.1 - - - +
269A VAL* 1.3 77.3 - - - +
271A GLN* 1.3 62.7 + - + +
273A ILE* 3.3 8.0 + - - +
274A ALA* 3.0 25.1 + - - +
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Residues in contact with GLN 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 3.2 24.2 + - - +
267A GLU* 3.0 34.6 + - - +
268A ARG* 3.6 8.5 + - - +
269A VAL 3.3 0.2 - - - -
270A ALA* 1.3 77.7 - - + +
272A ILE* 1.3 61.7 + - + +
274A ALA* 3.7 5.6 + - - +
275A GLU* 3.1 27.9 + - - +
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Residues in contact with ILE 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 4.0 26.2 - - + -
40A PRO* 4.1 11.7 - - + -
190A PHE* 3.7 17.5 - - + -
268A ARG 3.1 19.5 + - - +
269A VAL 3.2 3.8 + - - +
271A GLN* 1.3 78.0 - - + +
273A ILE* 1.3 61.3 + - - +
275A GLU* 3.3 3.1 + - - +
276A ARG* 2.8 27.9 + - - +
297A THR 4.7 1.6 - - - +
298A ASN* 3.6 35.4 - - + +
338A VAL* 3.8 26.8 - - + +
339A GLY 4.2 10.5 - - - +
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Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 3.6 30.5 - - + +
269A VAL* 2.9 34.5 + - + +
270A ALA* 3.7 6.7 - - - +
272A ILE* 1.3 77.1 - - - +
274A ALA* 1.3 64.6 + - - +
276A ARG* 3.2 37.2 + - - +
277A GLU* 3.0 29.4 + - + +
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Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ALA 3.0 16.9 + - - +
271A GLN* 3.9 6.3 - - - +
273A ILE* 1.3 77.0 - - - +
275A GLU* 1.3 63.8 + - - +
277A GLU* 3.2 10.1 + - - +
278A TYR* 3.1 20.1 + - - +
341A ARG* 4.9 2.6 + - - +
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Residues in contact with GLU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A GLN 3.1 16.5 + - - +
272A ILE* 3.7 4.7 - - + +
273A ILE 3.3 0.2 - - - -
274A ALA* 1.3 75.8 - - - +
276A ARG* 1.3 66.3 + - - +
278A TYR* 3.2 12.5 + - - +
279A LEU* 3.0 22.5 + - - +
338A VAL* 3.7 11.4 - - + -
339A GLY 3.6 22.0 - - - +
340A THR* 4.9 0.2 - - - -
341A ARG* 2.9 54.7 + - - +
344A SER* 2.8 29.3 + - - +
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Residues in contact with ARG 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 4.8 1.6 + - - +
272A ILE 2.8 22.8 + - - +
273A ILE* 3.2 37.0 + - - +
275A GLU* 1.3 72.4 - - - +
277A GLU* 1.3 79.5 + - - +
279A LEU* 3.3 4.5 + - - +
280A ILE* 3.0 45.1 + - + +
295A SER* 3.2 37.8 + - - +
296A GLU* 3.5 13.5 + - - +
297A THR 2.9 38.7 + - - +
299A TYR 4.8 0.4 - - - -
300A ILE* 4.2 4.7 - - + -
338A VAL* 3.7 24.9 - - + +
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Residues in contact with GLU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ILE* 3.0 19.2 + - + +
274A ALA* 3.2 9.8 + - - +
276A ARG* 1.3 106.3 + - - +
278A TYR* 1.3 65.5 + - - +
280A ILE* 3.5 16.2 + - - +
281A ALA* 3.2 22.9 + - - +
294A ASP* 5.1 5.1 - - - +
295A SER 5.0 0.9 - - - +
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Residues in contact with TYR 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ALA 3.1 9.8 + - - +
275A GLU* 3.2 15.7 + - - +
277A GLU* 1.3 77.8 - - - +
279A LEU* 1.3 63.9 + - - +
281A ALA* 3.3 6.8 + - + +
282A ALA* 3.1 26.8 + - + +
341A ARG* 3.5 59.0 - - - +
344A SER* 4.6 3.8 - - - -
345A GLN* 3.5 22.9 + - + +
348A ILE* 3.8 23.7 - - + +
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 6.3 0.7 - - + -
275A GLU 3.0 15.3 + - - +
276A ARG 3.3 5.1 + - - +
278A TYR* 1.3 81.4 - - - +
280A ILE* 1.3 56.1 + - - +
282A ALA* 4.7 1.8 - - - -
283A LEU* 3.1 47.5 + - + +
300A ILE* 3.8 20.4 - - + -
336A ILE* 4.3 20.9 - - + -
337A THR 4.7 0.7 - - - +
338A VAL* 4.3 22.7 - - + -
344A SER* 3.8 42.0 - - - +
347A VAL* 5.3 7.6 - - + -
348A ILE* 4.4 11.4 - - + -
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Residues in contact with ILE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ARG* 3.0 38.3 + - + +
277A GLU* 3.9 22.2 - - - +
278A TYR 3.2 0.4 - - - -
279A LEU* 1.3 75.2 - - - +
281A ALA* 1.3 66.7 + - - +
283A LEU* 3.5 1.6 + - - +
284A LYS* 3.3 39.8 + - + +
292A VAL* 4.1 20.5 - - + +
293A PHE 4.8 6.1 - - - +
294A ASP* 4.8 9.6 - - - +
295A SER 4.8 14.1 - - - +
300A ILE* 3.4 23.1 - - + -
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Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLU 3.2 17.7 + - - +
278A TYR* 3.3 8.5 + - + +
280A ILE* 1.3 80.3 - - - +
282A ALA* 1.3 62.1 + - - +
284A LYS* 3.5 17.5 + - - +
285A GLU* 3.8 15.0 - - - +
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR* 3.1 25.4 + - + +
279A LEU 4.1 2.5 - - - +
281A ALA* 1.3 76.8 - - - +
283A LEU* 1.3 62.1 + - - +
285A GLU* 3.3 27.8 + - - +
286A ILE* 3.8 12.4 + - - +
348A ILE* 3.6 35.8 - - + +
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 3.1 39.2 + - + +
280A ILE* 4.0 2.9 - - - +
281A ALA 3.4 0.2 - - - -
282A ALA* 1.3 73.6 - - + +
284A LYS* 1.3 64.6 + - - +
286A ILE* 3.2 17.6 + - + -
289A VAL* 3.3 31.4 - - + +
292A VAL* 3.8 28.7 - - + -
300A ILE* 4.5 10.8 - - + -
302A ALA* 4.6 7.9 - - + -
304A PHE* 5.1 1.3 - - + -
336A ILE* 4.1 24.9 - - + -
347A VAL* 5.4 1.6 - - + -
348A ILE* 5.5 3.6 - - + -
351A LEU* 3.5 31.2 - - + -
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Residues in contact with LYS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 3.3 29.6 + - + +
281A ALA* 3.7 11.9 - - - +
282A ALA 3.3 0.6 - - - -
283A LEU* 1.3 77.5 - - - +
285A GLU* 1.3 61.4 + - + +
286A ILE 3.4 5.4 + - - +
289A VAL* 4.8 4.6 - - - +
292A VAL* 4.0 30.5 - - + +
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Residues in contact with GLU 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ALA* 3.8 17.5 - - - +
282A ALA* 3.5 14.9 - - - +
283A LEU 3.2 0.8 - - - -
284A LYS* 1.3 77.7 - - + +
286A ILE* 1.3 61.4 + - + +
287A PRO* 3.5 6.6 - - - +
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Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ALA 3.9 15.3 - - - +
283A LEU* 3.2 18.8 + - + +
284A LYS 4.0 2.5 - - - +
285A GLU* 1.3 78.6 - - + +
287A PRO* 1.3 68.2 - - + +
288A CYS* 3.5 29.8 - - - -
289A VAL* 3.1 34.8 + - + +
348A ILE* 4.1 23.6 - - + +
351A LEU* 3.8 40.4 - - + +
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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