Contacts of the helix formed by residues 263 - 285 (chain A) in PDB entry 1XV9
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 ASP 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ASN* 3.9 0.4 - - - +
255A GLY* 4.5 5.2 - - - +
257A ASN 3.6 18.2 - - - +
258A PRO* 3.1 29.1 - - + +
260A SER* 3.1 16.4 + - - +
261A PRO 3.8 0.4 - - - -
262A ASN* 1.3 72.2 - - - +
264A PRO* 1.3 75.7 - - - +
265A VAL* 3.3 17.4 + - - +
266A THR* 3.0 26.8 + - - +
267A ASN* 2.7 29.0 + - - +
340A ALA* 5.7 0.5 - - - +
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Residues in contact with PRO 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ALA* 5.0 5.2 - - + -
253A ASN 3.9 12.1 - - - +
255A GLY* 3.2 23.3 - - - +
262A ASN 3.1 9.2 - - - +
263A ASP* 1.3 85.5 - - - +
265A VAL* 1.3 71.6 + - - +
267A ASN* 2.9 19.1 + - + +
268A ILE* 3.2 15.9 + - + +
332A VAL* 5.3 13.1 - - + +
336A SER* 3.9 23.8 - - - +
337A ALA* 5.9 1.1 - - - -
340A ALA* 4.1 14.8 - - + -
342A VAL* 6.2 2.5 - - + -
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Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASP* 3.3 9.2 + - - +
264A PRO* 1.3 80.2 - - - +
266A THR* 1.3 64.4 + - - +
268A ILE* 3.1 18.6 + - - +
269A CYS* 3.5 12.8 + - - -
340A ALA* 4.5 22.9 - - + +
342A VAL* 4.9 7.8 - - + +
439A PHE* 4.0 38.1 - - + -
445A THR* 3.4 33.0 - - + +
1003A F15 6.3 2.5 - - - -
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Residues in contact with THR 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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258A PRO* 4.8 7.0 + - - +
263A ASP* 3.0 32.6 + - + +
264A PRO 3.2 0.4 - - - -
265A VAL* 1.3 79.8 - - - +
267A ASN* 1.3 59.6 + - - +
269A CYS* 3.4 6.4 + - - +
270A GLN* 3.1 39.6 + - + +
445A THR* 4.4 10.4 - - - +
446A PRO* 3.8 37.7 - - + +
685H GLU 6.3 0.9 - - - +
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Residues in contact with ASN 267 (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 ALA* 4.5 0.4 - - - +
261A PRO 3.6 13.7 - - - +
262A ASN* 2.9 27.5 + - - +
263A ASP 2.7 24.2 + - - -
264A PRO* 2.9 14.6 + - + +
266A THR* 1.3 70.3 - - - +
268A ILE* 1.3 60.8 + - - +
270A GLN* 3.2 26.8 + - - +
271A ALA* 2.9 28.4 + - - +
326A LEU* 3.9 8.4 - - + +
328A THR* 4.2 3.1 + - - +
330A LEU* 3.2 34.8 - - + +
332A VAL* 5.8 0.7 - - + -
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Residues in contact with ILE 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 PRO 3.2 12.5 + - - +
265A VAL* 3.1 10.4 + - - +
267A ASN* 1.3 76.4 - - - +
269A CYS* 1.3 62.3 + - - +
271A ALA* 3.3 6.9 + - - +
272A ALA* 2.8 26.3 + - - +
324A ILE* 6.2 2.2 - - + -
326A LEU* 4.2 19.5 - - + -
332A VAL* 5.6 9.4 - - + -
342A VAL* 6.2 1.3 - - + -
1003A F15 3.6 81.6 - - + +
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Residues in contact with CYS 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 VAL* 3.5 17.7 - - - -
266A THR* 3.4 7.8 + - - +
267A ASN 3.2 0.4 - - - -
268A ILE* 1.3 77.6 - - - +
270A GLN* 1.3 63.7 + - - +
272A ALA* 3.8 2.0 - - - +
273A ASP* 3.2 22.9 + - - +
436A LEU* 4.7 15.3 - - - -
439A PHE* 5.4 4.7 - - - -
445A THR* 4.3 19.1 - - - -
446A PRO 4.5 14.4 - - - +
447A ILE* 5.0 9.0 - - - -
448A ASP* 5.0 5.4 + - - +
451A LEU* 3.7 28.1 - - + +
1003A F15 6.4 0.7 - - - -
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Residues in contact with GLN 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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261A PRO 5.4 2.5 + - - +
266A THR* 3.1 36.7 + - + +
267A ASN* 3.3 28.6 + - - +
269A CYS* 1.3 76.5 - - - +
271A ALA* 1.3 61.1 + - - +
273A ASP* 3.7 6.4 + - - +
274A LYS* 3.4 21.1 + - - +
328A THR* 4.2 19.1 - - + +
446A PRO 5.9 1.3 - - - +
448A ASP* 5.0 12.6 - - - +
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Residues in contact with ALA 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 ASN 2.9 16.7 + - - +
268A ILE* 3.6 5.8 - - - +
270A GLN* 1.3 77.3 - - - +
272A ALA* 1.3 58.8 + - - +
274A LYS* 3.6 3.5 - - - +
275A GLN* 2.9 33.8 + - - +
326A LEU* 4.0 12.3 - - + -
327A ALA 4.4 0.2 - - - +
328A THR* 3.8 28.0 - - + +
1003A F15 4.0 18.6 - - + +
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Residues in contact with ALA 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 ILE 2.8 22.0 + - - +
269A CYS* 4.2 3.6 - - - +
270A GLN 3.4 0.2 - - - -
271A ALA* 1.3 70.9 - - - +
273A ASP* 1.3 65.6 + - - +
275A GLN 3.9 0.2 - - - -
276A LEU* 3.0 28.2 + - - +
305A TRP* 5.3 0.9 - - + -
309A LEU* 3.7 10.3 - - + +
436A LEU* 6.1 0.2 - - + -
451A LEU* 4.2 20.9 - - + -
1003A F15 3.3 33.6 - - + +
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Residues in contact with ASP 273 (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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269A CYS 3.2 18.8 + - - +
270A GLN* 3.7 7.6 - - - +
272A ALA* 1.3 74.5 - - - +
274A LYS* 1.3 64.6 + - - +
276A LEU* 3.0 14.9 + - - +
277A PHE* 3.0 36.4 - - - -
448A ASP* 3.4 28.3 - - + +
449A THR* 3.9 5.9 + - - -
450A PHE* 3.4 13.0 + - - -
451A LEU* 3.3 27.1 + - + +
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Residues in contact with LYS 274 (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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244A PRO* 5.4 6.5 - - - -
270A GLN 3.4 13.2 + - - +
271A ALA 3.6 2.2 - - - +
273A ASP* 1.3 78.6 - - - +
275A GLN* 1.3 76.3 + - - +
276A LEU 2.9 6.2 + - - -
277A PHE* 2.9 26.9 + - - +
278A THR* 3.4 12.6 + - + +
327A ALA* 3.1 35.8 + - + +
328A THR* 4.3 14.3 - - + +
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Residues in contact with GLN 275 (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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242A VAL* 4.4 10.4 - - - +
244A PRO* 5.2 10.7 - - - +
271A ALA 2.9 15.0 + - - +
272A ALA 3.8 0.7 - - - -
274A LYS* 1.3 94.7 - - - +
276A LEU* 1.3 57.6 + - - +
278A THR* 3.1 27.5 + - - +
279A LEU* 3.2 14.7 + - - +
309A LEU* 3.1 36.3 - - + +
312A SER* 4.9 2.9 + - - -
316A ARG* 4.1 10.3 + - - -
327A ALA* 3.1 37.8 - - + +
1003A F15 3.5 14.4 - - + +
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Residues in contact with LEU 276 (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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272A ALA 3.0 15.8 + - - +
273A ASP 3.1 9.0 - - - +
274A LYS 2.9 1.4 + - - -
275A GLN* 1.3 75.3 - - - +
277A PHE* 1.3 68.1 - - - +
279A LEU* 2.9 26.2 + - + +
280A VAL* 3.3 3.6 + - - +
305A TRP* 3.7 34.8 - - + -
309A LEU* 3.7 17.9 - - + -
450A PHE* 3.2 25.7 - - + +
451A LEU* 3.6 28.0 - - + +
454A MET* 3.3 30.5 - - + -
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Residues in contact with PHE 277 (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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273A ASP* 3.0 43.1 - - - -
274A LYS* 2.9 12.0 + - - +
276A LEU* 1.3 78.1 - - - +
278A THR* 1.3 61.6 + - + +
280A VAL* 2.9 29.6 + - - +
281A GLU* 3.7 5.2 + - - +
449A THR* 4.9 6.1 - - - -
450A PHE* 3.3 37.4 - + + -
632E ILE* 5.2 6.1 - - + -
635E ARG* 6.3 0.4 - - - -
636E LEU* 5.0 23.5 - - + +
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Residues in contact with THR 278 (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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242A VAL* 3.8 21.7 - - - +
274A LYS* 3.4 19.7 + - + +
275A GLN* 3.1 36.5 + - - +
277A PHE* 1.3 76.9 - - + +
279A LEU* 1.3 65.3 + - - +
280A VAL 3.2 0.2 - - - -
281A GLU* 3.5 11.2 + - - +
282A TRP* 3.0 22.9 + - - +
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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
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275A GLN 3.2 11.4 + - - +
276A LEU* 2.9 25.2 + - + +
278A THR* 1.3 80.9 + - - +
280A VAL* 1.3 51.3 + - + +
282A TRP* 3.2 14.2 + - + +
283A ALA* 2.8 32.6 + - - +
301A LEU* 4.9 7.4 - - + -
305A TRP* 3.5 30.1 - - + +
308A LEU* 3.3 40.2 - - + -
309A LEU* 3.9 5.8 - - + -
371A ARG* 3.4 28.0 - - - +
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Residues in contact with VAL 280 (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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276A LEU 3.9 2.7 - - - +
277A PHE 2.9 13.3 + - - +
279A LEU* 1.3 78.5 - - + +
281A GLU* 1.3 69.3 - - - +
283A ALA* 3.0 10.3 - - - +
284A LYS* 2.9 29.3 + - - +
289A PHE* 5.1 0.5 - - - -
301A LEU* 4.5 17.0 - - + +
450A PHE* 3.7 27.8 - - + -
633E LEU* 4.5 5.6 - - + -
636E LEU* 3.8 35.9 - - + +
637E LEU* 4.3 14.4 - - + +
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Residues in contact with GLU 281 (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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242A VAL* 6.2 0.4 - - + -
277A PHE 4.4 8.5 - - - +
278A THR* 3.5 11.2 + - - +
279A LEU 3.3 0.4 - - - -
280A VAL* 1.3 82.4 - - - +
282A TRP* 1.3 67.0 + - - +
284A LYS* 3.2 33.0 + - - +
285A ARG* 2.9 44.5 + - + +
636E LEU* 4.3 12.5 - - + +
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Residues in contact with TRP 282 (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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238A ALA* 3.6 8.5 - - - +
239A GLU* 2.8 34.7 + - - +
242A VAL* 3.3 33.6 - - + +
278A THR 3.0 12.6 + - - +
279A LEU* 3.4 21.1 - - + +
281A GLU* 1.3 77.1 - - - +
283A ALA* 1.3 84.3 + - + +
285A ARG* 3.7 7.2 + - - +
286A ILE* 3.0 40.3 + - + +
308A LEU* 4.4 7.9 - - + -
368A GLY 4.2 3.6 - - - -
371A ARG* 3.0 63.5 - - + +
372A ALA* 3.7 7.0 - - - -
375A LEU* 3.5 28.3 - - + -
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Residues in contact with ALA 283 (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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279A LEU 2.8 13.3 + - - +
280A VAL* 3.0 12.1 - - - +
282A TRP* 1.3 89.7 - - + +
284A LYS* 1.3 66.7 + - - +
286A ILE* 2.7 24.0 + - - +
289A PHE* 3.6 29.9 - - + +
301A LEU* 4.0 19.7 - - + -
375A LEU* 4.2 4.0 - - + -
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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
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280A VAL* 2.9 13.4 + - + +
281A GLU* 3.3 37.2 + - - +
283A ALA* 1.3 79.3 - - - +
285A ARG* 1.3 55.8 + - + +
286A ILE 2.7 22.0 + - - +
289A PHE* 3.7 10.0 - - + +
290A SER* 3.8 23.7 + - - +
297A GLN* 5.8 0.7 - - - +
636E LEU 3.5 19.0 + - - -
637E LEU* 4.3 22.2 - - + +
638E GLN 4.2 0.6 + - - -
639E GLU* 2.7 31.5 + - - +
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Residues in contact with ARG 285 (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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234A ARG* 3.7 13.2 - - - +
237A GLU* 5.2 7.4 + - - +
238A ALA* 3.1 34.7 - - + +
241A ALA* 3.7 33.5 - - - +
242A VAL* 5.7 0.7 - - - -
281A GLU* 2.9 35.4 + - - +
282A TRP* 3.9 3.1 - - - +
283A ALA 3.2 0.6 + - - -
284A LYS* 1.3 75.1 - - + +
286A ILE* 1.3 56.8 + - - +
287A PRO* 4.0 1.9 - - - +
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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
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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) + - + + + + + -
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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