Contacts of the helix formed by residues 283 - 314 (chain D) in PDB entry 4LML
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 GLN 283 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D LEU* 3.1 29.3 + - + +
281D GLU* 4.3 9.2 + - + +
282D SER* 1.3 80.5 - - - +
284D PRO* 1.4 61.0 - - - +
285D ALA* 3.0 14.8 - - + +
286D ARG* 3.1 57.6 + - + +
287D ALA 3.5 6.1 + - - -
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Residues in contact with PRO 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D LYS* 4.1 28.9 - - + +
282D SER* 3.3 10.8 - - - +
283D GLN* 1.4 86.0 - - - +
285D ALA* 1.3 65.6 + - + +
286D ARG 3.1 0.4 - - - -
287D ALA* 3.5 13.7 - - + -
288D ALA* 2.9 29.2 + - + +
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Residues in contact with ALA 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D GLN* 4.6 11.4 - - + -
284D PRO* 1.3 80.6 - - + +
286D ARG* 1.3 60.3 + - - +
288D ALA* 4.7 2.4 - - - +
289D SER* 3.8 15.8 + - - -
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Residues in contact with ARG 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D LEU* 3.5 25.1 - - + +
283D GLN* 3.1 40.1 + - - +
284D PRO 3.1 0.2 - - - -
285D ALA* 1.3 78.4 - - - +
287D ALA* 1.3 60.1 + - - +
289D SER* 3.1 9.1 + - - -
290D ILE* 3.0 40.6 + - + +
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Residues in contact with ALA 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D GLN* 3.8 32.4 - - + +
278D LEU* 3.5 20.0 - - + +
279D LYS* 4.9 4.3 - - + +
283D GLN 3.5 0.4 + - - +
284D PRO* 3.0 21.4 + - + +
286D ARG* 1.3 79.5 - - - +
288D ALA* 1.3 57.5 + - - +
290D ILE* 3.4 5.9 + - - +
291D THR* 2.8 34.0 + - - -
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Residues in contact with ALA 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D GLN* 5.4 0.9 - - - -
284D PRO* 2.9 14.6 + - + +
285D ALA 4.7 2.5 - - - +
287D ALA* 1.3 73.6 - - - +
289D SER* 1.3 59.8 + - - +
291D THR* 3.9 5.9 - - - -
292D ARG* 3.0 32.1 + - - +
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Residues in contact with SER 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D ALA 3.8 12.4 + - - -
286D ARG* 3.1 16.0 + - - -
288D ALA* 1.3 77.1 - - - +
290D ILE* 1.3 65.7 + - - +
292D ARG* 3.4 4.7 + - - +
293D ALA* 3.0 23.7 + - - +
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Residues in contact with ILE 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D GLU* 4.4 20.0 - - + +
274D VAL* 3.9 28.7 - - + -
275D GLN* 6.3 2.7 - - + -
278D LEU* 3.9 18.6 - - + -
286D ARG* 3.0 21.7 + - + +
287D ALA* 3.6 6.1 - - - +
289D SER* 1.3 74.4 - - - +
291D THR* 1.3 65.1 + - - +
293D ALA* 3.0 10.7 + - - +
294D SER* 3.0 23.8 + - - +
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Residues in contact with THR 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D ALA 5.0 1.1 - - - +
215D PHE* 3.0 39.0 - - + +
217D SER 5.3 2.0 - - - +
271D GLU* 3.2 21.5 + - - +
275D GLN* 2.4 31.7 + - - +
287D ALA 2.8 12.2 + - - -
288D ALA* 3.9 6.5 - - - -
290D ILE* 1.3 78.1 - - - +
292D ARG* 1.3 61.7 + - - +
294D SER* 3.1 5.7 + - - -
295D ARG* 3.0 29.2 + - - +
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Residues in contact with ARG 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D ALA 3.0 19.6 + - - +
289D SER* 3.9 5.6 - - - +
291D THR* 1.3 74.6 - - - +
293D ALA* 1.3 65.9 + - - +
295D ARG* 3.4 50.5 + - - +
296D ILE* 4.0 26.7 + - - +
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Residues in contact with ALA 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D SER 3.0 14.2 + - - +
290D ILE* 3.0 11.9 + - + +
292D ARG* 1.3 73.1 - - - +
294D SER* 1.3 67.5 - - - +
295D ARG 3.3 0.2 + - - -
296D ILE* 3.4 5.1 + - - +
297D ALA* 3.0 26.7 + - + +
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Residues in contact with SER 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D PHE* 3.5 21.1 - - - -
271D GLU* 3.1 33.0 + - - +
290D ILE* 3.0 10.4 + - - +
291D THR 3.2 10.1 - - - -
293D ALA* 1.3 76.9 - - - +
295D ARG* 1.3 63.7 + - - +
296D ILE 2.9 0.2 + - - -
297D ALA* 4.4 2.5 - - - -
298D PHE* 2.9 44.1 + - - +
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Residues in contact with ARG 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TYR* 3.4 45.6 + - - -
215D PHE* 2.9 39.4 + - + -
216D TRP* 3.6 56.7 - - + +
291D THR* 3.0 18.6 + - - +
292D ARG* 3.6 47.6 - - - +
293D ALA 3.3 0.4 - - - -
294D SER* 1.3 74.4 - - - +
296D ILE* 1.3 62.1 + - - +
299D PRO* 3.3 18.5 - - - +
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Residues in contact with ILE 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D ARG* 4.0 27.8 + - - +
293D ALA* 3.4 5.4 + - - +
294D SER 3.1 0.2 - - - -
295D ARG* 1.3 82.3 - - - +
297D ALA* 1.3 70.3 + - - +
298D PHE 3.2 1.3 - - - -
299D PRO* 3.1 6.9 - - + +
300D VAL* 2.9 45.5 + - + +
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Residues in contact with ALA 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D ALA* 3.0 22.0 + - + +
294D SER* 4.1 3.6 - - - +
296D ILE* 1.3 77.8 - - - +
298D PHE* 1.3 58.6 + - + +
300D VAL* 4.2 6.3 - - - -
301D VAL* 2.5 50.0 + - + +
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Residues in contact with PHE 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D TRP* 3.3 34.4 - + + -
215D PHE* 3.4 27.4 - + + -
264D PHE* 4.2 9.0 - + + -
267D VAL* 3.9 29.4 - - + -
268D ALA* 4.0 25.8 - - + -
271D GLU* 4.8 4.0 - - + -
294D SER* 2.9 40.0 + - - +
297D ALA* 1.3 77.4 - - + +
299D PRO* 1.4 64.8 - - + +
301D VAL* 4.1 4.2 - - + +
302D PHE* 2.9 31.2 + - - +
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Residues in contact with PRO 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D PHE* 6.5 0.2 - - + -
212D TRP* 4.0 26.0 - - + +
215D PHE* 5.6 0.9 - - + -
216D TRP* 6.3 0.4 - - + -
295D ARG* 3.3 23.3 - - - +
296D ILE* 3.1 18.2 - - + +
298D PHE* 1.4 87.6 - - + +
300D VAL* 1.3 54.0 + - + +
302D PHE* 3.5 2.7 - - + +
303D LEU* 2.7 37.8 + - - +
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Residues in contact with VAL 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D ILE* 2.9 43.7 + - + +
297D ALA* 3.6 5.8 - - - +
299D PRO* 1.3 75.0 - - + +
301D VAL* 1.3 59.1 + - + +
303D LEU* 3.4 4.9 + - - +
304D LEU* 2.7 45.1 + - + +
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Residues in contact with VAL 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D PHE* 3.7 22.9 - - + -
297D ALA* 2.5 40.4 + - + +
298D PHE* 4.1 4.5 - - + +
300D VAL* 1.3 75.1 - - + +
302D PHE* 1.3 52.5 + - - +
304D LEU* 3.3 8.2 + - + +
305D ALA* 2.6 43.1 + - + +
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Residues in contact with PHE 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D LEU* 4.3 17.0 - - + -
208D LEU* 3.6 29.2 - - + -
209D PHE* 4.5 16.2 - + - -
212D TRP* 3.8 12.8 - + + -
260D MET* 4.7 3.4 - - - -
261D ILE* 4.5 15.0 - - + -
264D PHE* 3.3 32.0 - + + -
298D PHE 2.9 20.4 + - - +
299D PRO* 3.5 4.7 - - + +
301D VAL* 1.3 76.6 - - - +
303D LEU* 1.3 61.2 - - + +
304D LEU 3.1 0.3 + - - -
305D ALA* 3.1 1.8 + - - +
306D ASN* 2.8 70.1 + - + +
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Residues in contact with LEU 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299D PRO 2.7 22.3 + - - +
300D VAL* 3.9 4.9 - - - +
302D PHE* 1.3 80.1 - - + +
304D LEU* 1.3 60.9 + - + +
306D ASN* 4.1 5.1 - - - +
307D ILE* 3.1 51.1 + - + +
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Residues in contact with LEU 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D VAL* 2.7 30.3 + - + +
301D VAL* 3.4 7.6 - - + +
303D LEU* 1.3 74.0 - - + +
305D ALA* 1.3 54.4 + - - +
307D ILE* 2.9 16.9 + - + +
308D ILE* 2.7 51.6 + - + +
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Residues in contact with ALA 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D MET* 3.9 25.9 - - + +
264D PHE* 4.6 5.2 - - + -
301D VAL* 2.6 25.3 + - + +
302D PHE* 3.7 2.9 - - - +
304D LEU* 1.3 73.5 - - - +
306D ASN* 1.3 55.7 + - - +
308D ILE* 3.3 11.4 + - - +
309D LEU* 2.8 32.4 + - - +
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Residues in contact with ASN 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D LEU* 6.0 1.6 - - - +
253D TYR* 4.9 6.2 + - - -
257D ILE* 5.0 18.8 - - - +
260D MET* 3.9 16.0 - - - +
302D PHE* 2.8 65.2 + - + +
303D LEU* 4.2 5.6 - - - +
305D ALA* 1.3 72.5 - - - +
307D ILE* 1.3 57.7 + - + +
309D LEU* 4.0 2.1 - - - +
310D ALA* 3.0 32.1 + - - +
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Residues in contact with ILE 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D LEU* 3.1 40.3 + - + +
304D LEU* 2.9 16.9 + - + +
306D ASN* 1.3 80.0 - - + +
308D ILE* 1.3 69.2 + - + +
310D ALA* 4.0 4.4 - - - +
311D PHE* 3.5 20.4 + - + +
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Residues in contact with ILE 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D LEU* 2.7 46.8 + - + +
305D ALA* 3.4 11.4 - - - +
307D ILE* 1.3 81.5 - - + +
309D LEU* 1.3 68.0 + - + +
311D PHE* 3.7 6.2 + - - +
312D LEU* 3.4 23.4 + - + +
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Residues in contact with LEU 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D TYR* 4.2 5.4 - - + -
256D ALA* 4.1 11.0 - - + -
257D ILE* 3.6 32.3 - - + +
260D MET* 3.5 29.4 - - + -
305D ALA 2.8 18.4 + - - +
306D ASN* 4.0 3.4 - - - +
308D ILE* 1.3 75.2 - - + +
310D ALA* 1.3 66.3 + - - +
312D LEU* 3.0 32.7 + - + +
313D PHE* 3.4 26.5 + - + -
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Residues in contact with ALA 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D TYR* 3.7 26.8 - - + +
306D ASN 3.0 18.7 + - - +
307D ILE* 4.0 5.8 - - - +
309D LEU* 1.3 76.4 - - - +
311D PHE* 1.3 62.4 + - - +
313D PHE* 3.3 2.1 + - - -
314D PHE* 3.1 30.7 + - + +
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Residues in contact with PHE 311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D ILE* 3.5 14.6 + - + +
308D ILE* 4.0 5.6 - - - +
309D LEU 3.3 0.4 - - - -
310D ALA* 1.3 78.0 - - - +
312D LEU* 1.3 74.3 + - + +
313D PHE 2.9 2.0 + - - -
315D GLY* 3.1 45.8 + - - +
316D PHE* 3.5 33.1 + + + +
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Residues in contact with LEU 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D ILE* 3.4 16.2 + - + +
309D LEU* 3.0 26.5 + - + +
311D PHE* 1.3 90.4 - - + +
313D PHE* 1.3 65.8 + - + +
316D PHE* 4.6 24.2 - - + +
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Residues in contact with PHE 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D ARG* 4.0 22.4 - - + -
117D ARG* 4.5 12.4 + - + +
251D MET* 3.6 26.9 - - + -
252D THR 3.6 8.1 - - - -
253D TYR* 3.2 54.3 - + + -
256D ALA* 4.4 9.9 - - + -
309D LEU* 3.4 17.4 + - + -
310D ALA 3.3 3.0 + - - +
311D PHE 2.9 1.0 + - - -
312D LEU* 1.3 86.8 - - + +
314D PHE* 1.3 82.8 + - + +
316D PHE* 4.1 9.2 - - - +
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Residues in contact with PHE 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ARG* 3.9 54.8 + - + +
120D PHE* 3.5 45.1 - + + -
253D TYR* 3.9 33.0 - + + -
310D ALA* 3.1 17.0 + - + +
313D PHE* 1.3 87.3 - - + +
315D GLY* 1.3 60.2 + - - +
316D PHE* 3.1 13.6 + - - +
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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