Contacts of the helix formed by residues 283 - 314 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E LEU* 3.1 33.7 + - + +
281E GLU* 4.4 8.9 - - + +
282E SER* 1.3 79.5 - - - +
284E PRO* 1.4 64.2 - - - +
285E ALA* 3.1 10.2 + - + +
286E ARG* 3.3 52.1 + - + +
287E ALA* 3.3 9.9 + - - +
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Residues in contact with PRO 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E LYS* 4.4 23.6 - - + +
282E SER* 3.3 11.9 - - - +
283E GLN* 1.4 87.0 - - - +
285E ALA* 1.3 65.7 + - + +
286E ARG 3.2 0.2 - - - -
287E ALA* 3.5 11.7 - - + -
288E ALA* 2.9 28.7 + - + +
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Residues in contact with ALA 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E GLN* 3.1 8.7 - - + -
284E PRO* 1.3 80.4 - - + +
286E ARG* 1.3 60.4 + - - +
288E ALA* 4.6 2.6 - - - +
289E SER* 3.6 16.5 + - - -
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Residues in contact with ARG 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E LEU* 3.5 19.8 - - + +
283E GLN* 3.3 34.4 + - - +
284E PRO 3.2 0.2 - - - -
285E ALA* 1.3 77.6 - - - +
287E ALA* 1.3 60.6 + - - +
289E SER* 3.0 10.8 + - - -
290E ILE* 2.9 41.0 + - + +
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Residues in contact with ALA 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E GLN* 4.2 30.5 - - + +
278E LEU* 3.4 17.0 - - + +
279E LYS* 4.6 7.9 - - + +
283E GLN 3.3 5.6 + - - +
284E PRO* 3.1 21.2 + - + +
286E ARG* 1.3 79.7 - - - +
288E ALA* 1.3 60.8 + - - +
290E ILE* 3.6 5.1 + - - +
291E THR* 3.1 27.9 + - - -
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Residues in contact with ALA 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284E PRO* 2.9 15.9 + - + +
285E ALA* 4.6 2.5 - - - +
287E ALA* 1.3 75.6 - - - +
289E SER* 1.3 58.5 + - - +
291E THR* 4.0 4.8 - - - -
292E ARG* 2.9 34.0 + - - +
295E ARG* 5.9 0.3 + - - -
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Residues in contact with SER 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285E ALA 3.6 13.3 + - - -
286E ARG* 3.0 18.6 + - - -
288E ALA* 1.3 76.0 - - - +
290E ILE* 1.3 65.6 + - - +
292E ARG* 3.4 4.5 + - - +
293E ALA* 2.9 25.3 + - - +
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Residues in contact with ILE 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271E GLU* 4.3 17.3 - - + -
274E VAL* 3.5 34.1 - - + -
275E GLN* 6.2 1.6 - - + -
278E LEU* 3.8 20.2 - - + -
286E ARG* 2.9 23.0 + - + +
287E ALA* 3.9 5.4 - - - +
289E SER* 1.3 75.3 - - - +
291E THR* 1.3 58.9 + - - +
293E ALA* 3.1 9.9 + - - +
294E SER* 2.9 29.8 + - - +
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Residues in contact with THR 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E ALA 4.9 1.1 - - - +
215E PHE* 3.1 39.0 - - + +
217E SER 5.3 0.9 - - - +
271E GLU* 3.1 21.8 + - - +
275E GLN* 2.6 32.8 + - - +
287E ALA 3.1 14.2 + - - -
288E ALA* 4.0 5.6 - - - -
290E ILE* 1.3 77.3 - - - +
292E ARG* 1.3 58.5 + - - +
294E SER* 3.1 4.0 + - - -
295E ARG* 2.9 34.4 + - - +
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Residues in contact with ARG 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E ALA* 2.9 21.1 + - + +
289E SER* 3.9 4.9 - - - +
291E THR* 1.3 76.1 - - - +
293E ALA* 1.3 63.1 + - - +
295E ARG* 3.4 53.5 - - - +
296E ILE* 4.0 21.9 + - - +
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Residues in contact with ALA 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289E SER 2.9 14.7 + - - +
290E ILE* 3.2 11.0 - - - +
292E ARG* 1.3 74.9 - - - +
294E SER* 1.3 65.6 + - - +
296E ILE* 3.1 7.0 + - - +
297E ALA* 2.9 26.7 + - + +
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Residues in contact with SER 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E PHE* 3.4 27.4 - - - -
271E GLU* 3.0 34.1 + - - +
290E ILE* 2.9 14.4 + - - +
291E THR 3.2 9.6 - - - -
293E ALA* 1.3 75.6 - - - +
295E ARG* 1.3 57.4 + - - +
296E ILE 2.9 6.8 + - - -
297E ALA* 4.2 3.4 - - - -
298E PHE* 2.9 35.9 + - - +
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Residues in contact with ARG 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D TYR* 4.4 26.3 + - - -
215E PHE* 2.9 45.2 + - + -
216E TRP* 3.6 54.3 - - + +
288E ALA 5.9 0.4 + - - -
291E THR* 2.9 20.2 + - - +
292E ARG* 3.4 54.9 - - - +
293E ALA 3.2 0.6 - - - -
294E SER* 1.3 74.6 - - - +
296E ILE* 1.3 64.3 + - + +
299E PRO* 3.7 16.7 - - - +
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Residues in contact with ILE 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E ARG* 4.0 24.0 + - - +
293E ALA* 3.1 7.2 + - - +
294E SER 3.0 0.6 - - - -
295E ARG* 1.3 84.1 - - - +
297E ALA* 1.3 68.8 + - - +
298E PHE 3.3 1.6 - - - -
299E PRO* 3.1 13.3 - - + +
300E VAL* 3.2 31.2 + - + +
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Residues in contact with ALA 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293E ALA* 2.9 21.6 + - + +
294E SER* 4.1 4.3 - - - +
296E ILE* 1.3 80.1 - - - +
298E PHE* 1.3 61.4 + - + +
300E VAL* 3.3 4.3 + - - -
301E VAL* 2.9 43.4 + - + +
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Residues in contact with PHE 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E TRP* 3.5 37.1 - + + -
215E PHE* 3.4 33.2 - + + -
264E PHE* 3.9 7.6 - + + -
267E VAL* 3.6 38.8 - - + -
268E ALA* 3.5 28.3 - - + -
271E GLU* 4.4 5.2 - - + -
294E SER* 2.9 31.7 + - - +
297E ALA* 1.3 79.0 - - + +
299E PRO* 1.4 70.2 - - + +
301E VAL* 3.9 5.0 - - + +
302E PHE* 3.2 17.7 + - - +
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Residues in contact with PRO 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E TRP* 3.7 32.7 - - + +
215E PHE* 5.3 1.1 - - + -
216E TRP* 6.3 0.2 - - + -
294E SER 3.8 1.3 - - - +
295E ARG* 3.7 20.6 - - - +
296E ILE* 3.1 15.0 - - + +
298E PHE* 1.4 90.0 - - + +
300E VAL* 1.3 57.5 + - + +
302E PHE* 3.4 3.2 - - + +
303E LEU* 2.9 31.4 + - - +
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Residues in contact with VAL 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E ILE* 3.2 36.4 + - + +
297E ALA* 3.7 6.1 - - - +
299E PRO* 1.3 74.7 - - + +
301E VAL* 1.3 60.6 - - + +
303E LEU* 3.4 4.6 + - - +
304E LEU* 2.8 51.8 + - + +
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Residues in contact with VAL 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264E PHE* 3.3 25.6 - - + -
297E ALA* 2.9 29.3 + - + +
298E PHE* 3.9 5.6 - - + +
300E VAL* 1.3 78.0 - - + +
302E PHE* 1.3 58.3 + - - +
304E LEU* 3.6 8.8 - - + +
305E ALA* 2.8 35.8 + - + +
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Residues in contact with PHE 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205E LEU* 3.7 26.2 - - + -
208E LEU* 3.4 27.8 - - + -
209E PHE* 4.3 11.9 - + - -
212E TRP* 3.7 13.5 - + + -
257E ILE* 6.3 0.9 - - + -
260E MET* 4.1 5.4 - - - -
261E ILE* 4.1 17.9 - - + -
264E PHE* 3.3 32.6 - + + -
298E PHE 3.2 11.7 + - - +
299E PRO 3.4 9.2 - - - +
300E VAL 3.2 0.2 - - - -
301E VAL* 1.3 75.6 - - - +
303E LEU* 1.3 65.5 + - + +
304E LEU 3.1 0.5 + - - -
305E ALA* 3.1 2.9 + - - +
306E ASN* 2.8 61.4 + - - +
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Residues in contact with LEU 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E PRO 2.9 15.8 + - - +
300E VAL* 4.1 3.8 - - - +
302E PHE* 1.3 83.6 - - + +
304E LEU* 1.3 62.3 + - + +
306E ASN* 4.1 5.6 - - - +
307E ILE* 3.1 47.1 + - + +
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Residues in contact with LEU 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300E VAL* 2.8 30.0 + - + +
301E VAL* 3.6 8.7 - - + +
303E LEU* 1.3 76.7 - - + +
305E ALA* 1.3 54.6 + - - +
307E ILE* 2.9 15.9 + - + +
308E ILE* 2.8 48.8 + - + +
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Residues in contact with ALA 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E MET* 3.6 28.3 - - + +
264E PHE* 4.9 2.7 - - + -
301E VAL* 2.8 25.1 + - + +
302E PHE 3.7 0.7 - - - +
304E LEU* 1.3 72.9 - - - +
306E ASN* 1.3 53.7 + - - +
308E ILE* 3.3 13.3 - - - +
309E LEU* 2.7 36.9 + - - +
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Residues in contact with ASN 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E LEU* 5.9 2.0 - - - +
253E TYR* 4.7 9.4 + - - -
257E ILE* 4.4 24.9 - - - +
260E MET* 3.4 13.6 - - - +
302E PHE* 2.8 55.3 + - - +
303E LEU* 4.1 7.4 - - - +
305E ALA* 1.3 73.6 - - - +
307E ILE* 1.3 58.2 + - + +
309E LEU* 3.7 3.7 - - - +
310E ALA* 2.8 35.7 + - - +
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Residues in contact with ILE 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303E LEU* 3.1 37.2 + - + +
304E LEU* 2.9 14.9 + - + +
306E ASN* 1.3 75.0 - - + +
308E ILE* 1.3 72.7 + - + +
310E ALA* 3.7 6.5 - - - +
311E PHE* 3.2 24.3 + - + +
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Residues in contact with ILE 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304E LEU* 2.8 41.4 + - + +
305E ALA* 3.3 11.0 - - - +
307E ILE* 1.3 84.2 - - + +
309E LEU* 1.3 63.5 + - + +
311E PHE* 3.6 6.4 + - - +
312E LEU* 3.3 27.7 + - + +
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Residues in contact with LEU 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253E TYR* 4.4 7.0 - - + -
256E ALA* 3.8 17.7 - - + -
257E ILE* 3.6 40.4 - - + +
260E MET* 3.9 21.1 - - + -
305E ALA 2.7 17.3 + - - +
306E ASN* 3.7 5.2 - - - +
308E ILE* 1.3 74.2 - - + +
310E ALA* 1.3 65.7 + - - +
312E LEU* 3.1 24.3 + - + +
313E PHE* 3.3 29.8 + - + -
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Residues in contact with ALA 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253E TYR* 4.1 21.7 - - - +
306E ASN 2.8 22.7 + - - +
307E ILE* 3.7 8.1 - - - +
309E LEU* 1.3 73.7 - - - +
311E PHE* 1.3 61.8 + - - +
313E PHE 3.5 0.2 + - - -
314E PHE* 3.3 31.5 + - + +
315E GLY 4.0 0.2 + - - -
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Residues in contact with PHE 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307E ILE* 3.2 14.4 + - + +
308E ILE* 3.9 4.9 - - - +
310E ALA* 1.3 78.1 - - - +
312E LEU* 1.3 75.6 + - + +
313E PHE 3.0 1.4 + - - -
315E GLY* 3.3 29.0 + - - +
316E PHE* 3.2 48.9 + + + +
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Residues in contact with LEU 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E ILE* 3.3 17.7 + - + +
309E LEU* 3.1 20.6 + - + +
311E PHE* 1.3 89.1 - - + +
313E PHE* 1.3 66.7 + - + +
316E PHE* 4.0 33.2 - - + +
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Residues in contact with PHE 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E ARG* 3.8 27.4 - - + -
117E ARG* 4.7 11.1 + - + +
251E MET* 3.3 30.1 - - + -
252E THR 3.5 20.0 - - - -
253E TYR* 3.6 33.2 - + + -
256E ALA* 4.3 10.1 - - + -
309E LEU* 3.3 25.5 + - + +
311E PHE 3.1 0.4 - - - -
312E LEU* 1.3 84.6 - - + +
314E PHE* 1.3 84.2 + - + +
316E PHE* 3.6 12.7 - - - +
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Residues in contact with PHE 314 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E ARG* 3.8 63.3 + - + +
120E PHE* 3.8 34.5 - + + -
253E TYR* 3.8 37.5 - + + -
310E ALA* 3.3 13.5 + - + +
313E PHE* 1.3 91.1 - - + +
315E GLY* 1.3 59.8 + - - +
316E PHE* 3.2 8.2 + - - +
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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