Contacts of the helix formed by residues 283 - 314 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LEU* 3.4 29.6 + - + +
279B LYS* 4.5 0.8 + - - -
281B GLU* 3.3 10.4 - - + +
282B SER* 1.3 78.0 - - - +
284B PRO* 1.4 62.1 - - - +
285B ALA* 3.0 12.3 - - + +
286B ARG* 3.1 60.1 + - + +
287B ALA* 3.1 10.4 + - - +
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Residues in contact with PRO 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LYS* 5.1 14.6 - - + +
282B SER* 3.3 11.4 - - - +
283B GLN* 1.4 86.0 - - - +
285B ALA* 1.3 65.4 + - + +
286B ARG 3.2 0.2 - - - -
287B ALA* 3.5 12.6 - - + -
288B ALA* 2.9 28.3 + - + +
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B GLN* 3.0 9.6 - - + +
284B PRO* 1.3 81.9 - - + +
286B ARG* 1.3 60.4 + - - +
288B ALA* 4.9 1.2 - - - +
289B SER* 3.5 18.2 + - - -
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Residues in contact with ARG 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LEU* 3.4 26.4 - - + +
283B GLN* 3.1 40.0 + - - +
285B ALA* 1.3 79.0 - - - +
287B ALA* 1.3 60.2 + - - +
289B SER* 3.1 7.4 + - - -
290B ILE* 3.0 46.1 + - + +
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Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B GLN* 4.1 17.5 - - + +
278B LEU* 3.6 13.9 - - + +
279B LYS* 4.3 26.7 - - + -
283B GLN 3.1 7.3 + - - +
284B PRO* 3.2 20.6 + - + -
286B ARG* 1.3 78.0 - - - +
288B ALA* 1.3 63.0 + - - +
289B SER 3.4 0.2 + - - -
290B ILE* 3.8 2.6 + - - +
291B THR* 3.2 24.1 + - - -
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PRO* 2.9 16.3 + - + +
285B ALA 4.9 1.3 - - - +
287B ALA* 1.3 77.2 - - - +
289B SER* 1.3 57.5 + - - +
291B THR* 3.8 4.3 + - - -
292B ARG* 3.0 32.3 + - + +
295B ARG* 5.9 0.3 + - - -
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Residues in contact with SER 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ALA 3.5 15.3 + - - -
286B ARG* 3.1 15.0 + - - -
288B ALA* 1.3 77.5 - - - +
290B ILE* 1.3 67.6 + - - +
292B ARG* 3.2 6.8 + - - +
293B ALA* 3.0 22.9 + - - +
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Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B GLU* 4.3 21.1 - - + +
274B VAL* 3.9 22.7 - - + -
275B GLN* 6.0 2.9 - - + -
278B LEU* 3.6 25.4 - - + -
286B ARG* 3.0 26.1 + - + +
287B ALA* 4.3 3.6 - - - +
289B SER* 1.3 74.6 - - - +
291B THR* 1.3 58.5 + - - +
293B ALA* 3.0 10.6 + - + +
294B SER* 3.0 28.0 + - - +
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Residues in contact with THR 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ALA 5.2 0.2 - - - +
215B PHE* 3.1 42.2 - - + +
217B SER 5.3 2.2 - - - +
223B ASN* 6.4 0.4 - - - +
271B GLU* 3.2 19.8 + - - +
275B GLN* 2.4 35.6 + - - +
287B ALA 3.2 12.8 + - - -
288B ALA* 4.0 4.5 - - - -
289B SER 3.4 0.6 - - - -
290B ILE* 1.3 76.1 - - - +
292B ARG* 1.3 62.5 + - - +
294B SER* 3.0 4.5 + - - -
295B ARG* 3.0 28.3 + - - +
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Residues in contact with ARG 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ALA 3.0 21.5 + - - +
289B SER* 3.2 6.2 + - - +
291B THR* 1.3 75.8 - - - +
293B ALA* 1.3 61.6 + - - +
295B ARG* 3.4 52.4 + - - +
296B ILE* 4.2 23.4 + - - +
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B SER 3.0 12.7 + - - +
290B ILE* 3.2 13.0 - - + +
292B ARG* 1.3 75.8 - - - +
294B SER* 1.3 65.6 + - - +
296B ILE* 3.3 5.2 + - - +
297B ALA* 3.0 27.5 + - + +
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B PHE* 3.6 22.2 - - - -
271B GLU* 2.8 35.8 + - - +
290B ILE* 3.0 9.0 + - - +
291B THR 3.2 9.4 - - - -
293B ALA* 1.3 77.4 - - - +
295B ARG* 1.3 63.8 + - - +
296B ILE 3.0 1.9 + - - -
297B ALA* 4.5 1.8 - - - -
298B PHE* 3.0 43.0 + - - +
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Residues in contact with ARG 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B PHE* 3.2 36.8 + - + -
216B TRP* 3.5 58.6 - - + +
288B ALA 5.9 0.4 + - - -
291B THR* 3.0 19.1 + - - +
292B ARG* 3.4 54.9 - - - +
293B ALA 3.2 0.8 - - - -
294B SER* 1.3 74.4 - - - +
296B ILE* 1.3 62.5 + - + +
299B PRO* 3.4 19.7 - - - +
277E TYR* 3.6 38.3 + - - -
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Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ARG* 4.3 25.8 - - - +
293B ALA* 3.3 6.2 + - - +
294B SER 3.1 0.2 - - - -
295B ARG* 1.3 82.8 - - + +
297B ALA* 1.3 70.8 + - - +
298B PHE 3.2 1.6 - - - -
299B PRO* 3.1 14.0 - - + +
300B VAL* 3.1 30.3 + - + +
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ALA* 3.0 20.5 + - + +
294B SER* 4.3 1.3 - - - +
296B ILE* 1.3 81.2 - - - +
298B PHE* 1.3 62.9 + - + +
300B VAL* 3.1 5.5 + - - +
301B VAL* 2.8 46.8 + - + +
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Residues in contact with PHE 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B TRP* 3.5 33.5 - + + -
215B PHE* 3.5 25.8 - + + -
264B PHE* 4.1 8.4 - + + -
267B VAL* 3.9 25.1 - - + -
268B ALA* 3.5 38.4 - - + -
271B GLU* 4.6 7.0 - - + -
294B SER* 3.0 36.8 + - - +
297B ALA* 1.3 82.4 - - + +
299B PRO* 1.4 67.2 - - + +
301B VAL* 3.7 4.4 + - + +
302B PHE* 3.3 21.8 + - - +
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Residues in contact with PRO 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PHE* 6.1 1.6 - - + -
212B TRP* 4.2 29.4 - - + +
215B PHE* 5.7 0.4 - - + -
294B SER 3.8 0.9 - - - +
295B ARG* 3.4 21.8 - - - +
296B ILE* 3.1 18.4 - - + +
298B PHE* 1.4 87.6 - - + +
300B VAL* 1.3 57.7 + - + +
302B PHE* 3.4 3.6 - - + +
303B LEU* 2.9 30.8 + - - +
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ILE* 3.1 37.3 + - + +
297B ALA* 3.1 6.3 + - - +
299B PRO* 1.3 76.1 - - + +
301B VAL* 1.3 60.0 + - + +
303B LEU* 3.3 6.7 + - + +
304B LEU* 2.7 45.8 + - + +
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B PHE* 3.4 27.1 - - + -
297B ALA* 2.8 34.5 + - + +
298B PHE* 4.2 3.6 - - + +
300B VAL* 1.3 73.9 - - + +
302B PHE* 1.3 51.6 + - - +
304B LEU* 3.2 10.5 + - + +
305B ALA* 2.4 44.2 + - + +
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Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 3.4 34.8 - - + -
208B LEU* 3.4 24.2 - - + -
209B PHE* 4.5 14.8 - + - -
212B TRP* 4.0 5.2 - + + -
257B ILE* 5.4 1.8 - - + -
260B MET* 3.9 9.2 - - + -
261B ILE* 3.8 21.1 - - + -
264B PHE* 3.4 32.6 - + + -
298B PHE 3.3 9.3 + - - +
299B PRO* 3.4 9.0 - - + +
301B VAL* 1.3 77.1 - - - +
303B LEU* 1.3 60.1 + - + +
305B ALA* 2.9 2.0 + - - +
306B ASN* 2.6 64.6 + - + +
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Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PRO 2.9 20.7 + - - +
300B VAL* 3.8 6.7 - - + +
302B PHE* 1.3 78.2 - - + +
304B LEU* 1.3 60.4 + - + +
306B ASN* 4.1 4.7 - - - +
307B ILE* 3.1 51.0 + - + +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B VAL* 2.7 30.4 + - + +
301B VAL* 3.3 10.8 - - + +
303B LEU* 1.3 74.5 - - + +
305B ALA* 1.3 52.6 + - - +
307B ILE* 2.8 18.3 + - + +
308B ILE* 2.6 55.8 + - + +
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B MET* 3.5 32.3 - - + +
264B PHE* 4.6 4.0 - - + -
301B VAL* 2.4 37.5 + - + +
302B PHE* 3.6 1.6 - - - +
304B LEU* 1.3 67.4 - - - +
306B ASN* 1.3 58.3 + - - +
308B ILE* 3.4 11.9 - - - +
309B LEU* 2.7 31.9 + - - +
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Residues in contact with ASN 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 5.8 1.4 - - - +
253B TYR* 4.4 15.2 + - - -
257B ILE* 4.4 21.6 - - - +
260B MET* 3.8 9.1 - - - +
302B PHE* 2.6 58.4 + - - +
303B LEU* 4.3 5.8 - - - +
305B ALA* 1.3 70.1 - - - +
307B ILE* 1.3 57.2 + - + +
309B LEU* 3.7 3.8 - - - +
310B ALA* 2.5 40.4 + - + +
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LEU* 3.1 35.8 + - + +
304B LEU* 2.8 21.2 + - + +
306B ASN* 1.3 71.2 - - + +
308B ILE* 1.3 69.9 - - + +
310B ALA* 4.2 5.1 - - - +
311B PHE* 3.2 25.4 + - + +
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Residues in contact with ILE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 2.6 50.3 + - + +
305B ALA* 3.4 11.2 - - - +
307B ILE* 1.3 80.2 - - + +
309B LEU* 1.3 65.3 + - + +
311B PHE* 4.1 4.8 - - - +
312B LEU* 3.3 31.1 + - + +
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B TYR* 4.4 3.1 - - + -
256B ALA* 3.6 32.8 - - + +
257B ILE* 3.6 19.7 - - + +
260B MET* 3.6 26.9 - - + -
305B ALA 2.7 18.9 + - - +
306B ASN* 3.7 4.5 - - - +
308B ILE* 1.3 76.6 - - + +
310B ALA* 1.3 67.5 + - - +
312B LEU* 3.0 26.9 + - + +
313B PHE* 3.3 27.8 + - + -
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B TYR* 3.8 25.3 - - + +
306B ASN* 2.5 24.1 + - + +
307B ILE* 4.2 4.7 - - - +
309B LEU* 1.3 74.2 - - - +
311B PHE* 1.3 62.8 + - - +
313B PHE 3.4 0.2 + - - -
314B PHE* 3.4 28.8 + - + +
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Residues in contact with PHE 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ILE* 3.2 18.2 + - + +
308B ILE* 4.1 3.1 - - - +
310B ALA* 1.3 79.2 - - - +
312B LEU* 1.3 71.7 + - + +
313B PHE 2.9 6.1 + - - -
315B GLY* 3.3 42.2 + - - +
316B PHE* 3.5 30.7 + + + +
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Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ILE* 3.3 25.7 + - + +
309B LEU* 3.0 22.0 + - + +
311B PHE* 1.3 90.9 - - + +
313B PHE* 1.3 64.4 + - + +
316B PHE* 4.1 29.8 - - + +
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Residues in contact with PHE 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ARG* 3.8 30.7 - - + +
117B ARG* 4.7 11.4 + - + +
251B MET* 3.4 34.5 - - + -
252B THR 3.6 11.9 - - - -
253B TYR* 3.6 31.4 - + + -
256B ALA* 4.2 12.3 - - + -
309B LEU* 3.3 24.1 + - + +
310B ALA 4.0 2.5 - - - +
311B PHE 2.9 1.4 + - - -
312B LEU* 1.3 83.3 - - + +
314B PHE* 1.3 81.9 + - + +
315B GLY 3.7 0.2 - - - -
316B PHE* 3.6 11.8 - - - +
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Residues in contact with PHE 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ARG* 3.8 53.1 + - + +
120B PHE* 3.4 44.9 - + + -
253B TYR* 4.2 30.3 - + - -
310B ALA* 3.4 16.0 + - + +
313B PHE* 1.3 87.8 - - + +
315B GLY* 1.3 59.5 + - - +
316B PHE* 3.1 9.8 + - - +
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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