Contacts of the helix formed by residues 283 - 314 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 3.5 31.5 + - + +
279A LYS 4.8 0.4 + - - -
281A GLU* 3.4 7.2 - - + +
282A SER* 1.3 78.3 - - - +
284A PRO* 1.4 61.1 - - - +
285A ALA* 3.1 13.3 + - + +
286A ARG* 3.3 51.3 + - + +
287A ALA* 3.5 8.9 + - - +
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Residues in contact with PRO 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LYS* 5.1 15.3 - - + +
282A SER* 3.3 11.4 - - - +
283A GLN* 1.4 86.1 - - - +
285A ALA* 1.3 65.5 + - + +
286A ARG 3.3 0.4 - - - -
287A ALA* 3.6 12.8 - - + -
288A ALA* 2.9 28.3 + - + +
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLN* 3.1 9.4 - - + +
284A PRO* 1.3 80.8 - - - +
286A ARG* 1.3 59.9 + - - +
288A ALA* 4.7 2.1 - - - +
289A SER* 3.8 15.6 + - - -
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 3.6 23.2 - - + +
283A GLN* 3.3 35.5 + - - +
285A ALA* 1.3 78.6 - - - +
287A ALA* 1.3 60.5 + - - +
289A SER* 3.1 9.4 + - - -
290A ILE* 3.0 40.2 + - + +
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLN* 4.7 24.0 - - + +
278A LEU* 3.7 14.3 - - + +
279A LYS* 4.8 13.5 - - + -
283A GLN 3.5 5.2 + - - +
284A PRO* 3.2 20.8 + - + +
286A ARG* 1.3 80.2 - - - +
288A ALA* 1.3 62.1 + - - +
289A SER 3.4 0.2 + - - -
290A ILE* 3.6 4.8 + - - +
291A THR* 3.1 25.8 + - - -
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PRO 2.9 14.5 + - - +
285A ALA* 4.7 2.7 - - - +
287A ALA* 1.3 76.5 - - - +
289A SER* 1.3 57.6 + - - +
291A THR* 3.8 4.5 + - - -
292A ARG* 3.0 32.1 + - - +
295A ARG* 5.7 1.2 + - - -
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Residues in contact with SER 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ALA 3.8 12.2 + - - -
286A ARG* 3.1 14.9 + - - -
288A ALA* 1.3 76.4 - - - +
290A ILE* 1.3 68.0 + - - +
292A ARG* 3.2 6.2 + - - +
293A ALA* 2.9 23.4 + - - +
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A GLU* 4.5 20.4 - - + +
274A VAL* 4.0 27.8 - - + -
275A GLN* 5.8 4.3 - - + +
278A LEU* 4.1 19.7 - - + -
286A ARG* 3.0 23.6 + - + +
287A ALA* 3.9 5.2 - - - +
289A SER* 1.3 74.4 - - - +
291A THR* 1.3 64.4 + - - +
293A ALA* 2.9 18.0 + - - +
294A SER* 3.0 16.3 + - - +
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Residues in contact with THR 291 (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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214A ALA 4.7 1.6 - - - +
215A PHE* 3.0 43.3 - - + +
217A SER 4.9 2.5 - - - +
271A GLU* 3.6 16.0 + - - +
275A GLN* 2.5 31.9 + - - +
287A ALA 3.1 16.1 + - - -
288A ALA* 4.1 5.1 - - - -
289A SER 3.4 0.2 - - - -
290A ILE* 1.3 77.7 - - - +
292A ARG* 1.3 62.2 + - - +
294A SER* 3.2 4.2 + - - -
295A ARG* 3.0 30.6 + - - +
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Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TRP* 6.2 0.6 - - - -
288A ALA 3.0 19.5 + - - +
289A SER* 3.2 6.3 + - - +
291A THR* 1.3 76.0 - - - +
293A ALA* 1.3 61.5 + - - +
295A ARG* 3.4 52.6 - - - +
296A ILE* 4.0 25.5 + - - +
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A SER 2.9 12.7 + - - +
290A ILE* 3.2 11.9 - - + +
292A ARG* 1.3 74.2 - - - +
294A SER* 1.3 66.4 + - - +
296A ILE* 3.1 6.6 + - - +
297A ALA* 2.9 25.9 + - + +
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Residues in contact with SER 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A PHE* 3.4 21.0 - - - -
271A GLU* 2.9 38.3 + - - +
290A ILE* 3.0 11.0 + - - +
291A THR 3.2 6.0 + - - -
293A ALA* 1.3 74.9 - - - +
295A ARG* 1.3 64.1 + - - +
296A ILE 2.9 1.9 + - - -
297A ALA* 4.5 3.1 - - - -
298A PHE* 3.0 43.2 + - - +
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Residues in contact with ARG 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A PHE* 2.7 37.9 + - + -
216A TRP* 3.4 61.7 - - + +
288A ALA 5.7 1.2 + - - -
291A THR* 3.0 21.7 + - - +
292A ARG* 3.4 54.0 - - - +
293A ALA 3.2 0.4 - - - -
294A SER* 1.3 74.2 - - - +
296A ILE* 1.3 62.0 + - + +
299A PRO* 3.5 17.9 - - - +
277C TYR* 3.8 37.2 + - - -
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Residues in contact with ILE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ARG* 4.2 26.9 - - - +
293A ALA* 3.1 6.3 + - - +
294A SER 2.9 0.6 + - - -
295A ARG* 1.3 84.6 - - + +
297A ALA* 1.3 69.0 + - - +
298A PHE 3.2 1.6 - - - -
299A PRO* 3.1 7.9 - - + +
300A VAL* 2.9 41.4 + - + +
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ALA* 2.9 20.3 + - + +
294A SER* 4.3 3.4 - - - +
296A ILE* 1.3 77.7 - - - +
298A PHE* 1.3 61.1 + - + +
300A VAL* 4.0 8.1 - - - -
301A VAL* 2.5 48.6 + - + +
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Residues in contact with PHE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TRP* 3.4 33.8 - + + -
215A PHE* 3.3 32.5 - + + -
264A PHE* 4.1 7.8 - + + -
267A VAL* 3.7 41.3 - - + -
268A ALA* 4.0 15.3 - - + -
271A GLU* 4.7 4.3 - - + -
294A SER* 3.0 37.3 + - - +
297A ALA* 1.3 79.8 - - + +
299A PRO* 1.4 70.8 - - + +
301A VAL* 4.1 5.4 - - + +
302A PHE* 3.1 25.5 + - - +
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Residues in contact with PRO 299 (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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209A PHE* 6.2 0.9 - - + -
212A TRP* 4.2 29.4 - - + +
215A PHE* 5.6 0.7 - - + -
294A SER 3.8 0.4 - - - +
295A ARG* 3.5 21.8 - - - +
296A ILE* 3.1 18.2 - - + +
298A PHE* 1.4 88.3 - - + +
300A VAL* 1.3 56.4 + - + +
302A PHE* 3.7 2.3 - - + +
303A LEU* 2.9 33.8 + - + +
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Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE* 2.9 40.1 + - + +
297A ALA* 3.4 6.7 - - - +
299A PRO* 1.3 76.5 - - + +
301A VAL* 1.3 63.9 + - + +
303A LEU* 3.8 3.8 - - - +
304A LEU* 2.8 41.7 + - + +
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A PHE* 3.7 23.8 - - + -
297A ALA* 2.5 40.6 + - + +
298A PHE* 4.1 5.2 - - + +
300A VAL* 1.3 74.7 - - + +
302A PHE* 1.3 52.8 + - - +
304A LEU* 3.5 6.8 - - - +
305A ALA* 2.7 37.6 + - + +
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Residues in contact with PHE 302 (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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205A LEU* 4.0 22.0 - - + -
208A LEU* 3.4 28.9 - - + -
209A PHE* 4.5 11.9 - + - -
212A TRP* 3.8 12.6 - + + -
257A ILE* 6.4 1.8 - - + -
260A MET* 4.2 6.3 - - + -
261A ILE* 4.2 18.4 - - + -
264A PHE* 3.2 31.3 - + + -
298A PHE 3.1 17.3 + - - +
299A PRO* 3.7 4.5 - - + +
301A VAL* 1.3 79.3 - - - +
303A LEU* 1.3 64.4 + - + +
304A LEU 3.0 0.3 + - - -
305A ALA* 3.1 2.8 + - - +
306A ASN* 2.8 61.9 + - - +
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Residues in contact with LEU 303 (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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299A PRO* 2.9 23.3 + - + +
300A VAL* 4.1 3.4 - - - +
302A PHE* 1.3 80.9 - - + +
304A LEU* 1.3 60.1 + - + +
306A ASN* 4.1 4.8 - - - +
307A ILE* 3.1 49.6 + - + +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A VAL* 2.8 27.1 + - + +
301A VAL* 3.5 6.3 - - - +
303A LEU* 1.3 76.5 - - + +
305A ALA* 1.3 67.9 + - - +
306A ASN 3.1 1.1 - - - -
307A ILE* 2.9 25.1 + - + +
308A ILE* 2.9 31.5 + - + +
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A MET* 3.8 29.4 - - + +
264A PHE* 5.0 0.4 - - + -
301A VAL* 2.7 27.3 + - + +
302A PHE 3.7 2.9 - - - +
304A LEU* 1.3 72.9 - - - +
306A ASN* 1.3 56.8 + - - +
308A ILE* 3.4 11.1 - - - +
309A LEU* 3.0 30.0 + - - +
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Residues in contact with ASN 306 (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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205A LEU* 6.2 0.4 - - - +
253A TYR* 4.9 9.0 + - - -
257A ILE* 4.7 24.1 - - - +
260A MET* 3.5 13.3 - - - +
302A PHE* 2.8 53.8 + - + +
303A LEU* 4.1 6.3 - - - +
305A ALA* 1.3 75.2 - - - +
307A ILE* 1.3 61.5 + - + +
309A LEU* 3.3 5.8 + - - +
310A ALA* 2.9 31.8 + - - +
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Residues in contact with ILE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LEU* 3.1 37.4 + - + +
304A LEU* 2.9 19.8 + - + +
306A ASN* 1.3 74.8 - - + +
308A ILE* 1.3 70.1 + - + +
310A ALA* 3.5 6.6 + - - +
311A PHE* 3.4 20.5 + - + +
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Residues in contact with ILE 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 2.9 33.1 + - + +
305A ALA* 3.4 11.4 - - - +
307A ILE* 1.3 83.8 - - + +
309A LEU* 1.3 65.7 + - + +
311A PHE* 3.8 5.2 + - - +
312A LEU* 3.4 29.8 + - + +
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A TYR* 4.4 7.0 - - + -
256A ALA* 4.4 10.1 - - + -
257A ILE* 3.7 35.4 - - + +
260A MET* 3.8 22.7 - - + -
305A ALA 3.0 15.9 + - - +
306A ASN* 3.3 6.5 + - - +
308A ILE* 1.3 77.0 - - + +
310A ALA* 1.3 66.7 + - - +
312A LEU* 3.3 20.9 + - + +
313A PHE* 3.4 38.3 - - + -
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A TYR* 4.2 20.1 - - - +
306A ASN 2.9 17.7 + - - +
307A ILE* 3.7 8.3 - - - +
308A ILE 3.4 0.2 - - - -
309A LEU* 1.3 77.5 - - - +
311A PHE* 1.3 61.6 + - - +
313A PHE 3.5 0.2 + - - -
314A PHE* 3.2 32.0 + - + +
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Residues in contact with PHE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ILE* 3.4 13.4 + - + +
308A ILE* 4.2 4.0 - - - +
310A ALA* 1.3 74.3 - - - +
312A LEU* 1.3 71.0 + - + +
313A PHE 2.8 11.4 + - - -
315A GLY* 3.0 50.1 + - - +
316A PHE* 3.3 31.8 + + + -
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Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ILE* 3.4 22.6 + - + +
309A LEU* 3.3 17.3 + - + +
311A PHE* 1.3 89.4 - - + +
313A PHE* 1.3 65.8 + - + +
316A PHE* 3.9 33.2 - - + +
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Residues in contact with PHE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG* 4.0 32.3 - - + -
117A ARG* 4.4 15.1 + - + +
251A MET* 4.0 19.5 - - + -
252A THR 4.0 6.1 - - - -
253A TYR* 3.5 38.8 - + + -
256A ALA* 4.9 4.0 - - + -
309A LEU* 3.4 36.1 + - + +
310A ALA 3.5 0.4 + - - -
311A PHE 2.8 1.4 + - - -
312A LEU* 1.3 87.1 - - + +
314A PHE* 1.3 81.4 + - + +
316A PHE* 3.7 12.2 - - - +
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Residues in contact with PHE 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ARG* 3.9 52.3 + - + +
120A PHE* 4.0 40.2 - + + -
253A TYR* 4.3 27.4 - + + -
310A ALA* 3.2 18.9 + - + +
311A PHE* 5.5 0.2 - - - -
313A PHE* 1.3 93.8 - - + +
315A GLY* 1.3 59.8 + - - +
316A PHE* 3.2 8.1 + - - +
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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