Contacts of the helix formed by residues 309 - 340 (chain A) in PDB entry 6D6U
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 309 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ILE 2.8 15.0 - - - +
306A PHE* 3.4 8.6 + - - -
308A SER* 1.3 92.1 + - - +
310A PRO* 1.3 72.8 - - + +
311A ALA* 4.5 7.3 - - + +
312A ARG* 3.3 41.1 - - + +
313A ALA 3.8 5.4 + - - -
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Residues in contact with PRO 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TYR* 5.3 5.5 + - - +
306A PHE* 3.5 37.0 - - + +
309A GLN* 1.3 85.6 - - + +
311A ALA* 1.3 67.5 + - + +
313A ALA* 3.3 1.3 + - - +
314A ALA* 2.9 26.5 + - - +
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLN* 3.4 8.4 - - + +
310A PRO* 1.3 82.9 - - + +
312A ARG* 1.3 58.1 + - - +
314A ALA* 4.0 3.2 - - - +
315A ALA* 2.9 29.9 + - - +
318A ARG* 4.6 1.4 + - - -
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Residues in contact with ARG 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ILE* 3.8 22.4 - - + +
309A GLN* 3.3 36.3 + - + +
310A PRO 3.4 0.2 - - - -
311A ALA* 1.3 78.6 - - - +
313A ALA* 1.3 57.6 + - - +
315A ALA* 3.3 12.4 + - - +
316A ILE* 2.9 48.7 + - + +
319A TRP* 6.1 1.0 - - - +
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TYR* 6.0 0.9 - - + -
302A VAL* 4.1 12.8 - - + +
305A ILE* 3.7 11.8 - - - +
306A PHE* 3.6 46.7 - - + +
309A GLN 3.8 2.1 + - - +
310A PRO 3.3 8.8 + - - +
311A ALA 3.2 0.6 - - - -
312A ARG* 1.3 80.2 - - - +
314A ALA* 1.3 58.5 + - - +
316A ILE* 3.8 1.0 - - - +
317A ASP* 2.9 35.5 + - - +
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Residues in contact with ALA 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TYR* 4.8 23.1 - - + +
306A PHE* 5.5 0.2 - - - -
310A PRO 2.9 15.9 + - - +
311A ALA* 4.1 3.4 - - - +
313A ALA* 1.3 75.2 - - - +
315A ALA* 1.3 63.5 + - - +
317A ASP* 3.5 9.9 + - - +
318A ARG* 3.0 50.4 + - - +
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ALA 2.9 19.8 + - - +
312A ARG* 3.4 19.7 - - - +
314A ALA* 1.3 77.9 - - - +
316A ILE* 1.3 59.0 + - + +
318A ARG* 3.0 17.1 - - - +
319A TRP* 2.8 47.2 + - + +
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Residues in contact with ILE 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A GLU* 3.9 17.7 - - + +
301A LEU* 5.5 11.7 - - + -
302A VAL* 4.0 9.2 - - + -
305A ILE* 3.6 26.7 - - + -
312A ARG* 2.9 36.6 + - + +
313A ALA 4.1 2.0 - - - +
315A ALA* 1.3 74.3 - - + +
317A ASP* 1.3 63.1 + - - +
319A TRP* 4.0 11.2 - - + -
320A SER* 2.9 28.5 + - - +
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Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PHE* 4.2 7.7 - - + -
244A TYR* 4.1 22.5 - - + +
250A ARG* 6.1 2.9 - - - -
298A GLU* 3.6 7.6 - - - +
299A TYR* 5.2 4.3 - - - -
302A VAL* 3.2 36.7 - - - +
313A ALA* 2.9 25.7 + - - +
314A ALA* 3.5 9.2 - - - +
315A ALA 3.1 0.2 - - - -
316A ILE* 1.3 77.4 - - - +
318A ARG* 1.3 57.6 + - - +
320A SER* 3.8 2.4 - - - -
321A ARG* 2.9 48.3 + - - +
----------------------------------------------------------
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Residues in contact with ARG 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ALA 4.6 1.2 + - - -
314A ALA* 3.0 36.3 + - - +
315A ALA* 3.0 49.4 - - - +
317A ASP* 1.3 76.1 - - - +
319A TRP* 1.3 68.9 + - + +
321A ARG* 3.2 22.3 + - - +
322A ILE* 3.0 31.4 + - + +
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Residues in contact with TRP 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ARG* 6.1 1.0 - - - +
315A ALA* 2.8 47.0 + - + +
316A ILE* 3.7 11.9 - - + +
317A ASP 3.2 0.2 - - - -
318A ARG* 1.3 81.3 - - + +
320A SER* 1.3 57.9 + - - +
322A ILE* 3.1 32.3 - - + +
323A PHE* 2.8 61.8 + + + -
----------------------------------------------------------
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Residues in contact with SER 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PHE* 3.8 27.1 - - - -
298A GLU* 3.5 22.7 - - - +
316A ILE* 2.9 22.9 + - - +
317A ASP 3.8 0.4 - - - -
319A TRP* 1.3 75.7 - - - +
321A ARG* 1.3 63.2 + - - +
323A PHE* 4.1 8.7 - - - -
324A PHE* 3.0 42.3 + - - +
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Residues in contact with ARG 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PHE* 2.7 55.5 + - + +
241A TRP* 4.9 11.8 + - - +
242A ILE 3.9 11.1 + - - -
243A ASN* 5.3 1.4 - - - +
244A TYR* 5.1 12.3 - - - +
250A ARG* 4.8 2.2 - - - +
317A ASP* 2.9 39.4 + - - +
318A ARG* 3.3 21.2 - - - +
319A TRP 3.2 0.2 - - - -
320A SER* 1.3 77.0 - - - +
322A ILE* 1.3 60.8 + - + +
324A PHE* 5.7 0.2 - - - -
325A PRO* 3.3 25.3 - - - +
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Residues in contact with ILE 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ARG* 3.0 17.6 + - + +
319A TRP* 3.1 44.6 - - + +
321A ARG* 1.3 78.2 - - + +
323A PHE* 1.3 69.0 + - + +
325A PRO* 4.4 1.6 - - - +
326A VAL* 4.1 15.2 - - - +
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Residues in contact with PHE 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A TRP* 2.8 62.9 + + + +
320A SER* 3.2 6.9 + - - +
322A ILE* 1.3 81.9 - - + +
324A PHE* 1.3 75.4 + - + +
325A PRO 3.4 0.9 - - - -
326A VAL* 3.1 18.8 + - - +
327A VAL* 3.2 23.5 + - + +
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Residues in contact with PHE 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TRP* 4.1 19.2 - + + +
240A PHE* 3.6 39.7 - + + -
291A PHE 5.6 1.3 - - - -
294A MET* 4.9 8.5 - - + -
295A ALA* 4.2 22.9 - - + -
298A GLU* 4.6 11.2 - - + -
320A SER* 3.0 32.9 + - - +
321A ARG* 5.7 0.2 - - - -
323A PHE* 1.3 80.9 - - + +
325A PRO* 1.3 68.2 - - + +
327A VAL* 3.2 12.7 + - + +
328A PHE* 2.9 24.4 + - - +
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Residues in contact with PRO 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TRP* 3.6 34.7 - - + -
321A ARG* 3.3 22.2 - - - +
322A ILE 4.4 2.0 - - - -
323A PHE 3.6 3.1 - - - -
324A PHE* 1.3 92.8 - - + +
326A VAL* 1.3 59.5 + - + +
328A PHE* 3.8 1.4 - - - +
329A SER* 2.9 34.9 + - - +
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Residues in contact with VAL 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE 4.1 15.3 - - - +
323A PHE* 3.1 7.9 + - - +
325A PRO* 1.3 78.8 - - + +
327A VAL* 1.3 60.6 + - + +
329A SER* 3.4 5.0 + - - -
330A PHE* 2.9 32.0 + - + +
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Residues in contact with VAL 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PHE* 4.5 19.5 - - + -
323A PHE* 3.2 28.1 + - + +
324A PHE* 3.2 14.6 + - + +
326A VAL* 1.3 77.9 - - + +
328A PHE* 1.3 57.3 + - - +
330A PHE* 3.3 10.6 + - + +
331A PHE* 2.9 28.6 + - + +
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Residues in contact with PHE 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ILE* 4.8 15.3 - - + -
233A THR* 3.7 28.5 - - + -
234A ILE* 5.0 10.1 - - + -
237A TRP* 3.4 40.6 - + + +
284A TYR* 4.6 9.0 - + - -
288A CYS* 4.9 6.1 - - - -
291A PHE* 3.4 36.8 - + + -
324A PHE 2.9 9.3 + - - +
325A PRO 3.8 0.9 - - - +
327A VAL* 1.3 77.7 - - - +
329A SER* 1.3 65.8 + - - +
331A PHE* 3.2 3.3 + + - +
332A ASN* 2.8 62.1 + - - +
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Residues in contact with SER 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TRP* 5.4 1.0 - - - -
325A PRO* 2.9 18.3 + - - +
326A VAL* 3.8 6.1 - - - -
328A PHE* 1.3 80.2 - - - +
330A PHE* 1.3 58.7 + - - +
332A ASN* 3.3 7.0 + - - +
333A ILE* 2.9 43.2 + - - +
----------------------------------------------------------
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Residues in contact with PHE 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A VAL* 2.9 20.8 + - + +
327A VAL* 3.6 10.1 - - + +
329A SER* 1.3 77.2 - - - +
331A PHE* 1.3 60.2 + - - +
333A ILE* 3.3 9.9 + - + +
334A VAL* 2.9 57.8 + - + +
----------------------------------------------------------
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Residues in contact with PHE 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A MET 5.1 5.2 - - - -
284A TYR* 4.4 23.1 - + - -
287A GLY* 4.4 25.8 - - - -
288A CYS* 5.3 1.3 - - - -
291A PHE* 3.9 31.0 - + + -
327A VAL* 2.9 18.0 + - + +
328A PHE* 3.2 5.4 + + - +
330A PHE* 1.3 81.8 - - + +
332A ASN* 1.3 66.1 + - - +
334A VAL* 3.4 7.3 + - + +
335A TYR* 2.9 42.1 + + + +
----------------------------------------------------------
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Residues in contact with ASN 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ILE* 5.9 0.6 - - - +
284A TYR* 3.4 38.0 + - - -
328A PHE* 2.8 56.5 + - - +
329A SER* 3.8 5.5 + - - +
331A PHE* 1.3 77.7 - - - +
333A ILE* 1.3 60.3 + - + +
335A TYR* 3.3 2.6 + - - -
336A TRP* 2.9 50.9 + - + +
----------------------------------------------------------
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Residues in contact with ILE 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A SER* 2.9 30.6 + - - +
330A PHE* 3.3 9.4 + - + +
332A ASN* 1.3 76.8 - - + +
334A VAL* 1.3 65.3 + - + +
336A TRP* 3.9 2.9 - - - +
337A LEU* 2.9 54.6 + - + +
----------------------------------------------------------
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Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A PHE* 2.9 54.6 + - + +
331A PHE* 3.8 7.6 - - + +
333A ILE* 1.3 79.0 - - + +
335A TYR* 1.3 63.9 + - - +
337A LEU* 5.0 4.0 - - + -
338A TYR* 3.4 52.7 + - + +
----------------------------------------------------------
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Residues in contact with TYR 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 6.0 1.9 - - + +
226A TYR* 4.2 13.8 + + - -
280A ALA* 3.5 23.8 + - - +
283A MET* 5.0 5.2 - - + -
284A TYR* 3.6 40.9 - + + +
331A PHE* 2.9 34.3 + + + +
332A ASN* 3.6 6.3 - - - +
333A ILE 3.2 0.2 - - - -
334A VAL* 1.3 80.6 - - - +
336A TRP* 1.3 96.4 + + - +
337A LEU 3.6 0.2 + - - -
338A TYR* 3.6 8.5 + - - +
339A TYR* 3.5 53.3 + + - -
----------------------------------------------------------
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Residues in contact with TRP 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 4.0 22.0 - - + -
218A ILE* 5.4 1.8 - - + -
222A ILE* 4.0 14.4 - - + -
226A TYR* 3.6 39.7 - + + -
230A ILE* 5.9 4.7 - - + +
284A TYR* 4.8 7.6 + + - -
332A ASN* 2.9 49.6 + - + +
333A ILE* 4.4 2.5 - - - +
335A TYR* 1.3 99.6 - + - +
337A LEU* 1.3 66.4 + - + +
338A TYR 3.3 0.2 - - - -
339A TYR* 4.2 2.0 - - + +
340A VAL* 3.3 44.7 + - + +
----------------------------------------------------------
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Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ILE* 2.9 42.1 + - + +
334A VAL* 4.4 2.9 - - - +
336A TRP* 1.3 78.8 - - - +
338A TYR* 1.3 76.1 + - + +
339A TYR 3.7 0.2 + - - -
340A VAL 4.1 11.8 - - - -
----------------------------------------------------------
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Residues in contact with TYR 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ARG* 4.0 8.5 + - - -
334A VAL* 3.4 41.5 + - + +
335A TYR* 3.6 5.0 + - - +
336A TRP 3.3 0.4 - - - -
337A LEU* 1.3 91.9 - - + +
339A TYR* 1.3 74.5 + - + +
340A VAL 5.0 0.5 - - - -
----------------------------------------------------------
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Residues in contact with TYR 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG 5.4 1.4 + - - -
142A ARG* 2.8 48.1 + - + +
145A LEU* 4.3 29.0 - - + +
280A ALA* 3.6 30.2 - - + +
283A MET* 5.1 7.4 - - - +
335A TYR* 3.5 53.4 + + + +
336A TRP* 4.8 2.0 - - + +
337A LEU 3.5 0.2 - - - -
338A TYR* 1.3 90.8 - - + +
340A VAL* 1.3 64.3 + - + +
----------------------------------------------------------
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Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 3.6 26.7 - - + -
218A ILE* 5.1 7.4 - - + -
336A TRP* 3.3 31.3 + - + +
337A LEU* 4.1 13.2 - - - -
338A TYR 4.9 0.4 - - - -
339A TYR* 1.3 80.7 - - - +
----------------------------------------------------------
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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