Contacts of the helix formed by residues 305 - 339 (chain A) in PDB entry 3RHW
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 THR 305 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA* 3.1 12.8 + - + +
304A GLY* 1.3 75.5 - - - +
306A THR* 1.3 59.5 - - - +
307A GLU* 3.0 23.1 + - + +
308A TRP* 3.2 32.6 + - + +
309A ASN* 3.5 6.3 + - - +
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Residues in contact with THR 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLY 3.6 3.0 + - - -
305A THR* 1.3 69.8 - - - +
307A GLU* 1.3 74.8 + - - +
308A TRP 3.3 0.2 - - - -
309A ASN* 3.7 15.0 - - - +
310A ASP* 2.8 31.2 + - - +
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A THR* 3.0 19.0 - - + +
306A THR* 1.3 90.6 - - - +
308A TRP* 1.3 62.5 + - + +
310A ASP* 2.7 18.5 - - - +
311A ILE* 3.3 18.1 - - + +
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Residues in contact with TRP 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ILE* 3.2 50.5 - - + +
303A ALA* 4.2 18.8 - - + -
305A THR* 3.2 28.8 + - + +
306A THR 3.3 0.2 - - - -
307A GLU* 1.3 81.0 - - + +
309A ASN* 1.3 61.0 + - - +
311A ILE* 3.0 24.6 + - + +
312A SER* 2.8 26.0 + - - -
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Residues in contact with ASN 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ARG* 4.1 9.2 + - - +
300A ILE 3.8 6.9 + - - -
301A ALA* 4.0 19.7 + - - +
303A ALA 5.1 1.1 + - - +
304A GLY 5.9 0.2 - - - +
305A THR 3.5 6.1 + - - +
306A THR* 3.5 21.9 + - - +
307A GLU 3.4 0.8 - - - -
308A TRP* 1.3 78.0 - - - +
310A ASP* 1.3 60.1 + - - +
312A SER* 3.1 23.5 - - - -
313A LYS* 3.2 20.4 + - - +
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Residues in contact with ASP 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A THR* 2.8 15.9 + - - +
307A GLU* 2.7 30.5 - - - +
309A ASN* 1.3 73.2 + - - +
311A ILE* 1.3 61.5 + - - +
313A LYS* 3.4 19.9 + - + +
314A ARG* 3.0 25.5 + - - +
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Residues in contact with ILE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ILE* 3.5 18.8 - - + -
307A GLU 3.3 19.3 - - - +
308A TRP* 3.0 32.9 + - + +
310A ASP* 1.3 82.9 + - - +
312A SER* 1.3 64.8 + - - +
314A ARG* 2.9 18.4 + - + +
315A VAL* 2.9 20.1 + - + +
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Residues in contact with SER 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ARG* 3.1 24.1 - - - -
297A VAL* 3.0 27.2 + - - +
300A ILE* 3.5 22.9 - - - +
301A ALA* 3.5 12.4 - - - +
308A TRP 2.8 11.1 + - - -
309A ASN 3.1 12.1 - - - -
311A ILE* 1.3 77.5 - - - +
313A LYS* 1.3 61.3 + - - -
315A VAL* 3.3 12.5 + - - +
316A ASP 3.5 8.3 + - - -
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Residues in contact with LYS 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ARG* 3.2 44.9 - - - +
309A ASN* 3.4 14.1 - - - +
310A ASP* 3.5 22.7 - - + +
311A ILE 3.2 0.6 - - - -
312A SER* 1.3 76.2 - - - +
314A ARG* 1.3 62.8 + - - +
316A ASP* 3.3 4.3 + - - +
317A LEU* 3.1 36.2 + - + +
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Residues in contact with ARG 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ASP 3.0 12.9 + - - +
311A ILE* 2.9 15.3 + - + +
313A LYS* 1.3 75.2 - - - +
315A VAL* 1.3 65.0 + - + +
317A LEU* 3.4 17.7 + - - +
318A ILE* 3.1 49.8 + - + +
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Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLU* 3.4 25.6 - - + +
296A LEU* 4.4 23.8 - - + -
297A VAL* 3.5 13.5 - - + -
300A ILE* 4.6 6.7 - - + -
311A ILE* 2.9 27.6 + - + +
312A SER 3.3 7.2 + - - +
314A ARG* 1.3 78.3 - - + +
316A ASP* 1.3 57.3 + - - +
318A ILE* 3.5 8.5 + - + +
319A SER* 2.9 34.7 + - - +
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Residues in contact with ASP 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A PHE* 4.2 5.5 - - - +
237A PHE 4.6 0.3 - - - +
239A ARG* 3.2 23.3 + - - +
245A ARG* 2.6 34.7 + - - -
293A GLU* 2.7 29.5 - - - +
297A VAL* 3.3 12.6 - - - +
312A SER 3.5 2.8 + - - -
313A LYS* 3.3 10.2 + - - +
314A ARG 3.3 0.4 - - - -
315A VAL* 1.3 75.1 - - - +
317A LEU* 1.3 67.5 + - + +
319A SER* 3.0 2.4 + - - -
320A ARG* 2.9 48.9 + - - +
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ARG* 6.2 1.1 - - - +
313A LYS* 3.1 24.8 + - + +
314A ARG* 3.4 22.0 + - - +
316A ASP* 1.3 77.1 - - + +
318A ILE* 1.3 64.8 + - + +
320A ARG* 3.6 40.4 + - - +
321A ALA* 3.9 8.3 + - - +
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Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ARG* 3.1 41.7 + - + +
315A VAL* 3.8 8.5 - - + +
317A LEU* 1.3 76.1 - - + +
319A SER* 1.3 54.0 + - - +
321A ALA* 3.2 4.1 + - - +
322A LEU* 2.7 59.3 + - + +
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Residues in contact with SER 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A PHE* 3.7 21.4 - - - -
293A GLU* 3.2 29.1 + - - +
315A VAL* 2.9 25.1 + - - +
316A ASP 3.6 3.6 - - - -
318A ILE* 1.3 74.2 - - - +
320A ARG* 1.3 59.1 + - - +
321A ALA 2.8 11.6 + - - -
322A LEU* 4.3 3.4 - - - +
323A PHE* 3.1 40.6 + - - +
324A PRO* 3.6 0.2 - - - +
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Residues in contact with ARG 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A PHE* 2.8 46.1 + - + -
236A TRP* 3.6 62.9 + - + +
237A PHE 5.4 2.0 + - - -
239A ARG* 5.7 4.2 - - - +
316A ASP* 2.9 33.6 + - - +
317A LEU* 3.8 31.9 - - - +
318A ILE 3.3 0.2 - - - -
319A SER* 1.3 75.6 - - - +
321A ALA* 1.3 56.8 + - + +
324A PRO* 3.4 17.0 - - - +
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Residues in contact with ALA 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU 3.9 7.5 + - - +
318A ILE* 3.2 5.9 + - - +
319A SER 2.9 0.4 - - - -
320A ARG* 1.3 80.4 - - + +
322A LEU* 1.3 64.8 + - - +
323A PHE 3.4 1.1 - - - -
324A PRO* 3.3 5.9 - - - +
325A VAL* 3.1 33.4 + - + +
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Residues in contact with LEU 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ILE* 2.7 40.1 + - + +
319A SER* 4.4 2.9 - - - +
321A ALA* 1.3 72.5 - - - +
323A PHE* 1.3 63.7 + - + +
325A VAL* 3.4 7.5 + - + -
326A LEU* 2.8 66.8 + - + +
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Residues in contact with PHE 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A TRP* 3.7 27.1 - + + +
235A PHE* 3.4 33.4 - + + -
286A PHE* 3.5 36.1 - + - -
289A CYS* 3.8 31.9 - - + -
290A ALA* 3.8 7.0 - - - -
293A GLU* 4.7 4.9 - - + -
319A SER* 3.1 26.3 + - - +
322A LEU* 1.3 84.4 - - + +
324A PRO* 1.3 65.7 - - + +
326A LEU* 3.2 6.4 + - + +
327A PHE* 2.8 31.2 + - - +
----------------------------------------------------------
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Residues in contact with PRO 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A TRP* 3.3 39.5 - - + -
235A PHE* 5.7 0.2 - - + -
319A SER 3.6 1.8 - - - +
320A ARG* 3.4 20.4 - - - +
321A ALA* 3.3 14.1 - - - +
323A PHE* 1.3 94.6 - - + +
325A VAL* 1.3 64.3 + - + +
327A PHE* 3.1 2.3 + - - +
328A PHE* 2.8 26.0 + - - +
----------------------------------------------------------
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Residues in contact with VAL 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ALA* 3.1 23.6 + - + +
322A LEU* 3.7 9.2 - - + +
324A PRO* 1.3 80.4 - - + +
326A LEU* 1.3 63.3 + - + +
328A PHE* 3.2 8.6 + - + +
329A VAL* 2.9 43.3 + - + +
----------------------------------------------------------
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Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A PHE* 3.8 15.2 - - + -
322A LEU* 2.8 56.0 + - + +
323A PHE* 3.7 5.2 - - - +
325A VAL* 1.3 75.7 - - + +
327A PHE* 1.3 57.2 + - - +
329A VAL* 3.2 15.4 + - + +
330A PHE* 2.8 27.9 + - - +
----------------------------------------------------------
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Residues in contact with PHE 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A CYS* 4.0 26.0 - - + -
228A VAL* 3.9 33.7 - - + -
229A ILE* 5.9 2.9 - - + -
232A TRP* 3.6 24.0 - + + -
279A TRP* 4.8 1.3 - + - -
283A CYS* 4.0 19.3 - - - -
286A PHE* 3.3 38.1 - + + -
323A PHE 2.8 20.1 + - - +
324A PRO 3.6 0.4 - - - +
326A LEU* 1.3 73.9 - - - +
328A PHE* 1.3 59.3 + - - +
330A PHE* 3.3 10.4 + + - +
331A ASN* 3.0 51.4 + - - -
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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
----------------------------------------------------------
324A PRO 2.8 17.2 + - - +
325A VAL* 3.5 9.6 - - + +
327A PHE* 1.3 76.7 - - - +
329A VAL* 1.3 69.0 + - + +
331A ASN* 3.4 11.7 + - + +
332A ILE* 3.1 55.3 + - + +
----------------------------------------------------------
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A VAL* 2.9 34.0 + - + +
326A LEU* 3.4 18.2 - - + +
328A PHE* 1.3 83.1 - - + +
330A PHE* 1.3 61.4 + - - +
332A ILE* 3.3 7.2 + - + +
333A LEU* 3.1 47.4 + - + +
----------------------------------------------------------
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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
----------------------------------------------------------
278A VAL* 4.1 12.3 - - + -
279A TRP* 3.6 37.0 - + - -
282A ALA* 3.2 34.3 - - + -
283A CYS* 5.2 0.7 - - - -
286A PHE* 4.2 15.5 - + + -
326A LEU 2.8 13.5 + - - +
327A PHE* 3.4 22.9 - + - +
328A PHE 3.2 0.4 - - - -
329A VAL* 1.3 73.6 - - - +
331A ASN* 1.3 63.6 + - - +
333A LEU* 3.0 11.5 + - + +
334A TYR* 2.7 55.7 + + + +
----------------------------------------------------------
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Residues in contact with ASN 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A CYS* 4.6 7.3 - - - -
279A TRP* 3.7 22.0 + - - -
327A PHE* 3.0 42.3 + - - -
328A PHE* 3.6 15.8 - - + +
330A PHE* 1.3 79.1 - - - +
332A ILE* 1.3 58.5 + - + +
334A TYR* 3.2 2.2 + - - -
335A TRP* 2.8 59.8 + - + +
----------------------------------------------------------
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Residues in contact with ILE 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PHE* 3.1 52.3 + - + +
329A VAL* 3.5 10.5 - - + +
330A PHE 3.1 0.2 - - - -
331A ASN* 1.3 77.6 - - + +
333A LEU* 1.3 69.9 + - + +
335A TRP* 4.5 2.1 - - - +
336A SER* 3.0 27.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A VAL* 3.1 41.1 + - + +
330A PHE* 3.0 12.4 + - + +
332A ILE* 1.3 83.6 - - + +
334A TYR* 1.3 63.8 + - - +
336A SER* 2.9 20.7 + - - -
337A ARG* 3.1 15.0 + - - +
----------------------------------------------------------
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Residues in contact with TYR 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PRO* 4.6 0.2 - - - +
139A MET* 4.3 4.3 - - + +
221A TYR* 2.9 22.3 + + - -
275A ALA* 3.2 32.5 + - - +
276A ILE 4.4 0.2 + - - -
278A VAL* 4.1 6.1 - - + -
279A TRP* 3.4 40.3 - + + +
330A PHE* 2.7 43.1 + + + +
331A ASN* 3.6 3.8 - - - +
333A LEU* 1.3 73.8 - - - +
335A TRP* 1.3 93.4 + + - +
337A ARG* 3.1 2.9 + - - -
338A PHE* 3.0 65.7 + + - +
----------------------------------------------------------
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Residues in contact with TRP 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A MET* 3.8 32.3 - - + -
213A PHE* 3.8 17.3 - + - -
217A LEU* 6.1 1.1 - - + -
221A TYR* 3.4 54.7 - + + -
279A TRP* 4.6 1.6 - + - -
331A ASN* 2.8 55.3 + - + +
332A ILE* 4.5 2.0 - - - +
334A TYR* 1.3 83.7 - + - +
336A SER* 1.3 61.0 + - - +
339A GLY* 2.8 35.0 + - - +
----------------------------------------------------------
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Residues in contact with SER 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ILE* 3.0 19.5 + - - +
333A LEU* 2.9 22.7 + - - -
335A TRP* 1.3 76.1 - - - +
337A ARG* 1.3 59.3 + - - +
339A GLY 4.6 0.4 - - - -
340A HIS* 4.4 16.7 + - - +
----------------------------------------------------------
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Residues in contact with ARG 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TYR* 3.8 30.3 + - - -
333A LEU 3.1 17.9 + - - +
334A TYR 3.1 5.5 + - - +
336A SER* 1.3 80.6 - - - +
338A PHE* 1.3 88.5 + - + +
339A GLY 3.8 0.2 - - - -
340A HIS* 4.8 6.4 - - - +
----------------------------------------------------------
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Residues in contact with PHE 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLN 5.2 1.6 - - - -
136A TYR* 3.6 28.0 - + + +
139A MET* 3.2 40.1 - - + +
275A ALA* 3.4 28.0 - - + -
278A VAL* 4.3 23.1 - - + -
334A TYR* 3.0 55.4 + + + +
337A ARG* 1.3 113.6 - - + +
339A GLY* 1.3 64.4 + - - +
340A HIS* 3.2 3.6 + - - -
----------------------------------------------------------
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Residues in contact with GLY 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A MET* 4.1 11.3 - - - +
335A TRP* 2.8 26.4 + - - +
338A PHE* 1.3 77.7 - - - +
340A HIS* 1.3 69.0 + - - +
----------------------------------------------------------
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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