Contacts of the helix formed by residues 298 - 324 (chain A) in PDB entry 6QVC
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 ALA 298 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASP* 5.3 0.2 - - - +
297A PHE* 1.3 93.8 - - - +
299A VAL* 1.3 60.0 + - - +
300A ARG* 4.3 9.2 - - + +
301A ASN* 3.1 35.3 + - - +
295B THR* 3.7 7.9 - - + +
296B TYR* 3.9 19.1 - - + +
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A PHE* 4.5 5.8 - - + +
298A ALA* 1.3 70.6 - - - +
300A ARG* 1.3 66.6 + - - +
301A ASN 3.2 0.2 - - - -
302A TYR* 3.2 13.9 + - + +
303A TRP* 3.0 36.8 + - + +
290B ILE* 4.5 31.9 - - + +
291B GLU* 4.4 18.8 - - - +
292B VAL* 6.2 0.2 - - - -
294B SER* 4.6 15.9 - - - +
295B THR* 3.6 21.4 + - + +
296B TYR* 5.8 0.7 - - - -
297B PHE* 5.9 0.2 - - + -
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Residues in contact with ARG 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TYR* 5.1 15.0 + - - -
298A ALA* 3.1 7.8 - - + +
299A VAL* 1.3 82.5 - - - +
301A ASN* 1.3 60.0 + - - +
303A TRP* 3.2 14.2 + - + +
304A ARG* 2.9 66.4 + - + +
595B TRP* 4.3 10.5 - - - -
597B GLN* 3.2 30.9 - - - +
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Residues in contact with ASN 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASP* 2.8 37.2 + - - +
268A THR* 5.2 3.8 + - + +
269A VAL* 4.3 11.2 - - + +
297A PHE* 3.6 22.6 - - + -
298A ALA* 3.1 29.5 + - - +
300A ARG* 1.3 76.6 - - - +
302A TYR* 1.3 61.2 + - - +
304A ARG* 3.3 33.2 + - - +
305A GLY* 2.8 27.4 + - - -
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Residues in contact with TYR 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A VAL* 4.2 29.4 - - + +
287A LEU* 5.5 2.9 - - + -
290A ILE* 5.9 5.8 - - + -
297A PHE* 3.3 24.1 - + + -
298A ALA 3.3 3.6 + - - -
299A VAL* 3.2 17.2 + - + +
301A ASN* 1.3 78.7 - - - +
303A TRP* 1.3 75.1 + + - +
305A GLY 3.8 0.2 - - - -
306A PHE* 2.9 42.5 + + + +
287B LEU* 3.3 42.0 - - + +
290B ILE* 5.4 10.3 - - + -
291B GLU* 4.3 20.5 - - + +
540B VAL* 4.0 28.7 - - + +
541B SER* 5.3 0.9 - - - -
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Residues in contact with TRP 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 3.0 23.5 + - + +
300A ARG* 3.2 13.4 + - + +
302A TYR* 1.3 99.3 - + - +
304A ARG* 1.3 64.0 + - + +
306A PHE* 3.3 4.1 + - - +
307A PHE* 3.0 25.5 + - - +
291B GLU* 4.1 26.2 + - + +
292B VAL* 5.2 3.1 - - + -
538B HIS* 4.6 17.0 - - + -
539B THR* 5.7 3.3 - - - +
540B VAL* 5.1 10.8 - - + +
571B GLN* 4.6 26.7 - - - -
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Residues in contact with ARG 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASP* 4.5 21.6 + - - +
121A LEU* 3.6 27.9 - - + +
262A TYR* 5.4 13.7 - - - +
265A ASP* 3.8 22.0 + - - +
266A ILE* 6.1 1.8 - - - +
269A VAL* 4.3 12.6 - - + -
300A ARG* 2.9 54.6 + - + +
301A ASN* 3.3 25.0 + - - +
303A TRP* 1.3 77.0 - - + +
305A GLY* 1.3 57.0 + - - +
307A PHE* 3.3 2.3 + - - +
308A ALA* 2.9 28.3 + - - +
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Residues in contact with GLY 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A VAL* 4.2 14.1 - - - +
272A ALA* 4.4 10.8 - - - +
286A VAL* 3.5 11.3 - - - +
301A ASN 2.8 19.4 + - - -
302A TYR 4.1 0.2 - - - -
304A ARG* 1.3 74.1 - - - +
306A PHE* 1.3 57.7 + - - +
308A ALA* 3.8 7.6 - - - +
309A ALA* 2.8 32.1 + - - +
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Residues in contact with PHE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PRO* 4.7 3.4 - - + -
283A LEU* 3.8 30.1 - - + -
286A VAL* 3.7 26.0 - - + +
302A TYR* 2.9 33.5 + + + +
303A TRP* 3.8 6.3 - - - +
304A ARG 3.2 0.4 - - - -
305A GLY* 1.3 75.4 - - - +
307A PHE* 1.3 60.3 + - - +
309A ALA* 3.9 0.7 - - - +
310A THR* 3.0 31.3 + - - +
287B LEU* 6.2 1.1 - - + -
540B VAL* 3.7 37.9 - - + -
543B ALA* 6.4 0.7 - - + -
544B VAL* 5.7 6.1 - - + -
560B MET* 4.3 29.2 - - + -
563B VAL* 5.9 0.9 - - + -
564B ILE* 3.6 26.9 - - + -
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Residues in contact with PHE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLY* 3.3 35.7 - - - -
121A LEU* 4.1 20.0 - - + -
122A VAL* 4.4 19.5 - - + -
303A TRP 3.0 17.6 + - - +
304A ARG* 3.7 2.7 - - - +
306A PHE* 1.3 77.7 - - - +
308A ALA* 1.3 62.8 - - - +
310A THR* 3.2 12.8 - - + +
311A PHE* 3.1 32.0 + + + +
564B ILE* 3.9 28.0 - - + -
568B MET* 4.4 18.2 - - + -
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.0 31.2 - - + +
125A GLY* 4.8 1.5 - - - +
269A VAL* 4.3 0.7 - - + -
273A VAL* 3.6 22.9 - - + -
304A ARG 2.9 17.3 + - - +
305A GLY* 3.8 6.5 - - - +
307A PHE* 1.3 82.2 - - - +
309A ALA* 1.3 56.3 + - - +
311A PHE* 3.2 4.7 + - - +
312A SER* 2.9 34.1 + - - -
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ALA 4.4 16.2 - - - +
273A VAL* 4.5 5.8 - - - +
276A GLY* 4.7 5.4 - - - +
282A PRO* 3.7 30.7 - - + +
286A VAL* 4.2 5.4 - - + +
305A GLY 2.8 22.8 + - - +
306A PHE 4.0 2.7 - - - +
308A ALA* 1.3 72.5 - - - +
310A THR* 1.3 58.6 + - - +
312A SER* 3.8 5.2 - - - -
313A ALA* 3.0 30.1 + - - +
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Residues in contact with THR 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PRO* 3.8 17.9 - - - +
306A PHE* 3.0 19.1 + - - +
307A PHE* 3.2 20.4 - - + +
309A ALA* 1.3 76.5 - - - +
311A PHE* 1.3 60.5 + - + +
313A ALA* 3.6 1.4 + - - +
314A PHE* 2.9 28.4 + - - +
557B LEU* 4.6 4.9 + - - +
560B MET* 3.8 25.1 - - - +
561B VAL* 4.4 16.6 - - + +
564B ILE* 3.8 24.2 - - + -
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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
----------------------------------------------------------
121A LEU 5.9 0.2 - - - +
122A VAL* 3.5 48.0 - - + -
125A GLY* 5.0 1.8 - - - -
126A LEU* 4.7 17.5 - - + -
307A PHE* 3.1 29.4 + + + +
308A ALA* 3.2 4.0 + - - +
310A THR* 1.3 79.2 - - + +
312A SER* 1.3 57.8 + - - +
314A PHE* 3.6 20.3 - + + +
315A VAL* 3.0 56.7 + - + +
561B VAL* 6.1 4.0 - - + -
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Residues in contact with SER 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLY* 3.2 33.4 - - - -
129A ALA* 3.7 6.7 - - - +
273A VAL* 3.6 14.7 - - - +
276A GLY 4.8 1.3 - - - -
277A CYS* 4.3 25.7 - - - -
308A ALA 2.9 18.1 + - - -
309A ALA* 3.8 6.1 - - - -
311A PHE* 1.3 75.9 - - - +
313A ALA* 1.3 63.7 + - - +
315A VAL 3.5 0.2 + - - -
316A PHE* 3.2 23.7 + - - +
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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
----------------------------------------------------------
276A GLY 4.0 6.1 + - - +
280A GLY* 3.5 40.5 - - - +
282A PRO* 3.6 15.0 - - + -
309A ALA 3.0 17.7 + - - +
310A THR 3.9 1.1 - - - +
312A SER* 1.3 75.8 - - - +
314A PHE* 1.3 63.2 + - - +
316A PHE* 3.5 9.5 + - - +
317A ARG* 3.5 20.4 + - - +
557B LEU* 4.5 6.7 - - + +
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Residues in contact with PHE 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A THR* 2.9 21.1 + - - +
311A PHE* 3.6 24.0 - + - +
313A ALA* 1.3 78.1 - - - +
315A VAL* 1.3 74.6 + - + +
316A PHE 3.4 0.2 + - - -
317A ARG* 3.5 1.9 + - - +
318A VAL* 3.2 53.7 + - + +
329A ILE* 5.0 4.9 - - + -
348B LEU* 4.6 26.9 - - + -
557B LEU* 3.9 26.0 - - + +
558B PRO* 6.4 2.0 - - + -
561B VAL* 4.7 22.9 - - + -
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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
----------------------------------------------------------
125A GLY 5.1 0.7 - - - +
126A LEU* 4.8 19.5 - - + +
129A ALA* 3.9 21.1 - - + -
130A LEU* 5.7 1.3 - - + -
311A PHE* 3.0 45.4 + - + +
312A SER* 3.5 0.4 + - - -
314A PHE* 1.3 84.9 - - + +
316A PHE* 1.3 63.2 + - - +
318A VAL* 3.8 8.1 - - + -
319A LEU* 3.1 40.5 + - + +
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Residues in contact with PHE 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA* 4.0 14.1 - - + +
132A SER* 3.5 25.4 - - - -
133A TRP* 3.9 30.8 - + + -
136A ASP* 3.3 25.1 - - - -
277A CYS* 4.3 11.2 - - - +
278A CYS 4.4 15.0 - - - -
280A GLY* 4.9 10.1 - - - -
312A SER 3.2 17.6 + - - +
313A ALA* 3.8 7.4 - - - +
314A PHE 3.2 0.2 - - - -
315A VAL* 1.3 80.2 - - - +
317A ARG* 1.3 84.4 + - + +
319A LEU* 4.5 3.1 - - - +
320A ALA* 3.9 15.2 + - - +
332A LEU* 4.8 14.6 - - + -
421A ARG* 6.3 0.2 - - - -
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Residues in contact with ARG 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLY* 5.5 6.7 - - - +
313A ALA 3.5 16.1 + - - +
314A PHE 3.5 4.0 + - - +
315A VAL 3.2 0.2 - - - -
316A PHE* 1.3 102.9 - - + +
318A VAL* 1.3 64.1 + - + +
319A LEU 3.3 0.4 - - - -
320A ALA* 3.3 28.7 - - - +
321A VAL* 3.3 13.7 - - - +
326A ALA* 4.6 15.0 + - - +
328A THR 5.0 3.3 + - - +
329A ILE* 3.7 23.5 - - + +
330A THR* 2.8 41.1 + - - +
331A ALA* 2.9 22.0 + - - +
332A LEU* 4.7 10.3 - - - +
557B LEU* 4.8 4.9 - - + -
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE* 3.2 53.5 + - + +
315A VAL* 3.6 14.8 - - + +
317A ARG* 1.3 74.4 - - + +
319A LEU* 1.3 62.4 + - + +
321A VAL* 3.1 11.7 + - - +
322A TRP* 3.0 44.1 + - - +
329A ILE* 3.8 22.4 - - + -
345B LEU* 5.9 8.8 - - + +
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA 5.2 1.3 - - - +
130A LEU* 3.7 35.4 - - + -
133A TRP* 3.4 48.2 + - + -
315A VAL* 3.1 30.9 + - + +
316A PHE* 4.5 3.8 - - - +
318A VAL* 1.3 73.5 - - + +
320A ALA* 1.3 64.3 + - - +
322A TRP* 3.1 21.0 + - + +
323A ASN* 3.1 30.6 + - - +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TRP* 4.8 15.5 - - + +
316A PHE 3.9 11.4 + - - +
317A ARG* 3.3 25.9 + - - +
319A LEU* 1.3 79.0 - - - +
321A VAL* 1.3 57.1 + - - +
322A TRP 3.0 3.5 + - - -
324A LYS* 2.8 36.3 + - + +
325A ASP 5.1 1.1 - - - +
326A ALA* 3.7 16.2 - - + -
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ARG 3.3 16.8 - - - +
318A VAL* 3.1 11.6 + - - +
320A ALA* 1.3 72.6 - - - +
322A TRP* 1.3 63.7 + - - +
324A LYS 3.7 6.9 - - - +
326A ALA* 3.5 17.5 - - + +
327A VAL* 5.2 2.7 - - - -
328A THR* 3.2 34.8 - - - +
329A ILE* 4.7 3.8 - - + -
345B LEU* 3.9 33.0 - - + -
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Residues in contact with TRP 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A VAL* 3.0 44.3 + - + +
319A LEU* 3.5 12.6 - - + +
320A ALA 3.0 3.8 - - - -
321A VAL* 1.3 83.8 - - - +
323A ASN* 1.3 72.6 + - - +
324A LYS 3.8 1.9 - - - +
345B LEU* 5.6 14.1 - - + -
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Residues in contact with ASN 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TRP* 4.4 19.8 - - + -
319A LEU* 3.1 26.8 + - - +
322A TRP* 1.3 84.8 - - - +
324A LYS* 1.3 84.2 + - - +
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Residues in contact with LYS 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TRP* 4.3 14.8 - - + +
137A TYR* 4.1 39.7 + - + -
319A LEU 4.3 0.4 + - - -
320A ALA* 2.8 26.0 + - + +
321A VAL* 3.7 12.0 - - - +
322A TRP 3.8 1.6 - - - +
323A ASN* 1.3 110.1 + - - +
325A ASP* 1.3 70.7 + - - +
----------------------------------------------------------
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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