Contacts of the helix formed by residues 298 - 324 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A THR* 3.6 7.4 - - + +
296A TYR* 3.8 19.5 - - + +
265B ASP* 5.3 0.2 - - - +
297B PHE* 1.3 93.8 - - - +
299B VAL* 1.3 61.4 + - - +
300B ARG* 4.3 8.7 - - + +
301B ASN* 3.1 35.1 + - - +
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ILE* 4.4 33.2 - - + +
291A GLU* 4.3 17.0 - - - +
292A VAL* 6.0 0.4 - - - +
294A SER* 4.4 18.6 - - - +
295A THR* 3.5 21.6 + - + +
296A TYR* 5.7 0.7 - - - -
297A PHE* 5.9 0.2 - - + -
297B PHE* 4.5 5.2 - - + +
298B ALA* 1.3 70.5 - - - +
300B ARG* 1.3 67.0 + - - +
302B TYR* 3.2 13.4 - - + +
303B TRP* 3.0 37.4 + - + +
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Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A TRP* 4.2 10.9 - - - -
597A GLN* 3.0 32.6 - - - +
262B TYR* 5.1 15.2 + - - -
298B ALA* 4.7 7.6 - - + -
299B VAL* 1.3 83.0 - - + +
301B ASN* 1.3 59.8 + - - +
303B TRP* 3.2 14.4 + - + +
304B ARG* 2.9 69.5 + - + +
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Residues in contact with ASN 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ASP* 2.8 37.3 + - - +
268B THR* 5.2 2.8 + - + +
269B VAL* 4.3 11.8 - - + +
297B PHE* 3.6 22.9 - - + -
298B ALA* 3.1 30.3 + - - +
300B ARG* 1.3 75.3 - - - +
302B TYR* 1.3 59.3 + - - +
304B ARG* 3.3 33.7 + - - +
305B GLY* 2.8 27.0 + - - -
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Residues in contact with TYR 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 3.3 42.3 - - + +
290A ILE* 5.4 11.0 - - + -
291A GLU* 4.2 21.0 - - + +
540A VAL* 4.0 30.0 - - + +
541A SER* 5.2 0.5 - - - -
286B VAL* 4.2 30.2 - - + +
287B LEU* 5.5 2.9 - - + -
290B ILE* 5.9 5.2 - - + -
297B PHE* 3.3 24.7 - + + -
298B ALA 3.3 3.4 + - - -
299B VAL* 3.2 18.3 + - + +
301B ASN* 1.3 78.5 - - - +
303B TRP* 1.3 73.6 + + - +
305B GLY* 3.8 0.3 - - - -
306B PHE* 2.9 40.8 + + + +
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Residues in contact with TRP 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU* 3.9 27.2 + - + +
292A VAL* 5.0 4.3 - - + -
538A HIS* 4.5 19.7 + - + -
539A THR* 5.6 4.1 - - - +
540A VAL* 5.1 10.1 - - + +
571A GLN* 4.7 24.9 - - - -
299B VAL* 3.0 24.9 + - + +
300B ARG* 3.6 12.3 - - + +
302B TYR* 1.3 98.9 - + - +
304B ARG* 1.3 64.1 + - + +
306B PHE* 3.3 4.4 + - - +
307B PHE* 3.0 25.5 + - - +
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASP* 4.5 21.2 + - - +
121B LEU* 3.6 29.0 - - + +
262B TYR* 5.4 13.5 - - - +
265B ASP* 3.8 22.4 + - - +
266B ILE* 6.1 1.2 - - - +
269B VAL* 4.3 13.0 - - + -
300B ARG* 2.9 54.6 + - + +
301B ASN* 3.3 26.1 + - - +
303B TRP* 1.3 77.5 - - - +
305B GLY* 1.3 59.2 + - - +
307B PHE* 3.3 1.8 + - - +
308B ALA* 2.9 28.3 + - - +
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Residues in contact with GLY 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B VAL* 4.2 13.4 - - - +
272B ALA* 4.4 10.9 - - - +
286B VAL* 3.5 10.7 - - - +
301B ASN 2.8 19.3 + - - -
302B TYR* 4.1 0.4 - - - -
304B ARG* 1.3 73.9 - - - +
306B PHE* 1.3 58.4 + - - +
308B ALA* 3.8 7.7 - - - +
309B ALA* 2.8 32.2 + - - +
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Residues in contact with PHE 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 6.2 1.1 - - + -
540A VAL* 3.6 44.0 - - + -
543A ALA* 6.4 0.4 - - + -
544A VAL* 5.6 6.1 - - + -
560A MET* 4.3 27.4 - - + -
563A VAL* 5.8 0.7 - - + -
564A ILE* 3.6 24.0 - - + -
282B PRO* 4.7 4.7 - - + -
283B LEU* 3.8 29.8 - - + -
286B VAL* 3.7 25.3 - - + +
302B TYR* 2.9 32.3 + + + +
303B TRP* 3.8 5.2 - - - +
304B ARG 3.2 0.2 - - - -
305B GLY* 1.3 75.4 - - - +
307B PHE* 1.3 60.3 + - - +
309B ALA* 3.9 0.5 - - - +
310B THR* 3.0 31.0 + - - +
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Residues in contact with PHE 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A ILE* 3.6 29.8 - - + +
565A LEU* 6.5 0.2 - - + -
568A MET* 4.1 20.6 - - + -
118B GLY* 3.3 34.5 - - - -
121B LEU* 4.1 20.2 - - + -
122B VAL* 4.4 20.4 - - + -
303B TRP 3.0 16.8 + - - +
304B ARG* 3.7 2.5 - - - +
306B PHE* 1.3 77.0 - - - +
308B ALA* 1.3 65.0 + - - +
310B THR* 3.2 12.2 - - + +
311B PHE* 3.1 31.6 + + + +
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 4.0 33.0 - - + +
124B LEU* 5.5 0.4 - - + -
125B GLY* 4.8 1.5 - - - +
269B VAL* 4.3 0.4 - - + -
273B VAL* 3.6 23.1 - - + -
304B ARG 2.9 18.5 + - - +
305B GLY* 3.8 6.7 - - - +
307B PHE* 1.3 81.0 - - - +
309B ALA* 1.3 56.7 + - - +
311B PHE* 3.2 4.9 + - - +
312B SER* 2.9 33.6 + - - -
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ALA 4.4 17.0 - - - +
273B VAL* 4.5 6.2 - - - +
276B GLY* 4.7 5.3 - - - +
282B PRO* 3.7 31.0 - - + +
286B VAL* 4.2 4.9 - - + -
305B GLY 2.8 22.7 + - - +
306B PHE 4.0 2.7 - - - +
308B ALA* 1.3 73.3 - - - +
310B THR* 1.3 58.3 + - - +
312B SER* 3.8 5.5 - - - -
313B ALA* 3.0 30.5 + - - +
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Residues in contact with THR 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A LEU* 4.6 4.5 + - - +
560A MET* 3.7 25.9 - - - +
561A VAL* 4.3 15.6 - - + +
564A ILE* 3.6 25.6 - - + -
282B PRO* 3.8 17.7 - - - +
306B PHE* 3.0 18.4 + - - +
307B PHE* 3.2 20.2 - - + +
309B ALA* 1.3 77.6 - - - +
311B PHE* 1.3 60.1 + - + +
313B ALA* 3.8 1.0 - - - +
314B PHE* 2.9 29.0 + - - +
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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
----------------------------------------------------------
561A VAL* 6.0 4.9 - - + -
121B LEU 5.9 0.2 - - - +
122B VAL* 3.5 47.1 - - + -
125B GLY* 5.0 1.6 - - - -
126B LEU* 4.7 17.0 - - + -
307B PHE* 3.1 29.7 + + + +
308B ALA* 3.2 4.0 + - - +
310B THR* 1.3 80.5 - - + +
312B SER* 1.3 58.9 + - - +
314B PHE* 3.3 21.2 + + + +
315B VAL* 3.0 55.7 + - + +
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Residues in contact with SER 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLY* 3.2 32.2 - - - -
129B ALA* 3.7 7.3 - - - +
273B VAL* 3.6 16.0 - - - +
276B GLY 4.8 1.6 - - - -
277B CYS* 4.3 26.2 - - - -
308B ALA 2.9 17.4 + - - -
309B ALA* 3.8 6.1 - - - -
310B THR 3.3 0.2 - - - -
311B PHE* 1.3 74.8 - - - +
313B ALA* 1.3 65.2 + - - +
316B PHE* 3.2 23.2 + - - +
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A LEU* 4.3 7.8 - - + +
276B GLY 4.0 5.7 + - - +
280B GLY* 3.5 39.8 - - - +
282B PRO* 3.6 15.3 - - + -
309B ALA 3.0 18.3 + - - +
310B THR 3.9 1.1 - - - +
312B SER* 1.3 76.5 - - - +
314B PHE* 1.3 63.7 + - - +
316B PHE* 3.5 9.5 + - - +
317B ARG* 3.5 20.1 + - - +
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Residues in contact with PHE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 4.4 31.4 - - + -
557A LEU* 3.9 26.6 - - + +
558A PRO* 6.0 2.2 - - + -
561A VAL* 4.4 25.8 - - + -
310B THR 2.9 20.2 + - - +
311B PHE* 3.6 24.0 - + + +
312B SER 3.3 0.2 - - - -
313B ALA* 1.3 77.9 - - - +
315B VAL* 1.3 75.7 + - + +
316B PHE 3.4 0.2 + - - -
317B ARG* 3.5 1.7 + - - +
318B VAL* 3.2 52.9 + - + +
329B ILE* 5.0 3.1 - - + -
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLY 5.1 0.2 - - - +
126B LEU* 4.8 20.0 - - + +
129B ALA* 3.9 20.6 - - + -
130B LEU* 5.7 0.9 - - + -
311B PHE* 3.0 44.5 + - + +
312B SER* 5.0 0.4 - - - -
314B PHE* 1.3 84.3 - - + +
316B PHE* 1.3 62.7 + - - +
318B VAL* 3.6 9.4 - - + +
319B LEU* 3.1 41.0 + - + +
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Residues in contact with PHE 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA* 4.0 15.4 - - + +
132B SER* 3.5 24.9 - - - -
133B TRP* 3.9 30.4 - + + +
136B ASP* 3.3 24.2 - - - -
231B LYS* 5.2 0.2 - - - -
277B CYS* 4.3 11.4 - - - +
278B CYS 4.4 14.4 - - - -
280B GLY* 4.9 10.5 - - - -
312B SER 3.2 18.1 + - - +
313B ALA* 3.7 7.6 - - - +
314B PHE 3.2 0.6 - - - -
315B VAL* 1.3 77.7 - - - +
317B ARG* 1.3 84.8 + - + +
319B LEU* 4.5 3.6 - - - +
320B ALA* 3.9 15.4 + - - +
332B LEU* 4.8 14.1 - - + -
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Residues in contact with ARG 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A LEU* 4.6 5.8 - - + -
280B GLY* 5.5 7.0 - - - +
313B ALA 3.6 16.4 - - - +
314B PHE 3.5 3.4 + - - +
315B VAL 3.2 0.2 - - - -
316B PHE* 1.3 103.6 + - + +
318B VAL* 1.3 64.3 + - - +
319B LEU 3.3 0.2 - - - -
320B ALA* 3.3 27.9 - - - +
321B VAL* 3.3 12.9 - - - +
326B ALA* 4.6 14.5 + - - +
328B THR 5.0 3.0 + - - -
329B ILE* 3.7 24.6 - - + +
330B THR* 2.8 42.1 + - - +
331B ALA* 3.0 21.5 + - - -
332B LEU* 4.7 10.9 + - - +
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Residues in contact with VAL 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 5.7 8.4 - - + +
348A LEU* 6.3 1.3 - - + -
314B PHE* 3.2 52.4 + - + +
315B VAL* 3.6 15.5 - - + +
317B ARG* 1.3 74.3 - - - +
319B LEU* 1.3 62.6 + - + +
321B VAL* 3.1 12.2 + - + +
322B TRP* 3.0 45.3 + - + +
329B ILE* 3.8 22.0 - - + -
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA* 5.2 1.3 - - + +
130B LEU* 3.7 34.8 - - + -
133B TRP* 3.4 47.7 + - + -
315B VAL* 3.1 32.7 + - + +
316B PHE* 4.5 3.8 - - - +
318B VAL* 1.3 74.9 - - + +
320B ALA* 1.3 64.6 + - - +
322B TRP* 3.1 20.6 + - + -
323B ASN* 3.1 31.0 + - - +
----------------------------------------------------------
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B TRP* 4.8 15.5 - - + +
316B PHE 3.9 11.4 + - - +
317B ARG* 3.3 27.0 + - - +
319B LEU* 1.3 78.5 - - - +
321B VAL* 1.3 57.4 + - - +
322B TRP 3.0 3.3 + - - -
324B LYS* 2.8 35.7 + - + +
325B ASP 5.1 1.1 - - - +
326B ALA* 3.7 15.9 - - + -
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 3.6 38.0 - - + +
317B ARG* 3.3 16.8 - - - +
318B VAL* 3.1 10.5 + - - +
320B ALA* 1.3 73.1 - - - +
322B TRP* 1.3 63.7 + - - +
324B LYS 3.7 7.1 - - - +
326B ALA* 3.6 17.9 - - + +
327B VAL* 5.2 2.7 - - - -
328B THR 3.2 34.5 - - - +
329B ILE* 4.7 2.2 - - + -
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Residues in contact with TRP 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 5.6 12.8 - - + -
318B VAL* 3.0 44.1 + - + +
319B LEU* 3.5 13.2 - - + +
320B ALA 3.0 3.2 - - - -
321B VAL* 1.3 83.9 - - - +
323B ASN* 1.3 73.3 + - - +
324B LYS 3.8 1.9 - - - +
----------------------------------------------------------
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Residues in contact with ASN 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B TRP* 4.4 20.6 - - + -
319B LEU* 3.1 26.8 + - - +
322B TRP* 1.3 85.6 - - - +
324B LYS* 1.3 81.9 + - - +
----------------------------------------------------------
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Residues in contact with LYS 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B TRP* 4.3 14.3 - - + +
137B TYR* 4.1 40.0 + - + -
319B LEU 4.3 0.2 + - - -
320B ALA* 2.8 26.2 + - + +
321B VAL* 3.7 12.5 - - - +
322B TRP 3.8 1.6 - - - +
323B ASN* 1.3 110.0 + - - +
325B ASP* 1.3 69.6 + - - +
----------------------------------------------------------
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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