Contacts of the helix formed by residues 245 - 268 (chain A) in PDB entry 6J8H
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 LEU 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A SER 3.6 9.4 + - - +
242A VAL* 3.0 21.7 + - + +
244A LYS* 1.3 78.0 - - - +
246A SER* 1.3 62.8 + - - +
247A ASP 3.4 1.1 - - - -
248A VAL* 3.5 15.4 + - + +
249A MET* 3.1 42.4 + - + +
397A ILE* 4.5 15.0 - - + +
400A VAL* 3.4 31.0 - - + -
401A VAL* 4.2 25.1 - - + -
957A LEU* 4.9 13.2 - - + -
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Residues in contact with SER 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A VAL 3.9 1.8 + - - -
243A LYS* 3.2 15.3 + - - -
244A LYS 3.1 3.8 + - - -
245A LEU* 1.3 77.9 - - - +
247A ASP* 1.3 69.0 + - - +
249A MET* 3.4 6.3 + - - +
250A ILE* 3.3 30.4 + - - +
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Residues in contact with ASP 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LYS 4.2 5.3 + - - +
245A LEU 3.4 0.4 - - - -
246A SER* 1.3 81.8 + - - +
248A VAL* 1.3 66.8 + - + +
250A ILE* 3.2 11.2 + - - +
251A LEU* 3.1 21.7 + - - +
1629A GLY* 2.5 51.2 - - - +
1630A ILE* 2.8 10.2 + - - +
1633A LEU* 4.2 9.7 - - + +
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Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LYS 5.2 0.9 + - - +
245A LEU* 3.5 14.5 + - + +
246A SER 3.4 0.4 - - - -
247A ASP* 1.3 77.8 - - + +
249A MET* 1.3 57.0 + - - +
251A LEU* 3.4 2.2 + - + +
252A THR* 2.7 44.1 + - - +
393A LEU* 5.1 2.2 - - + +
396A LEU* 4.5 12.6 - - + +
397A ILE* 3.6 34.1 - - + +
400A VAL* 3.4 39.0 - - + -
1633A LEU* 3.9 21.1 - - + -
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Residues in contact with MET 249 (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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245A LEU* 3.1 43.8 + - + +
246A SER* 3.6 7.6 - - - +
247A ASP 3.2 0.2 - - - -
248A VAL* 1.3 84.8 - - - +
250A ILE* 1.3 62.4 + - + +
252A THR* 3.3 17.3 + - + +
253A VAL* 3.0 31.3 + - + +
397A ILE* 4.9 14.1 - - + -
953A VAL* 6.2 3.8 - - + -
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Residues in contact with ILE 250 (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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246A SER* 3.3 17.4 + - - +
247A ASP* 3.2 14.8 + - - +
249A MET* 1.3 79.2 - - + +
251A LEU* 1.3 62.5 + - - +
253A VAL* 3.4 5.0 + - - +
254A PHE* 3.0 22.3 + - + +
1630A ILE* 3.0 31.2 - - + -
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Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ASP 3.1 12.9 + - - +
248A VAL* 3.8 7.0 - - + +
250A ILE* 1.3 76.8 - - - +
252A THR* 1.3 58.2 + - - +
254A PHE* 3.3 12.1 + - + -
255A CYS* 2.7 37.9 + - - +
392A TYR* 4.9 2.9 - - + -
393A LEU* 4.3 16.2 - - + -
396A LEU* 3.9 27.8 - - + -
1630A ILE* 3.3 34.7 - - + +
1633A LEU* 3.9 20.2 - - + -
1634A LEU* 3.8 22.7 - - + -
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Residues in contact with THR 252 (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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248A VAL* 2.7 32.5 + - - +
249A MET* 3.7 19.4 - - + +
250A ILE 3.3 0.2 - - - -
251A LEU* 1.3 78.3 - - - +
253A VAL* 1.3 60.1 + - + +
255A CYS* 3.8 0.7 - - - +
256A LEU* 2.9 47.7 + - + +
355A PHE* 6.4 0.4 - - + -
358A MET* 4.7 12.8 - - + -
393A LEU* 4.2 25.1 + - + +
397A ILE* 4.8 6.8 - - + +
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Residues in contact with VAL 253 (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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249A MET* 3.0 19.3 + - + +
250A ILE* 3.9 5.6 - - - +
252A THR* 1.3 79.0 - - + +
254A PHE* 1.3 57.7 + - - +
256A LEU* 3.9 4.9 - - - +
257A SER* 2.9 41.3 + - - +
351A PHE* 4.4 15.1 - - + -
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Residues in contact with PHE 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ILE* 3.0 17.8 + - + +
251A LEU* 3.6 20.2 - - + +
253A VAL* 1.3 78.2 - - - +
255A CYS* 1.3 60.8 + - - +
257A SER* 3.2 5.3 + - - -
258A VAL* 2.9 55.7 + - + +
1529A MET* 4.7 9.9 - - + -
1620A ILE* 3.9 32.3 - - + -
1621A LEU* 4.6 7.2 - - + -
1623A LEU* 4.4 17.7 - - + -
1624A VAL* 3.6 31.4 - - + -
1630A ILE* 4.7 11.7 - - + -
1634A LEU* 5.7 1.3 - - + -
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Residues in contact with CYS 255 (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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251A LEU* 2.7 35.6 + - - +
252A THR 3.8 3.4 - - - +
254A PHE* 1.3 75.1 - - - +
256A LEU* 1.3 65.4 + - - +
258A VAL* 3.4 5.8 + - - +
259A PHE* 3.0 47.0 + - + -
388A LEU* 4.6 12.8 - - - -
392A TYR* 6.4 0.7 - - - -
393A LEU* 3.9 26.2 - - + -
1634A LEU* 5.9 2.9 - - - -
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Residues in contact with LEU 256 (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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252A THR* 2.9 34.8 + - + +
253A VAL* 3.9 1.1 - - - +
255A CYS* 1.3 77.5 - - + +
257A SER* 1.3 59.0 + - - +
259A PHE* 3.9 6.4 - - + +
260A ALA* 2.9 29.3 + - - +
351A PHE* 3.9 31.3 - - + -
354A LEU* 4.3 23.2 - - + +
355A PHE* 4.0 33.0 - - + +
358A MET* 4.1 26.5 - - + -
389A GLY* 5.6 1.8 - - - +
393A LEU* 4.6 8.5 - - + -
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Residues in contact with SER 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A VAL* 2.9 27.8 + - - +
254A PHE* 3.3 8.3 - - - -
255A CYS 3.1 0.2 - - - -
256A LEU* 1.3 75.5 - - - +
258A VAL* 1.3 64.3 + - - +
260A ALA* 3.3 7.7 + - - +
261A LEU* 3.0 28.2 + - - +
347A PHE* 3.9 19.1 - - - -
351A PHE* 4.1 8.0 - - - -
1529A MET* 3.8 21.8 - - - +
1533A MET* 4.8 1.4 - - - +
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Residues in contact with VAL 258 (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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254A PHE* 2.9 51.8 + - + +
255A CYS* 3.4 6.5 + - - +
257A SER* 1.3 75.5 - - - +
259A PHE* 1.3 69.1 + - + +
261A LEU* 3.2 10.8 + - - +
262A ILE* 3.0 30.8 + - + +
1529A MET* 5.2 0.4 - - + -
1617A ILE* 3.9 25.4 - - + -
1620A ILE* 4.4 11.0 - - + -
1621A LEU* 4.3 11.2 - - + -
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Residues in contact with PHE 259 (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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255A CYS* 3.0 35.0 + - + +
256A LEU* 4.0 3.1 - - + +
258A VAL* 1.3 79.1 - - + +
260A ALA* 1.3 54.7 + - - +
262A ILE* 3.2 19.2 + - + +
263A GLY* 2.7 33.6 + - - -
354A LEU* 3.0 34.6 - - + +
381A PHE* 4.4 4.9 - + + -
384A VAL* 4.8 14.4 - - + -
385A VAL* 3.9 32.8 - - + -
388A LEU* 4.2 30.1 - - + -
389A GLY* 4.3 12.8 - - - -
393A LEU* 6.4 0.2 - - + -
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Residues in contact with ALA 260 (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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256A LEU 2.9 19.5 + - - +
257A SER* 3.4 7.2 - - - +
259A PHE* 1.3 77.3 - - - +
261A LEU* 1.3 56.4 + - - +
263A GLY* 3.8 0.2 - - - -
264A LEU* 2.9 31.8 + - - +
347A PHE* 3.7 22.8 - - + -
350A ALA* 4.0 7.6 - - + +
351A PHE* 4.4 22.9 - - + +
354A LEU* 4.1 11.0 - - + +
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Residues in contact with LEU 261 (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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257A SER 3.0 18.3 + - - +
258A VAL* 3.2 11.4 + - - +
260A ALA* 1.3 74.1 - - - +
262A ILE* 1.3 64.2 + - - +
264A LEU* 3.5 9.3 + - + +
265A GLN* 3.1 24.6 + - - +
347A PHE* 4.3 17.9 - - + -
1529A MET* 4.2 29.2 - - + -
1532A MET* 3.7 44.2 - - + +
1533A MET* 4.2 5.4 - - + +
1617A ILE* 4.0 14.8 - - + +
1620A ILE* 4.7 15.3 - - + -
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Residues in contact with ILE 262 (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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258A VAL* 3.0 24.8 + - + +
259A PHE* 3.7 22.4 - - + +
261A LEU* 1.3 75.8 - - - +
263A GLY* 1.3 62.6 + - - +
265A GLN* 4.0 0.9 - - - +
266A LEU* 3.1 30.7 + - + +
381A PHE* 4.1 17.7 - - + -
1614A LEU* 4.3 24.5 - - + +
1617A ILE* 2.9 33.7 - - + -
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Residues in contact with GLY 263 (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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259A PHE 2.7 20.7 + - - -
260A ALA 3.8 1.1 - - - -
262A ILE* 1.3 74.5 - - - +
264A LEU* 1.3 55.4 + - - +
267A PHE* 2.9 48.0 + - - +
344A PHE* 3.9 15.8 - - - -
381A PHE* 4.1 12.8 - - - -
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Residues in contact with LEU 264 (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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260A ALA 2.9 17.5 + - - +
261A LEU* 3.8 14.4 - - + +
262A ILE 3.3 0.2 - - - -
263A GLY* 1.3 75.6 - - - +
265A GLN* 1.3 63.5 + - - +
268A MET* 2.9 49.6 + - + +
344A PHE* 3.3 29.2 - - - +
345A ASP 3.4 20.6 - - - +
346A THR* 4.3 5.2 - - - +
347A PHE* 4.6 16.6 - - + +
350A ALA* 4.5 5.6 - - + -
1532A MET 4.3 14.6 - - - +
1535A GLU* 4.0 23.3 - - + +
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Residues in contact with GLN 265 (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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261A LEU 3.1 17.8 + - - +
262A ILE 4.0 0.2 - - - +
264A LEU* 1.3 80.7 - - - +
266A LEU* 1.3 63.4 + - - +
268A MET* 4.3 16.2 + - - +
1535A GLU* 6.0 0.2 - - - -
1610A ARG* 3.9 29.5 - - - +
1613A ARG* 3.1 57.9 + - - +
1614A LEU* 3.4 29.2 - - + -
1616A ARG* 4.2 10.5 + - - +
1617A ILE* 5.9 1.1 - - + -
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ILE* 3.1 28.7 + - + +
263A GLY 4.1 1.3 - - - +
265A GLN* 1.3 81.0 - - - +
267A PHE* 1.3 77.7 + - + +
268A MET 3.8 0.2 - - - -
270A ASN* 4.5 0.5 + - - -
378A TYR* 3.9 32.3 - - + -
381A PHE* 4.5 11.2 - - + -
1610A ARG* 2.3 40.1 + - + +
1611A VAL* 4.6 21.1 - - + +
1614A LEU* 3.9 29.8 - - + -
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Residues in contact with PHE 267 (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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263A GLY* 2.9 33.3 + - - +
266A LEU* 1.3 86.4 - - + +
268A MET* 1.3 64.8 + - - +
269A GLY 3.3 0.5 + - - -
270A ASN* 3.2 37.5 + - + +
271A LEU* 4.7 1.5 + - + +
344A PHE* 3.8 36.6 - + + +
370A THR* 4.3 18.4 - - - -
374A ALA* 3.9 11.2 - - + -
378A TYR* 3.8 43.1 - + + -
381A PHE* 3.4 42.8 - + + -
382A PHE* 4.7 0.9 - + - -
1610A ARG* 5.5 0.2 - - - -
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Residues in contact with MET 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 2.9 47.2 + - + +
265A GLN* 4.3 17.2 + - - +
266A LEU 3.8 1.4 - - - -
267A PHE* 1.3 75.9 - - - +
269A GLY* 1.3 57.5 + - - +
270A ASN* 3.2 7.2 + - - +
332A LYS* 5.3 1.0 + - - -
344A PHE 3.9 17.9 - - - +
345A ASP* 4.7 0.2 - - - -
1535A GLU* 4.9 17.7 - - + +
1536A LYS 4.0 4.7 - - - +
1537A GLU* 3.9 37.0 - - + +
1539A GLN* 6.3 0.9 - - - +
1613A ARG* 5.9 2.5 - - - +
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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