Contacts of the helix formed by residues 244 - 270 (chain J) in PDB entry 2QJK
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 PHE 244 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J THR 4.6 4.5 - - - -
33J ILE* 3.4 33.9 - - + +
34J MET 4.0 2.0 + - - -
35J ILE* 3.0 31.8 + - + +
37J THR* 4.0 7.6 - - - -
242J VAL 3.5 0.4 + - - -
243J PRO* 1.3 71.7 - - - +
245J TRP* 1.3 56.9 + - - +
247J TYR 3.2 0.9 + - - -
248J PHE* 2.7 69.0 + + + -
249J ILE* 3.4 27.2 + - + -
252J ASP* 3.4 19.3 - - - -
505J ANJ 3.5 55.2 - + + -
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Residues in contact with TRP 245 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J ILE* 3.2 28.7 + - + +
34J MET* 3.8 22.0 - - + +
243J PRO* 3.4 21.4 - - - +
244J PHE* 1.3 80.2 - - - +
246J PRO* 1.3 88.9 - - + +
247J TYR 3.4 0.9 - - - -
249J ILE* 3.7 40.4 - - + -
250J ILE* 5.7 2.7 - - + -
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Residues in contact with PRO 246 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243J PRO* 4.8 0.9 - - + -
244J PHE 3.4 1.3 - - - -
245J TRP* 1.3 123.3 - - + +
247J TYR* 1.3 82.6 + - + +
248J PHE 3.4 2.2 - - - -
249J ILE* 4.0 0.7 - - + -
250J ILE* 3.0 32.8 + - + +
251K LEU* 3.5 26.5 - - + -
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Residues in contact with TYR 247 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242J VAL* 3.7 15.5 - - + -
243J PRO* 3.2 52.5 - - + +
244J PHE 3.2 0.8 + - - -
246J PRO* 1.3 88.1 - - + +
248J PHE* 1.3 62.1 + - - +
250J ILE* 3.9 2.6 - - - +
251J LYS 3.6 7.3 + - - -
251K LEU* 3.4 39.7 + - + +
252K TRP* 3.0 44.5 + + + -
254K GLY 5.0 2.9 + - - -
255K VAL* 3.5 32.8 - - + +
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Residues in contact with PHE 248 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J THR* 3.2 34.8 - - + -
38J PRO 3.2 23.1 - - - -
39J ARG 4.6 1.3 - - - -
41J LEU* 3.8 24.7 - - + -
242J VAL* 4.0 11.0 - - + -
244J PHE* 2.7 53.2 + + + -
247J TYR* 1.3 72.6 - - - +
249J ILE* 1.3 66.0 + - - +
250J ILE 2.6 6.9 + - - -
251J LYS* 2.8 28.1 + - + +
252J ASP* 2.8 27.3 + - - +
505J ANJ 4.0 10.8 - + + -
252K TRP* 3.6 25.6 - + - -
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Residues in contact with ILE 249 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J ILE* 3.3 30.3 - - + -
244J PHE* 3.4 22.8 + - + -
245J TRP* 3.7 42.2 - - + -
246J PRO 3.7 7.2 - - - +
248J PHE* 1.3 76.4 - - - +
250J ILE* 1.3 60.9 + - + +
252J ASP* 3.5 9.1 + - + +
253J VAL* 3.0 34.7 + - + +
505J ANJ 4.4 10.8 - - + -
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Residues in contact with ILE 250 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245J TRP* 5.7 2.7 - - + -
246J PRO* 3.0 24.2 + - + +
247J TYR 3.9 2.9 - - - +
248J PHE 2.6 4.8 + - - -
249J ILE* 1.3 75.4 - - + +
251J LYS* 1.3 52.9 + - - +
252J ASP 3.0 1.1 - - - -
253J VAL* 2.9 8.1 + - + +
254J PHE* 2.6 33.7 + - + +
244K LEU* 4.7 10.0 - - + +
247K THR* 4.1 22.4 - - + -
248K ASN* 3.2 37.5 - - + +
251K LEU* 3.4 25.1 - - + -
16L TYR* 6.1 4.0 - - + -
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Residues in contact with LYS 251 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J LEU 3.5 24.2 + - - -
42J ASN* 4.6 3.8 + - - +
43J TRP* 2.9 47.1 - - + -
46J ILE* 5.4 2.2 - - + -
247J TYR 3.6 1.8 + - - +
248J PHE* 2.8 47.8 + - + +
250J ILE* 1.3 75.9 - - - +
252J ASP* 1.3 61.9 + - - +
254J PHE* 2.7 7.1 + - - +
255J ALA* 2.5 38.5 + - - +
505J ANJ 4.7 7.4 + - - +
248K ASN* 3.3 21.8 + - - +
252K TRP* 3.9 16.5 - - + +
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Residues in contact with ASP 252 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J ILE* 4.5 6.3 - - - +
49J VAL* 3.9 27.6 - - + +
244J PHE* 3.4 20.4 - - - -
248J PHE 2.8 17.3 + - - +
249J ILE* 3.5 8.7 + - + +
251J LYS* 1.3 79.0 - - - +
253J VAL* 1.3 53.7 + - + +
255J ALA* 3.2 5.7 + - - +
256J LEU* 2.7 38.6 + - - +
505J ANJ 2.9 50.7 + - + +
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Residues in contact with VAL 253 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249J ILE* 3.0 24.4 + - + +
250J ILE* 2.9 9.3 + - + +
252J ASP* 1.3 80.8 - - + +
254J PHE* 1.3 64.9 + - - +
256J LEU* 3.3 15.6 - - + +
257J ALA* 2.9 22.0 + - - +
244K LEU* 3.5 28.9 - - + -
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Residues in contact with PHE 254 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J TRP* 3.8 36.3 - + - -
250J ILE 2.6 17.3 + - - +
251J LYS* 2.7 12.2 + - - +
253J VAL* 1.3 74.2 - - - +
255J ALA* 1.3 67.9 + - - +
257J ALA* 3.0 14.2 + - - +
258J VAL* 3.3 28.6 + - + +
241K SER* 3.9 12.1 - - - -
244K LEU* 4.1 21.3 - - + +
245K TYR* 3.8 50.9 - + + -
248K ASN* 4.3 14.1 - - + -
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Residues in contact with ALA 255 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J TRP* 5.0 8.3 - - + -
46J ILE* 3.7 42.4 - - + -
50J VAL* 6.0 0.4 - - + -
251J LYS 2.5 17.5 + - - +
252J ASP 3.6 2.9 - - - +
254J PHE* 1.3 77.9 - - + +
256J LEU* 1.3 65.9 + - - +
258J VAL* 2.7 24.7 + - - +
259J VAL* 2.9 16.3 + - + +
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Residues in contact with LEU 256 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J VAL* 3.3 31.2 - - + -
50J VAL* 4.0 22.1 - - + +
53J PHE* 4.1 35.0 - - + -
252J ASP 2.7 20.6 + - - +
253J VAL* 3.3 16.8 - - + +
255J ALA* 1.3 71.8 - - - +
257J ALA* 1.3 55.8 + - - +
259J VAL* 3.5 6.9 - - + +
260J LEU* 3.0 41.7 + - + +
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Residues in contact with ALA 257 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253J VAL 2.9 11.0 + - - +
254J PHE 3.1 11.4 - - - +
255J ALA 2.7 4.2 + - - -
256J LEU* 1.3 71.7 - - - +
258J VAL* 1.3 66.8 + - - +
260J LEU* 3.1 5.8 + - - +
261J LEU* 2.8 22.9 + - - +
237K LEU* 4.1 17.4 - - + +
240K LEU* 4.8 3.8 - - + -
241K SER* 3.9 20.0 - - - +
244K LEU* 3.9 19.7 - - + -
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Residues in contact with VAL 258 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254J PHE* 3.4 45.1 - - + +
255J ALA* 2.7 14.9 + - - +
257J ALA* 1.3 71.7 - - - +
259J VAL* 1.3 66.2 + - + +
261J LEU* 3.1 28.1 - - + +
262J VAL* 3.2 14.1 + - + +
241K SER* 4.3 9.9 - - - +
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Residues in contact with VAL 259 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J ILE* 4.7 10.3 - - + -
47J TRP* 5.2 9.6 - - + -
50J VAL* 4.0 36.6 - - + -
103J LEU* 4.1 22.7 - - + -
255J ALA* 2.9 20.4 + - - +
256J LEU* 3.5 10.1 - - + +
258J VAL* 1.3 76.3 - - + +
260J LEU* 1.3 55.7 + - + +
262J VAL* 2.9 11.5 + - - +
263J PHE* 2.8 30.8 + - + +
504J LOP 5.1 6.2 - - + +
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Residues in contact with LEU 260 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53J PHE* 3.3 54.5 - - + -
103J LEU* 4.9 5.4 - - + -
256J LEU* 3.0 28.2 + - + +
257J ALA* 3.6 5.4 - - - +
259J VAL* 1.3 78.8 - - + +
261J LEU* 1.3 58.2 + - - +
263J PHE* 3.7 20.0 - - + -
264J PHE* 2.6 54.6 + - + -
237K LEU* 4.2 12.8 - - + -
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Residues in contact with LEU 261 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257J ALA 2.8 12.2 + - - +
258J VAL* 3.1 20.2 - - + +
260J LEU* 1.3 78.5 - - - +
262J VAL* 1.3 67.5 + - + +
264J PHE* 3.9 1.7 - - - +
265J ALA* 3.0 21.5 + - + +
234K VAL* 3.6 41.6 - - + +
237K LEU* 4.1 12.9 - - + +
238K THR* 3.6 22.9 - - + +
241K SER* 4.1 17.0 - - - +
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Residues in contact with VAL 262 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258J VAL* 3.4 20.4 - - + +
259J VAL* 2.9 7.1 + - - +
261J LEU* 1.3 77.4 - - + +
263J PHE* 1.3 67.4 + - - +
265J ALA* 3.0 21.5 + - - +
266J ILE* 3.1 15.7 + - + +
431J BGL 3.7 25.4 - - + -
504J LOP 3.7 33.7 - - + -
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Residues in contact with PHE 263 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J PHE* 5.2 0.4 - + - -
57J LEU* 3.8 20.2 - - + -
96J LEU* 3.4 43.7 - - + -
99J ASN* 3.6 27.4 - - + -
100J GLY* 4.1 3.1 - - - -
103J LEU* 4.2 14.8 - - + -
259J VAL 2.8 16.7 + - - +
260J LEU* 3.4 27.6 - - + +
262J VAL* 1.3 71.7 - - - +
264J PHE* 1.3 73.9 + + - +
266J ILE* 3.0 13.6 + - + +
267J VAL* 2.9 35.8 + - + +
504J LOP 3.8 28.6 - - + +
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Residues in contact with PHE 264 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53J PHE* 5.6 3.1 - + - -
57J LEU* 6.5 0.2 - - + -
92J MET* 5.7 7.0 - - - -
96J LEU* 4.1 32.1 - - + -
260J LEU* 2.6 49.5 + - + +
261J LEU 3.9 2.7 - - - +
263J PHE* 1.3 83.9 - + - +
265J ALA* 1.3 53.1 + - - +
267J VAL* 3.5 7.7 - - + +
268J GLY* 2.6 36.0 + - - -
230K GLY* 5.4 2.1 - - - -
233K ALA* 3.7 31.4 - - + -
234K VAL* 5.2 2.9 - - + +
237K LEU* 3.6 20.6 - - + -
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Residues in contact with ALA 265 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261J LEU* 3.0 15.9 + - + +
262J VAL* 3.0 19.0 + - - +
264J PHE* 1.3 75.0 - - - +
266J ILE* 1.3 50.8 + - - +
269J PHE* 2.8 51.4 + - + +
270J MET* 4.7 0.5 - - - +
431J BGL 4.4 25.4 - - + +
234K VAL* 4.6 12.7 - - + +
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Residues in contact with ILE 266 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99J ASN* 4.1 16.6 - - - +
262J VAL* 3.1 23.3 - - + +
263J PHE* 3.0 7.1 + - + +
265J ALA* 1.3 72.4 - - - +
267J VAL* 1.3 62.5 - - + +
268J GLY 3.0 1.6 - - - -
270J MET* 2.6 74.6 + - + +
271J PRO 2.9 0.3 - - - -
273J TYR* 5.4 1.1 - - + -
274J LEU* 5.1 13.9 - - + -
431J BGL 4.1 20.6 - - + -
504J LOP 4.2 21.5 - - + -
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Residues in contact with VAL 267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92J MET* 4.5 12.1 - - - +
95J TYR* 3.9 26.2 - - + -
96J LEU* 4.0 26.0 - - + +
99J ASN* 4.3 7.9 - - + +
263J PHE* 2.9 52.7 - - + +
264J PHE* 3.7 9.9 - - + +
266J ILE* 1.3 73.3 - - + +
268J GLY* 1.3 61.7 + - - +
271J PRO* 3.7 19.5 - - - +
226K ARG* 4.1 10.7 - - - +
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Residues in contact with GLY 268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J MET* 5.5 3.4 - - - -
264J PHE 2.6 21.4 + - - -
265J ALA 3.9 0.2 - - - -
267J VAL* 1.3 74.0 - - - +
269J PHE* 1.3 64.3 + - - +
271J PRO* 4.6 0.2 - - - -
226K ARG* 3.2 40.0 + - - +
227K LYS* 4.5 2.3 - - - +
230K GLY* 4.4 18.6 - - - -
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Residues in contact with PHE 269 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265J ALA* 2.8 36.4 + - + +
268J GLY* 1.3 77.5 - - - +
270J MET* 1.3 58.8 + - - +
271J PRO* 3.6 5.1 - - - +
431J BGL 2.8 63.1 + - + +
16K PRO* 3.9 37.2 - - + -
226K ARG* 4.1 5.4 + - - +
227K LYS* 4.1 17.5 - - + -
230K GLY* 4.2 5.6 - - - -
231K PHE* 3.8 40.4 - + - -
234K VAL* 4.0 23.1 - - + -
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Residues in contact with MET 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99J ASN* 4.7 0.2 - - - +
266J ILE* 2.6 53.7 + - + +
269J PHE* 1.3 76.9 - - + +
271J PRO* 1.3 65.1 - - - +
272J ASN 3.3 2.5 - - - +
273J TYR* 3.2 48.1 + - + +
431J BGL 3.8 41.1 - - + +
121K LEU* 3.6 35.4 - - + +
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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