Contacts of the helix formed by residues 222 - 254 (chain B) 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 LYS 222 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A MET 4.2 7.2 - - - +
85A ARG* 3.0 28.1 + - - +
86A ASN 6.0 0.7 - - - -
91A PHE* 3.4 44.0 - - + -
52B GLU* 3.3 31.5 + - - +
220B GLU* 3.2 7.8 + - - +
221B PRO* 1.3 93.6 - - + +
223B LEU* 1.3 63.3 + - - +
224B MET 3.6 1.1 - - - -
225B ALA* 3.5 11.4 + - + +
226B ARG* 3.0 24.0 + - - +
42C ALA* 5.6 3.6 - - - +
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A BGL 4.2 14.1 - - - +
13B PHE* 4.4 16.2 - - + +
18B GLY 5.1 1.8 - - - +
20B PHE* 3.7 31.2 - - + -
216B MET* 4.5 12.1 - - + -
220B GLU* 3.0 19.9 + - + +
221B PRO 3.2 2.8 - - - -
222B LYS* 1.3 75.8 - - - +
224B MET* 1.3 72.4 + - + +
226B ARG* 2.8 39.6 + - - +
227B LYS* 2.9 49.1 + - + +
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Residues in contact with MET 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLY 4.7 2.0 - - - +
19B THR* 3.4 39.7 - - + -
20B PHE* 3.8 29.8 - - + +
54B GLY* 3.8 34.5 - - - +
221B PRO 4.8 1.9 + - - +
223B LEU* 1.3 84.0 - - + +
225B ALA* 1.3 64.7 + - - +
227B LYS* 3.0 7.0 + - - +
228B GLN* 2.8 42.8 + - + +
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Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 3.8 21.7 - - + -
222B LYS* 3.5 19.1 + - + +
223B LEU 3.2 0.2 - - - -
224B MET* 1.3 77.4 - - - +
226B ARG* 1.3 58.5 + - - +
228B GLN* 3.2 14.5 + - - +
229B ALA* 2.8 30.7 + - - +
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Residues in contact with ARG 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 3.5 24.0 - - + -
92A MET* 4.6 4.1 - - + +
95A TYR* 3.5 27.5 - - + -
267A VAL 4.0 10.3 - - - +
268A GLY* 3.0 27.1 + - - +
269A PHE 3.9 15.0 + - - -
271A PRO* 3.8 14.3 - - - +
272A ASN* 5.1 0.8 - - - +
431A BGL 4.4 8.3 + - - -
220B GLU* 2.4 39.9 + - - +
222B LYS 3.0 10.8 + - - +
223B LEU* 2.8 40.4 + - - +
225B ALA* 1.3 80.6 - - - +
227B LYS* 1.3 63.9 + - - +
229B ALA* 3.2 7.5 - - - +
230B GLY* 3.0 21.3 + - - -
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Residues in contact with LYS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLY 4.2 10.1 - - - +
269A PHE* 4.0 15.9 - - + -
431A BGL 3.5 31.5 + - - +
13B PHE 2.7 24.4 + - - -
15B GLY 2.6 23.4 + - - +
16B PRO* 3.7 23.6 - - + +
18B GLY 4.0 11.6 + - - +
223B LEU* 2.9 34.9 + - + +
224B MET* 3.0 7.8 + - - +
226B ARG* 1.3 79.0 - - - +
228B GLN* 1.3 62.2 + - + +
230B GLY* 2.9 15.0 + - - +
231B PHE* 3.1 21.5 + - + -
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Residues in contact with GLN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B MET* 2.8 48.7 + - + +
225B ALA* 3.5 11.6 + - - +
227B LYS* 1.3 69.9 - - - +
229B ALA* 1.3 66.7 + - - +
230B GLY 3.0 0.9 + - - -
231B PHE* 3.3 17.2 + - + +
232B THR* 3.1 24.5 + - - -
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Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 5.2 2.0 - - + -
92A MET* 4.2 24.9 - - + -
225B ALA 2.8 13.4 + - - +
226B ARG* 3.2 13.9 - - - +
228B GLN* 1.3 77.2 - - - +
230B GLY* 1.3 66.4 + - - +
232B THR* 3.3 7.0 - - - -
233B ALA* 3.0 21.4 + - - +
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Residues in contact with GLY 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A PHE 5.3 2.2 - - - -
268A GLY* 4.4 14.8 - - - -
269A PHE* 4.2 10.1 - - - -
226B ARG 3.0 10.1 + - - -
227B LYS 2.9 11.4 + - - -
229B ALA* 1.3 78.0 - - - +
231B PHE* 1.3 67.4 + - - +
233B ALA* 2.8 13.5 + - - +
234B VAL* 3.0 16.6 + - - +
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Residues in contact with PHE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A PHE* 3.9 13.6 - + - -
16B PRO* 3.1 28.3 - - + -
17B PHE* 2.9 46.4 - + - -
227B LYS* 3.1 29.4 + - + -
228B GLN* 3.8 16.2 - - + +
230B GLY* 1.3 68.6 - - - +
232B THR* 1.3 67.2 + - - +
234B VAL* 2.9 11.5 + - - +
235B MET* 2.7 36.6 + - + +
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Residues in contact with THR 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B GLN 3.1 12.7 + - - -
229B ALA* 3.3 12.0 - - - -
230B GLY 2.9 0.2 + - - -
231B PHE* 1.3 81.1 - - - +
233B ALA* 1.3 66.5 + - - +
235B MET* 2.8 16.5 + - - +
236B PHE* 3.0 41.5 + - + -
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A PHE* 3.7 40.4 - - + -
229B ALA 3.0 8.2 + - - +
230B GLY* 2.8 13.5 + - - +
232B THR* 1.3 78.2 - - - +
234B VAL* 1.3 61.6 + - - +
236B PHE* 3.6 11.4 + - - +
237B LEU* 3.0 33.0 + - + +
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Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 3.5 22.4 - - + +
264A PHE* 5.3 0.4 - - + -
265A ALA* 4.6 19.1 - - + +
269A PHE* 4.2 17.9 - - + -
230B GLY* 3.0 17.9 + - - +
231B PHE* 2.9 8.7 + - - +
233B ALA* 1.3 77.5 - - + +
235B MET* 1.3 65.5 + - + +
237B LEU* 3.2 1.3 + - - +
238B THR* 2.5 52.0 + - - +
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Residues in contact with MET 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B PHE* 2.7 30.2 + - + +
232B THR* 2.8 11.2 + - - +
234B VAL* 1.3 88.5 - - + +
236B PHE* 1.3 72.4 + - + +
238B THR* 3.1 11.4 + - + +
239B VAL* 2.9 30.7 + - + +
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Residues in contact with PHE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B THR* 3.0 39.1 + - + -
233B ALA* 3.7 11.9 - - - +
235B MET* 1.3 79.5 - - + +
237B LEU* 1.3 57.3 + - + +
239B VAL* 3.2 5.2 + - - +
240B LEU* 2.6 40.2 + - + +
22C ALA* 5.5 4.4 - - + +
25C VAL* 3.6 29.8 - - + -
26C ALA* 4.7 20.6 - - + -
29C ALA* 3.9 29.6 - - + -
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Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ALA* 4.0 22.4 - - + +
260A LEU* 4.1 20.0 - - + +
261A LEU* 4.1 18.2 - - + -
264A PHE* 3.6 33.9 - - + -
233B ALA* 3.0 24.6 + - - +
234B VAL 3.6 1.6 - - - +
235B MET 3.1 0.4 - - - -
236B PHE* 1.3 82.5 - - + +
238B THR* 1.3 55.2 + - - +
240B LEU* 4.0 20.2 - - + -
241B SER* 2.4 43.4 + - - +
26C ALA* 6.2 1.8 - - + -
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Residues in contact with THR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 3.7 16.2 - - + +
234B VAL* 2.5 44.9 + - - +
235B MET* 3.7 12.8 - - + +
237B LEU* 1.3 72.9 - - - +
239B VAL* 1.3 63.7 + - + +
241B SER* 3.3 6.1 - - - -
242B VAL* 3.0 32.2 + - + +
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Residues in contact with VAL 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B MET* 2.9 20.5 + - + +
236B PHE* 3.3 7.6 - - - +
238B THR* 1.3 75.0 - - + +
240B LEU* 1.3 60.7 + - - +
241B SER 2.8 3.8 - - - -
242B VAL* 2.7 30.8 + - + +
243B LEU* 2.9 31.3 + - + -
22C ALA* 5.0 7.0 - - + -
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Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ALA* 4.8 4.9 - - + -
236B PHE* 2.6 23.2 + - + +
237B LEU* 3.7 23.1 - - + +
239B VAL* 1.3 77.0 - - - +
241B SER* 1.3 56.1 + - - +
243B LEU* 3.9 6.3 - - + -
244B LEU* 2.9 59.4 + - + +
19C THR* 4.5 9.4 - - + +
22C ALA* 4.1 11.7 - - + +
23C GLY* 4.1 32.1 - - - +
26C ALA* 4.7 14.8 - - + -
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Residues in contact with SER 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A PHE* 3.9 6.1 - - - -
257A ALA* 3.9 23.2 - - - +
258A VAL* 4.1 15.0 + - - -
261A LEU* 4.1 12.0 - - - +
237B LEU 2.4 33.0 + - - -
238B THR* 3.3 8.7 - - - -
239B VAL 2.7 0.4 + - - -
240B LEU* 1.3 71.1 - - - +
242B VAL* 1.3 55.8 + - - -
244B LEU* 3.2 3.5 + - - +
245B TYR* 2.7 37.8 + - - +
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Residues in contact with VAL 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B THR* 3.0 23.3 - - + +
239B VAL* 2.7 13.8 + - + +
241B SER* 1.3 72.7 - - - +
243B LEU* 1.3 64.9 + - + +
245B TYR* 3.1 11.7 + - + +
246B LEU* 3.0 43.8 + - + +
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B VAL* 2.9 32.2 + - + +
240B LEU* 3.8 8.3 - - + +
242B VAL* 1.3 79.3 - - + +
244B LEU* 1.3 59.3 + - - +
245B TYR 3.0 0.7 + - - -
246B LEU* 3.0 12.7 + - + +
247B THR* 2.7 31.6 + - - -
15C LEU* 3.9 22.5 - - + +
18C ALA* 3.6 34.5 - - + +
19C THR* 3.1 20.2 - - + +
22C ALA* 4.2 10.5 - - + -
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ILE* 4.6 11.5 - - + +
253A VAL* 3.6 38.4 - - + +
254A PHE* 4.1 18.2 - - + +
257A ALA* 4.0 15.0 - - + -
240B LEU* 2.9 54.1 + - + +
241B SER 3.6 2.9 - - - +
243B LEU* 1.3 73.4 - - - +
245B TYR* 1.3 56.6 + - - +
247B THR* 3.4 10.6 - - + +
248B ASN* 2.8 30.1 + - - +
19C THR* 4.0 14.6 + - + -
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Residues in contact with TYR 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A PHE* 3.9 31.8 - + + -
241B SER 2.7 17.6 + - - +
242B VAL* 3.2 14.8 - - + +
244B LEU* 1.3 69.4 - - - +
246B LEU* 1.3 75.0 + - + +
248B ASN* 3.0 8.5 + - + +
249B LYS* 2.8 66.1 + - + +
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Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B VAL* 3.0 29.2 - - + +
243B LEU* 3.0 8.5 + - + +
245B TYR* 1.3 93.7 - - + +
247B THR* 1.3 67.2 + - - +
248B ASN 2.9 0.5 + - - -
249B LYS* 2.9 10.5 + - + +
250B ARG* 2.7 26.0 + - - +
15C LEU* 3.7 33.9 - - + -
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Residues in contact with THR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ILE* 4.1 22.7 - - + -
243B LEU 2.7 19.8 + - - -
244B LEU* 3.4 14.1 - - + -
246B LEU* 1.3 75.6 - - - +
248B ASN* 1.3 62.7 + - - +
250B ARG* 3.7 3.9 + - - +
251B LEU* 3.1 23.6 + - - +
15C LEU* 3.8 14.6 - - - +
16C TYR* 4.3 28.3 + - + -
19C THR* 3.3 26.2 + - + +
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Residues in contact with ASN 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TRP* 4.7 4.2 - - - -
250A ILE* 3.3 24.8 - - + +
251A LYS* 3.5 25.5 + - - +
254A PHE* 4.5 14.8 - - + -
244B LEU 2.8 15.3 + - - +
245B TYR* 3.2 13.7 + - - +
246B LEU 3.0 0.2 - - - -
247B THR* 1.3 74.4 - - - +
249B LYS* 1.3 70.7 + - - +
251B LEU* 2.8 15.5 + - - +
252B TRP* 2.9 44.3 + - - +
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Residues in contact with LYS 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B TYR* 2.8 50.4 + - + +
246B LEU* 3.5 11.7 - - + +
248B ASN* 1.3 75.5 - - - +
250B ARG* 1.3 54.0 + - - +
252B TRP* 3.8 3.7 - - - +
253B ALA* 2.7 41.5 + - + +
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Residues in contact with ARG 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B LEU 2.7 20.5 + - - +
247B THR 3.7 4.3 - - - +
249B LYS* 1.3 76.7 - - - +
251B LEU* 1.3 64.4 + - - +
253B ALA* 3.3 16.5 + - + +
254B GLY* 3.6 4.0 + - - -
9C GLY 5.7 2.4 - - - +
11C ARG* 5.1 8.5 - - - +
12C ARG* 2.7 60.2 - - - +
15C LEU* 4.7 8.7 - - + -
16C TYR* 4.0 19.1 + - - +
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A PRO* 3.5 41.3 - - + +
247A TYR* 3.3 40.6 + - + +
250A ILE* 3.6 26.9 - - + -
247B THR 3.1 15.0 + - - +
248B ASN* 2.8 9.5 + - - +
250B ARG* 1.3 78.2 - - - +
252B TRP* 1.3 62.5 + - + +
254B GLY* 3.4 10.0 + - - -
16C TYR* 4.6 12.7 + - - +
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Residues in contact with TRP 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG 4.2 15.5 - - - -
242A VAL* 4.1 20.0 - - + -
247A TYR* 3.1 45.8 + + + -
248A PHE* 3.6 39.0 - + - -
251A LYS* 4.2 19.4 - - + +
428A PHE* 4.9 13.7 - + - -
248B ASN* 2.9 49.7 + - - +
249B LYS* 4.1 3.4 - - - +
251B LEU* 1.3 73.1 - - + +
253B ALA* 1.3 64.9 + - - +
254B GLY 2.8 7.3 + - - -
255B VAL* 2.8 29.2 + - + +
256B LYS* 3.4 10.3 + - + +
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Residues in contact with ALA 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LYS* 2.7 29.2 + - + +
250B ARG* 3.4 9.6 - - - +
252B TRP* 1.3 72.0 - - - +
254B GLY* 1.3 57.3 + - - +
255B VAL 3.1 5.1 + - - -
256B LYS 3.7 18.6 + - - -
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Residues in contact with GLY 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A TYR* 5.1 2.3 + - - -
250B ARG 3.6 3.9 + - - -
251B LEU 3.4 9.4 + - - -
252B TRP 2.8 2.8 + - - -
253B ALA* 1.3 78.0 - - - +
255B VAL* 1.3 63.8 + - - +
----------------------------------------------------------
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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).
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