Contacts of the helix formed by residues 244 - 270 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A THR 4.6 4.3 - - - -
33A ILE* 3.4 33.9 - - + +
34A MET 4.1 1.6 + - - -
35A ILE* 3.0 31.6 + - + +
37A THR* 3.9 8.7 - - - -
242A VAL 3.5 0.6 + - - -
243A PRO* 1.3 71.5 - - - +
245A TRP* 1.3 57.8 + - - +
247A TYR 3.2 0.5 + - - -
248A PHE* 2.7 69.1 + + + -
249A ILE* 3.4 26.6 + - + -
252A ASP* 3.4 18.8 - - - -
504A ANJ 3.5 55.9 - + + -
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Residues in contact with TRP 245 (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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33A ILE* 3.2 28.2 + - + +
34A MET* 3.9 21.8 - - + +
243A PRO* 3.4 23.0 - - - +
244A PHE* 1.3 78.7 - - - +
246A PRO* 1.3 87.4 - - + +
247A TYR 3.4 0.7 - - - -
249A ILE* 3.7 39.9 - - + -
250A ILE* 5.7 3.1 - - + -
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Residues in contact with PRO 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A PRO* 4.8 0.9 - - + -
244A PHE 3.4 1.6 - - - -
245A TRP* 1.3 122.4 - - + +
247A TYR* 1.3 83.1 + - + +
248A PHE 3.4 2.0 - - - -
249A ILE 4.0 0.7 - - - -
250A ILE* 2.9 33.6 + - + +
251B LEU* 3.5 27.4 - - + -
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Residues in contact with TYR 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A VAL* 3.7 20.6 - - + -
243A PRO* 3.3 51.4 - - + +
244A PHE 3.2 1.0 + - - -
246A PRO* 1.3 86.3 - - + +
248A PHE* 1.3 60.3 + - - +
250A ILE* 3.9 2.8 - - - +
251A LYS 3.5 8.7 + - - -
251B LEU* 3.3 47.7 + - + +
252B TRP* 3.1 39.6 + + + -
254B GLY 5.1 2.4 + - - -
255B VAL* 3.7 24.9 - - + +
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Residues in contact with PHE 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR* 3.2 36.1 - - + -
38A PRO 3.2 22.0 - - - -
39A ARG 4.7 1.1 - - - -
41A LEU* 3.8 26.0 - - + -
242A VAL* 4.1 10.5 - - + -
244A PHE* 2.7 51.7 + + + -
247A TYR* 1.3 72.2 - - - +
249A ILE* 1.3 67.6 + - - +
250A ILE 2.6 4.1 + - - -
251A LYS* 2.7 17.2 + - + +
252A ASP* 2.7 28.9 + - - +
504A ANJ 3.9 17.0 - + - +
252B TRP* 3.6 29.4 - + - -
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Residues in contact with ILE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 3.4 29.4 - - + -
244A PHE* 3.4 23.8 + - + -
245A TRP* 3.7 43.1 - - + -
246A PRO 3.7 6.7 - - - +
248A PHE* 1.3 77.2 - - - +
250A ILE* 1.3 62.4 + - + +
252A ASP* 3.6 7.9 + - + +
253A VAL* 3.0 32.2 + - + +
504A ANJ 4.4 10.3 - - + -
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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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245A TRP* 5.7 2.7 - - + -
246A PRO* 2.9 24.9 + - + +
247A TYR 3.9 3.4 - - - +
248A PHE 2.6 4.8 + - - -
249A ILE* 1.3 77.0 - - + +
251A LYS* 1.3 55.5 + - - +
252A ASP 3.0 1.1 - - - -
253A VAL* 2.9 7.2 + - + +
254A PHE* 2.5 35.1 + - + +
244B LEU* 4.6 11.4 - - + +
247B THR* 4.1 22.9 - - + -
248B ASN* 3.3 34.5 - - + +
251B LEU* 3.6 24.9 - - + -
16C TYR* 6.3 2.2 - - + -
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Residues in contact with LYS 251 (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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41A LEU 4.2 19.3 + - - -
42A ASN* 4.8 6.7 - - - +
43A TRP* 3.5 45.9 - - + -
46A ILE* 5.4 2.9 - - + -
247A TYR 3.5 11.6 + - - +
248A PHE* 2.7 33.4 + - + +
250A ILE* 1.3 74.8 - - - +
252A ASP* 1.3 53.8 + - - +
254A PHE* 3.1 7.2 + - - +
255A ALA* 2.8 37.2 + - - +
504A ANJ 4.7 8.7 - - - +
248B ASN* 3.6 18.7 - - - +
252B TRP* 4.3 19.9 - - - +
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Residues in contact with ASP 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 4.5 6.3 - - - +
49A VAL* 3.9 26.1 - - + +
244A PHE* 3.4 17.0 - - - -
248A PHE 2.7 22.5 + - - +
249A ILE* 3.6 8.3 + - + +
251A LYS* 1.3 73.7 - - - +
253A VAL* 1.3 53.4 + - + +
255A ALA* 3.2 5.3 + - - +
256A LEU* 2.7 39.2 + - + +
504A ANJ 2.8 52.8 + - + +
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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
----------------------------------------------------------
249A ILE* 3.0 24.0 - - + +
250A ILE* 2.9 8.8 + - + +
252A ASP* 1.3 75.8 - - + +
254A PHE* 1.3 64.9 + - - +
256A LEU* 3.2 15.4 + - + +
257A ALA* 2.9 22.5 + - - +
244B LEU* 3.6 29.2 - - + -
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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
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43A TRP* 3.6 37.2 - + - -
250A ILE 2.5 17.2 + - - +
251A LYS* 3.2 9.4 - - - +
253A VAL* 1.3 76.9 - - - +
255A ALA* 1.3 65.3 + - - +
257A ALA* 3.0 14.2 + - - +
258A VAL* 3.3 27.8 + - + -
241B SER* 3.9 19.7 - - - -
244B LEU* 4.1 25.5 - - + +
245B TYR* 3.9 39.3 - + + -
248B ASN* 4.5 13.9 - - + -
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Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TRP* 4.4 8.3 - - + -
46A ILE* 3.6 41.1 - - + -
50A VAL* 6.0 0.4 - - + -
251A LYS 2.8 18.6 + - - +
252A ASP 3.6 3.6 - - - +
254A PHE* 1.3 76.2 - - - +
256A LEU* 1.3 64.9 + - - +
258A VAL* 2.7 24.7 + - - +
259A VAL* 2.9 16.6 + - + +
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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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49A VAL* 3.3 31.4 - - + -
50A VAL* 4.1 21.5 - - + +
53A PHE* 4.1 34.3 - - + -
252A ASP 2.7 20.8 + - - +
253A VAL* 3.3 15.9 - - + +
255A ALA* 1.3 72.4 - - - +
257A ALA* 1.3 57.2 + - - +
259A VAL* 3.6 6.1 - - + +
260A LEU* 3.0 42.2 + - + +
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Residues in contact with ALA 257 (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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253A VAL 2.9 11.2 + - - +
254A PHE 3.1 10.8 - - - +
255A ALA 2.8 1.2 + - - -
256A LEU* 1.3 74.7 - - - +
258A VAL* 1.3 54.9 + - - +
260A LEU* 3.1 6.4 + - - +
261A LEU* 2.8 34.7 + - - +
237B LEU* 4.0 17.6 - - + +
240B LEU* 4.8 3.6 - - + -
241B SER* 3.9 19.5 - - - +
244B LEU* 4.0 19.7 - - + -
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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* 3.4 44.6 - - + +
255A ALA* 2.7 14.5 + - - +
257A ALA* 1.3 72.6 - - - +
259A VAL* 1.3 65.1 + - + +
261A LEU* 3.1 27.9 - - + +
262A VAL* 3.2 14.7 + - + +
241B SER* 4.1 11.2 + - - +
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Residues in contact with VAL 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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46A ILE* 4.6 9.6 - - + -
47A TRP* 5.1 6.7 - - + -
50A VAL* 4.0 36.3 - - + -
103A LEU* 4.1 22.9 - - + -
255A ALA 2.9 20.4 + - - +
256A LEU* 3.6 10.5 - - + +
258A VAL* 1.3 77.4 - - + +
260A LEU* 1.3 56.4 + - + +
262A VAL* 3.0 11.3 + - - +
263A PHE* 2.8 31.6 + - - +
503A LOP 4.4 14.8 - - + +
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Residues in contact with LEU 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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53A PHE* 3.3 54.7 - - + -
103A LEU* 4.9 5.2 - - + -
256A LEU* 3.0 27.2 + - + +
257A ALA* 3.1 5.1 + - - +
259A VAL* 1.3 81.4 - - + +
261A LEU* 1.3 55.4 + - - +
263A PHE* 3.8 19.5 - - + -
264A PHE* 2.7 54.8 + - + -
237B LEU* 4.1 15.0 - - + -
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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 ALA 2.8 12.3 + - - +
258A VAL* 3.1 20.0 - - + +
259A VAL 3.1 0.4 - - - -
260A LEU* 1.3 76.6 - - - +
262A VAL* 1.3 66.6 + - + +
264A PHE* 3.9 2.1 - - - +
265A ALA* 3.0 24.3 + - + +
234B VAL* 3.5 43.3 - - + +
237B LEU* 4.1 13.6 - - + +
238B THR* 3.7 22.2 - - + +
241B SER* 4.1 16.2 - - - +
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Residues in contact with VAL 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* 3.4 21.1 - - + +
259A VAL* 3.0 6.2 + - - +
261A LEU* 1.3 77.9 - - + +
263A PHE* 1.3 67.6 + - - +
265A ALA* 3.1 15.7 - - - +
266A ILE* 3.1 26.3 - - + +
431A BGL 4.0 24.5 - - + -
503A LOP 4.3 24.0 - - + -
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Residues in contact with PHE 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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53A PHE* 5.2 0.2 - + - -
57A LEU* 3.8 21.1 - - + -
96A LEU* 3.4 46.7 - - + -
99A ASN* 3.7 26.0 - - + -
100A GLY* 4.2 3.6 - - - -
103A LEU* 4.1 14.4 - - + -
259A VAL 2.8 17.0 + - - +
260A LEU* 3.2 28.7 + - + +
262A VAL* 1.3 72.2 - - - +
264A PHE* 1.3 71.8 + + - +
266A ILE* 3.0 12.8 + - - +
267A VAL* 2.9 32.9 + - + +
503A LOP 3.5 30.6 - - + +
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Residues in contact with PHE 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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53A PHE* 5.6 3.4 - + - -
92A MET* 4.5 18.8 - - + -
96A LEU* 4.2 27.6 - - + -
260A LEU* 2.7 47.2 + - + +
261A LEU 3.9 2.7 - - - +
263A PHE* 1.3 80.3 - + - +
265A ALA* 1.3 55.9 + - - +
267A VAL* 3.7 6.5 - - + +
268A GLY* 2.6 35.2 + - - -
230B GLY* 5.3 2.5 - - - -
233B ALA* 3.7 32.1 - - + -
234B VAL* 5.2 2.7 - - + +
237B LEU* 3.6 20.4 - - + -
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Residues in contact with ALA 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* 3.0 17.4 + - + +
262A VAL* 3.1 16.2 - - - +
264A PHE* 1.3 75.1 - - - +
266A ILE* 1.3 52.6 + - - +
269A PHE* 2.8 53.8 + - + +
270A MET* 4.7 0.3 - - - +
431A BGL 4.5 23.7 - - + +
234B VAL* 4.6 10.0 - - + +
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Residues in contact with ILE 266 (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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99A ASN* 4.1 15.9 - - - +
262A VAL* 3.1 24.0 - - + +
263A PHE 3.0 6.9 + - - +
265A ALA* 1.3 73.1 - - - +
267A VAL* 1.3 60.6 + - + +
268A GLY 3.0 4.3 - - - -
270A MET* 2.6 79.3 + - + +
271A PRO 2.9 0.3 - - - -
273A TYR* 5.4 0.9 - - + -
274A LEU* 5.1 9.0 - - + -
431A BGL 4.3 16.8 - - + -
503A LOP 4.2 25.4 - - + -
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Residues in contact with VAL 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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92A MET* 4.3 12.9 - - + +
95A TYR* 3.9 27.3 - - + +
96A LEU* 4.0 25.8 - - + +
99A ASN* 4.3 7.6 - - + +
263A PHE* 2.9 52.7 + - + +
264A PHE* 3.7 10.8 - - + +
266A ILE* 1.3 74.2 - - + +
268A GLY* 1.3 62.1 + - - +
271A PRO* 3.8 18.4 - - - +
226B ARG* 4.0 11.1 - - - +
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Residues in contact with GLY 268 (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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92A MET* 5.2 4.0 - - - -
264A PHE 2.6 20.5 + - - -
265A ALA 3.9 0.2 - - - -
267A VAL* 1.3 76.0 - - - +
269A PHE* 1.3 63.6 + - - +
226B ARG* 3.0 44.9 + - - +
227B LYS* 4.2 5.4 - - - +
230B GLY* 4.4 12.6 - - - -
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Residues in contact with PHE 269 (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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265A ALA* 2.8 36.0 + - + +
268A GLY* 1.3 76.4 - - - +
270A MET* 1.3 57.5 + - - +
271A PRO* 3.5 5.7 - - - +
431A BGL 2.6 62.3 + - + +
16B PRO* 3.6 44.0 - - + -
226B ARG* 3.9 4.8 + - - +
227B LYS* 4.0 21.8 - - + -
230B GLY* 4.2 5.4 - - - -
231B PHE* 3.9 30.5 - + - -
234B VAL* 4.2 22.4 - - + -
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Residues in contact with MET 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASN* 4.7 0.2 - - - +
266A ILE* 2.6 52.1 + - + +
269A PHE* 1.3 77.7 - - + +
271A PRO* 1.3 64.8 - - - +
272A ASN 3.3 2.7 - - - +
273A TYR* 3.2 43.9 + - + +
431A BGL 3.8 42.2 - - + +
121B LEU* 3.6 38.8 - - + +
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il