Contacts of the helix formed by residues 238 - 261 (chain A) in PDB entry 2WWB
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 ASN 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A LEU* 3.1 42.3 + - - +
217A PHE* 3.6 26.3 - - + +
220A LEU* 3.9 20.3 - - - +
228A ARG* 3.2 43.4 + - - +
237A GLN* 1.4 87.2 + - - +
239A LEU* 1.4 60.3 + - - +
240A PRO* 3.5 4.5 - - - +
241A ASN 3.5 3.1 + - - -
242A LEU* 3.1 25.4 + - + +
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Residues in contact with LEU 239 (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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228A ARG* 4.4 1.6 - - - +
235A TYR* 4.2 24.7 - - + -
236A ARG* 3.5 52.4 - - + +
237A GLN 3.9 0.6 - - - +
238A ASN* 1.4 76.9 - - - +
240A PRO* 1.3 68.8 - - + +
242A LEU* 3.9 24.0 - - + -
243A MET* 3.0 44.0 + - + +
246A ILE* 5.7 4.7 - - + -
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Residues in contact with PRO 240 (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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199A THR* 4.2 19.3 - - + +
216A LEU* 3.9 16.4 - - + -
236A ARG* 3.5 30.1 - - - +
237A GLN* 5.0 1.1 - - - +
238A ASN 3.6 6.1 - - - +
239A LEU* 1.3 90.5 - - + +
241A ASN* 1.4 58.7 + - - +
243A MET* 3.7 13.0 - - + +
244A ASN* 3.2 14.7 + - - +
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Residues in contact with ASN 241 (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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194A LYS 3.5 12.0 - - - +
195A ALA* 3.4 26.4 + - - +
197A SER 3.2 23.6 + - - +
199A THR* 3.3 17.2 + - - +
215A ALA* 3.8 2.8 - - - +
216A LEU* 3.5 38.1 - - + +
217A PHE* 3.7 15.7 - - + -
238A ASN 3.5 2.0 + - - +
239A LEU 3.3 0.4 - - - -
240A PRO* 1.4 77.3 - - - +
242A LEU* 1.4 61.6 + - - +
243A MET 3.3 0.7 - - - -
244A ASN* 3.4 18.7 + - - +
245A LEU* 3.7 15.4 + - - +
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Residues in contact with LEU 242 (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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217A PHE* 4.0 14.1 - - + -
228A ARG* 5.3 9.9 - - - +
235A TYR* 4.7 16.4 - - + -
238A ASN* 3.1 20.0 + - + +
239A LEU* 3.7 26.7 - - + +
241A ASN* 1.4 76.2 - - - +
243A MET* 1.4 58.5 + - - +
244A ASN 3.3 0.2 - - - -
245A LEU* 3.4 16.2 + - + +
246A ILE* 3.1 44.2 + - + +
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Residues in contact with MET 243 (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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236A ARG* 5.0 10.1 - - - +
239A LEU* 3.0 42.0 + - + +
240A PRO* 3.7 10.3 - - + +
241A ASN 3.3 0.2 - - - -
242A LEU* 1.4 75.9 - - - +
244A ASN* 1.4 58.7 + - - +
246A ILE* 3.5 17.7 - - + +
247A ALA* 3.1 27.9 + - - +
351A PHE* 6.1 4.5 - - + +
353A SER* 5.5 6.5 - - - +
438A LEU 4.0 8.1 - - - +
439A GLY* 4.0 24.5 - - - -
440A ALA 4.2 8.1 + - - +
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Residues in contact with ASN 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE* 4.9 5.3 - - - +
194A LYS* 3.2 43.9 - - + +
195A ALA* 4.4 6.3 - - - +
240A PRO 3.2 19.8 + - - +
241A ASN* 3.4 11.4 - - - +
242A LEU 3.3 0.2 - - - -
243A MET* 1.4 79.0 - - - +
245A LEU* 1.4 59.8 + - - +
247A ALA* 3.4 14.4 - - - +
248A THR* 3.4 11.3 + - - -
440A ALA 3.2 22.3 + - - -
441A ILE* 3.8 21.8 - - + +
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Residues in contact with LEU 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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191A ILE* 5.2 7.0 - - + +
195A ALA* 3.6 25.6 - - + -
196A PHE* 5.6 4.9 - - + -
217A PHE* 3.8 31.0 - - + -
241A ASN 3.7 8.9 + - - +
242A LEU* 3.4 17.4 + - + +
243A MET 3.3 0.4 - - - -
244A ASN* 1.4 75.8 - - - +
246A ILE* 1.4 63.9 + - + +
247A ALA 3.2 0.9 + - - -
248A THR* 3.4 16.4 + - - -
249A ILE* 3.5 21.0 + - + +
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Residues in contact with ILE 246 (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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239A LEU* 5.7 4.7 - - + -
242A LEU* 3.1 34.7 + - + +
243A MET* 3.5 33.4 - - + +
245A LEU* 1.4 74.2 - - + +
247A ALA* 1.4 61.3 - - - +
248A THR 3.3 0.2 - - - -
249A ILE* 3.3 21.3 + - + +
250A PHE* 2.9 54.6 + - + -
438A LEU 4.6 1.6 - - - +
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Residues in contact with ALA 247 (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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243A MET 3.1 11.0 + - - +
244A ASN 3.4 13.7 - - - +
245A LEU 3.2 0.2 - - - -
246A ILE* 1.4 78.3 - - - +
248A THR* 1.4 59.7 + - - +
250A PHE* 3.7 9.3 + - - +
251A VAL* 3.4 25.5 + - - +
435A ALA 5.7 0.2 - - - +
439A GLY 3.4 35.3 - - - +
440A ALA* 3.5 7.0 - - - +
441A ILE* 4.3 0.2 - - + -
447A ILE* 3.6 18.1 - - + +
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Residues in contact with THR 248 (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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191A ILE* 3.6 32.7 - - + +
244A ASN 3.4 13.7 + - - -
245A LEU* 3.4 8.4 + - - -
246A ILE 3.3 0.2 - - - -
247A ALA* 1.4 77.2 - - - +
249A ILE* 1.4 58.5 + - - +
251A VAL* 3.3 3.9 + - + +
252A PHE* 3.0 34.6 + - + +
441A ILE* 4.9 1.2 - - - +
447A ILE* 4.5 20.3 - - + +
451A VAL* 5.9 4.7 - - + -
44B PHE* 4.7 14.1 - - + -
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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
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245A LEU* 3.5 20.2 - - + +
246A ILE* 3.3 25.7 + - + +
248A THR* 1.4 74.3 - - - +
250A PHE* 1.4 66.8 + - + +
252A PHE* 3.6 18.9 + - + +
253A ALA* 4.1 6.8 + - - +
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Residues in contact with PHE 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 ILE* 2.9 50.8 + - + -
247A ALA* 3.9 11.4 - - - +
248A THR 3.4 0.2 - - - -
249A ILE* 1.4 80.0 - - + +
251A VAL* 1.4 64.6 + - + +
252A PHE 3.6 0.2 + - - -
253A ALA* 4.1 5.9 + - - +
254A VAL* 3.9 16.8 - - - +
435A ALA* 5.7 2.0 - - - -
438A LEU* 3.4 68.6 - - + -
439A GLY 4.2 0.9 - - - -
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Residues in contact with VAL 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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247A ALA 3.4 16.2 - - - +
248A THR* 3.3 8.0 + - + +
250A PHE* 1.4 76.6 - - + +
252A PHE* 1.4 63.5 + - - +
254A VAL* 3.3 23.2 + - - +
255A VAL* 3.3 6.9 + - - +
435A ALA* 4.6 20.0 - - + +
447A ILE* 4.2 25.6 - - + +
448A LEU* 4.0 24.2 - - + +
451A VAL* 3.7 31.6 - - + -
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Residues in contact with PHE 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 THR* 3.0 22.8 + - + +
249A ILE* 3.7 12.6 - - + +
250A PHE 3.4 0.6 - - - -
251A VAL* 1.4 75.3 - - - +
253A ALA* 1.3 67.0 + - + +
255A VAL* 3.3 20.0 - - + +
256A ILE* 3.8 27.6 - - + +
451A VAL* 5.8 5.6 - - + -
455A TYR* 4.2 22.7 - + - -
37B ALA* 5.8 8.3 - - + -
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Residues in contact with ALA 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 ILE 4.1 6.0 + - - +
250A PHE 4.6 4.5 - - - +
251A VAL 3.4 0.6 - - - -
252A PHE* 1.3 83.5 - - + +
254A VAL* 1.4 66.4 + - + +
256A ILE* 3.3 26.2 - - - +
257A TYR* 3.8 21.9 - - + +
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Residues in contact with VAL 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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250A PHE 3.9 13.2 - - - +
251A VAL* 3.3 18.6 - - - +
253A ALA* 1.4 80.0 - - + +
255A VAL* 1.4 64.1 + - - +
257A TYR* 3.6 14.0 + - + +
258A PHE* 3.0 48.1 + - + -
431A LEU* 4.5 16.4 - - + -
448A LEU* 5.1 4.9 - - + -
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Residues in contact with VAL 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 VAL* 3.3 14.6 + - + +
252A PHE* 3.3 24.0 - - + +
254A VAL* 1.4 77.0 - - - +
256A ILE* 1.4 62.0 + - + +
258A PHE* 3.1 14.0 + - + +
259A GLN* 3.0 44.9 + - + +
448A LEU* 5.2 5.4 - - + -
451A VAL* 3.8 47.3 - - + +
452A THR* 4.4 9.9 - - + +
455A TYR* 5.7 2.9 - - + -
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Residues in contact with ILE 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 PHE* 3.8 33.2 - - + +
253A ALA* 3.3 22.2 - - - +
255A VAL* 1.4 77.0 - - + +
257A TYR* 1.4 72.0 + - + +
259A GLN* 3.5 18.7 + - - +
260A GLY 3.2 15.8 + - - -
455A TYR* 5.2 12.3 - - + -
28B PRO* 3.4 14.4 - - + +
33B PHE* 4.7 18.8 - - + -
36B ILE* 4.0 26.7 - - + -
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Residues in contact with TYR 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 ALA* 3.8 23.9 - - + +
254A VAL* 3.6 15.0 + - + +
255A VAL 3.3 0.6 - - - -
256A ILE* 1.4 82.7 - - + +
258A PHE* 1.4 60.0 + + + +
260A GLY* 3.2 3.1 + - - -
261A PHE* 2.9 55.9 + + + -
26B THR 4.4 0.3 - - - +
27B LYS* 3.3 52.5 + - + -
28B PRO* 4.4 4.3 - - + -
33B PHE* 4.2 16.4 - + - -
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Residues in contact with PHE 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 VAL* 3.0 34.1 + - + -
255A VAL* 3.1 11.5 + - + +
257A TYR* 1.4 76.4 - + + +
259A GLN* 1.4 59.3 + - + +
261A PHE* 2.8 45.5 - + - +
284A PHE* 3.3 50.9 - + + +
427A CYS* 6.5 0.7 - - + -
428A ILE* 6.5 0.4 - - + -
431A LEU* 3.7 35.2 - - + -
448A LEU* 5.9 2.0 - - + -
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Residues in contact with GLN 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 VAL* 3.0 34.7 + - + +
256A ILE* 3.8 18.3 - - - +
257A TYR 3.4 0.2 - - - -
258A PHE* 1.4 75.7 - - + +
260A GLY* 1.4 60.4 + - - +
262A ARG* 3.5 21.7 + - - +
451A VAL 5.1 1.1 - - - -
452A THR* 5.4 5.8 - - + +
455A TYR* 3.4 33.4 - - - +
456A GLN* 3.7 29.8 + - + +
459A GLU* 3.4 24.4 + - - -
28B PRO* 5.8 1.1 - - + -
36B ILE* 5.3 8.5 - - + +
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Residues in contact with GLY 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 ILE 3.2 13.7 + - - -
257A TYR 3.2 4.7 + - - -
259A GLN* 1.4 75.1 - - - +
261A PHE* 1.4 60.8 + - - +
262A ARG* 3.3 26.9 + - - -
25B CYS* 5.6 0.2 - - - -
26B THR* 3.0 23.9 + - - +
27B LYS 4.6 0.4 - - - -
28B PRO* 4.1 15.8 - - - +
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Residues in contact with PHE 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 TYR* 2.9 44.9 + + + +
258A PHE* 2.8 50.0 + + - +
260A GLY* 1.4 73.3 - - - +
262A ARG* 1.3 64.6 + - - +
283A LEU* 3.9 17.1 + - + +
284A PHE* 4.0 10.3 - + + -
21B LEU* 5.9 7.0 - - + -
25B CYS* 3.9 22.2 - - + -
26B THR* 3.4 33.4 - - - -
27B LYS* 4.0 8.5 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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