Contacts of the helix formed by residues 236 - 269 (chain A) in PDB entry 4YAY
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 ASP 236 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LEU* 3.9 30.0 - - + +
235A ASN* 1.4 75.7 + - - +
237A ASP* 1.4 74.7 + - - +
238A ILE 3.2 0.2 - - - -
239A PHE* 3.1 9.5 + - - +
240A LYS* 2.8 45.1 + - + +
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Residues in contact with ASP 237 (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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235A ASN 3.5 2.9 - - - +
236A ASP* 1.4 91.5 + - - +
238A ILE* 1.3 64.1 + - + +
240A LYS* 3.2 31.9 + - - +
241A ILE* 3.2 30.4 + - + +
304A PHE* 3.3 23.7 - - - +
305A LEU* 5.3 6.1 - - + -
308A LYS* 5.5 6.6 - - - +
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Residues in contact with ILE 238 (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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57A MET* 5.7 11.7 - - + -
61A THR* 5.2 12.1 - - + +
63A ALA* 4.0 16.2 - - + -
67A LEU* 4.0 22.0 - - + -
126A ARG* 4.6 7.4 - - - +
235A ASN* 3.5 30.0 + - - +
236A ASP 3.2 0.2 - - - -
237A ASP* 1.3 75.1 - - + +
239A PHE* 1.4 53.0 + - - +
241A ILE* 3.0 12.6 + - + +
242A ILE* 2.8 58.1 + - + +
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Residues in contact with PHE 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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126A ARG* 3.9 20.2 - - + +
130A ILE* 5.4 0.9 - - + -
215A TYR* 3.9 7.2 - + - -
218A ILE* 3.3 38.1 - - + -
219A TRP* 3.7 47.8 - + + -
222A LEU* 3.7 28.5 - - + -
235A ASN 3.0 20.4 + - - +
236A ASP* 3.1 7.4 + - - +
238A ILE* 1.4 74.4 - - - +
240A LYS* 1.4 58.7 + - + +
242A ILE* 3.7 2.3 - - - +
243A MET* 2.8 66.7 + - + +
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Residues in contact with LYS 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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222A LEU* 6.4 0.4 - - + -
236A ASP* 2.8 22.7 + - + +
237A ASP* 3.2 41.2 + - - +
239A PHE* 1.4 75.3 - - + +
241A ILE* 1.3 59.8 + - - +
243A MET* 3.8 5.2 - - - +
244A ALA* 3.0 31.4 + - - +
304A PHE* 3.7 43.0 + - + +
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Residues in contact with ILE 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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57A MET* 5.3 7.0 - - + -
67A LEU* 4.3 11.7 - - + -
237A ASP 3.2 17.7 + - - +
238A ILE* 3.0 13.8 + - + +
240A LYS* 1.3 75.6 - - - +
242A ILE* 1.3 57.2 + - - +
244A ALA* 3.3 3.0 + - - +
245A ILE* 3.0 53.1 + - + +
301A PHE 3.3 24.0 - - - +
302A TYR* 4.1 42.6 - - + +
304A PHE* 4.1 10.1 - - + -
305A LEU* 4.4 17.7 - - + -
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Residues in contact with ILE 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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63A ALA* 4.6 2.0 - - + -
67A LEU* 4.4 12.1 - - + -
119A LEU* 5.0 1.3 - - + +
122A LEU* 3.7 48.5 - - + +
125A ASP* 5.4 0.2 - - - +
126A ARG* 3.7 26.7 - - + +
215A TYR* 2.9 33.7 - - + +
238A ILE* 2.8 40.6 + - + +
239A PHE* 4.0 4.7 - - - +
241A ILE* 1.3 70.8 - - - +
243A MET* 1.3 55.5 - - - +
245A ILE* 3.6 6.8 + - - +
246A VAL* 3.1 31.7 + - + +
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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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215A TYR* 4.2 25.1 - - + -
219A TRP* 4.3 27.8 - - + -
239A PHE* 2.8 53.6 + - + +
240A LYS* 3.8 6.5 - - - +
242A ILE* 1.3 72.1 - - - +
244A ALA* 1.3 58.7 + - - +
246A VAL* 3.4 3.9 + - - +
247A LEU* 2.9 57.4 + - + +
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Residues in contact with ALA 244 (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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240A LYS 3.0 19.0 + - - +
241A ILE 3.3 3.8 + - - +
243A MET* 1.3 72.1 - - - +
245A ILE* 1.3 64.9 + - - +
247A LEU* 4.3 4.4 - - - +
248A PHE* 3.1 27.5 + - - +
301A PHE* 3.5 34.0 - - + -
304A PHE* 4.2 13.5 - - + -
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Residues in contact with ILE 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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67A LEU* 4.3 11.7 - - + -
70A LEU* 3.8 17.7 - - + -
119A LEU* 3.6 23.3 - - + -
122A LEU* 6.1 0.7 - - + -
241A ILE* 3.0 37.7 + - + +
242A ILE* 4.1 5.6 - - - +
244A ALA* 1.3 75.5 - - - +
246A VAL* 1.3 56.8 + - - +
248A PHE* 4.4 0.3 - - - +
249A PHE* 3.1 32.6 + - + +
298A ASN* 3.4 33.7 - - + +
301A PHE* 3.8 24.7 - - + -
302A TYR* 4.5 11.9 - - + -
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Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.7 33.7 - - + +
123A SER* 4.3 0.4 - - - +
211A ILE* 3.6 16.8 - - + -
215A TYR* 3.4 41.1 - - + +
242A ILE* 3.1 22.0 + - + +
243A MET* 3.8 4.0 - - - +
245A ILE* 1.3 74.2 - - - +
247A LEU* 1.4 71.8 + - + +
249A PHE* 3.6 2.7 + - - +
250A PHE* 3.3 34.9 + - + -
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Residues in contact with LEU 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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215A TYR* 6.2 0.9 - - + -
243A MET* 2.9 48.9 + - + +
244A ALA* 4.3 4.7 - - - +
246A VAL* 1.4 77.3 - - + +
248A PHE* 1.3 66.3 + - - +
250A PHE* 4.3 1.3 - - - +
251A PHE* 3.0 53.3 + - + -
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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
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244A ALA 3.1 19.6 + - - +
245A ILE 4.4 0.4 - - - +
247A LEU* 1.3 72.3 - - - +
249A PHE* 1.4 67.2 + - - +
251A PHE* 3.3 5.9 + - + +
252A SER* 3.1 42.3 + - - -
290A ILE* 4.8 4.0 - - + -
293A PHE* 4.4 16.6 - + + -
294A ASN* 3.7 39.7 - - + -
297A LEU* 3.6 31.4 - - + -
298A ASN* 5.1 0.7 - - - -
301A PHE* 3.7 16.2 - + + -
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Residues in contact with PHE 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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70A LEU* 6.5 0.4 - - + -
111A ASN* 5.2 2.9 - - - -
112A LEU* 4.1 9.4 - - + -
115A SER* 3.6 31.6 - - - -
116A VAL* 3.7 28.7 - - + -
119A LEU* 3.7 22.0 - - + -
204A PHE* 5.5 0.9 - + - -
245A ILE* 3.1 22.4 + - + +
246A VAL* 3.8 4.5 - - - +
247A LEU 3.5 0.2 - - - -
248A PHE* 1.4 79.1 - - - +
250A PHE* 1.3 78.0 + + - +
252A SER* 3.0 18.5 + - - -
253A TRP* 3.1 47.5 + + - -
294A ASN* 3.7 29.2 - - + -
298A ASN* 5.8 2.2 - - - -
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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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116A VAL* 4.9 9.2 - - + -
119A LEU* 5.4 2.2 - - + -
204A PHE* 3.5 41.0 - + + -
207A PRO* 5.3 1.6 - - + -
208A PHE* 3.9 37.9 - + + -
211A ILE* 3.7 40.4 - - + -
246A VAL* 3.3 32.0 + - + +
247A LEU* 4.5 2.5 - - - +
248A PHE 3.3 0.4 - - - -
249A PHE* 1.3 96.6 - + - +
251A PHE* 1.3 64.5 + - + +
252A SER 3.2 1.1 + - - -
253A TRP* 3.5 8.8 + - - +
254A ILE* 3.4 21.0 + - - +
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Residues in contact with PHE 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 LEU* 3.0 50.8 + - + +
248A PHE* 3.3 5.8 + - + +
250A PHE* 1.3 76.8 - - + +
252A SER* 1.4 57.3 + - - +
253A TRP 3.5 0.2 - - - -
254A ILE* 3.7 27.5 - - + +
255A PRO* 3.9 13.0 - - - +
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Residues in contact with SER 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 PHE* 3.1 30.9 + - - -
249A PHE* 3.0 18.0 + - - -
251A PHE* 1.4 75.2 - - - +
253A TRP* 1.4 63.1 + - - +
254A ILE 3.5 0.9 - - - -
255A PRO* 3.6 11.0 - - - +
256A HIS 4.9 0.2 + - - -
287A THR 4.5 1.6 - - - +
290A ILE* 3.3 37.3 + - - +
291A ALA* 3.5 23.8 + - - +
294A ASN* 4.7 2.8 + - - -
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Residues in contact with TRP 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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112A LEU* 3.4 36.8 - - + -
204A PHE* 3.7 24.2 - + + -
249A PHE* 3.1 53.6 + + - +
250A PHE 3.5 2.3 + - - +
252A SER* 1.4 80.2 + - - +
254A ILE* 1.4 57.4 - - - +
255A PRO 3.5 0.4 - - - -
256A HIS* 3.4 29.6 + + - +
257A GLN* 2.9 44.5 + - - +
291A ALA* 3.0 38.9 + - + -
292A TYR* 3.5 38.4 - + - -
1201A ZD7 5.0 4.5 - + - -
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Residues in contact with ILE 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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204A PHE* 5.1 8.0 - - + -
250A PHE 3.4 14.6 - - - +
251A PHE* 3.7 39.0 - - + +
253A TRP* 1.4 72.9 - - - +
255A PRO* 1.4 75.2 - - + +
257A GLN* 2.9 19.0 + - + +
258A ILE* 3.2 28.9 + - + +
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Residues in contact with PRO 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 PHE 3.9 10.3 - - - +
252A SER 3.6 16.8 - - - +
254A ILE* 1.4 91.9 - - + +
256A HIS* 1.4 61.5 + - - +
258A ILE* 3.3 17.3 + - + +
259A PHE* 3.3 24.0 - - + -
287A THR* 3.9 23.8 - - + -
290A ILE* 5.1 14.6 - - + -
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Residues in contact with HIS 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 SER 4.9 0.2 + - - -
253A TRP* 3.4 29.9 + + + +
254A ILE 3.3 0.6 - - - -
255A PRO* 1.4 78.6 - - - +
257A GLN* 1.3 54.2 + - - +
259A PHE* 3.8 1.0 - - - +
260A THR* 2.5 60.5 + - + +
284A MET* 3.7 31.0 - - + +
287A THR* 2.7 41.0 + - - +
288A ILE* 3.4 39.1 + - + +
291A ALA* 4.1 9.0 - - + -
1201A ZD7 5.8 1.8 - - - -
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Residues in contact with GLN 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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200A ASN* 4.6 12.6 + - - +
204A PHE* 3.3 53.4 - - + +
253A TRP* 2.9 30.8 + - - +
254A ILE* 2.9 13.9 + - + +
256A HIS* 1.3 75.9 - - - +
258A ILE* 1.4 63.7 + - + +
260A THR* 4.0 5.3 - - - -
261A PHE* 3.4 20.3 + - - +
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Residues in contact with ILE 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 ILE* 3.2 33.1 + - + +
255A PRO* 3.3 13.0 + - + +
257A GLN* 1.4 75.4 - - + +
259A PHE* 1.4 69.3 + - + +
261A PHE* 3.4 8.3 + - - +
262A LEU* 3.1 41.5 + - + +
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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 PRO* 3.3 27.1 + - + +
256A HIS 4.2 2.5 - - - +
258A ILE* 1.4 86.1 - - + +
260A THR* 1.4 55.7 + - - +
262A LEU* 3.3 15.4 + - + +
263A ASP* 2.8 34.9 + - - +
279A ILE* 4.0 18.2 - - + -
280A VAL* 3.7 32.7 - - + +
283A ALA* 3.7 27.8 - - + -
284A MET* 4.1 17.4 - - + +
287A THR* 3.9 18.2 - - + +
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Residues in contact with THR 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 HIS* 2.5 50.9 + - + +
257A GLN* 4.0 6.3 - - - -
259A PHE* 1.4 74.9 - - - +
261A PHE* 1.4 59.9 - - - +
263A ASP* 3.3 9.4 + - + +
264A VAL* 3.1 32.7 + - + +
284A MET* 4.7 8.3 - - + +
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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 GLN 3.4 10.1 + - - +
258A ILE* 3.4 9.6 + - - +
259A PHE 3.3 0.2 - - - -
260A THR* 1.4 77.2 - - - +
262A LEU* 1.4 69.7 + - + +
264A VAL* 3.2 18.6 + - + +
265A LEU* 3.2 50.6 + - + +
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Residues in contact with LEU 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 ILE* 3.1 31.4 + - + +
259A PHE* 3.3 23.8 + - + +
261A PHE* 1.4 80.5 - - + +
263A ASP* 1.4 62.3 + - - +
265A LEU* 3.3 31.4 + - + +
266A ILE* 3.3 20.8 + - - +
271A ILE* 5.0 10.1 - - + +
276A ILE* 5.6 5.2 - - + -
280A VAL* 4.0 24.2 - - + -
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Residues in contact with ASP 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PHE 2.8 19.7 + - - +
260A THR* 3.3 9.3 + - - +
262A LEU* 1.4 68.1 - - - +
264A VAL* 1.4 60.2 + - - +
266A ILE* 3.2 16.9 + - - +
267A GLN* 3.1 49.7 + - - +
280A VAL* 3.9 3.1 - - + +
281A ASP* 4.4 14.4 - - - +
284A MET* 3.8 28.1 - - - +
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Residues in contact with VAL 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A PRO 6.2 0.9 - - - +
193A ILE* 6.0 7.0 - - + -
196A GLY* 6.6 0.4 - - - -
260A THR* 3.1 21.6 + - + +
261A PHE* 3.2 19.9 + - + +
263A ASP* 1.4 76.0 - - + +
265A LEU* 1.4 57.6 + - + +
267A GLN* 3.2 17.9 + - + +
268A LEU* 3.0 54.0 + - + +
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Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A PHE* 3.2 46.3 + - + +
262A LEU* 3.3 22.2 + - + +
264A VAL* 1.4 76.5 - - + +
266A ILE* 1.4 60.2 + - - +
268A LEU* 4.5 5.8 - - + -
269A GLY 3.4 1.6 + - - -
270A ILE* 3.1 60.7 + - + -
271A ILE* 3.2 35.8 + - + -
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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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18A CYS* 5.9 4.0 - - + -
262A LEU 3.4 15.9 - - - +
263A ASP* 3.2 13.8 + - - +
265A LEU* 1.4 78.8 - - - +
267A GLN* 1.4 62.5 + - + +
268A LEU 3.4 1.0 + - - -
269A GLY* 3.7 9.5 + - - -
271A ILE* 3.6 27.0 - - + +
272A ARG* 5.9 0.5 - - - -
276A ILE* 5.1 1.8 - - + -
277A ALA* 3.8 33.7 - - + -
280A VAL* 3.8 34.3 - - + -
281A ASP* 4.4 8.1 - - - +
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Residues in contact with GLN 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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184A TYR* 3.7 37.9 + - + -
263A ASP* 3.1 40.8 + - - +
264A VAL* 3.6 21.9 - - - +
266A ILE* 1.4 77.3 - - + +
268A LEU* 1.4 60.2 + - + +
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Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A THR 5.2 10.3 - - - +
192A PRO* 6.2 3.8 - - + -
193A ILE* 5.1 23.3 - - + +
264A VAL* 3.0 39.1 + - + +
265A LEU* 4.3 5.2 - - + +
266A ILE 3.3 0.6 - - - -
267A GLN* 1.4 80.4 - - + +
269A GLY* 1.3 59.1 + - - +
270A ILE* 4.0 29.6 - - + -
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Residues in contact with GLY 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LEU 3.4 4.9 + - - -
266A ILE 3.7 7.6 + - - -
268A LEU* 1.3 77.6 - - - +
270A ILE* 1.3 67.9 + - - +
271A ILE 3.5 4.0 - - - -
272A ARG* 4.5 15.8 - - - +
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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
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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