Contacts of the helix formed by residues 226 - 251 (chain A) in PDB entry 6FWF
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 THR 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A THR* 5.2 3.1 + - - -
209A PHE* 3.9 32.9 - - + -
213A ASN* 5.7 1.8 - - + +
214A ASN* 3.7 13.5 - - - +
224A VAL 3.5 0.8 + - - -
225A PRO* 1.3 72.7 - - - +
227A THR* 1.3 73.9 + - - +
228A GLU* 3.5 24.8 + - + +
229A ASN* 2.9 29.2 + - - +
230A TYR* 3.1 20.8 - - - -
553A MET* 5.2 3.8 - - + -
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Residues in contact with THR 227 (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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226A THR* 1.3 82.9 + - - +
228A GLU* 1.3 58.8 + - - +
229A ASN 3.2 0.3 + - - -
230A TYR* 3.4 26.0 + - + +
231A MET* 2.8 50.5 + - + +
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Residues in contact with GLU 228 (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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207A GLU* 4.5 6.1 - - - +
209A PHE* 4.0 19.2 - - - -
226A THR* 3.5 21.7 + - + +
227A THR* 1.3 79.4 + - - +
229A ASN* 1.3 57.3 + - - +
231A MET* 4.0 22.0 - - + -
232A TRP* 2.8 45.1 + - + +
550A SER* 3.5 27.7 + - - +
553A MET* 4.5 11.9 - - + -
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Residues in contact with ASN 229 (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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213A ASN* 4.8 7.3 - - - +
214A ASN* 4.8 1.6 + - - -
225A PRO* 3.3 21.6 - - + +
226A THR* 2.9 36.9 + - - +
227A THR 3.2 0.4 - - - -
228A GLU* 1.3 76.6 - - - +
230A TYR* 1.3 54.5 + - - +
232A TRP* 3.8 1.1 - - - +
233A SER* 2.6 39.8 + - - -
545A PHE* 5.0 6.1 - - - -
553A MET* 3.4 29.8 - - - +
618A PRO* 3.2 32.8 - - + +
619A ILE 4.8 1.1 - - - +
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Residues in contact with TYR 230 (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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225A PRO 4.5 9.2 - - - -
226A THR 3.1 28.9 - - - -
227A THR* 3.4 26.7 + - + +
229A ASN* 1.3 75.5 - - - +
231A MET* 1.3 61.2 + - + +
233A SER* 3.8 9.9 - - - -
234A PHE* 3.0 43.4 - + + -
619A ILE* 4.4 23.8 - - + +
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Residues in contact with MET 231 (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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227A THR* 2.8 30.1 + - + +
228A GLU* 3.6 19.3 - - + +
229A ASN 3.2 0.2 - - - -
230A TYR* 1.3 78.6 - - + +
232A TRP* 1.3 88.0 + - + +
234A PHE* 3.3 6.3 + - - +
235A THR* 2.6 39.8 + - - +
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Residues in contact with TRP 232 (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 GLU* 2.8 40.0 + - + +
229A ASN* 4.3 1.1 - - - +
231A MET* 1.3 96.4 - - + +
233A SER* 1.3 56.3 + - - +
234A PHE 3.2 0.2 - - - -
235A THR* 3.6 29.4 - - + -
236A SER* 2.8 35.3 + - - -
239A LEU* 4.6 13.9 - - + -
550A SER* 5.3 2.9 + - - -
553A MET* 5.4 2.2 - - + +
554A ALA* 3.5 46.1 - - + +
557A ALA* 4.3 17.9 - - + +
558A CYS* 4.9 4.7 - - + -
618A PRO* 5.7 3.1 - - + -
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Residues in contact with SER 233 (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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229A ASN 2.6 27.7 + - - -
230A TYR* 3.8 10.6 - - - -
231A MET 3.3 0.2 - - - -
232A TRP* 1.3 77.0 - - - +
234A PHE* 1.3 68.0 + - - +
236A SER* 2.6 18.3 + - - -
237A VAL* 3.5 13.0 - - - +
617A PRO* 3.6 27.0 - - - +
618A PRO* 3.6 18.6 - - - +
619A ILE* 3.8 13.7 + - - +
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Residues in contact with PHE 234 (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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230A TYR* 3.0 39.9 - + + -
231A MET* 3.3 5.5 + - - +
233A SER* 1.3 85.7 - - - +
235A THR* 1.3 61.3 + - - +
236A SER 3.2 1.6 - - - -
237A VAL* 3.1 12.9 + - + +
238A VAL* 2.8 36.5 + - + +
619A ILE* 5.4 9.2 - - + -
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Residues in contact with THR 235 (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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231A MET* 2.6 39.2 + - - +
232A TRP* 3.6 36.2 - - + -
234A PHE* 1.3 76.6 - - - +
236A SER* 1.3 51.0 + - - +
238A VAL* 3.4 11.0 + - + +
239A LEU* 2.8 44.0 + - + +
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Residues in contact with SER 236 (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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232A TRP* 2.8 19.8 + - - -
233A SER* 2.6 28.4 + - - -
235A THR* 1.3 70.3 - - - +
237A VAL* 1.3 52.8 + - - +
239A LEU* 3.3 7.5 + - - +
240A LEU* 2.8 35.7 + - - +
557A ALA* 3.9 16.6 - - - -
558A CYS* 5.3 0.2 - - - +
561A ALA* 3.5 26.9 - - - +
613A PHE* 3.8 13.3 - - - -
616A ASN* 4.6 3.8 + - - -
617A PRO* 5.3 2.1 - - - +
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Residues in contact with VAL 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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233A SER 3.5 16.2 - - - +
234A PHE* 3.1 17.3 + - + +
236A SER* 1.3 79.9 + - - +
238A VAL* 1.3 57.3 + - + +
240A LEU* 3.3 4.3 + - - +
241A LEU* 2.8 54.3 + - + +
613A PHE* 3.8 24.9 - - + -
617A PRO* 6.1 1.3 - - + -
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Residues in contact with VAL 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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234A PHE* 2.8 28.0 + - + +
235A THR* 3.6 12.6 - - + +
236A SER 3.3 0.2 - - - -
237A VAL* 1.3 75.0 - - + +
239A LEU* 1.3 60.5 + - + +
241A LEU* 3.7 6.7 - - + +
242A MET* 2.8 34.5 + - + +
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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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232A TRP* 4.6 7.9 - - + -
235A THR* 2.8 39.3 + - + +
236A SER* 3.8 4.9 - - - +
238A VAL* 1.3 72.9 - - + +
240A LEU* 1.3 60.6 + - - +
242A MET* 3.3 14.8 - - + +
243A GLY* 2.8 26.0 + - - -
558A CYS* 3.9 37.0 - - + +
561A ALA* 5.2 3.4 - - + -
562A LEU* 4.6 16.8 - - + +
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Residues in contact with LEU 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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236A SER 2.8 22.0 + - - +
237A VAL* 3.7 6.5 - - - +
239A LEU* 1.3 73.0 - - - +
241A LEU* 1.3 57.7 + - + +
243A GLY* 3.2 1.8 + - - +
244A ILE* 2.8 53.4 + - + +
561A ALA* 3.5 23.7 - - + +
562A LEU* 5.3 3.6 - - + -
564A VAL* 3.8 37.9 - - + -
565A VAL* 4.0 19.1 - - + +
613A PHE* 4.2 23.1 - - + -
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Residues in contact with LEU 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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237A VAL* 2.8 40.0 + - + +
238A VAL* 4.0 5.4 - - - +
240A LEU* 1.3 70.7 - - + +
242A MET* 1.3 56.6 + - - +
244A ILE* 4.0 23.1 - - + +
245A GLY* 2.8 29.8 + - - -
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Residues in contact with MET 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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238A VAL* 2.8 29.5 + - + +
239A LEU* 3.3 20.4 - - + +
241A LEU* 1.3 72.4 - - - +
243A GLY* 1.3 52.6 + - - +
245A GLY* 3.8 0.6 - - - -
246A LEU* 2.8 68.6 + - + +
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Residues in contact with GLY 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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239A LEU 2.8 18.4 + - - -
240A LEU* 3.6 4.0 - - - -
242A MET* 1.3 70.6 - - - +
244A ILE* 1.3 58.1 + - - +
246A LEU* 3.3 7.2 + - - +
247A LEU* 2.9 35.9 + - - +
562A LEU* 5.5 7.2 - - - -
565A VAL* 4.6 12.1 - - - -
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Residues in contact with ILE 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 LEU* 2.8 49.8 + - + +
241A LEU* 4.0 22.0 - - + +
243A GLY* 1.3 71.2 - - - +
245A GLY* 1.3 53.8 + - - +
247A LEU* 3.4 3.5 + - - +
248A MET* 2.8 63.9 + - + +
564A VAL* 6.0 1.1 - - + -
565A VAL* 4.2 17.4 - - + +
568A VAL* 5.0 14.1 - - + -
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Residues in contact with GLY 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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241A LEU 2.8 22.2 + - - -
242A MET* 3.8 0.7 - - - -
244A ILE* 1.3 75.0 - - - +
246A LEU* 1.3 57.1 + - - +
248A MET* 3.7 3.3 - - - -
249A TRP* 2.8 51.8 + - - +
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Residues in contact with LEU 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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242A MET* 2.8 51.0 + - + +
243A GLY* 3.8 5.2 - - - +
245A GLY* 1.3 72.0 - - - +
247A LEU* 1.3 59.2 + - + +
249A TRP* 3.8 2.1 - - - +
250A GLY* 2.8 26.0 + - - +
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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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243A GLY* 2.9 15.6 + - - +
244A ILE* 3.9 3.6 - - - +
246A LEU* 1.3 76.9 - - + +
248A MET* 1.3 53.3 + - - +
250A GLY* 3.3 2.4 + - - -
251A TYR* 2.8 34.0 + - - +
565A VAL* 3.7 33.9 - - + +
569A LEU* 4.7 13.5 - - + -
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Residues in contact with MET 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 ILE* 2.8 47.8 + - + +
245A GLY* 3.9 4.5 - - - +
247A LEU* 1.3 73.1 - - - +
249A TRP* 1.3 70.8 + - + +
251A TYR* 3.6 21.8 + - + +
252A SER* 4.1 5.0 + - - -
572A ARG* 5.9 9.9 - - - -
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Residues in contact with TRP 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 GLY* 2.8 37.7 + - - +
246A LEU* 4.5 2.2 - - + +
248A MET* 1.3 80.5 - - + +
250A GLY* 1.3 61.4 + - - +
251A TYR 3.3 0.7 - - - -
252A SER* 3.1 30.9 + - - -
253A PHE* 5.5 3.1 - - - -
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Residues in contact with GLY 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 LEU 2.8 21.2 + - - -
247A LEU* 3.3 3.1 + - - -
249A TRP* 1.3 76.6 - - - +
251A TYR* 1.3 58.2 + - - +
252A SER 3.2 3.5 + - - -
253A PHE* 4.0 18.1 + - - +
254A LEU 5.2 0.2 + - - -
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Residues in contact with TYR 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 2.8 16.0 + - - +
248A MET* 3.6 17.5 - - + +
249A TRP 3.3 0.8 - - - -
250A GLY* 1.3 74.9 - - - +
252A SER* 1.3 61.4 + - - +
253A PHE 3.4 0.9 - - - -
254A LEU* 3.5 43.0 + - + +
572A ARG* 4.1 25.1 + - - -
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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