Contacts of the helix formed by residues 222 - 244 (chain D) in PDB entry 1XHU
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 222 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219D PHE* 3.6 10.9 - - - -
221D GLY* 1.3 76.1 - - - -
223D ARG* 1.3 61.7 + - - +
224D GLU* 3.1 18.1 + - + +
225D GLU* 3.3 25.2 + - + +
226D TRP 2.9 23.4 + - - -
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Residues in contact with ARG 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D MET* 4.8 9.9 - - + -
161D PHE* 3.3 37.9 - - + -
162D ASP* 5.0 8.7 - - - +
164D PHE 4.1 3.8 + - - -
165D ASP* 3.4 17.2 + - - -
189D GLU* 5.8 1.8 + - - -
191D PHE* 3.3 68.5 + - - +
192D LYS* 5.1 10.1 - - - +
219D PHE* 5.5 2.0 - - - -
222D THR* 1.3 74.1 + - - +
224D GLU* 1.3 65.4 + - - +
226D TRP* 3.1 10.2 + - - +
227D ALA* 2.8 22.7 + - - +
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Residues in contact with GLU 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D ILE* 4.1 3.3 - - + +
161D PHE* 3.3 34.4 - - + -
222D THR* 3.1 12.5 + - + +
223D ARG* 1.3 77.3 - - - +
225D GLU* 1.3 57.3 + - - +
227D ALA* 3.0 5.6 + - - +
228D LYS* 2.8 33.6 + - + +
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Residues in contact with GLU 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D PHE* 4.7 5.4 - - + -
221D GLY* 5.6 0.7 - - - -
222D THR* 3.3 31.1 + - + +
223D ARG 3.1 0.4 - - - -
224D GLU* 1.3 79.7 - - - +
226D TRP* 1.3 57.8 + - - +
228D LYS* 2.8 9.4 + - - -
229D SER* 2.6 38.3 + - - -
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Residues in contact with TRP 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D LEU* 4.0 19.7 - - + -
152D CYS* 3.8 19.3 - - - -
190D LEU* 3.2 32.5 + - + -
191D PHE* 3.5 30.7 - + - +
193D SER 2.8 22.8 + - - -
195D PRO* 3.7 9.1 - - + +
198D LEU* 3.6 30.5 - - + -
219D PHE* 3.5 32.2 - + + -
222D THR 2.9 14.0 + - - +
223D ARG* 3.3 16.8 - - - +
225D GLU* 1.3 73.2 - - - +
227D ALA* 1.3 63.8 + - - +
229D SER* 3.0 17.2 + - - -
230D TYR* 3.1 27.8 + + + +
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Residues in contact with ALA 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D CYS* 3.7 18.0 - - + +
155D MET* 3.5 25.1 - - + +
156D ILE* 3.3 24.5 - - + -
161D PHE* 4.6 0.2 - - + -
223D ARG 2.8 9.6 + - - +
224D GLU* 3.2 9.0 - - - +
226D TRP* 1.3 76.2 - - - +
228D LYS* 1.3 66.4 + - - +
230D TYR* 3.5 2.6 + - - +
231D LEU* 3.2 26.4 + - - +
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Residues in contact with LYS 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C TYR* 3.1 36.5 - - + +
257C ILE* 5.3 2.3 - - - +
258C LEU* 5.4 18.0 + - + +
156D ILE* 4.8 23.5 - - + +
224D GLU* 2.8 17.3 + - + +
225D GLU* 2.8 15.6 + - - +
227D ALA* 1.3 68.9 - - - +
229D SER* 1.3 67.4 + - - +
231D LEU* 2.8 23.2 + - + +
232D LYS* 3.2 9.7 + - - +
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Residues in contact with SER 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D PRO* 3.2 21.6 - - - +
196D SER* 4.8 9.3 + - - -
219D PHE* 5.1 2.2 - - - -
225D GLU* 2.6 28.3 + - - -
226D TRP* 3.0 15.2 + - - -
228D LYS* 1.3 72.1 - - - +
230D TYR* 1.3 61.0 + - - -
232D LYS* 3.1 11.1 + - - +
233D HIS* 3.0 20.2 + - - +
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Residues in contact with TYR 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D ALA* 3.1 38.3 + - - +
148D LEU* 3.4 35.2 - - + +
149D ALA* 3.6 17.3 - - - -
152D CYS* 4.0 16.8 - - + -
195D PRO* 4.1 19.5 - - + -
198D LEU* 4.4 9.4 - - + -
200D ILE* 4.1 15.4 - - + +
208D ILE* 4.1 3.9 - - + +
226D TRP* 3.1 34.4 + + + +
227D ALA 3.8 3.1 - - - +
228D LYS 3.0 0.2 + - - -
229D SER* 1.3 80.7 + - - +
231D LEU* 1.3 53.8 + - + +
233D HIS* 2.8 13.4 + + - +
234D PHE* 2.4 47.6 + - + +
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Residues in contact with LEU 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C PHE* 3.7 22.4 - - + -
256C TYR* 3.6 44.9 - - + -
257C ILE* 4.4 4.7 - - + -
149D ALA* 3.6 35.0 - - + +
152D CYS* 4.4 4.9 - - + -
153D ALA* 4.3 12.6 - - - +
156D ILE* 4.7 5.6 - - + -
227D ALA 3.2 19.7 - - - +
228D LYS* 2.8 16.2 + - + +
230D TYR* 1.3 74.8 - - + +
232D LYS* 1.3 55.0 + - - +
234D PHE* 4.1 4.0 - - + -
235D VAL* 2.9 38.5 + - + +
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Residues in contact with LYS 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C LYS* 5.3 5.9 - - - +
257C ILE* 3.7 43.2 - - + +
258C LEU* 6.1 3.4 - - + -
228D LYS 3.2 5.8 + - - +
229D SER* 3.1 13.9 + - - +
230D TYR 3.0 0.4 - - - -
231D LEU* 1.3 75.3 - - - +
233D HIS* 1.3 54.6 + - - +
235D VAL* 3.3 0.9 + - - +
236D THR* 2.5 53.2 + - - +
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Residues in contact with HIS 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D PRO 3.2 26.9 + - - +
196D SER* 3.6 25.4 + - - +
198D LEU 2.6 27.6 + - - -
199D TYR* 5.0 0.9 - - - -
200D ILE* 4.0 16.6 + - + +
229D SER 3.0 11.1 + - - +
230D TYR* 2.8 15.7 + + - +
232D LYS* 1.3 78.2 - - - +
234D PHE* 1.3 59.5 + - - +
236D THR* 3.5 5.0 - - - +
237D GLN* 3.0 66.5 + - + +
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Residues in contact with PHE 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C PHE* 3.2 41.3 - + + -
253C PHE* 4.0 9.9 - + - -
145D ALA* 3.5 46.0 - - + -
146D TYR* 3.5 19.5 - + - -
149D ALA* 3.5 23.8 - - + -
200D ILE* 4.2 9.0 - - + -
202D TRP* 3.6 23.5 - + - -
230D TYR* 2.4 39.5 + - + +
231D LEU* 3.9 7.0 - - + +
233D HIS* 1.3 74.7 - - - +
235D VAL* 1.3 63.9 + - + +
238D ALA* 3.2 23.7 + - - +
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Residues in contact with VAL 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C PHE 4.0 7.0 - - - +
250C VAL* 3.5 28.9 - - + +
253C PHE* 3.4 32.8 - - + +
254C LYS* 4.0 15.0 - - + +
257C ILE* 3.6 24.7 - - + -
231D LEU 2.9 27.3 + - - +
234D PHE* 1.3 76.4 - - + +
236D THR* 1.3 66.2 + - - +
238D ALA* 3.1 7.9 - - - +
239D GLU* 3.0 23.2 + - - +
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Residues in contact with THR 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C LYS* 6.3 0.4 - - - +
232D LYS* 2.5 45.7 + - - +
233D HIS* 3.5 9.3 - - - +
235D VAL* 1.3 73.7 - - - +
237D GLN* 1.3 76.0 + - - +
239D GLU* 3.0 12.5 + - - +
240D GLN* 2.8 27.1 + - + +
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Residues in contact with GLN 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D ILE* 4.5 8.5 - - + +
202D TRP* 3.6 24.0 - - + +
233D HIS* 3.0 49.7 + - + +
236D THR* 1.3 83.1 - - - +
238D ALA* 1.3 59.5 + - - +
240D GLN* 3.6 17.6 - - - +
241D ARG* 2.6 36.7 + - - +
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Residues in contact with ALA 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C MET* 4.4 7.5 - - - +
246C ILE* 4.0 3.1 - - - +
249C PHE* 4.1 13.5 - - + +
250C VAL* 3.3 22.2 - - + +
202D TRP* 3.5 17.9 - - + -
234D PHE 3.2 19.1 + - - +
235D VAL* 3.1 13.9 + - - +
236D THR 3.0 0.2 - - - -
237D GLN* 1.3 77.1 - - - +
239D GLU* 1.3 61.4 + - - +
241D ARG* 4.1 1.3 - - - +
242D ALA* 3.3 23.0 + - - +
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Residues in contact with GLU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C ILE* 4.2 17.3 - - + +
250C VAL* 3.8 25.7 - - + +
254C LYS* 3.9 22.4 + - - -
235D VAL* 3.0 10.5 + - - +
236D THR* 3.0 10.4 + - - +
238D ALA* 1.3 76.1 - - - +
240D GLN* 1.3 65.3 + - - +
242D ALA* 3.4 3.3 + - - +
243D ILE* 3.2 28.2 + - + +
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Residues in contact with GLN 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D THR* 2.8 22.1 + - + +
237D GLN* 3.7 22.0 - - - +
239D GLU* 1.3 73.4 - - - +
241D ARG* 1.3 52.6 + - - +
243D ILE* 3.0 10.2 + - - +
244D SER* 2.7 36.1 + - - -
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Residues in contact with ARG 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C TRP* 5.3 3.6 - - - +
206C MET* 4.0 25.9 - - - +
245C MET* 3.6 15.9 - - + +
202D TRP* 3.5 46.7 - - + +
203D ALA* 4.4 10.4 - - - +
237D GLN* 2.6 23.5 + - - +
238D ALA 4.1 1.3 - - - +
240D GLN* 1.3 72.6 - - - +
242D ALA* 1.3 64.6 + - - +
244D SER* 2.9 25.8 + - - +
245D MET* 3.0 41.7 + - - +
248D LYS* 5.6 0.2 - - - +
249D PHE* 4.0 15.8 - - - -
4K G 5.9 0.2 - - - -
5K G 3.8 22.3 + - - -
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Residues in contact with ALA 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C ALA* 3.7 23.2 - - + +
245C MET* 3.5 19.0 - - + +
246C ILE* 3.5 25.6 - - + -
238D ALA 3.3 16.5 + - - +
239D GLU 3.5 3.6 - - - +
241D ARG* 1.3 80.3 - - - +
243D ILE* 1.3 64.1 + - + +
245D MET* 3.3 13.2 + - - +
246D ILE* 3.7 9.6 + - - +
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Residues in contact with ILE 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D GLU* 3.2 15.0 + - + +
240D GLN* 3.0 10.8 + - - +
242D ALA* 1.3 77.0 - - + +
244D SER* 1.3 56.1 + - - +
245D MET 2.7 15.4 + - - -
246D ILE* 3.3 31.2 + - + +
247D ASP* 3.3 15.0 - - - +
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Residues in contact with SER 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D GLN* 2.7 20.9 + - - -
241D ARG* 2.9 16.7 + - - -
243D ILE* 1.3 70.1 - - - +
245D MET* 1.3 54.3 + - - +
247D ASP* 3.0 21.9 + - - +
248D LYS* 3.8 20.3 - - - +
249D PHE* 4.8 0.2 - - - -
4K G 4.8 9.2 + - - -
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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