Contacts of the helix formed by residues 217 - 239 (chain F) in PDB entry 4DVQ
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 SER 217 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211F LEU* 3.8 13.7 - - - +
215F SER 3.3 4.2 + - - -
216F PRO* 1.3 77.1 - - - +
218F SER* 1.3 58.9 + - - +
219F ALA* 3.6 8.1 + - - +
220F SER* 3.1 27.2 + - - -
221F LEU* 3.1 26.5 + - - +
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Residues in contact with SER 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F SER* 1.3 72.3 - - - +
219F ALA* 1.3 60.8 + - - +
220F SER 3.2 1.1 - - - -
221F LEU* 3.9 9.4 - - - +
222F ASN* 2.8 47.0 + - - -
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Residues in contact with ALA 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F SER* 3.6 7.3 + - - +
218F SER* 1.3 79.6 + - - +
220F SER* 1.3 63.6 + - - +
222F ASN* 3.9 8.1 - - - +
223F PHE* 3.0 26.5 + - - +
266F TYR* 4.1 19.6 - - + -
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Residues in contact with SER 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194F HIS* 2.5 38.4 + - - -
197F ILE* 4.0 8.0 - - - +
211F LEU* 3.9 17.6 - - - +
217F SER* 3.1 31.1 + - - -
219F ALA* 1.3 79.0 - - - +
221F LEU* 1.3 60.5 + - - +
223F PHE* 3.5 5.8 + - - +
224F LEU* 3.2 24.3 + - - +
266F TYR* 4.9 7.2 - - - -
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Residues in contact with LEU 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F HIS* 4.1 10.5 - - - +
216F PRO* 3.8 29.8 - - + +
217F SER 3.1 19.1 + - - +
218F SER* 3.4 8.3 + - - +
220F SER* 1.3 72.5 - - - +
222F ASN* 1.3 67.1 + - - +
224F LEU* 3.2 11.8 + - + +
225F HIS* 3.0 24.9 + - - +
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Residues in contact with ASN 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F SER* 2.8 35.4 + - - +
219F ALA* 3.9 7.5 - - - +
221F LEU* 1.3 76.0 - - - +
223F PHE* 1.3 53.3 + - - +
225F HIS* 3.4 6.2 + - - +
226F ALA* 2.8 36.9 + - - +
262F CYS* 4.2 18.3 - - - -
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Residues in contact with PHE 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197F ILE* 4.6 15.3 - - + -
219F ALA 3.0 18.1 + - - +
220F SER* 3.6 3.8 - - - +
222F ASN* 1.3 76.7 - - - +
224F LEU* 1.3 57.0 + - + +
226F ALA* 3.3 4.2 + - - +
227F LEU* 2.9 50.1 + - + +
262F CYS* 4.9 3.1 - - - -
263F ILE* 3.9 34.1 - - + -
266F TYR* 3.9 56.3 - + + -
312F THR* 3.7 23.8 - - + -
313F ALA* 4.3 2.5 - - - -
316F VAL* 4.0 22.2 - - + -
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Residues in contact with LEU 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F PRO* 6.1 1.3 - - + -
193F PHE* 3.5 42.6 - - + -
194F HIS* 3.6 29.2 - - + +
197F ILE* 3.7 20.6 - - + -
220F SER 3.2 16.0 + - - +
221F LEU* 3.2 15.0 + - + +
223F PHE* 1.3 76.4 - - + +
225F HIS* 1.3 62.3 + - - +
227F LEU* 3.7 8.2 + - + +
228F GLU* 3.2 21.7 + - - +
316F VAL* 3.8 10.1 - - + -
317F ASP* 5.2 2.1 - - - +
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Residues in contact with HIS 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221F LEU 3.0 17.0 + - - +
222F ASN* 3.7 7.0 - - - +
224F LEU* 1.3 75.1 - - - +
226F ALA* 1.3 67.1 + - - +
228F GLU* 2.9 24.6 + - - +
229F VAL* 2.9 44.2 + - + +
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Residues in contact with ALA 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F ASN 2.8 21.8 + - - +
223F PHE* 3.7 5.2 - - - +
225F HIS* 1.3 75.1 + - - +
227F LEU* 1.3 56.9 + - - +
229F VAL* 3.4 3.1 + - - +
230F MET* 2.8 30.1 + - - +
259F ALA* 3.4 31.3 - - - +
262F CYS* 3.7 19.7 - - + -
263F ILE* 3.9 9.2 - - + +
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Residues in contact with LEU 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F PHE* 2.9 48.3 + - + +
224F LEU* 3.8 8.1 - - - +
226F ALA* 1.3 76.2 - - - +
228F GLU* 1.3 57.3 + - - +
230F MET* 3.2 13.5 + - + +
231F PHE* 2.9 41.4 + - + -
263F ILE* 3.6 24.9 - - + +
313F ALA* 3.9 26.9 - - + +
316F VAL* 4.2 13.5 - - + -
317F ASP* 3.2 29.8 - - - +
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Residues in contact with GLU 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224F LEU 3.2 11.3 + - - +
225F HIS* 2.9 28.6 + - - +
227F LEU* 1.3 79.5 - - - +
229F VAL* 1.3 59.1 + - - +
231F PHE* 3.3 8.8 + - - +
232F LYS* 3.0 28.3 + - + +
317F ASP* 5.2 4.5 - - - +
486F SER* 5.3 0.7 + - - -
490F ARG* 5.2 17.3 + - - +
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Residues in contact with VAL 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225F HIS* 2.9 45.5 + - + +
226F ALA* 3.8 5.2 - - - +
228F GLU* 1.3 76.5 - - + +
230F MET* 1.3 64.0 + - - +
232F LYS* 3.7 10.6 - - + +
233F SER* 3.0 25.6 + - - -
255F GLU* 3.8 41.3 - - + +
259F ALA* 3.9 6.1 - - + -
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Residues in contact with MET 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F TRP* 3.5 13.0 - - + -
226F ALA 2.8 18.2 + - - +
227F LEU* 3.2 13.4 + - + +
229F VAL* 1.3 78.0 - - - +
231F PHE* 1.3 78.8 + - + +
233F SER* 3.1 7.4 + - - -
234F THR* 2.6 48.3 + - - -
256F HIS* 3.5 2.9 - - + +
259F ALA* 3.7 11.2 - - + -
260F TRP* 3.4 59.9 - - + +
263F ILE* 3.9 14.1 - - + -
313F ALA* 5.7 1.3 - - + -
602F 1CA 6.0 1.1 - - + -
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Residues in contact with PHE 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F TRP* 4.2 2.2 - + - -
227F LEU* 2.9 32.6 + - + +
228F GLU* 3.8 5.8 - - - +
230F MET* 1.3 96.7 - - + +
232F LYS* 1.3 68.1 + - - +
234F THR* 3.3 5.4 - - - -
235F VAL* 3.3 22.0 + - - +
313F ALA 5.5 2.5 - - - -
317F ASP* 3.8 35.9 - - + -
318F THR* 5.6 0.7 - - + -
486F SER* 3.5 18.6 - - - +
487F PHE* 3.5 36.9 - + + +
488F ILE* 4.1 20.6 - - + -
602F 1CA 4.0 26.7 - - + -
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Residues in contact with LYS 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F GLN* 4.0 32.8 - - + +
228F GLU* 3.0 17.4 + - + +
229F VAL* 3.4 14.4 + - + +
231F PHE* 1.3 75.8 - - - +
233F SER* 1.3 69.0 + - - +
235F VAL* 2.8 20.0 + - - +
236F GLN* 2.9 36.2 + - - +
255F GLU* 2.7 29.8 + - - -
486F SER* 4.1 12.3 + - - +
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Residues in contact with SER 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229F VAL 3.0 16.4 + - - -
230F MET 3.1 1.7 + - - -
232F LYS* 1.3 82.7 - - - +
234F THR* 1.3 63.2 + - - +
236F GLN* 3.1 15.9 + - - +
237F LEU* 3.0 27.0 + - - +
252F VAL* 3.9 13.9 - - - -
255F GLU* 4.7 3.4 - - - -
256F HIS* 2.5 50.4 + - - +
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Residues in contact with THR 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F LEU* 4.3 7.0 - - + -
115F PRO* 4.6 3.9 - - + +
116F TRP* 2.9 32.9 + - + +
230F MET* 2.6 29.7 + - - -
231F PHE* 3.3 9.6 - - - -
232F LYS 3.0 0.2 + - - -
233F SER* 1.3 76.4 + - - +
235F VAL* 1.3 59.2 + - - +
237F LEU* 3.1 2.3 + - - +
238F MET* 2.8 38.6 + - + +
256F HIS* 3.1 10.2 - - - -
487F PHE* 3.7 32.8 - - + -
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Residues in contact with VAL 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F ILE* 4.1 4.7 - - + +
60F GLY* 4.3 7.4 - - - -
61F TYR* 4.0 35.9 - - + +
231F PHE 3.7 8.5 - - - +
232F LYS* 2.8 12.7 + - - +
234F THR* 1.3 73.2 - - - +
236F GLN* 1.3 65.2 + - - +
237F LEU 3.3 0.2 + - - -
238F MET* 3.4 15.1 + - - -
239F PHE* 3.6 24.3 - - + -
485F TYR* 3.9 13.2 - - + +
486F SER* 3.9 7.9 - - - +
487F PHE* 3.3 33.2 - - + +
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Residues in contact with GLN 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F ILE* 3.9 19.8 - - + +
59F GLN* 3.8 56.0 - - - +
60F GLY* 4.3 0.4 - - - +
232F LYS* 2.9 37.6 + - - +
233F SER* 3.1 19.9 + - - +
235F VAL* 1.3 79.2 - - - +
237F LEU* 1.3 60.5 + - + +
239F PHE* 4.4 1.7 + - - +
240F MET* 4.1 17.3 - - - +
249F SER* 6.0 1.7 - - - +
252F VAL* 3.5 35.7 - - + +
255F GLU* 4.9 2.4 + - - -
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Residues in contact with LEU 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F GLU* 6.1 0.2 - - - +
115F PRO* 3.9 19.6 - - + +
233F SER 3.0 14.7 + - - +
234F THR 4.0 0.2 - - - +
236F GLN* 1.3 76.5 - - - +
238F MET* 1.3 63.2 + - - +
239F PHE 3.4 2.2 + - - -
240F MET* 3.2 25.0 - - - +
245F SER* 4.6 5.5 + - - -
249F SER* 4.4 9.9 - - - +
252F VAL* 3.4 26.7 - - + +
253F TRP* 3.4 69.3 - - + +
256F HIS* 4.1 20.2 - - + -
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Residues in contact with MET 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F LEU* 4.3 19.5 - - + -
115F PRO* 4.4 9.8 - - - +
234F THR* 2.8 20.6 + - + +
235F VAL* 3.7 11.2 - - - +
236F GLN 3.4 1.0 - - - -
237F LEU* 1.3 78.8 - - - +
239F PHE* 1.3 83.8 + - + +
240F MET 3.3 4.5 + - - +
381F PHE* 4.3 17.9 - - + -
383F GLU* 5.9 2.2 - - - +
485F TYR* 3.5 23.8 - - - +
487F PHE* 3.8 28.0 - - + -
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Residues in contact with PHE 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F ARG* 3.4 49.9 + - + +
52F LEU* 2.9 20.7 - - + +
55F ILE* 3.6 22.9 - - + -
61F TYR* 4.2 15.7 - + - -
64F LEU* 4.4 18.8 - - + -
83F LEU* 6.1 0.9 - - - +
235F VAL* 3.6 30.4 + - + +
236F GLN 4.4 2.3 + - - +
237F LEU 3.4 0.8 - - - -
238F MET* 1.3 110.5 - - + +
240F MET* 1.3 60.2 + - + +
241F PRO* 4.9 0.2 - - - +
381F PHE* 5.6 2.5 - + - -
485F TYR* 4.7 2.9 - + - -
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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