Contacts of the helix formed by residues 217 - 239 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211C LEU* 3.6 15.4 - - - +
215C SER 3.4 2.6 + - - -
216C PRO* 1.3 74.1 - - - +
218C SER* 1.3 64.5 + - - +
219C ALA* 3.4 10.9 + - - +
220C SER* 3.0 25.9 + - - -
221C LEU* 3.0 27.2 + - - +
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Residues in contact with SER 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C SER* 1.3 73.0 - - - +
219C ALA* 1.3 66.4 + - - +
221C LEU* 4.1 10.0 - - - +
222C ASN* 3.0 39.5 + - - +
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Residues in contact with ALA 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C SER* 3.1 10.5 + - - +
218C SER* 1.3 83.0 + - - +
220C SER* 1.3 63.2 + - - +
222C ASN* 3.8 7.2 - - - +
223C PHE* 3.1 24.6 + - - +
266C TYR* 4.3 18.8 - - + -
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Residues in contact with SER 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C HIS* 2.9 29.0 + - - -
197C ILE* 4.3 8.0 - - - +
211C LEU* 3.6 29.2 - - - -
216C PRO* 3.7 0.5 - - - +
217C SER* 3.0 30.4 + - - -
219C ALA* 1.3 77.5 - - - +
221C LEU* 1.3 55.1 + - - +
223C PHE* 3.4 6.6 + - - +
224C LEU* 2.9 34.5 + - - +
266C TYR* 5.1 4.7 - - - -
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Residues in contact with LEU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C HIS* 4.3 10.5 - - + -
216C PRO* 3.6 31.2 - - + +
217C SER 3.0 23.0 + - - +
218C SER* 4.1 7.0 - - - +
220C SER* 1.3 72.0 - - - +
222C ASN* 1.3 67.1 + - - +
224C LEU* 3.9 7.7 - - + +
225C HIS* 3.0 26.0 + - - +
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Residues in contact with ASN 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C SER* 3.0 34.4 + - - +
219C ALA* 3.8 7.1 - - - +
221C LEU* 1.3 78.0 - - - +
223C PHE* 1.3 58.9 + - - +
225C HIS* 3.3 6.4 + - - +
226C ALA* 2.9 30.1 + - - +
262C CYS* 4.0 17.3 - - - -
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Residues in contact with PHE 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C ILE* 4.5 16.4 - - + -
219C ALA 3.1 15.9 + - - +
220C SER* 3.5 3.6 - - - +
222C ASN* 1.3 79.2 - - - +
224C LEU* 1.3 63.2 + - - +
226C ALA* 3.3 4.1 + - - +
227C LEU* 3.1 44.0 + - + +
262C CYS* 4.6 3.5 - - - -
263C ILE* 4.0 32.1 - - + -
266C TYR* 3.6 57.0 - + + -
312C THR* 3.7 22.2 - - + -
313C ALA* 4.3 3.1 - - - -
316C VAL* 3.8 21.5 - - + -
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Residues in contact with LEU 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C PRO* 6.2 0.2 - - + -
193C PHE* 3.6 37.0 - - + -
194C HIS* 3.5 37.2 - - + +
197C ILE* 3.6 21.5 - - + -
220C SER 2.9 18.4 + - - +
221C LEU* 3.9 9.6 - - + +
222C ASN 3.3 0.4 - - - -
223C PHE* 1.3 75.8 - - + +
225C HIS* 1.3 62.8 + - - +
227C LEU* 3.4 6.5 + - + +
228C GLU* 3.1 21.9 + - - +
316C VAL* 3.7 12.6 - - + -
317C ASP* 4.7 4.8 - - - +
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Residues in contact with HIS 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C LEU 3.0 17.6 + - - +
222C ASN* 3.5 6.1 - - - +
224C LEU* 1.3 77.4 - - - +
226C ALA* 1.3 61.4 + - - +
228C GLU* 3.1 13.8 + - - +
229C VAL* 2.8 49.3 + - + +
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Residues in contact with ALA 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C ASN 2.9 19.4 + - - +
223C PHE* 3.8 4.3 - - - +
225C HIS* 1.3 77.1 - - + +
227C LEU* 1.3 52.9 - - - +
229C VAL* 3.3 2.1 + - - +
230C MET* 2.7 38.1 + - - +
259C ALA* 3.6 26.7 - - - +
262C CYS* 3.7 24.5 - - + -
263C ILE* 3.9 8.5 - - + -
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Residues in contact with LEU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C PHE* 3.1 50.4 + - + +
224C LEU* 3.6 8.1 - - - +
226C ALA* 1.3 74.9 - - - +
228C GLU* 1.3 59.2 + - - +
230C MET* 3.3 17.5 + - + +
231C PHE* 2.8 46.4 + - + -
263C ILE* 4.2 16.1 - - + +
313C ALA* 3.4 29.4 - - + +
316C VAL* 4.2 14.4 - - + -
317C ASP* 3.3 25.8 - - - +
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Residues in contact with GLU 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C LEU 3.1 12.3 + - - +
225C HIS* 3.1 16.7 + - - +
227C LEU* 1.3 77.7 - - - +
229C VAL* 1.3 63.6 + - + +
231C PHE* 3.5 8.0 + - - +
232C LYS* 3.0 24.6 + - + +
317C ASP* 5.1 4.8 + - - +
490C ARG* 4.2 24.2 + - - +
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Residues in contact with VAL 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C HIS* 2.8 45.7 + - + +
226C ALA* 3.8 6.1 - - - +
228C GLU* 1.3 73.0 - - + +
230C MET* 1.3 53.6 + - - +
232C LYS* 3.2 8.5 + - + +
233C SER* 2.7 39.8 + - - +
255C GLU* 3.8 40.6 - - + +
259C ALA* 3.8 16.8 - - + -
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Residues in contact with MET 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C TRP* 3.4 28.5 - - + -
226C ALA 2.7 21.0 + - - +
227C LEU* 3.5 16.8 - - + +
229C VAL* 1.3 72.2 - - - +
231C PHE* 1.3 90.1 + - + +
233C SER* 3.1 8.6 + - - -
234C THR* 2.6 37.6 + - - -
256C HIS* 3.6 3.9 + - + +
259C ALA* 3.8 10.1 - - + +
260C TRP* 3.4 48.7 - - + +
263C ILE* 3.9 12.1 - - + -
313C ALA* 5.6 1.8 - - + -
602C 1CA 5.7 1.3 - - + -
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Residues in contact with PHE 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C TRP* 4.5 0.9 - + - -
227C LEU* 2.8 44.8 + - + +
228C GLU* 3.9 6.5 - - + +
230C MET* 1.3 96.4 - - + +
232C LYS* 1.3 62.3 + - - +
234C THR* 3.1 16.1 + - - -
235C VAL* 3.3 14.9 + - - +
313C ALA 5.0 1.8 - - - -
317C ASP* 3.7 36.3 - - + -
318C THR* 5.7 0.7 - - + -
486C SER* 3.5 20.0 - - - +
487C PHE* 3.9 22.7 - + + +
488C ILE* 4.0 20.4 - - + -
602C 1CA 4.0 33.2 - - + -
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Residues in contact with LYS 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C GLU 4.6 2.6 + - - -
59C GLN* 2.9 43.3 + - - +
60C GLY* 5.0 2.8 - - - -
62C GLU* 5.2 7.1 + - - -
228C GLU* 3.0 21.3 + - + +
229C VAL* 3.6 8.1 - - + +
231C PHE* 1.3 73.4 - - - +
233C SER* 1.3 63.9 + - - +
235C VAL* 3.1 15.8 + - - +
236C GLN* 3.3 28.3 + - - +
255C GLU* 5.6 4.7 - - - +
486C SER* 4.6 15.2 - - - -
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Residues in contact with SER 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C VAL* 2.7 26.7 + - - +
230C MET* 3.1 4.5 + - - -
232C LYS* 1.3 74.6 - - - +
234C THR* 1.3 64.9 + - - +
236C GLN* 3.3 11.9 + - - -
237C LEU* 3.0 26.9 + - - +
252C VAL* 3.9 19.5 - - - -
255C GLU* 5.0 4.7 - - - -
256C HIS* 2.9 40.0 + - - +
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Residues in contact with THR 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU* 4.2 12.3 - - + -
115C PRO* 4.7 3.5 - - + +
116C TRP* 3.0 36.1 + - + +
230C MET* 2.6 26.6 + - - -
231C PHE* 3.1 10.0 + - - -
233C SER* 1.3 77.5 + - - +
235C VAL* 1.3 54.9 + - - +
237C LEU* 3.2 2.6 + - - +
238C MET* 2.7 41.2 + - + +
256C HIS* 3.3 8.8 + - + -
487C PHE* 4.0 29.8 - - + -
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Residues in contact with VAL 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ILE* 4.1 5.6 - - + +
60C GLY* 4.3 6.7 - - - -
61C TYR* 3.6 37.9 - - + +
231C PHE 3.6 11.2 - - - +
232C LYS* 3.1 7.5 + - - +
234C THR* 1.3 77.8 - - - +
236C GLN* 1.3 61.2 + - - +
237C LEU 3.1 1.0 + - - -
238C MET* 3.6 12.4 + - - -
239C PHE* 3.7 19.6 + - + -
485C TYR* 4.2 13.5 - - + +
486C SER* 3.6 11.9 - - - -
487C PHE* 3.3 33.2 - - + +
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Residues in contact with GLN 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ILE* 3.8 20.1 - - + +
56C TRP 5.8 0.4 + - - -
59C GLN* 3.5 57.6 - - - +
60C GLY* 4.8 0.4 - - - -
232C LYS* 3.5 30.2 - - - +
233C SER* 3.3 16.4 + - - +
235C VAL* 1.3 76.1 - - - +
237C LEU* 1.3 59.7 + - - +
239C PHE* 5.1 1.0 + - - +
240C MET* 4.1 19.9 - - - +
249C SER* 5.1 2.1 + - - +
252C VAL* 3.7 31.8 - - + +
255C GLU* 4.5 8.2 + - - +
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Residues in contact with LEU 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C PRO* 3.9 17.4 - - + +
233C SER 3.0 19.0 + - - +
236C GLN* 1.3 80.0 - - - +
238C MET* 1.3 59.1 + - - +
239C PHE 3.2 3.7 + - - -
240C MET* 3.1 26.8 + - - +
245C SER* 4.0 13.6 + - - -
249C SER* 4.5 4.0 - - - +
252C VAL* 3.5 28.5 - - + -
253C TRP* 3.4 61.4 - - + +
256C HIS* 4.0 24.7 - - + -
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Residues in contact with MET 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU* 4.1 23.3 - - + -
115C PRO* 4.3 8.7 - - + -
234C THR* 2.7 24.6 + - + +
235C VAL* 3.9 8.1 - - - +
237C LEU* 1.3 72.2 - - - +
239C PHE* 1.3 95.7 + - + +
240C MET 3.4 2.7 + - - -
381C PHE* 4.5 12.8 - - + -
485C TYR* 3.9 14.8 - - - +
487C PHE* 3.8 34.8 - - + -
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Residues in contact with PHE 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ARG* 5.4 1.0 - - - +
51C ARG* 3.7 46.0 + - - +
52C LEU* 3.0 20.5 - - + +
55C ILE* 3.6 33.9 - - + -
61C TYR* 3.8 17.5 - + - -
64C LEU* 4.1 21.3 - - + -
235C VAL* 3.7 14.3 + - + +
236C GLN 5.1 1.2 + - - +
237C LEU 3.2 1.2 + - - -
238C MET* 1.3 120.5 - - + +
240C MET* 1.3 59.7 + - - +
381C PHE* 5.4 4.9 - + - -
404C GLN* 6.0 1.8 - - - -
485C TYR* 4.5 5.4 - + - -
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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