Contacts of the helix formed by residues 198 - 220 (chain C) in PDB entry 1XFB
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 198 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C ASP 3.8 1.4 + - - -
197C HIS* 1.3 78.8 - - - +
199C LEU* 1.3 65.3 + - - +
200C LYS* 3.1 37.4 + - - +
201C ARG* 3.2 26.9 + - - +
202C CYS 3.3 8.0 + - - -
236C PRO* 4.1 3.1 - - - -
240C CYS* 4.0 15.3 - - - -
242C ILE* 4.3 9.0 - - + +
244C TYR* 3.4 14.1 + - - +
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Residues in contact with LEU 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C ASP* 1.3 74.1 - - - +
200C LYS* 1.3 65.3 + - - +
202C CYS* 3.1 3.6 + - - +
203C GLN* 3.0 21.0 + - - +
234C VAL* 3.3 19.7 - - + +
235C THR* 3.2 33.0 - - - -
236C PRO* 3.8 13.7 - - + +
244C TYR* 3.3 42.4 + - + -
248C GLU* 3.6 28.0 - - + +
249C ILE* 4.4 5.6 - - + -
252C ALA* 3.9 14.6 - - + -
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Residues in contact with LYS 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PRO* 4.4 20.3 - - - +
198C ASP* 3.1 20.3 + - - +
199C LEU* 1.3 78.1 - - - +
201C ARG* 1.3 62.5 + - - +
203C GLN* 3.1 10.5 + - - +
204C TYR* 3.0 21.4 + - - +
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Residues in contact with ARG 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ARG* 3.8 17.3 - - - +
3B HIS* 3.1 44.8 + - - +
4B SER* 4.1 15.0 + - - +
154C ILE* 3.4 19.8 - - + +
155C SER 3.3 25.4 + - - -
156C GLU* 4.6 1.2 + - - +
157C ARG* 5.6 0.2 - - - +
159C PRO* 4.8 3.6 - - - +
197C HIS* 3.7 23.6 - - + -
198C ASP* 3.2 20.4 + - - +
200C LYS* 1.3 79.8 - - - +
202C CYS* 1.3 63.7 + - - +
204C TYR* 3.1 7.1 + - - +
205C VAL* 2.9 36.6 + - + +
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Residues in contact with CYS 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ILE* 4.1 17.9 - - - +
191C ILE* 5.2 4.3 - - - -
197C HIS* 4.0 12.0 - - + -
198C ASP 3.3 2.6 + - - +
199C LEU 3.1 8.8 + - - +
201C ARG* 1.3 78.2 - - - +
203C GLN* 1.3 57.8 + - - +
205C VAL* 4.0 0.9 - - - +
206C THR* 2.8 42.2 + - - -
232C ASN* 4.2 7.2 - - - -
233C MET 4.4 0.7 - - - -
234C VAL* 3.5 10.8 - - - -
235C THR* 3.2 44.4 - - - +
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Residues in contact with GLN 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C LEU* 3.0 11.8 + - - +
200C LYS* 3.4 12.4 - - - +
202C CYS* 1.3 77.8 - - - +
204C TYR* 1.3 57.0 + - - +
206C THR* 3.2 3.1 + - - -
207C GLU* 2.6 60.0 + - - +
234C VAL* 3.8 15.9 - - + +
252C ALA* 3.4 37.8 - - + +
255C THR* 3.7 15.4 - - - +
256C ALA* 3.9 6.0 - - + +
259C ARG* 3.2 16.2 - - - +
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Residues in contact with TYR 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B HIS* 2.7 56.9 + + - +
4B SER* 3.2 31.4 - - - +
5B TYR 5.2 0.9 - - - -
221B HIS* 3.4 25.3 - - - -
200C LYS 3.0 12.7 + - - +
201C ARG* 3.3 11.0 - - - +
203C GLN* 1.3 75.1 - - - +
205C VAL* 1.3 67.8 + - + +
207C GLU* 3.1 13.3 + - - +
208C LYS* 3.0 55.9 + - + +
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Residues in contact with VAL 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B HIS* 4.1 13.2 - - + +
154C ILE* 3.9 25.8 - - + -
159C PRO* 3.6 31.6 - - + -
164C ILE* 6.0 0.2 - - + -
191C ILE* 3.7 16.6 - - + -
201C ARG* 2.9 40.4 + - + +
202C CYS 4.0 0.4 - - - +
204C TYR* 1.3 77.8 - - + +
206C THR* 1.3 65.2 + - - +
208C LYS* 3.2 5.8 + - + +
209C VAL* 2.9 26.1 + - + +
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Residues in contact with THR 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C ILE* 3.4 15.9 - - + +
202C CYS* 2.8 28.2 + - - -
203C GLN* 3.5 6.3 - - - -
205C VAL* 1.3 75.2 - - - +
207C GLU* 1.3 64.1 + - - +
209C VAL* 3.8 0.7 - - - +
210C LEU* 2.9 46.1 + - + +
231C PRO* 5.8 2.7 - - + -
232C ASN* 3.3 28.8 + - - +
234C VAL* 4.4 9.3 - - + +
256C ALA* 4.1 16.2 - - + -
257C LEU* 5.9 1.1 - - + -
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Residues in contact with GLU 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B SER* 5.8 0.2 - - - -
203C GLN* 2.6 52.2 + - - +
204C TYR* 3.1 11.5 + - - +
206C THR* 1.3 77.4 - - - +
208C LYS* 1.3 61.4 + - + +
210C LEU* 4.8 0.2 - - - -
211C ALA* 2.9 30.4 + - - +
256C ALA* 3.7 24.1 - - - +
259C ARG* 3.0 31.0 + - - +
260C THR* 3.4 16.0 - - + +
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Residues in contact with LYS 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B HIS* 6.2 1.8 - - + -
218B SER* 3.0 38.5 + - - +
219B ASP* 5.0 1.3 - - - +
221B HIS* 3.2 21.1 + - - +
164C ILE* 4.7 13.7 - - + +
204C TYR* 3.0 60.0 + - + +
205C VAL* 3.7 7.0 - - - +
207C GLU* 1.3 76.0 - - + +
209C VAL* 1.3 65.9 + - + +
211C ALA* 3.4 5.9 + - - +
212C ALA* 3.1 22.5 + - - +
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Residues in contact with VAL 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LEU* 3.3 37.0 - - + -
159C PRO* 4.8 0.2 - - + -
164C ILE* 4.4 22.6 - - + +
189C PRO* 4.2 15.9 - - + +
191C ILE* 3.6 19.1 - - + -
205C VAL* 2.9 29.3 + - + +
206C THR 3.8 2.9 - - - +
208C LYS* 1.3 75.7 - - - +
210C LEU* 1.3 65.8 + - + +
212C ALA* 3.0 5.5 + - - +
213C VAL* 2.9 36.0 + - + +
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Residues in contact with LEU 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C PRO* 4.0 16.6 - - + -
191C ILE* 6.5 0.2 - - + -
206C THR* 2.9 39.5 + - + +
207C GLU 4.0 0.4 - - - +
209C VAL* 1.3 77.5 - - + +
211C ALA* 1.3 63.3 + - - +
213C VAL* 2.9 16.4 + - + +
214C TYR* 2.9 25.2 + - + -
229C LEU* 3.9 33.0 - - + -
231C PRO* 4.7 7.4 - - + -
256C ALA 5.0 1.1 - - - +
257C LEU* 3.8 25.8 - - + -
260C THR* 3.5 28.9 - - - +
261C VAL* 4.5 0.2 - - + -
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Residues in contact with ALA 211 (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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215B LYS* 4.0 11.2 - - + +
218B SER* 3.6 30.1 - - - +
207C GLU 2.9 18.6 + - - +
208C LYS* 3.6 5.8 - - - +
210C LEU* 1.3 77.2 - - - +
212C ALA* 1.3 61.4 + - - +
214C TYR* 3.8 3.0 + - - +
215C LYS* 3.3 21.0 + - - +
260C THR* 4.1 14.9 - - + +
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Residues in contact with ALA 212 (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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215B LYS* 4.3 17.2 - - - +
164C ILE* 3.5 28.5 - - + +
165C LEU* 6.1 0.4 - - - -
168C ALA* 4.1 9.9 - - + +
208C LYS 3.1 8.4 + - - +
209C VAL 3.0 9.5 + - - +
211C ALA* 1.3 74.4 - - - +
213C VAL* 1.3 66.8 + - - +
215C LYS* 3.2 3.6 + - - +
216C ALA* 3.0 23.9 + - - +
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Residues in contact with VAL 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C ALA* 4.0 17.9 - - + +
171C LEU* 4.2 11.9 - - + -
187C VAL* 3.9 27.4 - - + -
189C PRO* 4.1 18.2 - - + -
209C VAL* 2.9 34.5 + - + +
210C LEU* 2.9 11.4 + - + +
212C ALA* 1.3 76.7 - - - +
214C TYR* 1.3 67.0 + - + +
216C ALA* 3.3 4.0 + - - +
217C LEU* 3.0 35.9 + - + +
229C LEU* 5.3 1.1 - - + -
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Residues in contact with TYR 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C VAL* 5.7 1.8 - - + +
210C LEU* 2.9 24.5 + - + +
211C ALA* 4.5 2.9 - - - +
213C VAL* 1.3 77.6 - - + +
215C LYS* 1.3 66.6 + - - +
217C LEU* 3.2 17.4 + - + +
218C SER* 2.9 22.2 + - - -
224C LEU* 3.6 35.2 - - + +
227C THR* 5.1 2.7 + - - -
228C LEU 5.2 0.9 - - - -
229C LEU* 3.4 40.7 - - + +
260C THR 3.9 16.8 - - - +
261C VAL* 3.7 21.6 - - + +
262C PRO* 3.7 19.5 - - + -
265C VAL* 3.5 25.7 - - + +
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Residues in contact with LYS 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ALA* 4.1 17.9 - - + +
212B ALA* 4.3 22.4 - - - +
215B LYS* 4.0 32.1 - - + -
211C ALA 3.3 17.8 + - - +
212C ALA 3.2 5.3 + - - +
214C TYR* 1.3 76.8 - - - +
216C ALA* 1.3 58.2 + - - +
218C SER* 3.2 9.3 + - - -
219C ASP* 2.9 66.5 + - - +
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Residues in contact with ALA 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C ALA* 3.4 35.2 - - + +
169C ASN* 4.3 4.3 - - - +
172C ALA* 3.8 7.0 - - + -
212C ALA 3.0 12.6 + - - +
213C VAL 3.4 7.9 - - - +
215C LYS* 1.3 74.4 - - - +
217C LEU* 1.3 66.6 + - - +
219C ASP* 2.9 10.4 + - - +
220C HIS* 2.9 28.9 + - + -
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Residues in contact with LEU 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C ALA 5.8 0.2 - - - +
171C LEU 4.7 0.4 - - - -
172C ALA* 3.7 22.0 - - + +
175C ALA* 3.9 8.7 - - + -
187C VAL* 4.4 18.4 - - + -
213C VAL* 3.0 27.4 + - + +
214C TYR* 3.5 38.8 - - + +
216C ALA* 1.3 75.7 - - - +
218C SER* 1.3 63.9 + - - +
220C HIS 3.2 1.2 + - - -
221C HIS 3.1 3.8 + - - -
222C VAL* 3.0 61.2 + - + +
224C LEU* 4.0 15.5 - - + -
227C THR* 5.5 2.5 - - - +
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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
----------------------------------------------------------
207B GLU 5.9 0.2 - - - -
208B LYS* 3.0 33.6 + - - +
211B ALA* 3.7 27.1 - - - +
214C TYR 2.9 14.2 + - - -
215C LYS* 3.3 12.2 - - - +
216C ALA 3.1 0.2 - - - -
217C LEU* 1.3 75.7 - - - +
219C ASP* 1.3 61.4 + - - +
221C HIS* 2.9 18.3 + - - +
222C VAL 5.0 2.9 - - - +
224C LEU* 6.0 0.2 - - - +
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Residues in contact with ASP 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LYS* 5.1 1.6 - - - +
215C LYS* 2.9 51.1 + - - +
216C ALA* 2.9 11.3 + - - +
218C SER* 1.3 78.6 + - - +
220C HIS* 1.3 62.5 + - + +
221C HIS* 3.4 12.5 + - - -
162D LEU* 3.5 21.7 - - + +
165D LEU* 3.7 30.2 - - + +
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Residues in contact with HIS 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ASN* 2.8 28.0 + - - -
172C ALA* 3.4 29.1 - - + +
173C ARG* 3.8 35.3 + - + +
176C SER* 3.7 19.8 + - - -
216C ALA* 2.9 23.1 + - - +
217C LEU 3.9 2.9 - - - +
218C SER 3.1 0.4 - - - -
219C ASP* 1.3 79.5 - - + +
221C HIS* 1.3 75.4 + - - +
222C VAL* 3.3 3.7 + - + -
116D LEU* 5.6 2.2 - - + +
117D ALA 4.1 3.3 - - - +
162D LEU* 3.6 30.4 - - + +
165D LEU* 3.9 5.1 - - + +
166D GLU* 3.8 11.4 - - + -
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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
------------------------------------------------------------
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