Contacts of the helix formed by residues 198 - 220 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196I ASP 3.8 1.2 + - - -
197I HIS* 1.3 79.1 - - - +
199I LEU* 1.3 65.4 + - - +
200I LYS* 3.1 37.3 + - - +
201I ARG* 3.2 26.7 + - - +
202I CYS 3.3 8.0 + - - -
236I PRO* 4.1 2.9 - - - -
240I CYS* 4.0 15.9 - - - -
242I ILE* 4.3 9.3 - - + +
244I TYR* 3.4 14.2 + - - +
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Residues in contact with LEU 199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198I ASP* 1.3 73.2 - - - +
200I LYS* 1.3 64.3 + - - +
202I CYS* 3.1 4.2 + - - +
203I GLN* 3.0 20.5 + - - +
234I VAL* 3.3 19.5 - - + +
235I THR* 3.2 33.2 - - - -
236I PRO* 3.8 14.4 - - + +
244I TYR* 3.3 43.3 + - + -
248I GLU* 3.7 28.3 - - + +
249I ILE* 4.4 5.6 - - + -
252I ALA* 3.9 13.9 - - + -
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Residues in contact with LYS 200 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198I ASP* 3.1 20.9 + - - +
199I LEU* 1.3 78.6 - - - +
201I ARG* 1.3 63.8 + - - +
203I GLN* 3.1 10.2 + - - +
204I TYR* 3.0 21.7 + - - +
244I TYR* 6.0 0.2 - - - +
6L PRO* 4.4 21.1 - - - +
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Residues in contact with ARG 201 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154I ILE* 3.4 20.0 - - + +
155I SER 3.3 18.8 + - - -
156I GLU* 5.8 0.4 - - - +
159I PRO* 4.8 1.4 - - - +
197I HIS* 3.7 22.4 - - + -
198I ASP* 3.2 20.0 + - - +
200I LYS* 1.3 79.4 - - - +
202I CYS* 1.3 64.4 + - - +
204I TYR* 3.1 8.4 + - - +
205I VAL* 2.9 34.5 + - + +
157K ARG* 3.0 24.6 - - - +
3L HIS* 2.5 50.9 + - - +
4L SER* 3.9 18.0 + - - +
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Residues in contact with CYS 202 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154I ILE* 4.1 17.7 - - - -
191I ILE* 5.2 4.7 - - - -
192I LEU 6.1 0.2 - - - -
197I HIS* 4.0 12.3 - - + +
198I ASP 3.3 3.6 + - - +
199I LEU 3.1 8.1 + - - +
201I ARG* 1.3 78.4 - - - +
203I GLN* 1.3 57.9 + - - +
205I VAL* 4.0 0.9 - - - +
206I THR* 2.8 41.9 + - - -
232I ASN* 4.2 7.0 - - - -
233I MET 4.4 0.4 - - - -
234I VAL* 3.5 11.0 - - - -
235I THR* 3.2 44.2 - - - +
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Residues in contact with GLN 203 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199I LEU* 3.0 11.6 + - - +
200I LYS* 3.4 13.2 - - - +
202I CYS* 1.3 78.4 - - - +
204I TYR* 1.3 56.8 + - - +
206I THR* 3.2 2.4 + - - -
207I GLU* 2.6 59.1 + - - +
234I VAL* 3.8 15.7 - - + +
252I ALA* 3.4 37.9 + - + +
255I THR* 3.7 15.2 - - - +
256I ALA* 3.9 5.8 - - + +
259I ARG* 3.2 16.6 - - - +
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Residues in contact with TYR 204 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200I LYS 3.0 12.1 + - - +
201I ARG* 3.3 11.9 - - - +
203I GLN* 1.3 75.5 - - - +
205I VAL* 1.3 69.1 + - + +
207I GLU* 3.1 13.7 + - + +
208I LYS* 3.0 53.9 + - + +
118K GLY 4.6 0.6 + - - -
3L HIS* 3.1 48.4 + + - +
4L SER* 3.5 28.0 - - - +
5L TYR 5.3 0.7 - - - -
221L HIS* 3.0 34.0 - + + -
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Residues in contact with VAL 205 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154I ILE* 3.9 25.8 - - + -
159I PRO* 3.6 31.9 - - + -
164I ILE* 6.0 0.2 - - + -
191I ILE* 3.7 16.2 - - + -
201I ARG* 2.9 27.2 + - + +
202I CYS 4.0 0.4 - - - +
204I TYR* 1.3 77.7 - - + +
206I THR* 1.3 64.9 + - - +
208I LYS* 3.2 5.9 + - + +
209I VAL* 2.9 25.4 + - + +
3L HIS* 3.9 26.0 - - + +
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Residues in contact with THR 206 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191I ILE* 3.4 16.8 - - + +
202I CYS* 2.8 28.6 + - - -
203I GLN* 3.5 6.1 - - - -
205I VAL* 1.3 75.5 - - - +
207I GLU* 1.3 64.0 + - - +
209I VAL* 3.8 0.3 - - - +
210I LEU* 2.9 46.3 + - + +
231I PRO* 5.8 2.2 - - + -
232I ASN* 3.3 28.0 + - - +
234I VAL* 4.4 8.7 - - + +
256I ALA* 4.1 14.8 - - + -
257I LEU* 5.9 1.1 - - + -
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Residues in contact with GLU 207 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203I GLN* 2.6 51.5 + - - +
204I TYR* 3.4 11.4 + - + +
206I THR* 1.3 77.4 - - - +
208I LYS* 1.3 60.9 + - + +
211I ALA* 2.9 30.4 + - - +
256I ALA* 3.7 23.7 - - - +
259I ARG* 3.0 32.0 + - - +
260I THR* 3.4 16.4 - - + +
218L SER* 5.5 0.4 - - - -
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Residues in contact with LYS 208 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I ILE* 4.7 13.7 - - + +
204I TYR* 3.0 60.7 + - + +
205I VAL* 3.7 7.4 - - + +
207I GLU* 1.3 76.0 - - + +
209I VAL* 1.3 67.5 + - - +
211I ALA* 3.4 6.1 + - - +
212I ALA* 3.1 22.7 + - - +
215L LYS* 5.6 0.5 - - - -
218L SER* 2.5 43.2 + - - +
219L ASP* 4.7 2.9 - - - +
221L HIS* 3.2 19.9 + - - +
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Residues in contact with VAL 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152I LEU* 3.3 37.2 - - + -
159I PRO* 4.8 0.7 - - + -
164I ILE* 4.4 22.0 - - + -
189I PRO* 4.2 15.5 - - + +
191I ILE* 3.6 18.8 - - + -
205I VAL* 2.9 28.2 + - + +
206I THR 3.8 3.1 - - - +
208I LYS* 1.3 76.3 - - - +
210I LEU* 1.3 65.0 + - + +
212I ALA* 3.0 5.7 + - - +
213I VAL* 2.9 37.7 + - + +
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Residues in contact with LEU 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I PRO* 4.0 17.3 - - + -
191I ILE* 6.5 0.2 - - + -
206I THR* 2.9 38.9 + - + +
209I VAL* 1.3 77.0 - - + +
211I ALA* 1.3 65.3 + - - +
213I VAL* 2.9 17.1 + - + +
214I TYR* 2.9 23.9 + - + -
229I LEU* 3.9 33.4 - - + -
231I PRO* 4.7 7.2 - - + -
256I ALA 5.0 0.7 - - - +
257I LEU* 3.8 26.5 - - + -
260I THR* 3.5 28.9 - - + +
261I VAL* 4.5 0.4 - - + -
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Residues in contact with ALA 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207I GLU 2.9 19.3 + - - +
208I LYS 3.6 4.5 - - - +
209I VAL 3.3 0.2 - - - -
210I LEU* 1.3 77.0 - - - +
212I ALA* 1.3 60.7 + - - +
214I TYR* 3.8 3.8 + - - +
215I LYS* 3.3 21.3 + - - +
260I THR* 4.1 14.5 - - + +
215L LYS* 3.8 13.3 - - + +
218L SER* 3.5 32.3 - - - +
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Residues in contact with ALA 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I ILE* 3.5 28.9 - - + -
165I LEU* 6.1 0.7 - - - -
168I ALA* 4.1 9.8 - - + +
208I LYS 3.1 8.4 + - - +
209I VAL 3.0 9.3 + - - +
211I ALA* 1.3 74.1 - - - +
213I VAL* 1.3 68.0 + - - +
215I LYS* 3.2 3.3 + - - +
216I ALA* 3.0 24.1 + - - +
215L LYS* 3.9 20.8 - - - +
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Residues in contact with VAL 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168I ALA* 4.0 16.7 - - + +
171I LEU* 4.2 12.8 - - + -
187I VAL* 3.9 28.0 - - + -
189I PRO* 4.1 18.6 - - + -
209I VAL* 2.9 35.6 + - + +
210I LEU* 3.3 11.0 - - + +
212I ALA* 1.3 75.8 - - - +
214I TYR* 1.3 67.0 + - + +
216I ALA* 3.3 4.1 + - - +
217I LEU* 3.0 36.0 + - + +
229I LEU* 5.3 1.1 - - + -
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Residues in contact with TYR 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I VAL* 5.7 1.5 - - + +
210I LEU* 2.9 24.7 + - + +
211I ALA* 4.5 2.5 - - - +
213I VAL* 1.3 78.3 - - + +
215I LYS* 1.3 66.0 + - - +
217I LEU* 3.2 17.0 + - + +
218I SER* 2.9 22.3 + - - -
224I LEU* 3.6 35.6 - - + +
227I THR* 5.1 2.9 + - - -
228I LEU 5.2 0.7 - - - -
229I LEU* 3.4 40.3 - - + +
260I THR 3.9 17.3 - - - +
261I VAL* 3.7 21.6 - - + +
262I PRO* 3.7 19.3 - - + -
265I VAL* 3.5 26.2 - - + +
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Residues in contact with LYS 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211I ALA 3.3 15.3 + - - +
212I ALA* 3.2 5.9 + - - +
214I TYR* 1.3 78.2 - - - +
216I ALA* 1.3 57.7 + - - +
218I SER* 3.2 5.2 + - - -
219I ASP* 2.9 68.4 + - - +
208L LYS 5.5 0.9 - - - -
211L ALA* 3.7 25.1 - - + +
212L ALA* 3.7 28.2 - - - +
215L LYS* 3.9 30.5 - - + -
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Residues in contact with ALA 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168I ALA* 3.4 35.4 - - + +
169I ASN* 4.3 4.7 - - - +
172I ALA* 3.8 6.3 - - + -
212I ALA 3.0 12.0 + - - +
213I VAL 3.4 8.1 - - - +
215I LYS* 1.3 75.7 - - - +
217I LEU* 1.3 68.5 + - - +
219I ASP* 2.9 10.8 + - - +
220I HIS* 2.9 28.9 + - + -
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Residues in contact with LEU 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171I LEU* 4.7 0.9 - - + -
172I ALA* 3.7 21.3 - - + +
175I ALA* 3.9 8.5 - - + -
187I VAL* 4.4 18.6 - - + -
213I VAL* 3.0 27.4 + - + +
214I TYR* 3.2 39.9 + - + +
216I ALA* 1.3 76.8 - - - +
218I SER* 1.3 63.6 + - - +
220I HIS 3.2 1.4 + - - -
221I HIS 3.1 3.8 + - - -
222I VAL* 3.0 61.0 + - + +
224I LEU* 4.0 15.3 - - + -
227I THR* 5.5 1.8 - - - +
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Residues in contact with SER 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214I TYR 2.9 13.5 + - - -
215I LYS 3.3 10.3 - - - -
217I LEU* 1.3 76.7 - - - +
219I ASP* 1.3 58.5 + - - +
221I HIS* 2.9 12.0 + - - -
222I VAL 5.0 2.9 - - - +
224I LEU* 6.0 0.2 - - - +
207L GLU 4.8 0.5 + - - -
208L LYS* 2.4 46.2 + - - +
211L ALA* 3.4 30.5 - - - +
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Residues in contact with ASP 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215I LYS* 2.9 51.5 + - - +
216I ALA* 2.9 11.0 + - - +
218I SER* 1.3 78.3 + - - +
220I HIS* 1.3 66.6 + - + +
221I HIS* 3.4 18.7 + - - -
162J LEU* 3.9 14.7 - - + +
165J LEU* 4.1 22.9 - - + +
208L LYS* 4.5 4.5 - - - +
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Residues in contact with HIS 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169I ASN* 2.8 29.3 + - - -
172I ALA* 3.4 29.7 - - + +
173I ARG* 3.8 34.9 + - + +
176I SER* 3.7 18.9 + - - -
216I ALA* 2.9 22.4 + - - +
217I LEU 3.2 2.7 + - - +
218I SER 3.1 0.2 - - - -
219I ASP* 1.3 81.9 - - + +
221I HIS* 1.3 76.0 + - - +
222I VAL* 3.3 2.4 + - + -
116J LEU* 5.9 2.1 - - + +
117J ALA 4.4 3.3 - - - +
162J LEU* 3.6 29.4 - - + +
165J LEU* 4.2 3.4 - - + +
166J GLU* 4.2 9.4 - - + -
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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) + - + + + + + -
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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