Contacts of the helix formed by residues 207 - 219 in PDB entry 2IIL
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 HIS 207
.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176 TYR* 3.7 19.4 + - - +
177 GLN 4.5 0.7 + - - -
194 ASP 5.1 0.2 - - - -
196 TYR* 4.9 16.7 - + + -
203 PRO* 5.2 7.3 - - + +
204 SER* 3.0 31.5 + - - -
205 ASP 6.1 0.2 - - - -
206 SER* 1.3 71.6 + - - +
208 ARG* 1.3 62.7 + - - +
209 LEU* 3.4 2.5 - - + +
210 SER* 3.0 37.0 + - - +
211 TYR* 3.4 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 208
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12 HIS 5.2 0.2 + - - -
177 GLN* 2.7 68.7 - - - +
178 VAL* 3.2 33.6 - - - +
190 ASP* 3.4 10.9 + - - +
193 LYS 3.2 22.7 - - - +
194 ASP* 3.3 7.7 + - - +
195 LYS* 3.1 65.1 - - - +
205 ASP* 5.6 2.2 - - - +
206 SER* 2.9 39.3 + - - +
207 HIS* 1.3 69.2 - - - +
209 LEU* 1.3 60.2 + - - +
211 TYR 3.2 1.2 + - - -
212 THR* 2.9 21.2 + - - -
291 GLN* 4.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194 ASP* 3.0 40.8 + - + +
196 TYR* 5.1 6.5 - - + -
198 CYS* 6.3 1.6 - - - -
207 HIS* 3.4 2.4 - - + +
208 ARG* 1.3 77.7 - - - +
210 SER* 1.3 61.3 + - - +
212 THR* 3.4 2.4 + - - -
213 THR* 3.1 25.4 + - - +
288 TRP* 3.6 20.9 + - + +
291 GLN* 3.0 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176 TYR* 2.7 27.5 + - - -
207 HIS* 3.0 24.6 + - - +
209 LEU* 1.3 78.1 - - - +
211 TYR* 1.3 62.7 + - - +
213 THR* 3.1 26.0 - - - +
214 LEU* 3.2 11.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 211
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168 ALA 3.2 6.3 + - - -
169 SER* 2.6 24.4 + - - -
172 PRO* 3.1 35.8 - - + +
173 PHE* 3.5 27.8 - + - -
176 TYR* 3.3 22.0 - + + -
177 GLN* 3.2 40.6 - - + +
189 LEU* 4.1 0.9 - - + -
207 HIS 3.4 11.0 + - - +
208 ARG 3.2 1.4 + - - -
210 SER* 1.3 79.1 + - - +
212 THR* 1.3 59.9 + - - +
214 LEU* 3.0 23.3 + - + +
215 LEU* 2.9 60.0 + - + +
219 GLN* 4.2 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 212
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177 GLN* 3.2 1.5 + - - -
189 LEU* 3.1 38.3 - - + +
190 ASP 4.1 2.9 + - - -
191 ALA* 5.3 0.9 - - + -
208 ARG 2.9 19.1 + - - -
209 LEU 3.8 0.7 - - - -
211 TYR* 1.3 74.6 - - - +
213 THR* 1.3 55.1 + - - +
215 LEU* 3.2 2.8 + - - +
216 LEU* 3.0 52.5 + - + +
284 THR* 6.1 2.9 - - + -
288 TRP* 3.1 43.3 - - + +
291 GLN* 5.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 213
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209 LEU 3.1 16.6 + - - +
210 SER* 3.1 28.7 - - - +
212 THR* 1.3 74.8 - - - +
214 LEU* 1.4 55.3 - - - +
216 LEU* 3.4 5.6 + - - +
217 VAL* 3.0 35.8 + - - +
288 TRP* 4.8 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168 ALA 6.0 2.2 - - - +
176 TYR* 5.9 1.8 - - + -
210 SER 3.2 14.3 + - - +
211 TYR* 3.0 33.1 + - + +
213 THR* 1.4 74.9 - - - +
215 LEU* 1.3 58.4 + - + +
217 VAL* 3.4 8.0 - - + +
218 LEU* 2.9 57.7 + - + +
219 GLN* 4.7 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121 CYS* 5.3 1.8 - - - -
169 SER* 4.3 0.7 - - - +
173 PHE* 3.2 36.1 - - + -
189 LEU* 3.2 15.0 - - + -
211 TYR* 2.9 60.9 + - + +
212 THR 3.4 8.5 - - - +
214 LEU* 1.3 77.2 - - + +
216 LEU* 1.3 63.1 + - + +
219 GLN* 3.0 66.0 + - - +
220 TYR* 3.4 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189 LEU* 5.9 0.2 - - + -
212 THR* 3.0 49.1 + - + +
213 THR* 4.0 5.6 - - - +
215 LEU* 1.3 81.0 - - + +
217 VAL* 1.3 56.3 + - - +
220 TYR* 3.3 14.5 - - + +
221 PHE* 2.9 30.8 + - - +
280 THR* 3.7 30.5 - - + +
284 THR* 5.3 11.2 - - + -
285 VAL* 4.8 21.8 - - + -
288 TRP* 5.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 217
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213 THR* 3.0 25.2 + - + +
214 LEU* 3.4 12.8 - - + +
216 LEU* 1.3 76.0 - - - +
218 LEU* 1.3 73.9 + - + +
221 PHE* 3.5 9.6 + - + -
222 GLY* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129 PHE* 4.3 9.6 - - + -
165 LEU* 5.9 8.3 - - + -
168 ALA* 5.4 12.3 - - + -
214 LEU* 2.9 39.2 + - + +
217 VAL* 1.3 78.6 - - + +
219 GLN* 1.3 65.6 + - + +
222 GLY* 5.5 0.7 - - - -
223 PRO* 2.9 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 219
.
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121 CYS* 5.1 1.0 - - - -
125 THR* 5.1 1.4 + - - -
128 ILE* 2.8 35.0 - - + +
129 PHE* 4.3 8.7 - - + -
165 LEU 5.3 0.9 - - - +
168 ALA 4.4 1.4 - - - +
169 SER* 2.8 50.6 + - - +
211 TYR* 4.2 0.7 + - - -
214 LEU* 4.5 4.7 - - + +
215 LEU* 3.0 53.9 + - - +
218 LEU* 1.3 87.6 - - + +
220 TYR* 1.3 63.2 + - - +
223 PRO* 4.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
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