Contacts of the helix formed by residues 206 - 229 (chain C) in PDB entry 3AP3
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 206 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ALA* 4.4 21.2 - - - +
193C ILE* 4.0 11.0 - - - +
207C TYR* 1.3 60.3 + - - +
208C ARG* 3.3 11.3 + - - +
209C ASP* 2.8 34.5 + - - +
210C CYS* 2.9 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ARG 5.6 0.2 - - - -
189C VAL* 3.8 13.7 - - + -
190C HIS* 3.3 40.3 + - + -
193C ILE* 3.4 37.4 - - + +
194C THR* 4.2 3.6 - - - +
206C SER* 1.3 69.4 + - - +
208C ARG* 1.3 60.4 + - - +
210C CYS* 3.0 1.8 + - - -
211C LEU* 2.8 45.7 + - + +
304C HIS* 4.4 14.3 + - - +
305C ILE* 3.6 31.9 - - + -
306C PRO* 4.2 21.5 - - + -
309C VAL* 4.3 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C SER* 3.5 7.6 - - - +
207C TYR* 1.3 79.5 - - - +
209C ASP* 1.3 55.0 + - + +
212C THR* 2.7 35.6 + - - +
308C ASP* 3.1 33.5 + - - -
309C VAL* 3.8 15.9 - - + +
311C ARG* 4.2 1.8 - - - +
312C ASP* 2.8 31.5 + - - +
316C ILE* 3.7 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ILE 5.5 0.2 - - - +
200B ALA* 4.9 2.3 - - - -
201B GLY* 3.6 38.3 + - - +
202B PHE 5.7 0.7 - - - +
213B LYS* 5.1 3.1 + - - -
206C SER* 2.8 31.5 + - - +
208C ARG* 1.3 74.1 - - + +
210C CYS* 1.3 72.7 + - - +
212C THR* 3.4 7.1 + - - -
213C LYS* 3.1 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 210 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ALA* 6.1 4.9 - - - -
189C VAL* 3.2 35.2 - - + +
192C MET* 4.5 17.6 - - - +
193C ILE* 3.8 19.3 - - - -
206C SER 2.9 30.0 + - - +
207C TYR 3.0 0.6 + - - +
209C ASP* 1.3 81.0 + - - +
211C LEU* 1.3 56.8 + - - +
213C LYS* 3.5 6.6 - - - +
214C TRP* 3.0 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C GLY* 3.8 23.6 - - - +
186C ARG* 4.0 14.6 - - + +
189C VAL* 3.7 27.4 - - + -
207C TYR* 2.8 32.0 + - + +
210C CYS* 1.3 70.6 - - - +
212C THR* 1.3 55.9 + - - +
213C LYS 2.9 1.3 - - - -
214C TRP* 3.1 10.5 + - + +
215C ASN* 2.7 37.2 + - - +
305C ILE* 5.6 1.6 - - + -
309C VAL* 3.9 25.6 - - + -
313C MET* 4.8 11.0 - - + -
316C ILE* 3.5 18.6 - - + -
317C ALA* 5.0 8.9 - - + +
320C LEU* 5.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ARG* 2.7 26.9 + - - +
209C ASP* 3.7 6.1 - - - -
211C LEU* 1.3 74.8 - - - +
213C LYS* 1.3 58.2 + - + +
215C ASN* 3.1 5.2 - - + +
216C LYS* 3.0 30.7 + - + +
316C ILE* 3.6 25.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLY 5.7 0.6 + - - -
202B PHE 4.1 7.9 + - - +
203B ASP* 3.2 44.3 + - - +
204B LEU 5.5 1.1 - - - +
209B ASP* 5.4 0.4 + - - -
209C ASP* 3.1 25.5 + - - +
210C CYS* 3.5 9.0 - - - +
211C LEU 2.9 0.4 - - - -
212C THR* 1.3 78.3 - - + +
214C TRP* 1.3 67.0 + - - +
215C ASN 3.1 0.7 - - - -
216C LYS* 3.3 9.5 + - - +
217C ALA* 2.9 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C VAL* 3.6 37.2 - - + +
79C SER* 5.0 1.2 + - - -
183C ARG 3.7 12.9 + - - -
184C ASP* 5.0 0.2 - - - -
185C GLY* 3.1 37.2 - - - -
188C SER* 4.2 11.1 + - - -
189C VAL* 4.0 9.6 - - + -
192C MET* 5.4 2.0 - - + -
210C CYS 3.0 19.7 + - - +
211C LEU* 3.5 9.9 - - + +
213C LYS* 1.3 74.0 - - - +
215C ASN* 1.3 87.2 + - + +
217C ALA* 3.6 5.1 - - - +
218C ILE* 2.9 54.9 + - + +
317C ALA* 4.0 8.7 - - + -
319C MET* 4.0 10.8 - - + -
320C LEU* 3.6 35.4 - - + -
323C LEU* 3.9 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C LEU 2.7 16.4 + - - +
212C THR* 3.1 13.7 - - - +
214C TRP* 1.3 85.8 - - + +
216C LYS* 1.3 64.0 + - - +
218C ILE* 3.5 3.1 - - - +
219C GLU* 2.9 40.2 + - - +
316C ILE 3.6 15.5 - - - +
317C ALA* 3.4 4.8 - - - +
318C PRO* 3.3 18.7 - - - +
319C MET* 3.1 43.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C THR* 3.0 12.9 + - + +
213C LYS* 4.0 9.0 - - - +
215C ASN* 1.3 84.5 + - - +
217C ALA* 1.3 63.6 + - - +
219C GLU* 3.2 37.0 + - - +
220C VAL* 3.0 50.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C VAL* 3.9 16.4 - - + -
161C PHE* 4.9 15.7 - - + -
164C LYS* 5.0 8.5 - - - +
213C LYS 2.9 18.7 + - - +
214C TRP* 3.6 4.3 - - - +
216C LYS* 1.3 78.1 - - - +
218C ILE* 1.3 57.3 + - - +
220C VAL* 3.3 6.7 + - - +
221C MET* 3.1 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C VAL* 4.0 20.4 - - + +
180C LEU* 4.7 15.7 - - + -
181C MET 5.2 3.1 - - - +
182C VAL* 4.1 23.6 - - + -
183C ARG 6.0 0.4 - - - +
214C TRP* 2.9 51.6 + - + +
215C ASN 3.5 9.6 - - - +
217C ALA* 1.3 71.2 - - - +
219C GLU* 1.3 61.9 + - - +
221C MET* 4.2 7.6 - - - -
222C TYR* 3.0 30.1 + - + +
319C MET* 4.2 7.6 - - + -
323C LEU* 4.1 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C ASN* 2.9 27.8 + - - +
216C LYS* 3.2 45.3 + - - +
218C ILE* 1.3 73.7 - - - +
220C VAL* 1.3 67.7 + - - +
222C TYR* 4.0 1.9 - - - +
223C ALA* 3.3 19.2 + - - +
319C MET* 3.8 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C LYS* 4.0 39.5 - - - +
216C LYS* 3.0 43.2 + - + +
217C ALA* 3.5 7.4 - - - +
219C GLU* 1.3 77.1 - - - +
221C MET* 1.3 60.8 + - - +
222C TYR 3.0 0.4 - - - -
223C ALA* 2.9 25.0 + - - +
224C GLN* 3.1 16.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C GLY* 3.6 39.3 - - - +
76C VAL* 3.7 15.9 - - + +
160C PRO 4.0 11.2 - - - +
161C PHE* 3.9 21.5 - - + -
163C LEU* 4.1 19.3 - - - +
164C LYS* 3.8 33.4 - - + +
166C SER* 5.0 0.2 + - - -
180C LEU* 3.3 29.1 - - + +
217C ALA 3.1 20.8 + - - +
218C ILE* 3.4 8.0 + - - +
220C VAL* 1.3 75.6 - - - +
222C TYR* 1.3 57.4 + - - +
224C GLN* 3.9 4.4 - - - +
225C CYS* 3.3 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C LEU* 4.1 15.7 - - + +
182C VAL* 5.5 1.3 - - + -
218C ILE* 3.0 19.4 + - + +
219C GLU 4.0 3.4 - - - +
221C MET* 1.3 75.4 - - - +
223C ALA* 1.3 56.7 + - - +
224C GLN 3.2 1.3 - - - -
225C CYS* 3.1 1.7 + - + +
226C MET* 2.7 82.9 + - + +
235C PRO* 4.0 20.4 - - + +
237C TYR* 5.5 4.0 + - - -
319C MET* 4.5 16.2 - - + -
323C LEU* 4.3 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C GLU 3.3 11.5 + - - +
220C VAL* 2.9 12.1 + - - +
222C TYR* 1.3 77.3 - - - +
224C GLN* 1.3 53.2 + - + +
226C MET* 3.3 7.4 + - - +
227C GLU* 2.8 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C LEU 4.3 2.5 - - - +
164C LYS 3.0 21.5 + - - +
165C SER* 3.3 2.8 - - - -
166C SER* 3.0 24.8 + - - +
167C VAL* 2.7 55.0 + - + +
220C VAL* 3.1 19.4 + - + +
221C MET 3.9 7.2 - - - +
223C ALA* 1.3 73.3 - - + +
225C CYS* 1.3 56.5 + - - +
226C MET 3.0 1.3 - - - -
227C GLU* 3.0 8.2 + - - +
228C VAL* 2.8 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 225 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C LEU* 5.7 0.9 - - + -
166C SER* 4.3 2.6 + - - +
180C LEU* 3.9 12.6 - - + -
221C MET 3.3 16.8 + - - +
222C TYR* 3.1 5.7 + - - +
224C GLN* 1.3 78.7 - - - +
226C MET* 1.3 76.3 + - + +
228C VAL* 4.0 2.0 - - - -
229C GLY 3.8 12.8 + - - +
233C CYS* 2.0 70.9 - - - +
234C LEU 4.1 0.9 - - - -
235C PRO* 4.2 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 226 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C TYR* 2.7 73.5 + - + +
223C ALA* 3.6 7.2 - - - +
225C CYS* 1.3 90.8 - - - +
227C GLU* 1.3 65.4 + - - +
228C VAL 3.3 0.2 - - - -
229C GLY* 3.5 11.0 + - - -
230C LYS* 6.1 9.2 - - + +
233C CYS 4.9 2.0 - - - +
235C PRO* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C VAL* 3.8 30.0 - - + +
171C ARG* 4.8 6.1 + - - -
223C ALA 2.8 22.7 + - - +
224C GLN* 3.0 7.9 + - - +
226C MET* 1.3 74.8 - - - +
228C VAL* 1.3 63.5 + - - +
229C GLY* 3.2 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C SER* 4.3 12.3 - - - +
167C VAL* 4.1 29.6 - - + +
170C SER* 4.7 7.4 - - - -
178C PHE* 4.8 4.3 - - + -
224C GLN 2.8 24.0 + - - +
225C CYS* 3.9 5.8 - - - +
226C MET 3.3 0.2 - - - -
227C GLU* 1.3 73.8 - - - +
229C GLY* 1.3 56.6 + - - +
231C GLU* 6.0 0.2 - - - +
232C LYS* 3.0 49.5 - - + +
233C CYS* 3.7 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C CYS 3.8 6.7 + - - -
226C MET 3.5 10.7 + - - -
227C GLU 3.2 5.6 + - - -
228C VAL* 1.3 78.6 - - - +
230C LYS* 1.3 55.4 + - - -
231C GLU* 2.8 18.0 + - - -
232C LYS 2.9 14.0 + - - -
233C CYS* 3.0 12.5 + - - +
----------------------------------------------------------
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