Contacts of the helix formed by residues 197 - 221 (chain C) in PDB entry 1XPM
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 197 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C TYR 4.2 6.1 - - - +
184C ASP 2.9 13.7 + - - +
186C TRP* 4.9 2.4 - - + -
196C VAL* 1.3 74.1 - - - +
198C GLY* 1.3 64.4 + - - +
199C ALA* 3.9 5.9 + - - +
200C LEU* 2.8 49.4 + - + +
201C SER* 2.8 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 198 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C VAL* 3.4 15.7 + - - +
197C ASP* 1.3 71.2 - - - +
199C ALA* 1.3 60.8 + - - +
201C SER* 2.5 26.7 + - - -
202C LYS* 3.6 8.1 + - - +
3402C CAA 4.0 28.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C ASP* 3.4 5.4 + - - +
198C GLY* 1.3 72.6 - - - +
200C LEU* 1.3 64.8 + - - +
202C LYS* 3.1 22.4 + - - +
203C ASP* 3.5 6.9 + - - +
3402C CAA 5.0 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C VAL* 3.9 21.8 - - + -
183C TYR 3.7 24.5 - - - +
184C ASP* 3.8 10.8 - - - -
197C ASP* 2.8 33.5 + - + +
199C ALA* 1.3 75.6 - - - +
201C SER* 1.3 63.2 + - - +
202C LYS 3.2 0.3 + - - -
203C ASP* 3.3 12.8 + - + +
204C ALA* 3.0 26.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 201 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C ASP* 3.6 26.7 - - - +
185C PHE* 5.4 1.1 - - - -
196C VAL* 4.7 4.3 - - - -
197C ASP 2.8 11.4 + - - -
198C GLY* 2.5 25.2 + - - -
200C LEU* 1.3 76.4 - - - +
202C LYS* 1.3 60.5 + - - +
204C ALA* 4.0 1.3 - - - +
205C TYR* 3.1 24.9 + - - +
3402C CAA 2.8 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 202 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C GLY 3.8 13.0 - - - +
199C ALA* 3.1 9.8 + - - +
200C LEU 3.1 0.6 - - - -
201C SER* 1.3 78.5 + - - +
203C ASP* 1.3 66.1 + - - +
205C TYR* 3.3 1.9 + - - +
206C ILE* 3.0 33.2 + - + +
236C PHE* 5.4 4.0 - - + -
239C MET* 4.1 30.3 - - + -
242C LYS* 5.9 5.4 - - + -
3402C CAA 4.9 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C ALA 3.5 6.9 + - - +
200C LEU* 3.3 16.2 + - + +
202C LYS* 1.3 78.6 - - - +
204C ALA* 1.3 58.4 + - - +
206C ILE* 3.4 5.5 + - - +
207C ARG* 2.8 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C VAL* 4.3 17.9 - - + -
184C ASP* 4.0 17.3 - - + +
200C LEU* 3.0 19.7 + - + +
201C SER 4.1 0.7 - - - +
203C ASP* 1.3 76.4 - - - +
205C TYR* 1.3 62.3 + - - +
207C ARG* 3.9 5.8 - - - +
208C SER* 3.0 25.8 + - - -
305C TYR* 3.4 18.9 + - - +
309C SER* 5.0 2.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C SER 3.1 18.7 + - - +
202C LYS* 3.6 6.3 - - - +
204C ALA* 1.3 80.1 - - - +
206C ILE* 1.3 68.5 + - + +
208C SER* 3.5 2.9 + - - -
209C PHE* 3.2 19.5 + - + +
232C PHE* 3.7 17.0 - + - +
233C HIS* 2.9 40.6 + + + +
235C PRO* 4.3 0.2 - - + -
239C MET* 4.3 25.4 - - + -
240C GLY* 4.7 4.3 - - - -
243C ALA* 3.6 29.4 - - + -
303C PHE* 4.3 16.5 - + - -
305C TYR* 3.5 28.8 + + + -
3402C CAA 3.1 28.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C LYS* 3.0 20.9 + - + +
203C ASP* 4.0 4.0 - - - +
205C TYR* 1.3 75.2 - - - +
207C ARG* 1.3 64.9 + - - +
209C PHE* 3.2 5.7 + - + +
210C GLN* 2.9 43.2 + - - +
239C MET* 4.3 14.4 - - + -
242C LYS* 4.1 27.1 - - + +
243C ALA* 4.0 17.5 - - + -
246C SER* 3.7 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C TYR* 3.2 19.9 + - + -
180C GLU* 2.8 36.0 + - - +
203C ASP 2.8 23.2 + - - +
204C ALA* 3.9 5.8 - - - +
206C ILE* 1.3 72.6 - - - +
208C SER* 1.3 58.6 + - - +
210C GLN* 3.2 10.2 + - - +
211C GLN* 2.8 63.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C TYR* 4.2 18.1 + - - -
204C ALA 3.0 19.7 + - - -
205C TYR 3.6 0.7 - - - -
207C ARG* 1.3 76.1 - - - +
209C PHE* 1.3 58.2 + - - +
211C GLN* 4.0 0.5 - - - +
212C SER* 2.8 35.9 + - - -
303C PHE* 3.6 1.5 - - - -
305C TYR* 3.5 22.8 - - - -
309C SER* 4.8 5.6 + - - -
310C VAL 4.0 0.2 - - - -
311C GLY* 3.2 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C TYR* 3.2 11.5 + - + +
206C ILE* 3.5 9.6 - - - +
208C SER* 1.3 80.4 - - - +
210C GLN* 1.3 58.1 + - - +
212C SER* 3.9 0.5 - - - -
213C TRP* 2.9 35.5 + - + +
230C LEU* 4.4 2.7 - - + -
232C PHE* 3.3 33.2 - + - -
243C ALA* 3.6 28.5 - - + -
246C SER* 4.3 3.4 - - - -
247C ILE* 3.3 44.4 - - + -
303C PHE* 3.4 48.8 - + + -
313C PHE* 4.2 17.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 210 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ILE* 2.9 32.9 + - + +
207C ARG* 3.2 8.6 + - - +
209C PHE* 1.3 79.7 - - + +
211C GLN* 1.3 65.7 + - - +
213C TRP* 3.9 3.8 - - - +
214C ASN* 2.9 43.2 + - - +
246C SER* 3.5 40.7 + - - +
247C ILE* 4.3 12.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C TYR* 3.6 44.1 + - + +
207C ARG* 2.8 53.8 + - + +
210C GLN* 1.3 82.4 + - - +
212C SER* 1.3 61.2 + - - +
214C ASN* 3.9 14.8 + - - +
215C GLU* 3.2 23.9 + - - +
101D PHE* 4.0 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C VAL* 3.6 12.6 - - - +
177C ALA 5.7 0.2 - - - -
178C TYR* 3.4 21.9 - - - +
208C SER 2.8 22.0 + - - -
209C PHE 3.9 0.7 - - - -
211C GLN* 1.3 74.8 - - - +
213C TRP* 1.3 67.8 + - - +
215C GLU* 3.5 2.1 + - - +
216C TYR* 3.0 23.2 + - - +
303C PHE* 3.7 14.3 - - - -
311C GLY 3.6 14.7 - - - -
313C PHE* 4.2 19.1 - - - -
101D PHE* 5.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C PHE* 2.9 26.0 + - + +
210C GLN* 3.9 2.5 - - - +
212C SER* 1.3 77.6 - - - +
214C ASN* 1.3 71.2 + - - +
216C TYR* 3.1 21.0 + + - +
217C ALA* 2.8 46.6 + - + +
222C LYS 4.4 0.7 - - - -
223C SER* 3.7 26.2 - - - -
224C LEU* 3.5 40.9 - - + +
227C PHE* 3.5 26.0 - + - -
247C ILE* 4.3 23.8 - - + +
313C PHE* 3.5 33.6 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C GLN* 2.9 35.0 + - - +
211C GLN* 3.9 17.7 + - - +
212C SER 3.4 0.2 - - - -
213C TRP* 1.3 88.0 + - - +
215C GLU* 1.3 61.0 + - - +
217C ALA* 3.4 4.8 + - - +
218C LYS* 3.0 24.3 + - - +
247C ILE* 6.0 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C VAL* 3.7 11.4 - - + -
211C GLN 3.2 7.0 + - - +
212C SER 4.0 2.7 - - - +
214C ASN* 1.3 76.2 - - - +
216C TYR* 1.3 61.1 + - - +
218C LYS* 3.3 22.9 + - - +
219C ARG* 2.7 74.1 + - - +
101D PHE* 3.4 50.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ASP* 2.7 58.5 + - + -
176C VAL* 3.5 12.3 - - + +
212C SER 3.0 18.8 + - - +
213C TRP* 3.1 20.4 + + - +
215C GLU* 1.3 77.4 - - - +
217C ALA* 1.3 60.1 + - - +
219C ARG* 3.3 3.8 + - - -
220C GLN* 2.9 39.4 + - + +
222C LYS* 3.5 32.1 - - + +
227C PHE* 3.6 21.8 - + - -
313C PHE* 3.5 29.2 - + + -
314C TYR* 4.3 3.4 - - - -
315C SER* 3.5 10.5 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
213C TRP* 2.8 40.5 + - + +
214C ASN* 3.8 6.1 - - - +
216C TYR* 1.3 79.2 - - - +
218C LYS* 1.3 56.5 + - - +
221C GLY* 2.8 27.0 + - - -
222C LYS 3.2 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C ASN 3.0 18.2 + - - +
215C GLU* 3.6 24.1 + - - +
216C TYR 3.2 0.2 - - - -
217C ALA* 1.3 79.3 - - - +
219C ARG* 1.3 62.6 + - + +
221C GLY* 3.6 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B GLN 5.4 1.0 - - - +
221B GLY 5.3 4.0 - - - +
175C ALA 4.8 4.0 + - - -
176C VAL* 3.7 28.9 - - - +
215C GLU* 2.7 46.8 + - - +
216C TYR* 3.9 3.4 - - - +
218C LYS* 1.3 79.6 - - + +
220C GLN* 1.3 76.4 + - - +
99D GLN* 5.1 2.0 + - - -
101D PHE* 3.6 31.7 + - - +
131D GLU* 5.6 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ARG 5.4 1.0 - - - +
220B GLN* 3.8 18.1 - - - +
221B GLY 5.7 0.4 - - - -
173C GLU 4.7 3.6 + - - +
174C ASP* 3.5 30.4 + - + +
216C TYR* 2.9 42.5 + - + +
219C ARG* 1.3 91.8 + - + +
221C GLY* 1.3 62.7 + - - +
222C LYS* 3.3 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LYS 5.8 0.2 - - - +
219B ARG 5.2 5.0 - - - +
221B GLY* 4.9 16.4 + - - -
217C ALA 2.8 11.6 + - - -
218C LYS 3.6 5.4 + - - -
219C ARG 3.5 2.2 - - - -
220C GLN* 1.3 80.1 - - - +
222C LYS* 1.3 60.3 + - - +
226C ASP* 4.7 0.7 - - - +
----------------------------------------------------------
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