Contacts of the helix formed by residues 223 - 244 (chain C) in PDB entry 5YL4
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 THR 223 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C VAL* 5.8 0.9 - - - -
221C ARG* 4.2 11.4 - - - +
222C PRO* 1.3 76.8 - - - +
224C TYR* 1.3 64.3 + - - +
225C THR* 3.4 14.3 + - - -
226C ASN* 2.9 29.9 + - - +
227C LEU* 3.0 25.8 + - - +
323D MET* 5.7 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLN* 3.7 14.8 - - - -
15C GLN* 4.3 7.0 - - - +
177C VAL* 3.0 32.1 + - + +
179C THR* 4.0 8.7 - - - +
223C THR* 1.3 73.5 - - - +
225C THR* 1.3 57.5 + - - +
227C LEU* 4.4 10.5 - - + -
228C ASN* 2.8 39.4 + - - +
501C GTP 2.9 88.3 + + - +
245D GLN* 4.0 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 225 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C THR* 3.1 13.3 + - - -
224C TYR* 1.3 77.5 - - - +
226C ASN* 1.3 62.8 + - - +
228C ASN* 4.3 4.9 - - - +
229C ARG* 3.4 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 226 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C CYS* 3.9 11.2 - - - -
217C LEU* 5.6 1.6 - - - +
219C ILE* 3.6 30.4 - - + +
221C ARG 4.5 0.5 - - - +
222C PRO* 3.5 13.6 - - + +
223C THR* 2.9 36.8 + - - +
225C THR* 1.3 79.0 - - - +
227C LEU* 1.3 64.1 + - - +
229C ARG* 3.6 8.5 + - - +
230C LEU* 3.5 14.4 + - - +
367C ASP* 3.0 28.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C VAL* 4.4 17.7 - - + -
206C ASN* 3.9 29.2 - - - +
209C ILE* 3.5 28.2 - - + +
210C TYR* 3.6 26.0 - - + +
213C CYS* 4.1 7.2 - - - -
222C PRO* 4.1 10.3 - - + -
223C THR 3.0 18.8 + - - +
224C TYR* 3.8 17.9 - - + +
226C ASN* 1.3 77.0 - - - +
228C ASN* 1.3 62.7 + - - +
230C LEU* 3.2 5.2 + - - +
231C ILE* 2.9 32.2 + - + +
501C GTP 4.3 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLN* 3.6 23.0 + - - +
16C ILE* 3.4 17.1 - - + +
19C ALA* 3.6 18.7 - - + +
224C TYR* 2.8 28.4 + - - +
225C THR* 4.3 5.6 - - - +
227C LEU* 1.3 72.1 - - - +
229C ARG* 1.3 57.3 + - - +
231C ILE* 3.6 6.8 - - - +
232C SER* 2.9 31.7 + - - -
501C GTP 2.7 47.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ALA* 4.6 7.4 - - + -
22C GLU* 5.6 0.4 + - - -
225C THR* 3.4 38.9 + - + +
226C ASN* 3.9 7.3 - - - +
227C LEU 3.3 0.4 - - - -
228C ASN* 1.3 79.3 - - + +
230C LEU* 1.3 59.5 + - - +
232C SER* 2.6 19.6 + - - -
233C GLN* 3.5 16.1 + - - +
363C VAL* 4.1 30.0 - - + +
364C PRO 4.1 10.5 + - - -
365C GLY* 3.4 26.0 + - - -
366C GLY* 3.8 15.8 - - - -
367C ASP* 4.1 15.8 + - - +
368C LEU* 4.4 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C ILE* 3.9 25.4 - - + -
212C ILE* 3.5 32.5 - - + -
213C CYS* 4.0 13.7 - - - -
217C LEU* 5.0 2.2 - - + -
226C ASN 3.5 9.3 + - - +
227C LEU 3.2 9.0 + - - +
229C ARG* 1.3 75.4 - - - +
231C ILE* 1.3 65.7 + - - +
233C GLN* 3.0 14.8 + - + +
234C ILE* 3.1 33.5 + - + +
272C TYR* 4.5 5.2 - - + -
275C VAL* 3.7 27.4 - - + -
302C MET* 5.7 1.1 - - + -
368C LEU* 4.3 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ILE* 3.8 36.6 - - + -
169C PHE* 6.5 0.2 - - + -
171C ILE* 4.8 2.7 - - + -
204C VAL* 3.9 38.1 - - + -
206C ASN* 4.6 0.7 - - - +
209C ILE* 4.1 13.9 - - + -
227C LEU* 2.9 23.7 + - + +
228C ASN* 3.6 6.7 - - - +
230C LEU* 1.3 75.2 - - - +
232C SER* 1.3 57.4 + - - +
234C ILE* 3.0 12.8 + - + +
235C VAL* 2.8 35.5 + - + +
501C GTP 3.6 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ALA* 3.8 26.9 + - - +
20C CYS* 3.9 19.2 - - - -
23C LEU* 3.4 18.1 - - - +
24C TYR* 5.4 0.3 - - - -
228C ASN 2.9 14.6 + - - -
229C ARG* 2.6 28.6 + - - +
231C ILE* 1.3 73.0 - - - +
233C GLN* 1.3 58.2 + - - +
235C VAL* 3.9 0.5 - - - +
236C SER* 2.8 30.5 + - - -
363C VAL* 5.9 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 3.7 23.4 - - - +
27C GLU* 5.2 1.2 - - - +
229C ARG 3.5 15.1 + - - +
230C LEU* 3.0 9.4 + - + +
232C SER* 1.3 78.8 + - - +
234C ILE* 1.3 57.1 + - - +
236C SER* 3.4 2.5 + - - -
237C SER* 3.0 31.1 + - - -
272C TYR* 3.8 31.8 + - + +
320C ARG* 4.8 6.2 + - - -
360C PRO* 4.5 9.4 - - - +
361C THR 2.8 28.6 + - - +
362C VAL* 4.2 11.2 - - - +
363C VAL* 4.9 2.8 - - - +
368C LEU* 3.9 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C PHE* 5.5 1.3 - - + -
204C VAL* 5.7 6.1 - - + -
209C ILE* 5.0 0.2 - - + -
230C LEU* 3.1 47.3 + - + +
231C ILE* 3.0 9.2 + - + +
233C GLN* 1.3 75.5 - - - +
235C VAL* 1.3 68.1 + - + +
237C SER* 3.2 8.7 + - - -
238C ILE* 3.1 39.3 + - + +
270C ALA* 4.3 7.4 - - + -
272C TYR* 3.6 27.1 - - + -
302C MET* 3.4 46.7 - - + -
376C CYS* 4.5 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 235 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ILE* 4.9 0.2 - - + -
20C CYS* 3.8 20.4 - - - -
24C TYR* 3.3 21.3 - - - +
138C PHE* 3.9 24.9 - - + -
169C PHE* 3.7 38.6 - - + -
204C VAL* 6.1 0.4 - - + -
231C ILE* 2.8 36.6 + - + +
232C SER 3.9 0.4 - - - +
234C ILE* 1.3 71.8 - - + +
236C SER* 1.3 58.1 + - - +
238C ILE* 3.2 3.3 + - - +
239C THR* 2.9 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 236 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 4.0 8.7 - - - -
24C TYR* 4.1 7.4 - - - -
27C GLU* 2.5 29.3 + - - -
232C SER 2.8 23.4 + - - -
233C GLN* 3.7 5.8 - - - -
234C ILE 3.2 0.4 - - - -
235C VAL* 1.3 74.0 - - - +
237C SER* 1.3 51.9 + - - +
239C THR* 3.6 2.9 - - - -
240C ALA* 2.7 34.3 + - - +
243C ARG* 2.7 27.1 + - - +
320C ARG* 2.9 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 237 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C GLN 3.0 16.5 + - - -
234C ILE 3.2 10.1 + - - -
236C SER* 1.3 76.1 - - - +
238C ILE* 1.3 61.5 + - - +
240C ALA* 3.8 11.4 + - - +
241C SER* 4.7 1.9 + - - -
272C TYR* 3.4 18.8 + - - -
318C LEU* 3.7 20.2 + - - +
320C ARG* 3.7 23.3 + - - +
356C ASN* 5.4 1.7 + - - -
374C ALA* 5.6 0.5 - - - +
375C VAL 5.1 0.5 - - - -
376C CYS* 3.6 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C PHE* 3.9 33.2 - - + -
202C PHE* 4.1 16.6 - - + -
234C ILE* 3.1 34.8 + - + +
235C VAL 3.2 5.1 + - - +
237C SER* 1.3 77.6 - - - +
239C THR* 1.3 59.8 + - + +
241C SER* 3.3 18.4 + - - -
252C LEU* 3.7 37.1 - - + +
270C ALA* 4.9 2.2 - - + -
318C LEU* 4.0 6.5 - - + +
376C CYS* 4.3 7.6 - - - -
378C LEU* 4.0 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C TYR* 3.0 20.2 + - - +
52C PHE* 3.7 23.6 - - + -
136C LEU* 3.9 17.5 - - + -
169C PHE* 5.0 2.5 - - + -
235C VAL* 2.9 21.7 + - + +
238C ILE* 1.3 78.9 - - + +
240C ALA* 1.3 54.6 + - - +
241C SER 3.2 2.9 - - - -
242C LEU* 2.8 36.2 + - + +
243C ARG* 3.0 35.0 + - - -
252C LEU* 5.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C SER 2.7 22.7 + - - +
237C SER* 3.8 9.6 - - - +
238C ILE 3.4 1.2 - - - -
239C THR* 1.3 71.7 - - - +
241C SER* 1.3 61.4 + - - +
243C ARG* 3.6 14.1 - - - +
244C PHE* 3.0 35.5 + - + +
320C ARG* 4.0 23.6 - - - +
356C ASN* 3.6 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C SER 4.7 2.0 + - - -
238C ILE 3.3 18.0 + - - -
240C ALA* 1.3 77.0 - - - +
242C LEU* 1.3 60.6 + - - +
244C PHE 3.8 4.3 - - - +
249C ASN* 3.1 32.2 - - - +
250C VAL 3.2 27.4 - - - -
251C ASP* 4.9 6.3 - - - +
252C LEU* 3.6 20.3 + - - +
255C PHE* 5.2 4.3 - - - -
318C LEU* 5.4 3.2 - - - +
356C ASN* 4.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C CYS* 4.5 13.0 - - + -
48C SER* 3.1 11.3 + - - +
51C THR* 3.0 26.6 + - + +
52C PHE* 3.8 32.1 - - + -
133C GLN* 3.8 27.1 - - - +
136C LEU* 5.2 3.8 - - + -
167C LEU* 6.1 0.2 - - + -
239C THR* 2.8 22.0 + - + +
241C SER* 1.3 77.3 - - - +
243C ARG* 1.3 57.5 + - - +
244C PHE 3.5 1.1 + - - -
251C ASP* 5.5 2.9 - - + -
252C LEU* 4.1 40.2 - - + +
253C THR* 5.4 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C TYR* 3.4 26.2 - - - -
27C GLU* 2.7 22.4 + - - +
28C HIS* 3.4 45.8 + - + +
48C SER* 3.3 25.1 - - - +
49C PHE* 3.3 5.3 + - - +
51C THR* 4.3 0.7 - - - +
52C PHE* 3.6 42.2 - - + -
236C SER* 2.7 45.9 + - - +
239C THR* 3.0 22.0 + - - +
240C ALA* 3.2 11.7 + - - +
242C LEU* 1.3 77.1 - - - +
244C PHE* 1.3 68.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLU* 3.5 21.8 - - + -
28C HIS* 3.4 28.0 - + - -
48C SER* 3.6 11.1 + - - -
240C ALA* 3.0 25.4 + - + +
241C SER 3.8 4.2 - - - +
242C LEU 3.5 0.8 - - - -
243C ARG* 1.3 103.5 - - + +
245C ASP* 1.3 67.2 + - - +
249C ASN* 3.2 21.7 - - - +
320C ARG* 3.7 9.9 - - - -
356C ASN* 3.8 11.4 - - + +
358C GLN* 3.7 41.5 - - + -
----------------------------------------------------------
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