Contacts of the strand formed by residues 238 - 250 (chain C) in PDB entry 5BZZ
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 PHE 238 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C MET* 3.7 20.6 - - + -
200C PHE 3.4 15.5 - - - +
201C GLU* 4.0 30.5 - - + -
234C ARG* 3.4 8.0 - - - +
235C GLU* 2.9 52.2 + - + +
237C LYS* 1.3 96.2 - - + +
239C MET* 1.3 60.4 + - - +
240C TYR* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C MET* 3.1 6.8 - - - +
200C PHE* 2.8 48.1 + - + +
203C ILE* 3.5 41.5 - - + -
210C THR* 4.3 4.5 - - - +
211C CYS* 4.0 22.4 - - - +
213C PRO* 4.0 19.1 - - - -
231C PRO* 3.9 27.1 - - + -
233C ARG 3.6 3.6 - - - -
234C ARG* 4.1 17.7 - - - +
237C LYS 3.9 1.0 + - - -
238C PHE* 1.3 74.7 - - - +
240C TYR* 1.3 62.9 + - - +
241C PHE* 4.0 13.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C LYS* 4.6 24.2 - - + -
198C MET 3.6 4.7 - - - +
199C MET* 3.5 36.0 - - + -
231C PRO* 3.2 6.8 - - - +
232C THR* 2.8 40.4 + - - +
233C ARG* 2.8 49.9 + - + +
235C GLU* 3.4 44.3 + - + -
238C PHE* 3.9 14.9 - - + +
239C MET* 1.3 76.7 - - - +
241C PHE* 1.3 56.0 + - - +
242C GLU* 4.3 5.2 - - + +
346C TYR* 5.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C LYS* 3.0 4.4 - - - -
198C MET* 2.9 50.5 + - + +
200C PHE* 3.7 33.7 - + - -
213C PRO* 3.3 47.8 - - + -
215C PHE* 3.9 34.8 - + + -
227C SER* 5.6 0.4 - - - -
230C GLY 4.4 3.8 - - - -
231C PRO* 3.8 24.0 - - + -
232C THR* 3.8 4.9 - - - -
239C MET* 4.0 16.2 - - + -
240C TYR* 1.3 72.7 - - - +
242C GLU* 1.3 60.8 + - - +
243C PHE* 4.1 3.8 + - - -
257C PHE* 3.8 13.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLN* 6.0 0.5 - - - +
99B GLU* 4.3 8.7 - - - +
220B LEU* 3.3 27.3 - - + +
196C HIS 3.6 5.2 - - - +
197C LYS* 3.7 25.2 - - + +
215C PHE* 6.1 1.6 - - - -
225C TYR* 5.0 1.4 + - - -
232C THR* 2.5 37.3 + - + +
233C ARG* 3.2 31.1 + - - +
240C TYR* 4.5 5.8 - - + -
241C PHE* 1.3 75.8 - - - +
243C PHE* 1.3 66.9 + - - +
244C PRO* 3.6 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 4.9 1.9 - - - +
195C PHE* 3.3 58.1 - + - +
196C HIS 2.9 35.4 + - - +
197C LYS* 4.1 5.8 - - - -
198C MET* 4.6 2.0 - - + -
215C PHE* 3.7 23.3 - + - -
217C VAL* 4.3 0.9 - - + -
225C TYR* 3.4 46.4 - + + -
241C PHE 4.8 0.7 - - - -
242C GLU* 1.3 75.0 - - - +
244C PRO* 1.3 72.2 - - + +
245C GLN 3.3 21.0 + - - +
246C PRO* 4.6 1.2 - - - +
247C LEU* 3.5 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B GLN* 2.7 31.5 + - - +
220B LEU* 4.4 11.2 - - + -
222B VAL* 3.6 40.8 - - + -
224B ILE* 5.3 2.2 - - + -
250B CYS* 5.2 3.3 - - - +
225C TYR* 3.5 26.7 - - + +
242C GLU 3.6 6.0 - - - +
243C PHE* 1.3 85.9 - - + +
245C GLN* 1.3 78.8 + - - +
246C PRO* 4.8 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B GLN* 5.3 2.7 - - - +
224B ILE* 4.5 18.0 - - - +
248B PRO* 5.3 18.8 + - + +
225C TYR* 6.0 0.5 - - - -
243C PHE* 3.3 16.9 - - - +
244C PRO* 1.3 92.5 + - - +
246C PRO* 1.4 80.9 - - + +
247C LEU* 3.4 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LEU* 3.9 27.3 - - + +
195C PHE 3.5 8.1 - - - +
196C HIS* 3.5 38.6 - - + +
243C PHE* 4.5 3.8 - - + +
244C PRO 4.8 0.4 - - - +
245C GLN* 1.4 92.6 - - + +
247C LEU* 1.3 60.9 + - - +
248C PRO* 3.4 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LEU* 3.3 2.1 - - - -
195C PHE* 2.7 47.0 + - + +
217C VAL* 4.0 20.2 - - + -
224C ILE* 3.9 28.9 - - + +
225C TYR* 3.7 19.7 - - + -
243C PHE* 3.5 35.9 - - + -
245C GLN 3.4 1.5 + - - +
246C PRO* 1.3 71.3 - - - +
248C PRO* 1.3 84.5 - - + +
249C VAL* 3.3 8.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C LEU 3.6 6.5 - - - +
194C LEU* 3.8 13.9 - - + -
219C GLN* 4.2 1.6 - - - +
224C ILE* 3.7 14.4 - - - +
246C PRO 3.4 9.9 - - - +
247C LEU* 1.3 90.0 - - + +
249C VAL* 1.3 63.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C VAL 4.1 0.5 - - - +
192C ALA* 3.7 1.6 - - - +
193C LEU* 2.8 53.8 + - + +
195C PHE* 4.0 20.6 - - + -
217C VAL* 4.9 0.2 - - + -
219C GLN* 3.5 4.7 - - - -
224C ILE* 4.0 16.2 - - + -
247C LEU* 3.8 13.5 - - + +
248C PRO* 1.3 78.8 - - - +
250C CYS* 1.3 63.6 + - - +
253C ILE* 3.9 20.4 - - + -
277C THR* 3.9 15.7 - - + +
347C PHE* 4.1 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C PRO* 3.8 28.3 - - - -
191C VAL 4.1 14.8 - - - -
192C ALA* 4.2 9.4 - - + -
219C GLN* 2.7 41.4 + - - +
220C LEU* 5.6 0.3 - - - +
249C VAL* 1.3 78.9 - - - +
251C GLY* 1.3 67.3 + - - +
252C ASP 3.5 0.9 + - - -
253C ILE* 3.7 2.6 - - - +
277C THR* 4.0 4.3 - - - -
----------------------------------------------------------
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