Contacts of the strand formed by residues 197 - 206 (chain C) in PDB entry 5E5R
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 ILE 197 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C PHE* 3.8 7.0 - - - -
177C PHE* 4.7 8.5 - - + -
178C PHE 3.2 13.9 - - - +
179C TYR* 4.7 2.9 - - + +
180C ASN 5.8 0.2 - - - +
187C PHE* 4.1 17.3 - - + -
190C ALA* 4.0 24.7 - - + -
191C ILE* 4.1 18.2 - - + -
195C ARG 3.5 12.3 - - - +
196C ILE* 1.3 77.8 - - - +
198C GLY* 1.3 61.0 + - - +
256C LEU* 3.8 28.7 - - + -
264C ILE* 2.8 21.5 + - + +
265C VAL* 3.9 12.3 - - + -
266C GLU* 2.9 28.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
139C LEU* 5.4 5.8 - - - -
143C PHE* 3.8 10.4 - - - -
177C PHE* 3.5 5.5 - - - +
178C PHE* 2.8 44.6 + - - +
197C ILE* 1.3 77.5 - - - +
199C ALA* 1.3 64.5 + - - +
265C VAL* 4.6 2.0 - - - -
266C GLU* 3.5 10.3 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
176C ILE 3.1 11.9 - - - +
177C PHE* 4.0 15.5 - - + -
178C PHE* 4.4 1.5 - - - -
198C GLY* 1.3 75.9 - - - +
200C MET* 1.3 56.9 + - - +
265C VAL* 3.9 14.6 - - + -
266C GLU 3.0 7.5 + - - +
267C TRP* 3.3 29.5 - - + -
268C ILE* 2.7 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 200 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LEU* 4.5 2.5 - - + -
104C LEU* 3.7 17.0 - - + -
107C PHE* 4.7 1.6 - - - -
134C VAL* 3.6 31.9 - - + -
174C MET 3.5 0.3 - - - +
175C GLN* 3.1 10.6 - - - +
176C ILE* 3.0 44.5 + - + +
178C PHE* 3.7 27.6 - - + -
199C ALA* 1.3 75.7 - - - +
201C ALA* 1.3 60.2 + - - +
202C ILE* 3.8 14.1 - - + -
242C LEU* 4.4 8.1 - - - -
267C TRP* 4.5 1.8 - - - -
268C ILE* 3.3 22.2 - - + +
270C PHE* 4.1 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C HIS* 4.1 2.0 - - - +
173C GLU* 3.5 27.6 - - - +
174C MET 3.5 4.0 - - - -
175C GLN* 4.6 0.4 - - + -
200C MET* 1.3 73.2 - - - +
202C ILE* 1.3 62.0 + - - +
203C PHE* 4.3 1.5 + - + -
267C TRP* 4.1 11.6 - - + -
268C ILE 2.6 15.2 + - - +
269C VAL* 3.6 22.6 - - + +
270C PHE* 3.1 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C GLU* 3.3 3.2 - - - -
174C MET* 2.6 58.8 + - + +
176C ILE* 4.3 4.5 - - + -
200C MET* 3.8 23.6 - - + +
201C ALA* 1.3 77.1 - - - +
203C PHE* 1.3 76.8 + - - +
204C PHE* 3.7 11.8 - - + -
241C LEU 3.8 3.8 - - - +
242C LEU* 3.6 29.4 - - + -
243C PRO* 3.8 8.5 - - + -
270C PHE* 3.7 22.9 - - + -
274C VAL* 3.6 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C SER* 3.8 9.9 - - - -
163C HIS* 3.7 35.0 - - + -
164C SER* 4.3 3.1 - - - -
165C ILE* 4.0 15.0 - - + -
170C PHE* 3.4 47.3 - + + -
172C VAL 3.7 1.6 - - - -
173C GLU* 3.6 25.8 - - + -
201C ALA* 5.1 1.6 - - + -
202C ILE* 1.3 80.3 - - - +
204C PHE* 1.3 67.2 + - - +
269C VAL* 3.6 25.6 - - + -
270C PHE* 3.5 18.7 + - - +
271C ARG 4.6 6.1 - - - -
272C ARG 5.2 1.4 + - - -
273C PRO* 3.4 9.9 - - + +
274C VAL 2.8 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C PHE* 4.4 9.6 - + - -
170C PHE* 3.6 5.7 - - - +
171C PRO* 3.1 25.1 - - - +
172C VAL* 3.0 41.5 + - + +
174C MET* 4.1 28.9 - - + -
202C ILE* 3.7 17.3 - - + -
203C PHE* 1.3 84.7 - - - +
205C GLN* 1.3 60.0 + - - +
214C LEU* 4.3 25.6 - - + -
217C ILE* 6.2 1.3 - - + -
218C ILE* 6.5 0.2 - - + -
241C LEU* 4.3 4.0 - - + -
273C PRO* 4.3 1.3 - - - -
274C VAL* 3.1 30.5 - - + +
276C ILE* 3.6 30.7 - - + -
284C PHE* 4.9 5.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PRO* 4.4 12.6 + - + +
183A ASP* 5.3 2.2 + - - +
168C ARG* 2.9 34.3 - - - +
169C ARG 4.8 2.8 + - - -
170C PHE* 3.4 20.1 - - + -
171C PRO* 3.5 14.4 - - - +
204C PHE* 1.3 74.4 - - - +
206C VAL* 1.3 97.1 + - + +
273C PRO* 3.7 22.7 - - + +
274C VAL 2.9 7.4 + - - +
275C PRO* 3.7 5.2 - - + +
276C ILE* 3.1 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PRO* 3.6 30.7 - - + -
196A ILE* 4.0 17.7 - - + +
157C GLY* 4.4 5.6 - - - +
171C PRO* 3.9 12.3 - - + +
205C GLN* 1.3 91.3 + - + +
207C SER* 1.3 59.0 + - - +
276C ILE* 3.1 9.0 - - - +
278C TYR* 3.9 35.9 - - + +
281C LEU* 3.7 26.2 - - + -
----------------------------------------------------------
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