Contacts of the strand formed by residues 175 - 178 (chain E) in PDB entry 3STJ
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 175 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E SER 5.8 0.2 - - - -
162E LEU* 3.7 1.4 - - - -
163E GLY 3.2 9.2 + - - -
164E ARG* 3.0 40.8 + - + +
167E LEU* 3.7 19.5 - - + -
169E LEU* 4.0 18.6 - - + -
170E GLU* 4.0 23.3 - - + -
172E LEU 5.3 0.7 - - - -
173E GLU* 3.7 33.9 - - + -
174E ASN* 1.3 78.1 - - - +
176E ILE* 1.3 60.9 + - - +
177E GLN 4.0 0.2 + - - -
203E THR* 4.1 16.2 - - + -
204E ALA* 5.0 0.7 - - + -
217E PHE* 3.7 27.8 - - + -
218E ALA 3.4 19.7 - - - +
219E ILE* 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 176 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E SER* 4.7 0.2 - - - -
135E LEU* 3.7 13.9 - - + -
159E VAL* 4.0 30.5 - - + -
161E ALA 3.7 4.3 - - - +
162E LEU* 3.9 15.9 - - + -
163E GLY 5.9 0.2 - - - +
174E ASN 3.8 0.6 + - - +
175E PHE* 1.3 73.7 - - - +
177E GLN* 1.3 66.1 + - - +
178E THR* 4.1 1.1 + - - +
191E LEU* 4.0 20.6 - - + -
199E ILE 3.2 30.3 - - - +
200E GLY* 4.4 3.6 - - - -
216E GLY 3.5 0.2 - - - +
217E PHE* 3.3 6.1 - - - -
218E ALA* 2.9 37.3 + - + +
220E PRO* 3.6 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 177 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D LEU* 3.8 5.8 - - - +
153D THR* 3.3 36.6 + - - +
159E VAL* 3.6 3.5 - - - -
160E SER* 2.7 33.6 + - - -
161E ALA* 2.8 25.1 + - + +
164E ARG* 2.9 32.9 + - + -
175E PHE 4.0 0.4 + - - -
176E ILE* 1.3 76.1 - - - +
178E THR* 1.3 58.9 + - - +
214E GLY 5.2 0.4 + - - -
215E ILE* 3.9 25.2 - - + +
216E GLY 3.2 7.4 - - - +
217E PHE* 3.5 28.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E ALA* 4.2 7.4 - - - +
158E ILE 2.8 22.5 + - - -
159E VAL* 4.9 1.3 - - - -
160E SER* 3.7 5.4 - - - -
176E ILE* 5.2 2.0 - - - +
177E GLN* 1.3 76.1 - - - +
179E ASP* 1.4 59.3 + - - +
180E ALA* 3.3 17.0 + - + +
182E ILE* 3.5 30.7 - - + -
191E LEU* 3.9 26.9 - - + -
202E ASN* 4.9 0.9 - - - +
214E GLY 3.3 3.8 - - - +
215E ILE* 4.0 0.3 - - - -
216E GLY* 3.0 36.2 + - - +
217E PHE* 5.5 0.9 - - - -
218E ALA* 5.5 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