Contacts of the strand formed by residues 166 - 172 (chain B) in PDB entry 4TR8
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 166 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLU 3.6 1.2 - - - +
162B VAL* 3.5 7.4 - - - +
163B ASN* 3.2 35.8 + - - -
164B GLY 3.4 0.6 - - - +
165B GLY* 1.4 81.5 + - - +
167B LEU* 1.3 65.1 + - - +
168B ARG* 4.1 7.2 - - + +
181B SER* 3.9 18.2 - - - +
182B LEU 3.4 25.1 - - - +
183B ASP* 4.2 5.6 - - - +
184B ALA* 4.8 0.9 - - - -
186B ILE* 5.0 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 3.8 24.0 - - + -
130B ILE* 3.7 21.5 - - + -
135B LEU* 4.3 12.3 - - + -
138B LEU* 3.6 31.6 - - + +
160B LEU* 4.8 12.1 - - + -
161B GLU 3.6 20.6 - - - +
162B VAL* 3.8 18.4 - - + -
165B GLY 4.3 0.6 + - - -
166B THR* 1.3 73.4 - - - +
168B ARG* 1.3 62.0 + - - +
181B SER* 3.5 1.9 - - - -
182B LEU* 2.8 37.6 + - + +
184B ALA* 4.2 13.2 - - + +
186B ILE* 4.4 3.1 - - + -
219B LEU* 6.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 5.0 0.9 - - - -
159B LEU 3.6 0.7 - - - +
160B LEU* 3.4 7.5 - - - +
161B GLU* 2.8 57.4 + - + +
166B THR* 4.1 8.0 - - + +
167B LEU* 1.3 76.6 - - - +
169B SER* 1.3 68.6 + - - +
170B VAL* 3.8 9.1 + - + -
179B MET* 3.5 24.1 - - + +
180B CYS 3.2 11.2 - - - +
181B SER* 2.8 25.2 + - - +
245B TYR* 2.9 39.3 + - - -
246B GLU* 4.9 5.5 + - - +
249B LEU* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 2.8 41.2 + - - +
142B THR* 3.4 15.4 - - - +
158B MET* 3.9 5.8 - - - -
159B LEU 3.1 6.7 - - - -
160B LEU* 3.9 13.7 - - - -
168B ARG* 1.3 71.6 - - - +
170B VAL* 1.3 66.0 + - - +
179B MET* 3.2 5.3 - - - +
180B CYS* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B THR* 5.1 0.2 - - - -
158B MET* 3.7 3.3 - - - +
159B LEU* 2.9 51.9 + - + +
168B ARG* 3.8 24.2 - - + -
169B SER* 1.3 80.6 - - - +
171B ALA* 1.3 64.8 + - - +
177B LEU* 3.9 22.7 - - + -
178B ALA 3.4 9.6 - - - +
179B MET* 4.1 7.6 - - + -
242B PHE* 3.7 27.9 - - + -
245B TYR* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B THR* 3.3 31.9 - - - +
145B ALA* 3.4 2.9 - - - +
146B MET* 3.6 28.5 - - + +
157B GLY 4.6 3.6 - - - +
158B MET* 4.6 3.1 - - + -
170B VAL* 1.3 76.4 - - - +
172B THR* 1.3 64.1 + - - +
177B LEU* 3.3 2.8 - - - +
178B ALA 2.9 33.3 + - - +
242B PHE* 4.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ALA 3.0 12.2 + - - +
146B MET* 4.4 1.0 - - - +
147B ALA 3.6 6.6 + - - -
152B ARG* 6.3 0.2 - - - +
155B LEU* 3.6 43.0 + - + +
157B GLY 5.2 0.2 + - - -
171B ALA* 1.3 75.2 - - - +
173B ASP* 1.3 57.5 + - - +
174B GLY* 3.4 12.7 + - - +
176B ARG 2.7 21.5 + - - -
177B LEU* 3.7 20.6 - - + +
242B PHE* 3.9 18.8 - - + -
243B PRO* 5.1 4.9 - - + -
245B TYR* 5.9 0.9 - - + -
248B VAL* 5.8 2.3 - - - +
----------------------------------------------------------
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