Contacts of the strand formed by residues 189 - 195 (chain B) in PDB entry 3BEQ
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 TRP 189 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B SER* 3.4 46.9 - - - -
124B CYS 3.9 6.1 - - - -
125B SER* 4.2 16.1 - - - -
128B GLU* 4.9 6.9 + - + +
130B ARG* 4.1 19.8 - - + +
132B PHE* 3.7 26.9 - + - -
172B ARG* 3.7 29.6 - - - +
174B GLU* 5.7 1.1 - - - +
182B ALA* 4.7 0.2 - - + -
183B CYS* 3.6 22.9 - - - -
184B HIS* 3.6 27.9 + + + -
188B GLY* 1.3 70.7 - - - -
190B LEU* 1.3 61.9 + - - +
191B THR* 4.1 8.4 + - + +
206B LYS 3.6 1.2 - - - +
207B TYR* 3.2 5.9 - - - -
208B ASN* 2.9 34.2 + - - +
209B GLY 4.6 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ALA* 3.2 5.9 - - - +
183B CYS* 2.8 39.0 + - - +
188B GLY 3.6 2.2 + - - +
189B TRP* 1.3 73.2 - - - +
191B THR* 1.3 68.3 + - - +
192B ILE* 4.3 9.9 - - + -
205B LEU* 4.4 9.2 - - + -
206B LYS 3.2 15.7 - - - +
207B TYR* 4.2 8.3 - - + -
230B CYS* 4.1 15.5 - - - -
237B CYS* 4.0 24.0 - - + -
257B ILE* 3.8 35.4 - - + -
260B GLY* 3.8 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PHE* 4.2 9.0 - - + -
158B LEU* 4.2 11.7 - - + -
174B GLU* 3.6 32.3 + - + +
175B SER* 4.7 3.5 - - - -
181B SER 3.5 4.5 - - - -
182B ALA* 3.8 13.9 - - + -
189B TRP* 4.1 8.7 - - + +
190B LEU* 1.3 79.8 - - - +
192B ILE* 1.3 65.4 + - - +
193B GLY 4.2 0.4 - - - -
204B VAL 3.7 0.9 - - - +
205B LEU* 3.4 3.6 - - - -
206B LYS* 3.0 55.2 + - - +
209B GLY* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU* 4.3 1.9 - - - +
175B SER* 4.9 0.7 - - - -
180B ALA* 3.2 9.0 - - - +
181B SER* 2.8 46.6 + - - +
190B LEU* 4.3 13.9 - - + -
191B THR* 1.3 79.6 - - - +
193B GLY* 1.3 61.5 + - - +
194B ILE* 4.3 1.6 - - + -
203B ALA* 4.1 12.1 - - + -
204B VAL 3.5 3.6 - - - -
205B LEU* 4.1 16.4 - - + -
225B THR* 4.6 10.8 - - + +
230B CYS* 4.8 2.7 - - - -
239B THR* 3.9 28.9 - - + -
241B MET* 3.7 26.5 - - + -
257B ILE* 3.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B SER* 3.8 14.7 + - - -
176B VAL 3.8 9.0 - - - +
177B ALA* 3.6 18.8 - - - -
179B SER 3.7 0.4 - - - -
180B ALA* 4.6 0.2 - - - -
192B ILE* 1.3 75.9 - - - +
194B ILE* 1.3 62.4 + - - -
195B SER 3.9 0.5 + - - -
202B VAL 3.7 1.6 - - - +
204B VAL* 2.9 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ALA* 3.3 0.6 - - - +
178B TRP* 2.8 48.9 + - + -
179B SER* 2.9 19.3 + - - +
192B ILE* 4.7 2.0 - - + -
193B GLY* 1.3 72.2 - - - -
195B SER* 1.3 59.2 + - - +
201B ALA* 3.6 14.4 - - + -
202B VAL 3.4 8.5 - - - +
203B ALA* 3.6 23.1 - - + -
223B LEU* 3.5 27.8 - - + +
224B ARG* 3.6 37.0 - - - +
225B THR* 3.9 18.8 - - + +
241B MET* 4.5 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 4.8 6.1 - - - -
454A VAL* 4.7 0.4 - - - +
456A TRP* 3.5 8.3 - - - -
458A TRP* 3.2 28.9 + - - -
153B SER 4.5 2.1 + - - -
176B VAL* 3.8 26.2 - - - +
177B ALA 4.5 1.1 + - - -
178B TRP* 3.5 15.7 - - - +
193B GLY 3.9 1.2 + - - -
194B ILE* 1.3 74.6 - - - +
196B GLY* 1.3 66.3 + - - +
201B ALA* 3.4 2.9 - - - -
202B VAL* 2.9 33.2 + - - +
----------------------------------------------------------
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