Contacts of the strand formed by residues 196 - 201 (chain B) in PDB entry 3KTC
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 VAL 196 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B MSE 4.4 5.2 - - + -
155B ALA* 3.4 33.4 - - + -
163B PHE* 3.4 10.8 - - + +
165B ILE* 3.5 32.5 - - + -
188B ILE* 3.8 15.6 - - + +
191B ILE* 4.2 27.1 - - + -
193B LEU* 3.6 7.6 + - + +
194B ASP 3.3 1.4 - - - -
195B ASN* 1.3 82.1 - - - +
197B GLY* 1.3 59.8 + - - +
224B ARG* 2.9 28.6 + - - -
226B PHE* 3.6 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B PHE 2.8 10.6 + - - +
164B ALA* 4.0 1.8 - - - -
165B ILE* 2.9 30.8 + - - +
188B ILE* 3.8 10.0 - - - +
196B VAL* 1.3 74.8 - - - +
198B VAL* 1.3 64.5 + - - -
224B ARG* 3.5 11.9 - - - -
226B PHE* 3.1 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ALA* 4.2 4.3 - - - -
165B ILE 3.4 10.8 - - - +
167B TYR* 3.7 23.6 - - + -
181B ALA* 5.8 0.2 - - - -
184B THR* 3.9 11.7 - - + -
185B LEU* 4.3 8.1 - - + -
188B ILE* 3.7 19.5 - - + -
197B GLY* 1.3 77.2 - - - -
199B LEU* 1.3 71.6 + - - +
200B LEU 3.8 1.5 + - - +
219B ILE* 3.8 32.1 - - + -
224B ARG* 2.7 18.7 + - + +
225B LEU* 3.9 1.4 - - + -
226B PHE* 2.9 25.6 + - - +
227B GLY 3.4 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TYR* 3.3 40.8 - - + +
124B LYS* 4.0 15.7 - - + -
164B ALA* 4.0 12.1 - - + +
165B ILE 2.9 9.3 + - - +
166B GLU* 3.5 36.1 - - + +
167B TYR* 4.0 4.2 + - - +
198B VAL* 1.3 74.5 - - - +
200B LEU* 1.3 63.0 + - - +
201B ASP 3.5 2.9 + - - -
227B GLY* 3.4 17.9 - - - +
228B MSE 3.8 11.2 - - - +
229B ASP* 3.5 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TYR* 3.7 21.8 - - + +
198B VAL* 3.8 4.1 - - + -
199B LEU* 1.3 71.1 - - - +
201B ASP* 1.3 76.8 + - - +
202B PHE* 3.7 4.4 + - - +
205B ALA* 4.2 7.0 - - + -
212B PRO 5.0 0.7 - - - +
215B SER* 3.8 3.8 - - - -
216B ALA* 3.5 43.3 - - + +
219B ILE* 3.8 18.6 - - + -
225B LEU* 3.6 19.5 - - + -
227B GLY 3.0 8.0 + - - +
228B MSE 3.1 7.8 - - - +
229B ASP 2.8 24.0 + - - +
254B PHE* 3.8 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLU* 3.2 17.9 - - + +
167B TYR* 5.0 2.9 + - - -
199B LEU 3.5 3.4 + - - -
200B LEU* 1.3 76.6 - - - +
202B PHE* 1.3 64.9 + - - +
203B GLY 2.9 15.8 + - - -
204B HIS* 3.0 33.8 + - + +
205B ALA 3.0 18.9 + - - -
229B ASP* 3.4 15.6 - - + +
231B ASN* 3.0 17.1 + - - -
270B ASP* 3.1 6.1 - - - +
333B FE 3.9 0.2 - - - -
334B FE 2.2 27.9 - - - -
----------------------------------------------------------
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