Contacts of the strand formed by residues 196 - 201 (chain Y) in PDB entry 2PKA
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 GLY 196 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43X GLY 3.6 5.6 - - - -
44X GLY* 3.3 18.2 - - - -
45X VAL* 3.9 0.2 - - - +
53X LEU 3.7 3.5 - - - +
54X THR* 3.4 18.2 - - - -
55X ALA* 3.6 12.9 - - - +
194Y ASP 3.5 0.2 + - - -
195Y SER* 1.3 72.7 - - - +
197Y GLY* 1.3 63.8 + - - +
212Y ILE* 3.6 18.0 - - - +
213Y THR* 3.0 16.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 197 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30X GLN* 4.2 5.6 - - - -
43X GLY 3.8 1.8 - - - -
44X GLY 4.0 9.4 - - - -
45X VAL* 4.1 0.9 - - - -
139Y SER 4.8 4.0 - - - -
194Y ASP 3.3 10.5 + - - -
195Y SER 3.2 5.5 + - - -
196Y GLY* 1.3 82.0 - - - +
198Y PRO* 1.3 72.9 - - - +
212Y ILE* 3.3 2.8 - - - -
213Y THR* 2.8 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 198 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29X TRP* 3.2 36.3 - - + -
30X GLN* 3.6 20.0 - - - +
45X VAL* 3.5 18.6 - - + -
121Y LEU* 4.4 1.6 - - + -
137Y GLU 3.7 0.9 - - - +
138Y ALA* 3.5 23.6 - - - +
139Y SER* 3.9 7.0 + - - +
197Y GLY* 1.3 88.0 - - - +
199Y LEU* 1.3 59.2 + - - +
200Y ILE* 3.9 19.5 - - + -
209Y TRP* 4.0 9.9 - - + +
211Y GLY 3.6 7.0 - - - +
213Y THR* 4.3 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136Y CYS* 3.5 25.4 - - + -
137Y GLU 3.5 8.7 - - - +
138Y ALA* 4.5 1.6 - - + -
160Y LEU* 4.2 15.9 - - + -
162Y LEU* 4.7 2.9 - - + -
181Y LEU* 4.6 16.2 - - + -
183Y ALA* 4.0 23.6 - - + -
198Y PRO* 1.3 71.9 - - - +
200Y ILE* 1.3 58.9 + - - +
201Y CYS* 4.0 16.2 - - - -
209Y TRP* 3.7 1.6 - - - -
210Y GLN* 3.0 23.9 + - - +
211Y GLY* 3.0 18.3 + - - +
228Y TYR* 3.8 41.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 200 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29X TRP* 3.5 41.1 - - + +
121Y LEU* 3.9 19.1 - - + -
135Y THR 4.2 0.2 - - - +
136Y CYS* 3.3 1.0 - - - -
137Y GLU* 2.9 44.9 + - + +
198Y PRO* 3.9 13.0 - - + -
199Y LEU* 1.3 77.2 - - - +
201Y CYS* 1.3 59.8 + - - +
202Y ASN 4.0 1.2 + - - -
203Y GLY* 3.5 14.2 + - - +
208Y MET 3.4 29.4 - - - +
209Y TRP* 3.9 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 201 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129Y PRO* 4.2 6.5 - - + +
134Y SER* 4.0 14.1 - - - +
135Y THR 3.6 4.0 - - - -
136Y CYS* 2.0 44.6 - - - -
162Y LEU* 4.4 7.6 - - - -
199Y LEU* 4.0 16.8 - - - -
200Y ILE* 1.3 73.0 - - - +
202Y ASN* 1.3 60.8 + - - +
203Y GLY 3.3 0.9 - - - -
208Y MET* 2.8 34.8 + - - +
210Y GLN* 4.1 19.6 + - + +
----------------------------------------------------------
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