Contacts of the strand formed by residues 208 - 215 (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 MET 208 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123Y LEU 5.6 0.7 - - - +
124Y PRO* 3.8 4.7 - - + -
125Y THR* 3.1 42.4 - - - +
127Y GLN* 3.2 39.9 - - + +
200Y ILE* 3.5 4.5 - - - +
201Y CYS 2.8 38.1 + - - +
202Y ASN* 4.1 5.4 - - + +
203Y GLY* 1.3 80.3 - - - +
209Y TRP* 1.3 70.2 + - - +
210Y GLN* 3.0 18.9 + - - +
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Residues in contact with TRP 209 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45X VAL* 3.7 24.5 - - + -
47X VAL* 3.7 19.7 - - + -
53X LEU* 3.9 8.7 - - + -
121Y LEU* 3.5 50.9 - - + +
122Y GLU 3.7 23.3 + - - +
123Y LEU* 3.5 17.5 - - + -
124Y PRO* 3.1 30.4 - - - +
198Y PRO* 4.0 16.1 - - + +
199Y LEU 3.7 7.2 - - - -
200Y ILE* 3.9 6.6 - - - +
203Y GLY 4.1 0.8 + - - -
208Y MET* 1.3 71.2 - - - +
210Y GLN* 1.3 59.4 + - - +
211Y GLY 2.8 29.9 + - - -
212Y ILE* 3.6 23.9 - - + +
231Y LEU* 3.3 24.1 - - + +
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Residues in contact with GLN 210 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124Y PRO* 3.8 7.5 - - - +
127Y GLN* 3.3 24.0 + - - +
128Y GLU* 4.1 1.8 + - - +
129Y PRO* 3.3 44.2 - - + +
181Y LEU* 3.5 22.6 - - + +
199Y LEU* 3.0 10.1 + - + +
201Y CYS* 4.1 14.7 + - + -
208Y MET* 3.0 36.4 + - - +
209Y TRP* 1.3 78.3 - - - +
211Y GLY* 1.3 60.8 + - - +
230Y LYS* 4.0 1.0 - - - +
231Y LEU* 3.1 29.7 + - - +
232Y ILE* 4.5 4.5 + - - +
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Residues in contact with GLY 211 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181Y LEU* 4.4 6.3 - - - -
199Y LEU* 3.0 28.5 + - - +
209Y TRP* 2.8 21.9 + - - -
210Y GLN* 1.3 83.3 - - - +
212Y ILE* 1.3 63.1 + - - +
228Y TYR* 4.4 3.1 - - - -
229Y THR 3.2 12.1 - - - -
231Y LEU* 3.9 2.7 - - - -
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Residues in contact with ILE 212 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45X VAL* 4.4 0.7 - - + -
53X LEU* 3.5 41.7 - - + +
54X THR 4.4 7.4 - - - +
55X ALA* 4.5 0.9 - - - +
102Y ASP 4.3 17.7 - - - +
103Y LEU* 4.2 3.4 - - + -
196Y GLY* 3.6 29.2 - - - +
197Y GLY 3.3 6.3 - - - +
199Y LEU 4.6 0.4 - - - +
209Y TRP* 3.6 23.1 - - + +
211Y GLY* 1.3 77.6 - - - +
213Y THR* 1.3 72.7 + - - +
214Y SER* 5.8 0.2 - - - -
228Y TYR* 3.2 6.0 - - - -
229Y THR* 2.8 33.4 + - - -
231Y LEU* 3.6 9.0 - - + -
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Residues in contact with THR 213 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X ALA* 4.1 5.9 - - - +
1Y BEN 3.5 33.4 - - + -
138Y ALA* 5.0 0.7 - - - +
139Y SER 5.3 1.6 + - - -
190Y THR* 3.7 22.5 - - + +
194Y ASP* 3.6 22.1 + - - +
195Y SER* 3.7 6.2 - - - +
196Y GLY* 3.0 21.8 + - - +
197Y GLY 2.8 20.4 + - - -
198Y PRO 4.3 4.7 + - - -
212Y ILE* 1.3 74.5 - - - +
214Y SER* 1.3 57.8 + - - +
228Y TYR* 3.6 21.4 - - + -
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Residues in contact with SER 214 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57X HIS* 3.1 23.3 + - - -
1Y BEN 3.6 11.9 - - - -
99Y TYR* 3.9 1.6 + - - -
102Y ASP* 2.8 29.7 + - - +
212Y ILE 3.3 0.6 + - - -
213Y THR* 1.3 74.3 - - - +
215Y TRP* 1.3 79.6 + - - +
227Y ILE* 3.1 24.8 + - - +
229Y THR* 4.2 19.5 - - - -
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Residues in contact with TRP 215 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1Y BEN 3.7 14.3 - - + -
99Y TYR* 3.5 47.0 - + + +
172Y HIS* 3.7 34.3 - + + -
174Y ASP* 3.5 36.8 - - + -
175Y LYS 4.2 14.4 - - - -
176Y VAL* 4.3 4.5 - - + -
180Y MET* 4.4 3.8 - - - +
214Y SER* 1.3 106.0 - - - +
216Y GLY* 1.3 69.0 + - - +
226Y SER* 3.3 3.1 - - - -
227Y ILE* 2.7 72.9 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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