Contacts of the strand formed by residues 156 - 163 (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 GLN 156 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16X ILE* 3.3 22.6 - - + +
19X GLY 4.2 6.2 + - - +
20X ARG* 3.6 17.9 - - - +
21X GLU* 3.2 27.3 - - - +
22X CYS* 3.6 1.1 - - - -
139Y SER* 3.2 3.5 - - - -
140Y GLY 2.9 37.7 + - - +
144Y ILE* 3.8 26.5 - - + +
152Y PRO* 4.0 15.3 - - + +
154Y GLU* 3.3 20.9 + - - +
155Y ILE* 1.3 75.2 - - - +
157Y CYS* 1.3 57.1 - - - +
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Residues in contact with CYS 157 (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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19X GLY* 3.2 1.2 - - - -
20X ARG* 2.7 42.4 + - + +
22X CYS* 2.0 48.2 - - + -
26X SER* 4.8 4.3 - - - -
27X HIS* 5.4 2.0 - - - -
29X TRP* 6.4 0.4 - - - -
137Y GLU* 3.8 33.4 - - - +
138Y ALA 3.5 3.4 - - - -
139Y SER* 3.8 11.0 - - - -
156Y GLN* 1.3 71.0 - - - +
158Y VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 158 (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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16X ILE* 3.6 26.9 - - + -
17X ILE 3.8 7.6 - - - +
18X GLY 3.7 26.5 - - - +
19X GLY* 3.8 2.9 - - - -
136Y CYS 3.7 0.2 - - - +
137Y GLU* 3.3 5.9 - - - +
138Y ALA* 2.8 51.4 + - + +
157Y CYS* 1.3 75.5 - - - +
159Y GLN* 1.3 67.6 + - - +
160Y LEU* 3.9 12.2 + - + +
188Y LYS* 3.9 21.1 - - + +
189Y ASP 4.4 7.9 - - - +
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Residues in contact with GLN 159 (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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135Y THR* 3.4 27.5 - - + +
136Y CYS 3.3 6.5 - - - +
137Y GLU* 4.6 15.1 + - + +
158Y VAL* 1.3 78.4 - - - +
160Y LEU* 1.3 68.0 + - - +
184Y TYR* 5.1 3.1 - - - -
188Y LYS* 3.8 21.4 + - - +
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Residues in contact with LEU 160 (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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135Y THR* 3.4 8.3 - - - +
136Y CYS* 2.7 39.9 + - + +
138Y ALA* 4.3 11.7 - - + -
158Y VAL* 4.5 10.8 - - + +
159Y GLN* 1.3 82.1 - - - +
161Y THR* 1.3 61.8 + - - +
183Y ALA* 4.3 12.8 - - + +
184Y GLY* 3.9 23.6 - - - +
188Y LYS* 3.7 32.3 - - + +
189Y ASP* 4.3 3.8 - - - +
190Y THR* 4.9 3.8 - - + +
199Y LEU* 4.2 11.9 - - + -
228Y TYR* 3.2 33.2 - - + +
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Residues in contact with THR 161 (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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148B ASP* 2.9 41.0 + - - +
149B PHE* 4.6 4.0 - - + -
133Y GLY* 4.0 18.0 + - - +
134Y SER 3.3 5.3 + - - +
135Y THR* 5.2 4.0 + - - +
160Y LEU* 1.3 75.7 + - - +
162Y LEU* 1.3 68.2 + - - +
163Y LEU* 3.3 25.1 + - + +
183Y ALA* 3.2 4.7 - - - -
184Y GLY* 2.9 34.7 + - - +
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Residues in contact with LEU 162 (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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41A GLN* 5.6 0.9 - - - +
192B MET* 3.9 1.6 - - - +
128Y GLU* 6.0 0.7 - - - +
129Y PRO* 3.6 42.4 - - + +
130Y GLU 3.3 28.0 - - - +
132Y LEU* 3.8 11.3 - - + +
133Y GLY* 2.7 31.5 + - - -
134Y SER* 2.8 18.2 + - - +
136Y CYS* 3.9 17.3 - - - -
161Y THR* 1.3 72.9 - - - +
163Y LEU* 1.3 63.0 + - - +
181Y LEU* 4.3 24.2 - - + -
182Y CYS 3.6 13.5 - - - +
183Y ALA* 4.3 2.2 - - + -
199Y LEU* 4.7 4.7 - - + -
201Y CYS* 4.4 2.2 - - - -
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Residues in contact with LEU 163 (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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147B PRO 5.3 0.9 - - - +
149B PHE* 4.2 18.6 - - + -
192B MET* 3.9 6.3 - - - -
132Y LEU* 4.1 3.6 - - - +
161Y THR* 3.6 29.4 - - + +
162Y LEU* 1.3 81.3 - - - +
164Y GLN* 1.3 65.6 + - - +
165Y ASN* 3.5 1.9 + - - -
167Y PHE* 3.5 24.7 - - + -
182Y CYS* 2.8 27.2 + - - +
184Y GLY* 4.2 13.5 - - - +
185Y LEU* 3.7 37.5 - - + -
225Y PRO* 3.9 22.4 - - + -
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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