Contacts of the strand formed by residues 133 - 140 (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 133 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B PHE* 4.8 12.1 - - - +
151B PHE* 4.5 8.7 - - - -
192B MET* 4.0 4.9 - - - +
132Y LEU* 1.3 73.9 - - - +
134Y SER* 1.3 66.7 + - - +
135Y THR* 3.6 2.9 + - - -
161Y THR* 4.0 15.8 + - - +
162Y LEU 2.7 20.1 + - - -
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Residues in contact with SER 134 (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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129Y PRO* 4.3 1.8 - - - +
130Y GLU* 2.7 42.1 + - - +
132Y LEU 3.2 0.8 + - - -
133Y GLY* 1.3 78.1 - - - +
135Y THR* 1.3 61.7 + - - +
136Y CYS 3.5 0.7 + - - -
161Y THR* 3.3 3.7 - - - -
162Y LEU* 2.8 35.3 + - - +
201Y CYS* 4.0 23.2 - - - +
202Y ASN* 4.3 15.4 + - - +
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Residues in contact with THR 135 (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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133Y GLY 3.6 3.2 + - - -
134Y SER* 1.3 70.6 - - - +
136Y CYS* 1.3 62.3 - - - +
159Y GLN* 3.4 41.5 - - + +
160Y LEU 3.4 11.2 - - - +
161Y THR* 4.8 3.6 + - - +
200Y ILE 4.2 0.3 - - - +
201Y CYS* 3.6 0.5 - - - -
202Y ASN* 3.3 31.0 + - - +
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Residues in contact with CYS 136 (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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134Y SER 3.7 13.2 - - - -
135Y THR* 1.3 75.8 - - - +
137Y GLU* 1.3 61.7 + - - +
159Y GLN* 3.3 5.1 - - - +
160Y LEU* 2.7 43.9 + - + +
162Y LEU* 3.9 19.5 - - - -
183Y ALA* 4.9 0.4 - - - -
199Y LEU* 3.5 21.1 - - + -
200Y ILE 3.3 4.7 - - - +
201Y CYS* 2.0 47.6 - - - -
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Residues in contact with GLU 137 (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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26X SER* 5.7 2.3 + - - +
29X TRP* 5.0 12.1 - - - -
136Y CYS* 1.3 76.2 - - - +
138Y ALA* 1.3 64.6 + - - +
139Y SER* 5.0 2.6 - - - -
157Y CYS* 3.8 28.4 - - - +
158Y VAL 3.3 20.6 - - - +
159Y GLN* 4.6 13.8 + - + +
198Y PRO 3.7 1.2 - - - +
199Y LEU* 3.5 5.1 - - - -
200Y ILE* 2.9 44.4 + - + +
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Residues in contact with ALA 138 (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* 3.8 3.8 - - + +
137Y GLU* 1.3 77.1 - - - +
139Y SER* 1.3 61.4 + - - +
157Y CYS* 3.5 1.2 - - - -
158Y VAL* 2.8 41.1 + - + +
160Y LEU* 4.3 12.1 - - + +
190Y THR* 3.7 29.6 - - + -
198Y PRO 3.5 11.9 - - - +
199Y LEU* 4.5 6.2 - - + +
213Y THR* 5.0 1.1 - - - +
228Y TYR* 4.9 2.9 - - + +
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Residues in contact with SER 139 (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* 3.9 8.7 - - - +
22X CYS* 4.1 4.7 - - - -
27X HIS* 5.5 1.6 - - - -
29X TRP* 4.1 9.3 - - - -
30X GLN* 2.7 33.2 + - - +
137Y GLU* 5.0 2.9 - - - -
138Y ALA* 1.3 76.5 - - - +
140Y GLY* 1.3 59.3 + - - +
155Y ILE* 4.3 3.1 - - - -
156Y GLN 3.2 7.2 - - - -
157Y CYS* 3.8 22.0 - - - -
190Y THR* 5.5 0.3 - - - +
194Y ASP* 4.3 10.6 - - - +
197Y GLY* 4.8 1.9 - - - -
198Y PRO* 3.9 20.1 + - - +
213Y THR* 5.3 1.4 + - - -
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Residues in contact with GLY 140 (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 1.6 - - - +
30X GLN* 4.7 7.2 - - - -
139Y SER* 1.3 78.6 - - - +
141Y TRP* 1.3 63.0 + - - -
142Y GLY 3.3 6.0 + - - +
152Y PRO* 4.7 0.3 - - - +
154Y GLU 4.4 0.3 - - - +
155Y ILE* 3.7 10.8 - - - +
156Y GLN* 2.9 38.0 + - - +
194Y ASP* 3.2 15.5 - - - -
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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