Contacts of the helix formed by residues 164 - 172 (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 164 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLN* 4.5 19.2 + - - +
42A CYS* 5.0 5.1 - - - -
57A HIS* 4.6 9.7 + - - -
1B BEN 4.8 4.9 - - - -
192B MET* 3.4 43.9 - - + +
193B GLY 3.8 5.1 + - - -
195B SER* 3.9 15.4 + - - -
132Y LEU* 3.9 16.3 - - + +
163Y LEU* 1.3 74.4 - - - +
165Y ASN* 1.3 53.3 + - - +
166Y THR* 2.8 36.1 + - + +
167Y PHE* 2.8 32.3 + - + +
182Y CYS* 3.9 1.1 - - - -
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Residues in contact with ASN 165 (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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57A HIS 6.2 0.4 - - - +
163Y LEU 4.4 1.8 + - - -
164Y GLN* 1.3 70.9 - - - +
166Y THR* 1.3 53.1 + - - +
167Y PHE 3.0 1.1 - - - -
168Y CYS* 3.0 9.6 + - - +
169Y ALA* 2.8 29.0 + - - +
176Y VAL* 3.3 17.6 - - + +
177Y THR 3.0 26.5 - - - +
178Y GLU* 4.8 2.1 - - - -
180Y MET 3.1 21.9 + - - +
181Y LEU* 3.9 4.6 - - - +
182Y CYS* 3.6 26.5 - - - +
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Residues in contact with THR 166 (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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57A HIS* 4.2 25.9 - - + +
99B TYR* 3.1 34.0 + - - -
164Y GLN* 2.8 33.4 + - + +
165Y ASN* 1.3 78.4 - - - +
167Y PHE* 1.3 61.0 + - + +
168Y CYS 3.1 0.7 - - - -
169Y ALA* 3.2 11.0 - - - +
170Y ASP* 2.8 35.4 + - - +
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Residues in contact with PHE 167 (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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1B BEN 6.5 1.1 - + - -
149B PHE* 4.7 3.6 - + - -
192B MET* 3.7 35.7 - - + -
218B THR* 3.7 32.1 - - + -
163Y LEU* 3.5 17.9 - - + -
164Y GLN* 2.8 34.0 + - + +
166Y THR* 1.3 81.9 - - + +
168Y CYS* 1.3 60.1 + - - +
170Y ASP* 3.8 7.0 - - - +
171Y ALA* 3.3 23.2 + - - +
182Y CYS* 4.0 8.5 - - - -
185Y LEU* 3.5 32.7 - - + +
223Y ASN* 4.8 3.9 - - - +
225Y PRO* 3.7 11.8 - - + +
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Residues in contact with CYS 168 (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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165Y ASN 3.0 8.0 + - - +
167Y PHE* 1.3 77.5 - - - +
169Y ALA* 1.3 68.3 - - - +
170Y ASP 3.1 1.1 - - - -
171Y ALA* 3.0 11.8 + - - +
172Y HIS* 3.0 23.3 + - - +
176Y VAL* 4.0 9.8 - - + +
182Y CYS* 2.0 45.3 - - + -
225Y PRO* 3.7 14.1 - - - -
226Y SER 3.6 18.4 - - - -
227Y ILE* 3.6 24.0 - - + -
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Residues in contact with ALA 169 (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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95A ASN* 5.3 13.4 - - - +
99B TYR* 4.3 6.5 - - - +
165Y ASN* 2.8 13.9 + - + +
166Y THR* 3.2 18.2 - - - +
168Y CYS* 1.3 77.2 - - - +
170Y ASP* 1.3 61.3 - - - +
172Y HIS 3.2 18.2 - - - +
174Y ASP 5.0 0.6 - - - +
176Y VAL* 4.0 21.5 - - + +
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Residues in contact with ASP 170 (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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97B LYS* 4.7 13.0 + - - +
99B TYR* 2.8 35.4 + - - -
174B ASP* 4.6 15.4 - - - +
215B TRP* 5.5 5.5 - - - +
166Y THR* 2.8 15.1 + - - +
167Y PHE* 3.8 9.4 - - - +
169Y ALA* 1.3 80.9 - - - +
171Y ALA* 1.3 57.9 + - - +
172Y HIS 3.5 0.6 - - - +
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Residues in contact with ALA 171 (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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167Y PHE 3.3 17.2 + - - +
168Y CYS* 3.0 6.7 + - - +
170Y ASP* 1.3 81.3 - - - +
172Y HIS* 1.3 66.3 + - - +
173Y PRO* 4.5 1.9 - - - +
223Y ASN 3.3 24.5 - - - +
224Y LYS* 3.1 31.6 + - + +
225Y PRO* 3.9 10.5 - - + -
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Residues in contact with HIS 172 (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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95A LEU* 6.0 1.2 - - - +
168Y CYS 3.0 21.5 + - - +
169Y ALA 3.2 14.9 - - - +
170Y ASP 3.5 1.2 - - - +
171Y ALA* 1.3 91.6 + - + +
173Y PRO* 1.3 73.5 - - + +
174Y ASP 3.1 10.8 + - - +
176Y VAL* 5.0 0.4 - - + -
215Y TRP* 3.7 26.1 - + + -
216Y GLY* 4.2 3.0 - - - -
217Y HIS* 3.5 42.6 + - + +
224Y LYS* 4.2 7.9 - - + -
225Y PRO 2.7 28.2 + - - -
227Y ILE* 3.5 25.6 - - + +
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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