Contacts of the helix formed by residues 230 - 246 (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 LYS 230 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A TYR* 4.0 2.0 - - - -
60A ASN* 2.8 23.8 + - - +
61A ASP* 3.3 16.0 + - - -
128Y GLU* 3.1 28.4 + - + +
178Y GLU 2.8 26.6 + - - +
179Y SER* 3.0 24.6 + - - -
180Y MET 3.7 6.5 - - - +
181Y LEU* 3.7 32.3 - - + -
210Y GLN* 4.1 4.0 - - - +
228Y TYR 3.3 2.8 + - - -
229Y THR* 1.3 66.9 - - - +
231Y LEU* 1.3 65.8 - - - +
232Y ILE* 3.1 23.6 - - + +
233Y PHE* 3.1 25.9 + - - +
234Y TYR* 3.3 7.9 - - - -
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Residues in contact with LEU 231 (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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53X LEU* 4.2 9.2 - - + -
103Y LEU* 4.4 7.4 - - + -
123Y LEU* 3.8 10.8 - - + -
124Y PRO* 3.7 24.2 - - + -
209Y TRP* 3.3 40.8 - - + +
210Y GLN 3.1 14.1 + - - +
211Y GLY 3.9 15.0 - - - -
212Y ILE* 3.6 30.7 - - + -
229Y THR 3.0 10.9 + - - +
230Y LYS* 1.3 71.6 - - - +
232Y ILE* 1.3 62.3 + - - +
234Y TYR* 3.0 20.9 + - - +
235Y LEU* 3.4 14.8 + - - +
238Y ILE* 4.5 5.8 - - + +
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Residues in contact with ILE 232 (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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36A TYR* 3.7 52.0 + - + -
124Y PRO* 4.0 12.0 - - + +
125Y THR* 3.7 19.5 - - - +
127Y GLN 3.6 27.4 - - - +
128Y GLU* 4.1 10.8 - - + -
210Y GLN* 4.5 3.5 + - - +
230Y LYS* 3.1 18.8 - - + -
231Y LEU* 1.3 78.5 - - - +
233Y PHE* 1.3 63.1 + - - +
234Y TYR 3.2 1.0 + - - -
235Y LEU* 3.3 36.8 + - + +
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Residues in contact with PHE 233 (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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36A TYR* 4.4 8.2 + - - -
61A ASP* 3.5 43.9 - - + +
101Y HIS* 4.2 13.2 - + - -
178Y GLU* 4.2 12.8 - - + -
179Y SER* 3.8 29.2 - - - -
230Y LYS* 3.1 23.7 + - - +
232Y ILE* 1.3 81.5 - - - +
234Y TYR* 1.3 85.7 + + + +
235Y LEU 3.6 0.4 + - - -
236Y ASP* 5.1 3.3 + - - +
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Residues in contact with TYR 234 (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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91X HIS* 3.9 30.5 - + - -
101Y HIS* 2.7 46.2 + + - -
103Y LEU* 3.5 28.5 - - + -
179Y SER* 3.2 18.8 + - - -
229Y THR* 3.5 23.9 - - + +
230Y LYS 3.3 18.6 - - - -
231Y LEU* 3.0 9.1 + - - +
233Y PHE* 1.3 101.6 - + + +
235Y LEU* 1.3 63.7 + - - +
236Y ASP* 3.0 3.8 - - - -
237Y TRP* 3.0 11.4 + - + +
238Y ILE* 2.9 26.5 + - + +
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Residues in contact with LEU 235 (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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123Y LEU* 3.4 37.9 - - + -
124Y PRO* 3.2 30.3 - - + +
125Y THR* 5.1 1.8 - - - -
231Y LEU 3.4 15.3 + - - +
232Y ILE* 3.3 32.7 + - + +
233Y PHE 3.6 0.6 - - - -
234Y TYR* 1.3 75.0 - - - +
236Y ASP* 1.3 64.9 + - - +
238Y ILE* 3.8 4.4 + - + -
239Y ASP* 3.2 35.3 + - - +
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Residues in contact with ASP 236 (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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233Y PHE 5.1 2.4 + - - +
234Y TYR* 3.0 1.8 - - - -
235Y LEU* 1.3 83.4 - - - +
237Y TRP* 1.3 57.0 + - - +
239Y ASP* 3.9 2.4 - - - +
240Y ASP* 3.0 45.9 + - - +
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Residues in contact with TRP 237 (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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53X LEU* 4.6 0.9 - - + -
89X PHE* 3.4 33.2 - - + -
90X PRO 4.1 2.0 - - - -
91X HIS* 3.6 38.1 - + + +
92X PRO* 3.6 19.0 - - + +
103Y LEU* 3.7 37.7 - - + -
105Y LEU* 4.0 25.4 - - + -
234Y TYR* 3.0 11.4 + - + +
236Y ASP* 1.3 75.4 - - - +
238Y ILE* 1.3 92.5 + - + +
240Y ASP* 3.2 6.7 + - + +
241Y THR* 2.9 42.1 + - - -
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Residues in contact with ILE 238 (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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47X VAL* 4.7 6.5 - - + -
53X LEU* 3.7 25.8 - - + -
103Y LEU* 4.2 3.4 - - + -
105Y LEU* 4.1 12.8 - - + -
123Y LEU* 4.0 26.2 - - + -
231Y LEU* 4.5 10.8 - - + +
234Y TYR* 2.9 31.0 + - + +
235Y LEU* 4.0 3.8 - - - +
237Y TRP* 1.3 98.3 - - + +
239Y ASP* 1.3 66.7 + - - +
241Y THR* 3.3 1.7 + - - -
242Y ILE* 2.9 52.3 + - + +
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Residues in contact with ASP 239 (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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123Y LEU* 3.7 22.6 - - - +
235Y LEU* 3.2 23.5 + - - +
236Y ASP* 4.0 3.1 - - - +
238Y ILE* 1.3 75.9 - - - +
240Y ASP* 1.3 64.2 + - - +
242Y ILE* 3.6 6.9 + - - +
243Y THR* 3.0 36.0 + - - +
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Residues in contact with ASP 240 (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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236Y ASP* 3.0 28.5 + - - +
237Y TRP* 3.2 8.3 + - + +
239Y ASP* 1.3 82.9 - - - +
241Y THR* 1.3 53.2 + - - +
243Y THR* 3.1 4.8 + - - +
244Y GLU* 2.7 54.0 + - - +
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Residues in contact with THR 241 (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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51X TRP* 4.2 3.5 - - + -
89X PHE* 3.8 35.0 - - + -
105Y LEU* 3.3 28.9 - - + -
237Y TRP* 2.9 34.6 + - + -
240Y ASP* 1.3 72.2 - - - +
242Y ILE* 1.3 64.1 + - - +
243Y THR 3.0 4.9 + - - -
245Y ASN* 2.9 41.5 + - - +
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Residues in contact with ILE 242 (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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47X VAL* 4.1 25.1 - - + +
48X ASN* 4.4 19.3 - - + +
51X TRP* 4.0 40.1 + - + +
105Y LEU* 3.8 12.8 - - + -
238Y ILE* 2.9 37.0 + - + +
239Y ASP* 4.1 7.2 - - - +
241Y THR* 1.3 76.3 - - - +
243Y THR* 1.3 59.7 + - - +
245Y ASN 3.4 13.1 - - - +
246Y PRO 5.0 0.2 - - - +
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Residues in contact with THR 243 (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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239Y ASP* 3.0 21.0 + - - +
240Y ASP* 3.7 3.8 - - - +
241Y THR 3.0 0.2 - - - -
242Y ILE* 1.3 82.4 + - - +
244Y GLU* 1.3 73.2 + - + +
245Y ASN 3.3 6.5 + - - +
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Residues in contact with GLU 244 (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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240Y ASP* 2.7 34.5 + - - +
243Y THR* 1.3 84.8 - - + +
245Y ASN* 1.3 66.9 + - - +
246Y PRO* 4.5 1.9 - - - +
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Residues in contact with ASN 245 (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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51X TRP* 4.1 15.4 - - + -
89X PHE* 3.7 28.6 - - + -
107Y ARG* 6.1 0.4 - - + -
241Y THR* 2.9 39.2 + - - +
242Y ILE 3.4 17.0 - - - +
243Y THR 3.8 4.4 - - - +
244Y GLU* 1.3 85.4 - - - +
246Y PRO* 1.3 79.3 - - + +
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Residues in contact with PRO 246 (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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50X LYS* 4.4 15.5 + - - +
51X TRP* 3.9 15.4 + - - -
107Y ARG* 2.8 37.6 + - - +
242Y ILE 5.0 0.3 - - - +
244Y GLU 4.5 2.0 - - - +
245Y ASN* 1.3 97.0 - - + +
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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