Contacts of the helix formed by residues 223 - 234 (chain A) in PDB entry 2PUA
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 PRO 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A PHE 4.0 0.4 - - - -
222A GLU* 1.3 104.3 - - + +
224A GLU* 1.3 63.8 + - - +
226A GLY 3.7 0.4 - - - -
227A TYR* 3.1 20.4 + - - +
249A ILE* 3.4 43.3 - - + +
250A MET* 4.2 0.9 - - - -
252A MET* 5.3 7.0 - - + -
253A GLY* 3.4 15.5 - - - +
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Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A ASP* 6.0 0.4 - - - +
222A GLU* 2.8 6.5 + - + +
223A PRO* 1.3 79.9 - - - +
225A SER* 1.3 64.5 + - - +
227A TYR* 3.0 21.3 - - - +
228A ARG* 2.9 74.2 + - - +
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Residues in contact with SER 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A GLN 5.0 1.8 - - - +
219A GLY* 3.7 9.3 - - - -
220A ASP* 2.8 48.6 + - - -
222A GLU* 2.5 21.8 + - - +
224A GLU* 1.3 75.1 - - - +
226A GLY* 1.3 61.0 + - - +
228A ARG* 3.5 9.8 + - - +
229A ALA* 2.8 25.9 + - - +
250A MET* 3.2 11.0 - - - +
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Residues in contact with GLY 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ILE* 5.0 5.2 - - - -
222A GLU 3.1 4.8 + - - -
223A PRO 3.3 2.0 + - - -
224A GLU 3.1 0.2 - - - -
225A SER* 1.3 81.0 + - - +
227A TYR* 1.3 54.8 - - - +
229A ALA* 2.7 29.1 + - - +
230A MET* 2.9 13.7 + - - +
250A MET* 3.3 31.0 - - - -
254A ALA* 3.9 9.7 - - - +
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Residues in contact with TYR 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A PRO 3.1 12.3 + - - +
224A GLU* 3.0 27.8 + - - +
226A GLY* 1.3 71.0 - - - +
228A ARG* 1.3 70.2 + - + +
230A MET* 3.2 2.3 + - - +
231A GLN* 2.8 44.3 + - - +
253A GLY* 3.4 22.9 - - - -
254A ALA* 4.5 0.4 - - - +
256A CYS* 3.2 30.5 - - - -
257A ALA* 3.5 22.4 - - + +
260A GLU* 2.4 34.1 + - - +
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Residues in contact with ARG 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLU* 2.9 61.9 + - - +
225A SER* 4.0 7.0 - - - +
227A TYR* 1.3 76.3 - - + +
229A ALA* 1.3 57.9 + - - +
231A GLN* 3.3 15.4 + - - +
232A GLN* 2.7 37.5 + - + +
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Residues in contact with ALA 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ILE* 3.3 36.6 - - + -
217A VAL* 3.8 24.5 - - + +
218A GLN 4.9 1.8 - - - +
225A SER 2.8 13.4 + - - +
226A GLY 2.7 14.0 + - - +
228A ARG* 1.3 68.6 - - - +
230A MET* 1.3 65.9 + - - +
232A GLN* 3.0 5.5 + - - +
233A ILE* 2.8 27.5 + - - +
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Residues in contact with MET 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ILE* 3.8 11.5 - - - +
226A GLY 2.9 4.8 + - - +
227A TYR 3.6 6.5 - - - +
229A ALA* 1.3 75.4 - - - +
231A GLN* 1.3 56.5 + - - +
233A ILE* 2.7 28.5 + - - +
234A LEU* 2.9 46.5 + - + +
243A VAL* 4.7 11.7 - - + -
254A ALA* 3.4 39.3 - - + +
255A LEU* 5.5 0.2 - - + -
257A ALA* 4.5 3.1 - - + -
258A ALA* 4.6 14.4 - - + +
265A VAL* 5.6 1.6 - - + -
269A VAL* 4.5 16.6 - - + -
271A LEU* 3.6 31.0 - - + -
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Residues in contact with GLN 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A TYR* 2.8 41.1 + - - +
228A ARG* 3.3 16.4 + - - +
230A MET* 1.3 77.0 - - - +
232A GLN* 1.3 68.4 + - + +
234A LEU* 3.3 1.3 + - - +
235A SER* 2.9 35.7 + - - +
257A ALA* 4.6 6.9 - - + +
261A MET* 4.8 17.5 - - - +
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Residues in contact with GLN 232 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A SER 5.1 0.6 - - - +
217A VAL* 4.5 22.8 - - + +
228A ARG* 2.7 24.2 + - + +
229A ALA* 3.4 6.5 - - - +
231A GLN* 1.3 79.3 - - + +
233A ILE* 1.3 63.0 + - - +
235A SER* 3.7 11.7 + - - -
236A GLN* 3.6 17.2 + - - +
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Residues in contact with ILE 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A VAL 5.1 0.2 - - - +
184A ILE* 3.8 31.2 - - + -
214A SER 4.4 6.5 - - - +
215A TRP* 4.1 21.3 - - + +
217A VAL* 4.1 17.5 - - + -
229A ALA 2.8 20.9 + - - +
230A MET* 2.7 16.9 + - - +
232A GLN* 1.3 70.1 - - - +
234A LEU* 1.3 63.7 + - + +
235A SER 3.0 4.9 - - - -
236A GLN* 3.0 27.5 + - - +
239A ARG* 3.9 5.0 - - - +
240A PRO* 3.4 37.5 - - + -
243A VAL* 4.5 13.2 - - + -
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A MET* 2.9 36.1 + - + +
231A GLN 3.8 1.1 - - - +
233A ILE* 1.3 94.5 - - + +
235A SER* 1.3 56.4 + - - +
236A GLN 3.1 4.8 + - - -
239A ARG* 2.6 52.5 + - + +
240A PRO* 4.3 3.6 - - + -
258A ALA* 4.5 5.8 - - + -
261A MET* 3.9 25.3 - - + +
263A LEU* 3.3 27.4 - - + -
269A VAL* 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