Contacts of the helix formed by residues 227 - 235 (chain K) in PDB entry 2ONM
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 THR 227 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53K GLU* 5.2 7.6 + - - +
54K GLY 3.9 4.8 + - - -
55K ASP* 3.5 36.9 - - - +
56K LYS* 4.5 0.9 + - - +
224K PHE* 2.9 33.2 + - + +
225K GLY 3.0 0.4 + - - -
226K PRO* 1.3 84.8 - - + +
228K ALA* 1.3 71.8 + - - -
230K ALA* 4.3 0.2 - - - +
231K ALA* 3.1 24.1 + - - +
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Residues in contact with ALA 228 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54K GLY 3.7 22.6 + - - +
55K ASP* 4.5 3.1 - - - +
59K VAL* 3.5 16.8 - - + +
192K LYS* 3.7 22.7 - - + -
221K VAL* 4.2 5.6 - - + -
223K GLY* 4.6 3.1 - - - -
224K PHE 3.0 9.1 + - - +
227K THR* 1.3 78.7 + - - +
229K GLY* 1.3 66.6 + - - +
231K ALA* 3.2 5.4 + - - +
232K ILE* 3.2 25.5 + - - +
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Residues in contact with GLY 229 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K ILE* 3.8 10.5 - - - +
192K LYS* 3.8 16.2 - - - +
224K PHE 3.4 3.4 + - - -
225K GLY 3.0 11.9 + - - -
228K ALA* 1.3 78.7 - - - +
230K ALA* 1.3 60.3 + - - +
232K ILE* 3.2 7.0 + - - +
233K ALA* 3.1 21.0 + - - +
511K ADP 3.4 19.3 - - - -
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Residues in contact with ALA 230 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225K GLY 3.0 7.1 + - - +
226K PRO* 3.5 25.8 - - + +
227K THR 3.7 0.6 + - - +
228K ALA 3.4 0.4 - - - -
229K GLY* 1.3 72.8 - - - +
231K ALA* 1.3 60.8 + - - +
233K ALA* 3.9 5.8 - - - +
234K SER* 3.0 36.0 + - - +
252K VAL* 5.8 4.9 - - + -
256K ALA* 6.1 0.4 - - - -
511K ADP 3.5 15.1 - - + +
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Residues in contact with ALA 231 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56K LYS* 3.8 41.6 - - + +
59K VAL* 3.9 13.0 - - + -
60K ASP* 5.6 0.4 - - - +
227K THR 3.1 19.4 + - - +
228K ALA 3.3 8.1 - - - +
229K GLY 3.2 0.2 - - - -
230K ALA* 1.3 77.3 - - - +
232K ILE* 1.3 56.6 + - - +
234K SER* 3.9 2.3 - - - -
235K HIS* 3.1 32.1 + - - +
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Residues in contact with ILE 232 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59K VAL* 3.6 23.3 - - + -
163K GLY* 3.6 30.5 - - - -
165K ILE* 4.8 6.7 - - + -
190K VAL* 4.0 28.0 - - + +
191K MET 4.7 0.2 - - - -
192K LYS* 3.6 37.7 - - + +
221K VAL* 5.6 1.1 - - + -
228K ALA 3.2 8.4 + - - +
229K GLY 3.2 7.2 + - - +
231K ALA* 1.3 75.1 - - - +
233K ALA* 1.3 66.5 - - - +
235K HIS* 3.2 17.3 + - - +
238K VAL* 3.8 17.8 - - + +
241K VAL* 4.6 6.9 - - + +
263K LYS* 4.0 1.6 - - - -
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Residues in contact with ALA 233 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229K GLY 3.1 8.9 + - - +
230K ALA* 3.4 6.7 + - - +
232K ILE* 1.3 81.5 - - - +
234K SER* 1.3 58.5 + - - +
241K VAL* 4.5 11.7 - - + -
253K ILE* 3.7 38.8 - - + +
256K ALA* 3.7 25.5 - - + +
257K ALA* 4.0 1.0 + - - -
263K LYS* 2.9 25.3 + - - +
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Residues in contact with SER 234 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56K LYS* 6.3 3.4 - - - -
230K ALA* 3.0 19.9 + - - +
231K ALA* 3.9 2.7 - - - -
233K ALA* 1.3 74.6 - - - +
235K HIS* 1.3 66.9 + - - +
236K GLU* 3.4 5.0 + - - +
256K ALA* 3.5 28.7 + - - +
260K SER* 3.3 15.8 - - - -
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Residues in contact with HIS 235 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56K LYS* 6.1 0.4 - - - -
59K VAL* 4.2 5.2 - - + -
60K ASP* 3.3 34.3 + - - -
63K VAL* 3.7 36.6 - - + +
64K LYS* 6.2 3.8 - - + -
231K ALA 3.1 19.0 + - - +
232K ILE* 3.2 4.6 + - - +
234K SER* 1.3 76.0 - - - +
236K GLU* 1.3 68.6 + - + +
237K ASP* 2.9 34.2 + - + -
238K VAL* 3.4 24.5 + - + -
261K ASN* 3.8 1.0 - - - +
263K LYS* 3.0 25.1 + - - -
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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