Contacts of the helix formed by residues 229 - 240 (chain A) in PDB entry 2HDH
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 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A TYR* 2.9 51.7 + - + -
228A SER* 1.3 73.3 - - - +
230A GLU* 1.3 78.6 + - - +
232A ILE* 3.3 2.6 + - - +
233A ASP* 3.0 23.2 + - - +
247A PHE* 3.8 24.2 - - + -
298A PHE* 3.2 42.1 + - + +
299A TYR* 3.4 21.8 + - + +
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Residues in contact with GLU 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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228A SER* 3.4 19.9 - - - +
229A LYS* 1.3 89.7 + - - +
231A ASP* 1.3 60.8 + - - +
233A ASP* 3.5 3.7 + - - +
234A THR* 2.9 31.7 + - - +
299A TYR* 3.3 32.3 - - + +
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Residues in contact with ASP 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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228A SER* 3.1 23.7 + - - +
230A GLU* 1.3 79.8 - - - +
232A ILE* 1.3 55.8 + - - +
234A THR* 3.3 2.6 + - - -
235A ALA* 2.7 37.2 + - - +
195B HIS* 5.8 1.0 + - - -
196B PRO 4.9 1.2 - - - +
197B VAL* 3.7 24.6 - - + +
198B SER* 2.9 42.6 + - - +
206B ILE* 4.3 4.7 - - + -
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Residues in contact with ILE 232 (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 ALA* 4.0 13.5 - - + +
221A LEU* 4.1 11.4 - - + -
222A TYR* 4.1 8.1 - - + +
227A ALA* 3.8 28.0 - - + +
228A SER 3.0 18.2 + - - +
229A LYS 3.7 4.0 - - - +
231A ASP* 1.3 76.2 - - - +
233A ASP* 1.3 61.7 + - - +
235A ALA* 3.3 1.0 + - - +
236A MSE 3.0 25.2 + - + +
246A PRO* 3.5 24.5 - - + -
247A PHE* 3.8 19.3 - - + -
206B ILE* 4.2 14.8 - - + -
210B LEU* 3.8 21.3 - - + -
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Residues in contact with ASP 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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229A LYS 3.0 16.1 + - - +
230A GLU* 3.7 4.9 - - - +
232A ILE* 1.3 76.0 - - - +
234A THR* 1.3 63.0 + - - +
236A MSE 3.4 0.9 + - - -
237A LYS* 3.0 34.0 + - - +
245A GLY* 3.7 12.6 - - - -
246A PRO* 3.3 6.9 - - - +
247A PHE* 2.9 30.6 + - - +
248A GLU* 3.1 36.6 - - - +
299A TYR* 2.7 24.6 + - - +
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Residues in contact with THR 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 GLU 2.9 18.0 + - - -
231A ASP* 3.3 6.4 + - - -
233A ASP* 1.3 78.1 - - - +
235A ALA* 1.3 58.9 + - - +
237A LYS* 3.3 11.7 + - - +
238A LEU* 2.9 43.3 + - + +
168B LEU* 4.5 1.3 - - + -
195B HIS* 3.6 36.5 + - + +
197B VAL* 3.8 18.4 - - + -
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Residues in contact with ALA 235 (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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231A ASP 2.7 21.5 + - - +
232A ILE 3.6 0.7 - - - +
233A ASP 3.2 0.2 - - - -
234A THR* 1.3 73.7 - - - +
236A MSE 1.3 54.6 + - - +
239A GLY* 2.7 33.4 + - - -
168B LEU* 3.5 16.8 - - + +
197B VAL* 4.4 6.7 - - + +
206B ILE* 3.5 34.3 - - + -
207B VAL* 3.7 14.5 - - + +
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Residues in contact with MSE 236 (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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214A TYR* 3.7 18.4 - - + +
232A ILE 3.0 17.3 + - - +
233A ASP 4.2 0.7 - - - +
235A ALA* 1.3 74.3 - - - +
237A LYS* 1.3 62.1 + - - +
240A ALA* 3.1 40.1 + - + +
241A GLY 3.2 3.3 + - - -
242A TYR* 3.3 39.0 + - + +
245A GLY* 4.7 1.1 - - - -
246A PRO* 3.8 18.2 - - + -
206B ILE* 4.4 2.9 - - - +
207B VAL* 4.0 31.6 - - + +
210B LEU* 4.0 37.7 - - + -
211B LEU* 4.6 4.3 - - + -
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Residues in contact with LYS 237 (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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233A ASP* 3.0 29.7 + - - +
234A THR* 3.9 9.4 + - - +
236A MSE 1.3 77.5 - - - +
238A LEU* 1.3 64.9 + - + +
241A GLY* 3.0 26.5 + - - -
242A TYR 3.4 20.2 - - - +
243A PRO 3.8 11.2 - - - +
244A MSE 3.9 0.4 - - - -
245A GLY 3.6 13.0 - - - +
248A GLU* 3.3 35.7 + - - +
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Residues in contact with LEU 238 (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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234A THR* 2.9 25.6 + - + +
237A LYS* 1.3 85.1 - - + +
239A GLY* 1.3 62.9 + - - +
241A GLY* 4.2 2.4 + - - -
166B MSE 3.7 15.9 - - - +
167B LYS* 4.7 18.9 + - + +
168B LEU* 3.9 20.9 + - + +
195B HIS* 3.8 37.9 - - + +
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Residues in contact with GLY 239 (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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235A ALA 2.7 22.8 + - - -
238A LEU* 1.3 76.1 - - - +
240A ALA* 1.3 58.5 + - - +
160B PHE* 4.7 8.6 - - - -
166B MSE 3.7 20.1 - - - +
168B LEU* 3.7 17.3 - - - +
207B VAL* 4.4 13.5 - - - +
211B LEU* 5.9 0.9 - - - +
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Residues in contact with ALA 240 (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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235A ALA 3.7 1.2 + - - -
236A MSE 3.1 36.6 + - + +
239A GLY* 1.3 75.6 - - - +
241A GLY* 1.3 63.8 - - - +
242A TYR* 3.4 29.6 + - + +
207B VAL* 5.0 4.5 - - + -
211B LEU* 4.9 11.0 - - + -
243B PRO* 3.9 10.0 - - - +
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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