Contacts of the helix formed by residues 229 - 243 (chain A) in PDB entry 4O5A
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 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A ASP* 2.8 36.3 + - - +
228A TYR* 1.3 80.6 - - - +
230A PRO* 1.3 70.9 - - + +
231A GLU* 3.4 16.4 + - - +
232A SER* 3.1 16.3 + - - -
233A GLY 3.0 18.0 + - - -
257A MSE 3.4 5.3 - - - +
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Residues in contact with PRO 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 TYR 4.4 0.9 - - - +
229A THR* 1.3 88.3 - - - +
231A GLU* 1.3 71.5 + - - +
233A GLY 4.4 0.2 - - - +
234A ALA* 2.8 32.5 + - - +
256A VAL* 4.0 30.0 - - + +
257A MSE 4.7 1.3 - - + -
260A ALA* 3.5 23.9 - - + +
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Residues in contact with GLU 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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229A THR* 3.4 20.6 + - - +
230A PRO* 1.3 88.8 - - - +
232A SER* 1.3 58.7 + - - +
234A ALA* 3.4 6.2 + - - +
235A GLU* 3.0 29.5 + - - +
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Residues in contact with SER 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A HIS 4.9 0.3 + - - -
226A THR* 3.1 27.9 - - - +
227A ASP* 3.1 31.8 + - - -
229A THR* 3.1 11.0 + - - -
231A GLU* 1.3 78.6 - - - +
233A GLY* 1.3 56.3 + - - +
235A GLU* 3.4 14.5 + - - +
236A ALA* 3.0 29.1 + - - +
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Residues in contact with GLY 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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194A VAL* 4.5 7.9 - - - -
229A THR 3.0 10.9 + - - -
230A PRO 3.7 2.0 - - - -
232A SER* 1.3 77.3 - - - +
234A ALA* 1.3 55.2 + - - +
236A ALA* 3.5 1.7 + - - +
237A THR* 2.8 37.9 + - - -
252A TYR* 4.4 1.4 - - - -
257A MSE 3.7 34.0 - - - -
260A ALA* 4.8 3.6 - - - -
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Residues in contact with ALA 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 PRO 2.8 17.9 + - - +
231A GLU* 3.6 7.9 - - - +
233A GLY* 1.3 74.9 - - - +
235A GLU* 1.3 59.7 + - - +
237A THR* 3.3 3.5 + - - -
238A LYS* 3.0 37.9 + - - +
260A ALA* 4.3 10.4 - - + +
264A VAL* 3.7 22.9 - - + +
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Residues in contact with GLU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLU 3.0 17.3 + - - +
232A SER* 3.7 14.5 + - - +
233A GLY 3.3 0.2 - - - -
234A ALA* 1.3 75.0 - - - +
236A ALA* 1.3 64.2 + - - +
238A LYS* 3.4 11.3 + - - +
239A ARG* 3.0 24.0 + - + +
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Residues in contact with ALA 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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194A VAL* 3.9 25.1 - - + -
224A LEU* 3.6 23.2 - - + +
226A THR* 4.1 7.4 - - + -
232A SER 3.0 17.2 + - - +
233A GLY 3.8 4.5 - - - +
235A GLU* 1.3 78.6 - - - +
237A THR* 1.3 57.1 + - - +
239A ARG* 3.3 5.1 + - - +
240A LEU* 2.9 34.1 + - - +
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Residues in contact with THR 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 GLY 2.8 22.9 + - - -
234A ALA 3.7 4.7 - - - -
235A GLU 3.2 0.2 - - - -
236A ALA* 1.3 75.0 - - - +
238A LYS* 1.3 65.5 + - - +
240A LEU* 3.2 7.7 + - - +
241A LEU* 2.9 45.4 + - + +
250A ILE* 4.3 5.6 - - + -
252A TYR* 2.8 32.9 + - - +
261A GLY* 3.4 27.3 - - - +
264A VAL* 3.8 6.1 - - + -
276A LEU* 5.2 1.8 - - + -
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Residues in contact with LYS 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 ALA* 3.0 21.2 + - - +
235A GLU* 3.4 11.9 + - - +
237A THR* 1.3 76.1 - - - +
239A ARG* 1.3 60.6 + - - +
241A LEU* 3.5 3.1 + - - -
242A SER* 2.6 34.2 + - - +
264A VAL* 3.8 27.8 - - + +
268A LYS* 5.6 4.7 - - + +
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Residues in contact with ARG 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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224A LEU* 3.6 37.6 - - + +
235A GLU* 3.0 16.1 + - + +
236A ALA* 3.5 10.1 - - - +
238A LYS* 1.3 76.5 - - - +
240A LEU* 1.3 62.7 + - + +
242A SER* 3.3 12.1 + - - -
243A VAL* 3.4 27.6 - - + +
402A GOL 2.8 55.9 + - - -
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Residues in contact with LEU 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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192A ALA* 3.9 31.0 - - + -
193A ARG 4.9 2.0 - - - +
194A VAL* 3.6 30.1 - - + -
222A ARG* 5.1 11.0 - - + +
224A LEU* 3.7 23.1 - - + -
236A ALA 2.9 18.4 + - - +
237A THR* 3.2 4.0 + - - +
239A ARG* 1.3 77.2 - - + +
241A LEU* 1.3 62.1 + - - +
242A SER 3.4 0.9 + - - -
243A VAL* 3.7 12.5 + - - +
246A ARG* 4.2 0.3 - - - +
247A PRO* 3.2 34.9 - - + +
250A ILE* 4.0 16.8 - - + -
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Residues in contact with LEU 241 (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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237A THR* 2.9 37.0 + - + +
238A LYS 4.2 1.3 - - - +
240A LEU* 1.3 76.3 - - - +
242A SER* 1.3 59.1 + - - +
243A VAL 3.6 0.4 - - - -
246A ARG* 3.6 44.4 + - + +
247A PRO* 4.6 1.6 - - + +
250A ILE* 4.3 10.5 - - + -
264A VAL* 4.4 3.1 - - + -
265A ALA* 4.0 28.0 - - + -
268A LYS* 3.7 32.7 - - + -
270A VAL* 4.4 9.6 - - + -
276A LEU* 4.2 22.7 - - + -
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Residues in contact with SER 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A LYS* 2.6 24.0 + - - +
239A ARG* 3.3 4.7 + - - -
240A LEU 3.2 0.4 - - - -
241A LEU* 1.3 76.3 - - - +
243A VAL* 1.3 65.3 + - - +
244A GLU 3.9 2.0 + - - -
268A LYS* 3.6 20.4 + - - +
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Residues in contact with VAL 243 (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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220A ARG* 6.2 1.3 - - - +
239A ARG* 3.4 27.6 + - + +
240A LEU* 3.7 6.6 + - - +
241A LEU 3.6 0.8 - - - -
242A SER* 1.3 80.5 - - - +
244A GLU* 1.3 72.5 + - - +
245A PRO 3.3 15.1 - - - +
246A ARG* 3.5 7.8 + - - -
247A PRO* 4.6 0.9 - - - +
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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