Contacts of the helix formed by residues 232 - 241 (chain A) in PDB entry 5JMO
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 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A GLU* 3.1 30.7 + - + +
231A VAL* 1.3 76.9 - - - +
233A ASP* 1.3 65.0 + - - +
234A ALA* 3.5 9.6 + - - +
235A VAL* 3.2 26.6 + - + +
236A GLU* 3.1 23.0 + - - +
268B ARG* 6.0 3.8 - - - +
269B LEU* 6.2 3.5 - - + +
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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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232A THR* 1.3 73.6 - - - +
234A ALA* 1.3 57.4 + - - +
236A GLU* 3.4 8.3 + - - +
237A ALA* 3.0 26.3 + - - +
267A ALA* 3.4 25.9 + - + +
268A ARG* 3.4 7.1 + - - +
269A LEU* 2.8 34.9 + - + +
270A ALA* 3.0 30.3 + - - +
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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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232A THR* 3.2 8.5 + - - +
233A ASP* 1.3 75.5 - - - +
235A VAL* 1.3 60.7 + - - +
237A ALA* 3.3 3.6 + - - +
238A ARG* 2.9 37.5 + - + +
269A LEU* 4.0 21.4 - - + +
234B ALA* 4.5 16.2 - - + -
238B ARG* 4.2 12.8 - - - +
269B LEU* 4.7 12.8 - - + -
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Residues in contact with VAL 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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175A VAL* 3.8 20.8 - - + +
176A ASN* 4.3 6.7 - - - +
226A MET* 3.6 33.9 - - + +
230A GLU 3.5 18.8 - - - +
231A VAL* 4.3 4.9 - - - -
232A THR* 3.2 26.1 + - + +
234A ALA* 1.3 74.6 - - - +
236A GLU* 1.3 59.2 + - - +
238A ARG 3.4 0.9 + - - -
239A SER* 2.7 32.1 + - - -
238B ARG* 3.6 22.0 - - - +
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Residues in contact with GLU 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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226A MET* 4.4 5.8 - - + -
231A VAL* 3.8 18.7 - - + +
232A THR 3.1 15.2 + - - +
233A ASP* 3.7 9.9 - - - +
234A ALA 3.3 0.2 - - - -
235A VAL* 1.3 77.2 - - - +
237A ALA* 1.3 57.3 + - - +
239A SER* 3.2 4.4 + - - -
240A LEU* 3.0 37.5 + - + +
254A TRP* 4.0 17.3 - - + -
266A PRO* 4.5 0.2 - - - +
267A ALA 5.1 0.9 + - - -
270A ALA* 3.7 15.6 - - + +
308A TYR* 2.5 31.6 + - - -
2G ARG* 2.9 37.8 + - - +
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Residues in contact with ALA 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 18.3 + - - +
234A ALA* 3.8 5.4 - - - +
235A VAL 3.3 0.2 - - - -
236A GLU* 1.3 76.2 - - - +
238A ARG* 1.3 60.7 + - + +
240A LEU 3.6 0.2 + - - -
241A GLY* 3.0 27.5 + - - -
269A LEU* 3.5 35.4 - - + +
270A ALA* 4.2 3.1 - - - +
273A ALA* 3.7 16.3 - - + +
178B GLN* 3.8 4.7 + - - +
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Residues in contact with ARG 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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175A VAL* 4.1 20.3 - - + +
234A ALA* 2.9 22.9 + - + +
235A VAL 3.9 3.8 - - - +
237A ALA* 1.3 77.9 - - - +
239A SER* 1.3 61.4 + - - +
242A LEU* 3.5 23.0 + - - +
173B PHE* 5.8 2.4 - - - -
175B VAL* 3.3 34.5 + - - +
178B GLN* 3.7 28.9 + - - +
232B THR* 5.2 0.2 + - - -
234B ALA* 4.4 9.9 + - - +
235B VAL* 3.6 36.8 - - - +
238B ARG* 3.7 38.4 - - - +
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Residues in contact with SER 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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152A LEU* 4.0 19.3 - - - +
175A VAL* 3.7 3.1 - - - +
224A VAL* 3.7 23.8 - - - +
226A MET* 3.3 33.3 - - - +
235A VAL 2.7 19.2 + - - -
236A GLU 3.6 4.3 - - - -
238A ARG* 1.3 75.7 - - - +
240A LEU* 1.3 64.2 + - - +
241A GLY 3.1 2.5 + - - -
242A LEU* 3.3 16.6 + - - +
250A TYR* 3.9 7.8 - - - -
254A TRP* 6.0 0.2 - - - -
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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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152A LEU* 3.7 22.7 - - + -
236A GLU* 3.0 23.0 + - + +
239A SER* 1.3 76.0 - - - +
241A GLY* 1.3 57.4 + - - +
242A LEU 3.4 0.2 - - - -
244A PRO* 5.8 0.2 - - - +
250A TYR* 3.6 13.1 + - - -
254A TRP* 5.3 3.1 - - + -
270A ALA* 4.0 24.7 - - + +
273A ALA* 4.0 12.9 - - + +
274A PHE* 3.6 44.6 - - + -
277A GLY* 5.6 1.0 - - - -
287A SER* 5.2 0.7 + - - -
289A PHE* 3.4 38.4 - - + -
291A TRP* 4.0 16.6 - - + -
308A TYR* 5.4 2.7 - - + -
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Residues in contact with GLY 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 ALA 3.0 11.4 + - - -
239A SER 3.1 0.2 - - - -
240A LEU* 1.3 78.9 - - - +
242A LEU* 1.3 61.7 + - - +
243A ASN 3.3 2.9 + - - -
244A PRO* 3.5 5.4 - - - +
250A TYR* 4.4 1.8 - - - -
273A ALA* 4.7 7.4 - - - -
276A ARG* 3.0 28.2 + - - -
277A GLY* 6.4 1.1 - - - -
178B GLN* 3.1 26.7 - - - +
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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