Contacts of the helix formed by residues 229 - 241 (chain A) in PDB entry 2JI8
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 CYS 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A ALA 4.7 1.2 + - - -
227A ALA* 4.0 9.2 - - - -
228A GLN* 1.3 78.0 - - - +
230A ASP* 1.3 64.5 + - - +
231A ASP 3.3 2.9 - - - -
232A GLU* 3.3 13.2 + - + -
233A ILE* 3.0 44.2 + - - +
326A ILE* 3.8 20.9 - - - -
327A LYS* 3.8 41.1 - - + +
330A VAL* 5.4 0.4 - - - -
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Residues in contact with ASP 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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224A ALA 5.2 0.7 - - - +
225A ALA* 4.7 0.7 - - - +
228A GLN* 3.7 2.2 - - - -
229A CYS* 1.3 80.0 + - - +
231A ASP* 1.3 64.3 + - - +
233A ILE* 3.6 1.7 + - - +
234A ARG* 3.0 30.9 + - - +
253A LEU* 3.7 35.0 - - - +
254A LEU* 4.5 0.2 - - - +
416A PRO* 3.3 20.6 - - + +
417A ARG* 3.0 43.6 + - - -
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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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229A CYS 3.3 0.6 - - - -
230A ASP* 1.3 79.8 - - - +
232A GLU* 1.3 61.6 + - + +
234A ARG* 3.6 8.5 + - - +
235A ALA* 3.0 30.7 + - - +
334A ARG* 5.2 0.4 - - - -
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Residues in contact with GLU 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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229A CYS* 3.3 22.9 + - + +
231A ASP* 1.3 80.3 - - + +
233A ILE* 1.3 60.8 + - - +
235A ALA 3.4 0.9 + - - -
236A LEU 3.1 17.5 + - - -
327A LYS* 4.5 14.4 - - + +
330A VAL* 3.6 13.9 - - + +
331A SER* 3.5 37.7 + - - -
334A ARG* 2.9 45.3 + - - +
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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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220A LEU* 4.0 28.0 - - + -
224A ALA* 3.8 34.5 - - + +
229A CYS* 3.0 41.2 + - - +
230A ASP 4.0 3.6 - - - +
232A GLU* 1.3 74.5 - - - +
234A ARG* 1.3 66.5 + - - +
236A LEU* 3.3 6.0 + - + +
237A VAL* 3.1 24.5 + - + +
253A LEU* 4.0 11.7 - - + -
254A LEU* 4.0 14.4 - - + -
279A ILE* 4.9 6.7 - - + -
326A ILE* 4.2 3.4 - - + -
330A VAL* 4.3 19.7 - - + -
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Residues in contact with ARG 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 ASP 3.0 18.8 + - - +
231A ASP* 3.9 9.6 - - - +
233A ILE* 1.3 76.8 - - - +
235A ALA* 1.3 58.2 + - - +
237A VAL* 3.4 2.1 + - - +
238A GLU* 2.9 60.2 + - - +
253A LEU 5.8 0.7 - - - +
254A LEU* 3.5 31.8 - - + +
255A PRO* 3.6 26.6 - - - +
258A HIS* 4.1 14.6 + - - -
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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 3.0 19.5 + - - +
232A GLU 3.6 2.5 - - - +
234A ARG* 1.3 77.0 - - - +
236A LEU* 1.3 57.5 + - - +
238A GLU* 4.1 6.2 - - - +
239A GLU* 2.9 43.1 + - - +
334A ARG* 3.4 32.3 - - - +
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Residues in contact with LEU 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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210A ILE* 5.9 0.7 - - + -
218A ILE* 4.5 14.8 - - + -
232A GLU 3.1 13.3 + - - +
233A ILE* 3.5 9.2 - - + +
234A ARG 3.3 0.2 - - - -
235A ALA* 1.3 76.8 - - - +
237A VAL* 1.3 54.1 + - + +
239A GLU* 4.2 1.6 - - - +
240A THR* 2.7 43.5 + - + +
277A VAL* 5.6 1.6 - - + -
279A ILE* 3.9 28.0 - - + -
330A VAL* 4.1 14.8 - - + -
333A LEU* 4.2 23.1 - - + -
334A ARG* 3.9 25.7 - - + +
337A LEU* 3.9 28.3 - - + -
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Residues in contact with VAL 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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218A ILE* 3.6 26.9 - - + -
220A LEU* 5.2 1.8 - - + -
233A ILE* 3.1 20.9 + - + +
234A ARG 3.4 6.0 + - - +
236A LEU* 1.3 77.3 - - + +
238A GLU* 1.3 55.5 + - - +
240A THR* 3.4 5.6 + - - -
241A GLY 3.0 15.6 + - - -
242A ILE 3.5 9.3 + - - +
244A PHE* 3.7 29.2 - - + -
254A LEU* 4.0 17.3 - - + -
258A HIS* 4.8 1.6 - - + -
260A GLN* 2.7 40.8 + - + +
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Residues in contact with GLU 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 ARG* 2.9 50.1 + - - +
235A ALA* 4.1 5.6 - - - +
237A VAL* 1.3 74.6 - - - +
239A GLU* 1.3 63.7 + - + +
241A GLY* 3.4 7.4 + - - -
258A HIS* 2.8 33.5 + - + +
260A GLN* 3.5 14.6 - - - +
342A LYS* 2.8 25.0 + - - +
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Residues in contact with GLU 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* 2.9 28.3 + - - +
236A LEU* 4.2 2.0 - - - +
238A GLU* 1.3 75.9 - - + +
240A THR* 1.3 64.0 + - + +
334A ARG* 2.9 56.4 + - - +
338A LYS* 3.6 26.1 + - + +
340A ALA 5.0 5.5 - - - +
342A LYS* 3.5 22.9 - - - +
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Residues in contact with THR 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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210A ILE* 4.9 3.4 - - + -
218A ILE* 4.4 1.6 - - - +
236A LEU* 2.7 30.4 + - + +
237A VAL* 3.4 4.9 + - - -
239A GLU* 1.3 80.5 - - + +
241A GLY* 1.3 61.2 + - - +
242A ILE* 3.4 33.2 + - + +
337A LEU* 3.6 37.2 - - + -
341A PRO 4.4 3.1 - - - +
342A LYS* 3.3 7.5 - - - +
343A ALA* 2.9 24.8 + - - +
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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 VAL 3.0 5.7 + - - -
238A GLU 3.4 9.5 + - - -
240A THR* 1.3 77.6 - - - +
242A ILE* 1.3 62.0 + - - +
243A PRO 3.5 0.2 - - - -
260A GLN* 3.4 21.1 + - - +
342A LYS* 4.1 12.3 - - - +
343A ALA* 3.5 6.9 - - - +
348A THR* 3.5 23.7 - - - +
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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