Contacts of the helix formed by residues 227 - 239 (chain A) in PDB entry 1J71
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 SER 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A PHE* 1.3 78.2 - - - +
228A GLN* 1.3 65.0 + - - +
229A SER* 4.4 13.0 - - - -
230A THR* 3.1 11.6 + - - -
231A ALA 3.0 15.2 + - - -
294A ASN 3.6 1.7 + - - -
295A ASP* 2.9 35.6 + - - +
297A ASN* 3.2 20.3 + - - -
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Residues in contact with GLN 228 (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 PHE 3.5 1.2 + - - -
227A SER* 1.3 72.9 - - - +
229A SER* 1.3 65.6 + - - +
231A ALA* 4.4 0.2 - - - -
232A ASP* 2.8 43.8 + - - +
293A ARG* 3.4 52.9 + - + +
294A ASN 5.1 0.6 - - - +
295A ASP* 4.5 4.4 + - - -
577A EOH 4.1 9.5 + - - -
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Residues in contact with SER 229 (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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227A SER* 4.4 8.7 - - - -
228A GLN* 1.3 80.3 - - - +
230A THR* 1.3 67.9 + - - +
232A ASP* 3.9 6.7 + - - +
233A LYS* 3.4 24.2 + - - +
236A ARG* 5.6 0.5 + - - -
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Residues in contact with THR 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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210A SER 4.5 3.2 + - - +
211A THR* 4.0 22.7 + - + -
226A PHE* 4.2 15.5 - - + -
227A SER* 3.1 13.8 + - - -
229A SER* 1.3 81.3 + - - +
231A ALA* 1.3 66.1 + - - +
232A ASP 3.1 1.6 - - - -
233A LYS* 3.0 34.0 + - - +
234A PHE* 3.4 35.5 + - + -
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Residues in contact with ALA 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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226A PHE* 4.1 7.1 - - + +
227A SER 3.0 15.9 + - - +
228A GLN 3.9 1.8 - - - +
230A THR* 1.3 75.3 - - - +
232A ASP* 1.3 61.9 + - - +
234A PHE* 3.2 16.9 + - - +
235A ALA* 3.1 21.7 + - - +
249A TYR* 3.5 23.5 + - + +
289A PHE* 5.8 0.3 - - - -
291A ILE* 4.9 3.8 - - + -
292A SER 3.8 22.9 - - - +
293A ARG* 4.2 4.9 - - + -
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Residues in contact with ASP 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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228A GLN* 2.8 40.5 + - - +
229A SER* 4.0 7.3 - - - +
231A ALA* 1.3 74.2 - - - +
233A LYS* 1.3 66.0 + - - +
235A ALA* 3.3 5.6 + - - +
236A ARG* 3.0 40.9 + - + +
249A TYR* 2.5 29.1 + - - -
293A ARG* 2.9 16.5 + - - -
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Residues in contact with LYS 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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209A VAL* 3.6 25.5 - - + +
210A SER* 2.9 32.9 + - - +
229A SER 3.4 13.9 + - - +
230A THR* 3.0 24.6 + - - +
232A ASP* 1.3 77.6 - - - +
234A PHE* 1.3 63.0 + - - +
236A ARG* 3.3 32.5 + - - +
237A ILE* 3.5 19.1 + - + +
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Residues in contact with PHE 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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202A ILE* 3.8 9.2 - - + -
204A PHE* 3.2 29.1 - + + -
209A VAL* 3.5 28.3 - - + -
211A THR* 3.8 15.9 - - + -
226A PHE* 3.4 31.0 - + - -
230A THR* 3.4 27.8 - - + -
231A ALA* 3.2 12.1 + - - +
233A LYS* 1.3 76.2 - - - +
235A ALA* 1.3 62.1 + - - +
237A ILE* 3.1 18.5 + - - +
238A VAL* 3.3 17.7 + - - +
289A PHE* 4.1 14.8 - - + -
291A ILE* 3.7 30.1 - - + -
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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 ALA 3.1 5.1 + - - +
232A ASP* 3.6 9.2 - - - +
234A PHE* 1.3 79.9 - - - +
236A ARG* 1.3 57.0 + - + +
238A VAL* 3.4 10.6 + - - -
239A GLY* 2.9 25.5 + - - -
240A ALA* 2.9 24.4 + - + +
249A TYR* 3.5 39.7 - - + -
289A PHE* 4.9 2.4 - - + -
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Residues in contact with ARG 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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229A SER 5.6 0.2 + - - -
232A ASP* 3.0 29.4 + - + +
233A LYS* 3.5 29.3 - - - +
234A PHE 3.2 0.4 - - - -
235A ALA* 1.3 75.6 - - + +
237A ILE* 1.3 64.5 + - + +
239A GLY* 3.4 10.5 + - - -
240A ALA 5.4 0.4 - - - -
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Residues in contact with ILE 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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204A PHE* 4.2 34.5 - - + +
205A ASP* 6.1 0.7 - - + -
207A THR* 4.0 27.6 - - + +
209A VAL* 3.3 33.7 - - + -
233A LYS* 3.5 13.2 - - + +
234A PHE* 3.1 7.1 + - - +
236A ARG* 1.3 79.8 - - + +
238A VAL* 1.3 64.3 + - + +
239A GLY 3.3 0.7 + - - -
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Residues in contact with VAL 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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204A PHE* 5.2 8.1 - - + -
234A PHE 3.5 16.2 - - - +
235A ALA* 3.5 14.4 - - - +
237A ILE* 1.3 82.9 - - + +
239A GLY* 1.3 58.7 + - - +
240A ALA* 3.5 13.1 + - + -
251A LEU* 4.0 14.4 - - + +
252A PRO* 3.7 17.7 - - - +
256A LEU* 4.2 32.8 - - + +
274A LEU* 5.1 9.9 - - + -
289A PHE* 4.3 20.6 - - + -
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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 2.9 6.4 + - - -
236A ARG* 3.4 7.9 + - - -
237A ILE 3.3 4.8 + - - -
238A VAL* 1.3 78.9 - - - +
240A ALA* 1.3 63.1 + - - +
241A THR* 4.1 3.8 + - - -
250A ARG 4.5 0.2 - - - +
252A PRO* 3.4 21.5 - - - +
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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