Contacts of the helix formed by residues 228 - 238 (chain A) in PDB entry 2ABJ
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 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ARG* 5.3 3.1 - - - -
224A ASN 4.3 9.0 - - - -
225A TYR* 2.8 23.9 + - - -
227A SER* 1.3 78.5 + - - +
229A LEU* 1.3 64.6 + - - +
230A PHE 3.4 1.7 + - - -
231A ALA* 3.5 6.2 + - - +
232A GLN* 3.1 21.7 + - - +
245A TRP* 3.5 34.6 - - - -
173D VAL* 4.4 10.6 - - - +
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Residues in contact with LEU 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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225A TYR 3.9 5.2 - - - +
226A GLY 3.9 14.4 - - - +
227A SER 3.4 1.2 - - - -
228A SER* 1.3 77.3 + - - +
230A PHE* 1.3 60.0 + - - +
232A GLN* 3.3 7.3 + - + +
233A CYS* 3.0 33.1 + - - -
88D TYR* 5.9 0.7 - - + -
90D VAL* 3.5 31.0 - - + -
125D ALA 3.9 7.2 - - - +
126D THR* 3.7 28.0 - - + +
173D VAL* 3.7 20.9 - - + +
174D LYS* 3.5 44.4 - - - +
175D LYS 4.1 1.3 - - - +
176D PRO* 4.2 3.1 - - + -
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Residues in contact with PHE 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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208A TYR* 3.2 35.4 - + - -
227A SER 4.5 2.2 + - - +
228A SER 3.4 0.4 - - - -
229A LEU* 1.3 77.3 - - - +
231A ALA* 1.3 63.9 + - - +
233A CYS* 3.2 5.8 + - + +
234A GLU* 3.1 28.2 + - + +
123D VAL* 3.5 40.4 - - + -
124D ARG* 3.6 39.3 + - - +
126D THR* 3.6 11.7 - - + +
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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
----------------------------------------------------------
203A TRP* 4.2 3.6 - - + -
208A TYR* 3.7 39.9 - - + -
227A SER 5.1 1.7 + - - +
228A SER* 3.5 4.3 + - - +
229A LEU 3.4 0.2 - - - -
230A PHE* 1.3 78.9 - - - +
232A GLN* 1.3 56.9 + - - +
234A GLU* 3.4 3.7 + - - +
235A ASP* 2.8 28.6 + - - +
243A VAL* 3.6 11.3 - - + +
245A TRP* 3.8 28.5 - - + -
124D ARG* 5.9 0.4 - - - +
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Residues in contact with GLN 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 SER* 3.1 15.1 + - - +
229A LEU* 3.5 12.8 - - + +
230A PHE 3.2 0.2 - - - -
231A ALA* 1.3 75.1 - - - +
233A CYS* 1.3 61.7 + - - +
235A ASP* 3.2 17.4 + - - +
236A VAL* 3.0 41.3 + - + +
241A GLN 3.0 21.4 + - - +
242A GLN* 3.6 24.1 + - - +
243A VAL* 3.7 13.1 + - + +
257A GLY* 5.9 0.5 - - - -
173D VAL 4.5 16.5 + - - +
174D LYS* 5.2 8.9 - - + +
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Residues in contact with CYS 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 LEU 3.0 18.4 + - - -
230A PHE* 3.2 9.6 + - + +
232A GLN* 1.3 75.0 - - - +
234A GLU* 1.3 60.2 + - - +
236A VAL* 3.2 8.0 + - - +
237A ASP* 2.8 39.0 + - - +
126D THR* 4.0 10.3 - - + -
175D LYS* 3.7 43.3 - - - -
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Residues in contact with GLU 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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203A TRP* 2.9 29.5 + - + +
205A ASN* 3.0 20.9 + - - -
208A TYR* 2.8 24.9 + - - +
230A PHE* 3.1 20.4 + - + +
231A ALA* 3.6 8.5 - - - +
233A CYS* 1.3 73.2 - - - +
235A ASP* 1.3 64.3 + - - +
237A ASP* 3.4 10.1 + - + +
238A ASN* 2.8 39.0 + - - +
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Residues in contact with ASP 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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203A TRP* 3.3 20.8 - - + +
231A ALA 2.8 16.3 + - - +
232A GLN* 3.2 21.7 + - - +
234A GLU* 1.3 74.5 - - - +
236A VAL* 1.3 61.5 + - - +
238A ASN* 3.1 9.5 + - - +
239A GLY 3.4 0.2 + - - -
240A CYS* 2.6 60.6 + - - +
241A GLN 3.2 13.5 - - - -
242A GLN 2.6 29.6 - - - +
243A VAL* 3.8 5.8 - - + -
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Residues in contact with VAL 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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232A GLN* 3.0 38.4 + - + +
233A CYS* 3.2 9.6 + - - +
235A ASP* 1.3 71.6 - - - +
237A ASP* 1.3 62.6 + - - +
238A ASN 3.0 4.5 - - - -
239A GLY* 3.0 18.9 + - - -
240A CYS 3.4 11.9 - - - +
241A GLN* 5.0 1.6 - - - +
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Residues in contact with ASP 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 CYS* 2.8 24.7 + - - +
234A GLU* 3.6 10.8 - - + +
235A ASP 3.3 0.2 - - - -
236A VAL* 1.3 79.6 - - - +
238A ASN* 1.3 63.9 + - - +
239A GLY 3.4 0.8 + - - -
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Residues in contact with ASN 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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203A TRP* 3.4 49.8 - - + -
234A GLU* 2.8 25.4 + - - +
235A ASP 3.1 3.8 + - - +
236A VAL 3.0 1.0 - - - -
237A ASP* 1.3 83.9 + - - +
239A GLY* 1.3 59.2 + - - +
240A CYS* 3.3 9.4 + - - -
342A LEU* 4.7 10.2 - - + +
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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