Contacts of the helix formed by residues 228 - 238 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173G VAL* 4.5 10.0 - - - +
210J ARG* 5.3 4.0 - - - -
224J ASN 4.2 10.8 - - - -
225J TYR* 2.9 22.1 + - - +
227J SER* 1.3 76.9 + - - +
229J LEU* 1.3 65.0 + - - +
230J PHE 3.3 3.4 - - - -
231J ALA* 3.3 7.4 + - - +
232J GLN* 3.1 21.9 + - - +
245J TRP* 3.5 32.7 - - - -
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Residues in contact with LEU 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G TYR* 5.8 1.6 - - + -
90G VAL* 3.7 28.3 - - + -
125G ALA 3.8 7.0 - - - +
126G THR* 3.4 28.5 - - + +
173G VAL* 3.9 20.4 - - + +
174G LYS* 3.6 46.0 - - - +
175G LYS 4.9 1.7 + - - +
176G PRO* 4.1 3.6 - - + -
225J TYR 4.0 5.6 - - - +
226J GLY* 3.9 13.9 - - - +
227J SER 3.5 0.8 - - - -
228J SER* 1.3 79.1 + - - +
230J PHE* 1.3 57.8 + - - +
232J GLN* 3.2 8.2 + - + +
233J CYS* 2.9 32.6 + - - -
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Residues in contact with PHE 230 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G VAL* 3.4 41.5 - - + -
124G ARG* 3.7 38.8 + - - +
126G THR* 3.7 12.0 - - + +
208J TYR* 3.3 35.9 - + - -
226J GLY 5.1 0.2 + - - -
227J SER 4.6 3.5 + - - +
228J SER 3.3 0.8 - - - -
229J LEU* 1.3 77.1 - - - +
231J ALA* 1.3 62.5 + - - +
233J CYS* 3.3 5.5 + - + +
234J GLU* 3.1 27.4 + - + +
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Residues in contact with ALA 231 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G ARG* 5.9 0.4 - - - +
203J TRP* 4.1 4.0 - - + -
208J TYR* 3.6 40.8 - - + -
227J SER 5.1 1.3 + - - +
228J SER* 3.3 10.7 + - - +
230J PHE* 1.3 78.8 - - - +
232J GLN* 1.3 57.5 + - - +
234J GLU* 3.5 3.7 + - - +
235J ASP* 2.8 28.1 + - - +
243J VAL* 3.6 11.7 - - + +
245J TRP* 3.8 21.1 - - + -
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Residues in contact with GLN 232 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173G VAL 4.4 17.4 + - - +
174G LYS* 5.2 7.1 - - + +
175G LYS 6.0 0.2 - - - +
228J SER* 3.1 14.6 + - - +
229J LEU* 3.2 13.4 + - + +
231J ALA* 1.3 74.7 - - - +
233J CYS* 1.3 61.3 + - - +
235J ASP* 3.1 23.0 + - - +
236J VAL* 3.0 41.0 + - + +
241J GLN 3.0 25.1 + - - +
242J GLN* 3.6 22.1 + - - +
243J VAL* 3.7 13.0 + - + +
245J TRP* 6.2 0.2 - - + -
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Residues in contact with CYS 233 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126G THR* 4.0 11.4 - - + -
175G LYS* 3.7 46.9 - - - +
229J LEU 2.9 17.6 + - - +
230J PHE* 3.3 10.3 + - + +
232J GLN* 1.3 74.3 - - - +
234J GLU* 1.3 59.9 + - - +
236J VAL* 3.2 8.3 + - - +
237J ASP* 2.9 37.0 + - - +
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Residues in contact with GLU 234 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203J TRP* 2.9 27.5 + - + +
205J ASN* 2.9 28.8 + - - -
208J TYR* 2.8 23.5 + - - +
230J PHE* 3.1 21.3 + - + +
231J ALA* 3.6 8.5 - - - +
233J CYS* 1.3 72.8 - - - +
235J ASP* 1.3 64.4 + - - +
237J ASP* 3.3 9.8 + - + +
238J ASN* 2.8 35.6 + - - +
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Residues in contact with ASP 235 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203J TRP* 3.5 20.4 - - + +
231J ALA 2.8 16.3 + - - +
232J GLN* 3.1 34.5 + - - +
234J GLU* 1.3 75.4 - - - +
236J VAL* 1.3 63.1 + - - +
238J ASN* 3.2 9.7 + - - +
240J CYS* 2.7 60.0 + - - +
241J GLN 3.3 2.3 - - - -
242J GLN 2.6 29.5 - - - +
243J VAL* 3.8 4.5 - - + -
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Residues in contact with VAL 236 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232J GLN* 3.0 32.2 + - + +
233J CYS* 3.6 10.1 - - - +
235J ASP* 1.3 77.4 - - - +
237J ASP* 1.3 63.1 + - - +
238J ASN 3.0 4.5 - - - -
239J GLY* 2.9 19.4 + - - -
240J CYS 3.4 11.2 - - - +
241J GLN* 4.9 1.6 - - - +
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Residues in contact with ASP 237 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233J CYS* 2.9 20.6 + - - +
234J GLU* 3.3 13.5 + - + +
236J VAL* 1.3 78.7 - - - +
238J ASN* 1.3 64.5 + - - +
239J GLY 3.4 0.8 + - - -
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Residues in contact with ASN 238 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203J TRP* 3.6 47.6 - - + -
234J GLU* 2.8 25.4 + - - +
235J ASP 3.2 3.4 + - - +
236J VAL 3.0 1.2 - - - -
237J ASP* 1.3 82.8 + - - +
239J GLY* 1.3 61.2 + - - +
240J CYS* 3.3 9.8 + - - -
342J LEU* 4.7 10.5 - - + +
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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