Contacts of the helix formed by residues 228 - 238 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A VAL* 4.5 7.1 - - - +
210D ARG* 5.4 2.7 - - - -
224D ASN 4.4 8.3 - - - -
225D TYR* 2.8 27.5 + - - -
227D SER* 1.3 78.3 - - - +
229D LEU* 1.3 64.2 + - - +
230D PHE 3.3 2.7 - - - -
231D ALA* 3.3 7.5 + - - +
232D GLN* 3.1 26.8 + - - +
245D TRP* 3.4 31.4 - - - -
258D THR* 5.7 2.4 - - - +
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Residues in contact with LEU 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A TYR* 5.2 1.8 - - + -
90A VAL* 3.7 26.9 - - + -
125A ALA 3.9 5.8 - - - +
126A THR* 3.5 26.7 - - + +
173A VAL* 3.6 27.4 - - + +
174A LYS* 3.4 34.3 - - - +
175A LYS 4.1 0.7 - - - +
176A PRO* 4.1 3.6 - - + -
225D TYR 3.5 18.6 - - - +
226D GLY* 3.6 10.5 + - - +
228D SER* 1.3 75.3 - - - +
230D PHE* 1.3 60.8 + - - +
232D GLN* 3.4 7.9 + - + +
233D CYS* 3.0 33.1 + - - -
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Residues in contact with PHE 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A VAL* 3.3 39.0 - - + -
124A ARG* 3.4 34.3 + - + +
126A THR* 3.6 11.7 - - + +
208D TYR* 3.3 37.2 - + + -
226D GLY 5.0 0.4 + - - -
227D SER 5.1 4.7 - - - +
228D SER 3.3 1.4 - - - +
229D LEU* 1.3 77.4 - - - +
231D ALA* 1.3 58.9 + - - +
233D CYS* 3.3 5.4 + - + +
234D GLU* 3.0 34.2 + - + +
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Residues in contact with ALA 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D TRP* 4.3 3.8 - - + -
208D TYR* 4.0 27.8 - - + -
227D SER 5.3 1.7 + - - +
228D SER* 3.3 11.2 + - - +
230D PHE* 1.3 83.1 - - - +
232D GLN* 1.3 56.1 + - - +
234D GLU* 3.5 7.9 + - - +
235D ASP* 2.9 27.5 + - - +
243D VAL* 3.4 13.6 - - + +
245D TRP* 3.8 23.8 - - + -
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Residues in contact with GLN 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A VAL 4.7 14.3 + - - +
174A LYS* 5.9 2.9 - - - -
228D SER* 3.1 15.9 + - - +
229D LEU* 3.8 8.7 - - + +
230D PHE 3.2 0.2 - - - -
231D ALA* 1.3 74.2 - - - +
233D CYS* 1.3 62.4 + - - +
235D ASP* 2.9 45.4 + - - +
236D VAL* 2.9 25.6 + - + +
241D GLN 2.9 25.4 + - - +
242D GLN* 3.5 21.7 + - - +
243D VAL* 3.7 9.8 + - + +
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Residues in contact with CYS 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A THR* 4.0 12.8 - - + -
175A LYS* 3.9 41.1 - - - -
229D LEU 3.0 23.8 + - - +
230D PHE* 3.6 7.4 - - + +
232D GLN* 1.3 73.4 - - - +
234D GLU* 1.3 60.2 + - - +
236D VAL* 3.2 8.6 + - - +
237D ASP* 2.9 37.5 + - - +
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Residues in contact with GLU 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D TRP* 2.9 21.9 + - + +
205D ASN* 2.9 28.8 + - - -
207D LYS* 4.5 5.0 + - - -
208D TYR* 2.6 27.0 + - - -
230D PHE* 3.0 24.1 + - + +
231D ALA* 3.5 10.3 - - - +
233D CYS* 1.3 71.6 - - - +
235D ASP* 1.3 63.9 + - - +
237D ASP* 3.3 16.2 + - + +
238D ASN* 2.7 35.0 + - - +
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Residues in contact with ASP 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D TRP* 3.6 22.2 - - + -
231D ALA 2.9 15.8 + - - +
232D GLN* 2.9 34.8 + - - +
234D GLU* 1.3 75.5 - - - +
236D VAL* 1.3 74.5 + - - +
238D ASN* 3.0 13.0 + - - +
239D GLY 3.5 0.2 + - - -
240D CYS* 2.9 43.8 + - - +
241D GLN 3.6 0.3 - - - -
242D GLN 2.5 28.7 + - - +
243D VAL* 3.8 7.4 - - + -
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Residues in contact with VAL 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D GLN* 2.9 24.8 + - + +
233D CYS* 3.2 10.3 + - - +
235D ASP* 1.3 86.6 + - - +
237D ASP* 1.3 62.0 + - - +
238D ASN 2.9 11.3 + - - -
239D GLY* 2.9 14.2 + - - -
240D CYS 3.4 11.2 - - - +
241D GLN* 5.3 1.1 - - - -
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Residues in contact with ASP 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D CYS* 2.9 22.2 + - - +
234D GLU* 3.3 17.2 - - + +
236D VAL* 1.3 76.8 - - - +
238D ASN* 1.3 64.2 + - - +
239D GLY 3.5 0.4 + - - -
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Residues in contact with ASN 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D TRP* 3.5 46.8 - - + -
234D GLU* 2.7 28.5 + - - +
235D ASP 3.0 7.2 + - - +
236D VAL 2.9 1.4 + - - -
237D ASP* 1.3 86.5 - - - +
239D GLY* 1.3 60.7 + - - +
240D CYS* 3.2 3.1 + - - -
342D LEU* 3.8 19.0 - - + +
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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