Contacts of the strand formed by residues 226 - 235 (chain B) in PDB entry 2ADM
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 GLY 226 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B GLU* 4.2 21.3 - - - -
221B GLN 3.6 0.3 - - - +
222B GLU* 2.9 17.0 - - - +
223B SER* 2.8 35.5 + - - -
224B GLU 3.3 2.0 + - - -
225B SER* 1.3 81.4 - - - +
227B PHE* 1.3 60.2 + - - -
228B THR* 5.5 0.2 - - - -
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Residues in contact with PHE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLU* 4.0 26.8 + - + -
27B VAL* 3.9 24.2 - - + -
30B PHE* 4.0 34.0 - + + +
192B LEU* 4.0 17.9 - - + -
195B VAL* 3.8 31.4 - - + -
220B THR* 4.0 25.4 - - + -
221B GLN 3.3 4.7 - - - +
222B GLU* 3.7 42.2 - - + -
225B SER 4.3 0.6 + - - -
226B GLY* 1.3 73.7 - - - -
228B THR* 1.3 63.0 + - - +
229B PRO* 4.1 3.4 - - - +
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Residues in contact with THR 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B THR* 3.1 6.1 - - - -
221B GLN* 2.9 43.4 + - + +
223B SER* 4.8 8.5 + - - -
225B SER* 5.3 2.8 + - - -
227B PHE* 1.3 74.0 + - - +
229B PRO* 1.3 78.6 - - + +
230B ILE* 4.0 7.7 - - + +
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Residues in contact with PRO 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PHE* 3.4 31.0 - - + -
34B LEU* 5.3 4.0 - - + -
190B TYR* 4.3 12.8 - - + -
218B TRP* 3.9 22.0 - - + -
219B ASP 3.5 7.9 - - - +
220B THR* 4.3 2.0 - - + -
227B PHE 4.1 2.2 - - - +
228B THR* 1.3 94.4 - - + +
230B ILE* 1.3 66.8 + - - +
231B LEU 4.3 0.4 - - - -
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Residues in contact with ILE 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B TRP* 3.8 2.2 - - - -
219B ASP* 2.7 49.0 + - + +
220B THR* 4.6 3.8 - - - +
221B GLN* 4.2 36.1 - - + +
228B THR* 4.0 9.2 - - + +
229B PRO* 1.3 82.0 - - - +
231B LEU* 1.3 72.2 + - - +
232B TRP* 3.3 2.5 + - + -
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Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B SER* 4.2 3.4 - - - -
217B LEU 3.6 16.6 - - - +
218B TRP* 3.4 49.7 - - + +
230B ILE* 1.3 78.8 - - - +
232B TRP* 1.3 61.4 + - - +
233B ALA* 4.1 4.0 - - - +
234B GLU* 3.9 39.9 - - + +
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Residues in contact with TRP 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B LEU* 2.8 30.0 + - + +
218B TRP* 4.5 0.4 - - - -
219B ASP* 4.1 16.2 - - + +
230B ILE* 3.3 6.6 + - + +
231B LEU* 1.3 77.2 - - - +
233B ALA* 1.3 74.4 + - + +
245B PHE* 3.5 37.6 - + + -
246B GLU 2.8 38.6 + - - +
247B THR* 3.5 21.1 - - + -
386B THR* 5.2 3.4 - - + -
389B ARG* 3.8 22.7 - - - -
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B LEU* 2.8 32.0 + - + +
231B LEU* 3.9 1.5 - - - +
232B TRP* 1.3 98.6 - - + +
234B GLU* 1.3 66.3 + - - +
235B TYR* 4.0 26.1 - - + +
246B GLU* 5.6 1.6 - - + +
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Residues in contact with GLU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B LEU 3.5 6.9 - - - +
216B SER* 2.9 22.5 + - - +
218B TRP* 5.9 0.9 - - - -
231B LEU* 3.9 31.6 - - + +
233B ALA* 1.3 79.8 - - - +
235B TYR* 1.3 71.8 + - - +
236B PRO* 3.4 13.5 - - + +
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Residues in contact with TYR 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B LEU* 2.7 54.1 + - + +
217B LEU* 4.7 8.1 - - + -
232B TRP* 5.5 0.2 - - - -
233B ALA* 4.0 31.5 - - + +
234B GLU* 1.3 77.5 - - - +
236B PRO* 1.3 64.0 - - - +
237B HIS 3.1 6.1 + - - +
238B TRP* 3.1 25.9 + + + +
243B ILE* 5.9 1.8 - - + -
244B ARG 4.2 12.4 + - - -
246B GLU* 2.9 39.1 + - - +
251B ARG* 5.3 6.7 - - - -
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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