Contacts of the strand formed by residues 215 - 223 (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 LEU 215 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B THR* 3.1 21.3 - - + +
189B VAL* 3.9 22.4 - - + -
214B GLY* 1.3 75.0 - - - +
216B SER* 1.3 82.1 + - - +
217B LEU* 5.1 2.2 - - + +
234B GLU* 3.5 2.6 - - - +
235B TYR* 2.7 63.4 + - + +
236B PRO* 4.8 0.2 - - - +
238B TRP* 3.7 38.6 - - + -
243B ILE* 4.0 30.7 - - + -
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Residues in contact with SER 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LYS* 5.6 5.9 - - - +
187B THR 3.0 6.8 + - - -
188B SER* 3.5 12.1 + - - -
189B VAL 3.0 26.9 + - - -
215B LEU* 1.3 80.4 + - - +
217B LEU* 1.3 58.8 + - - +
218B TRP* 3.4 24.5 - - - -
231B LEU* 4.2 5.8 - - - -
233B ALA 3.7 4.7 - - - -
234B GLU* 2.9 25.7 + - - +
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LEU* 5.8 1.1 - - + -
189B VAL* 3.6 24.9 - - + +
191B TYR* 5.4 0.4 - - + -
215B LEU* 4.7 2.6 - - + +
216B SER* 1.3 72.3 - - - +
218B TRP* 1.3 67.0 + - - +
231B LEU* 3.6 2.9 - - - +
232B TRP* 2.8 31.7 + - + +
233B ALA 2.8 22.8 + - - +
235B TYR* 4.7 11.2 - - + -
243B ILE* 3.9 21.8 - - + -
244B ARG 3.5 27.6 - - - +
245B PHE* 3.5 46.0 - - + -
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Residues in contact with TRP 218 (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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188B SER* 3.8 11.0 + - - -
189B VAL 2.8 16.0 + - - +
190B TYR* 3.5 41.6 + + + -
191B TYR* 3.1 23.7 + - - +
216B SER* 3.4 29.9 - - - -
217B LEU* 1.3 88.3 - - - +
219B ASP* 1.3 63.6 + - - +
229B PRO* 3.9 19.7 - - + -
230B ILE 3.4 7.4 - - - +
231B LEU* 3.4 50.9 - - + -
232B TRP* 4.6 0.4 - - - -
234B GLU* 5.9 0.7 - - - -
245B PHE* 3.9 2.4 - - - -
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Residues in contact with ASP 219 (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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191B TYR* 3.8 9.6 - - - +
218B TRP* 1.3 76.3 - - - +
220B THR* 1.3 87.1 + - - +
229B PRO* 3.5 1.6 - - - +
230B ILE* 2.7 44.9 + - + +
232B TRP* 4.1 21.1 - - + +
245B PHE* 4.4 3.6 - - + -
389B ARG* 3.1 42.0 + - - -
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Residues in contact with THR 220 (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* 4.1 20.2 - - + -
190B TYR* 4.4 8.3 - - + -
191B TYR* 2.6 26.3 + - - +
192B LEU* 3.7 28.0 + - + +
219B ASP* 1.3 94.2 + - - +
221B GLN* 1.3 61.0 + - - +
222B GLU 4.2 0.4 + - - -
227B PHE* 4.0 15.2 - - + -
228B THR 3.1 12.8 - - - +
229B PRO* 4.3 2.5 - - + -
230B ILE* 4.6 4.1 - - - +
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Residues in contact with GLN 221 (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* 1.3 75.6 - - - +
222B GLU* 1.3 70.5 + - - +
223B SER* 3.9 5.1 + - - -
226B GLY 3.6 0.9 - - - +
227B PHE* 3.3 6.2 - - - -
228B THR* 2.9 43.7 + - + +
230B ILE* 4.2 19.5 - - + +
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Residues in contact with GLU 222 (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* 4.5 10.2 - - - +
220B THR 4.2 0.6 + - - -
221B GLN* 1.3 79.8 - - - +
223B SER* 1.3 70.3 - - - +
226B GLY* 2.9 35.8 - - - +
227B PHE* 3.7 34.4 - - + -
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Residues in contact with SER 223 (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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221B GLN* 5.0 6.5 + - - -
222B GLU* 1.3 87.9 - - - +
224B GLU* 1.3 71.3 + - - +
225B SER* 3.1 21.9 + - - -
226B GLY 2.8 27.0 + - - +
228B THR* 4.8 7.7 + - - -
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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