Contacts of the helix formed by residues 218 - 231 (chain B) in PDB entry 2D2O
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 ASP 218 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172B LEU* 4.8 0.3 - - - +
212B ILE* 3.9 13.5 - - - +
217B GLY* 1.3 75.2 - - - +
219B LEU* 1.3 63.0 + - - +
220B PRO* 3.5 19.1 - - + +
221B THR* 2.6 35.3 + - - -
222B PHE* 3.0 19.2 + - - +
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Residues in contact with LEU 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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212B ILE* 4.1 8.3 - - + +
218B ASP* 1.3 72.0 - - - +
220B PRO* 1.3 68.3 - - + +
222B PHE* 3.0 8.2 + - + +
223B ARG* 2.8 64.5 + - + +
313B PHE* 4.2 19.3 - - + -
314B TRP* 3.9 30.3 - - + -
317B GLN* 3.8 18.4 - - + +
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Residues in contact with PRO 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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218B ASP* 3.5 20.9 - - + +
219B LEU* 1.3 96.0 - - + +
221B THR* 1.3 56.8 + - - +
223B ARG* 3.5 13.1 + - + +
224B ARG* 3.1 43.4 + - - +
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Residues in contact with THR 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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172B LEU* 4.0 23.1 - - + -
173B LYS* 4.3 13.9 - - + +
176B ILE* 3.9 13.8 - - + +
216B PHE 5.1 0.2 - - - +
217B GLY* 4.8 5.0 - - - -
218B ASP* 2.6 33.6 + - - +
220B PRO* 1.3 73.1 - - - +
222B PHE* 1.3 61.3 + - - +
224B ARG* 3.2 10.1 + - - +
225B LEU* 2.9 26.9 + - - +
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Residues in contact with PHE 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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172B LEU* 4.2 15.8 - - + +
192B PHE* 5.8 1.3 - + - -
195B ILE* 3.6 27.4 - - + -
212B ILE* 3.9 16.2 - - + -
218B ASP 3.0 12.0 + - - +
219B LEU* 3.5 10.1 - - + +
221B THR* 1.3 77.1 - - - +
223B ARG* 1.3 63.3 + - - +
225B LEU* 3.0 17.4 + - + +
226B VAL* 2.9 42.1 + - + +
236B ILE* 4.5 4.7 - - + -
238B LEU* 3.7 17.3 - - + -
314B TRP* 3.8 28.0 - + - -
317B GLN* 3.9 18.2 - - + -
319B ILE* 3.7 23.8 - - + -
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Residues in contact with ARG 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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219B LEU* 2.8 43.7 + - + +
220B PRO* 3.6 12.3 - - + +
222B PHE* 1.3 78.4 - - + +
224B ARG* 1.3 62.4 + - - +
226B VAL* 3.4 9.5 + - - +
227B ASP* 3.1 31.4 + - - +
313B PHE* 5.8 0.2 - - - -
316B GLU 4.9 3.0 + - - -
317B GLN* 2.7 53.4 + - - +
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Residues in contact with ARG 224 (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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176B ILE* 4.2 14.6 - - + -
220B PRO* 3.1 28.5 + - - +
221B THR* 3.4 12.8 - - - +
223B ARG* 1.3 76.2 - - - +
225B LEU* 1.3 60.3 + - - +
227B ASP* 3.3 5.9 + - - +
228B GLU* 2.9 48.2 + - + +
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Residues in contact with LEU 225 (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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172B LEU* 4.1 27.4 - - + +
175B VAL* 3.5 28.5 - - + -
176B ILE* 3.8 27.5 - - + +
179B LEU* 4.4 11.4 - - + -
190B LEU* 5.2 0.2 - - + -
192B PHE* 3.9 26.7 - - + -
221B THR 2.9 13.8 + - - +
222B PHE* 3.0 20.6 + - + +
224B ARG* 1.3 76.9 - - - +
226B VAL* 1.3 58.1 + - + +
228B GLU* 3.9 0.6 - - - +
229B ALA* 2.9 37.3 + - + +
236B ILE* 4.7 5.8 - - + -
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Residues in contact with VAL 226 (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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222B PHE* 2.9 50.0 + - + +
223B ARG* 3.6 8.3 - - - +
225B LEU* 1.3 76.8 - - + +
227B ASP* 1.3 62.4 + - - +
229B ALA* 3.8 0.5 - - - +
230B HIS* 2.9 63.5 + - + +
236B ILE* 4.2 20.4 - - + -
317B GLN 3.9 15.5 - - - +
318B GLY* 3.7 11.2 - - - +
319B ILE* 4.9 2.7 - - + -
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Residues in contact with ASP 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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223B ARG* 3.1 23.6 + - - +
224B ARG* 3.7 7.5 - - + +
225B LEU 3.3 0.2 - - - -
226B VAL* 1.3 81.2 - - - +
228B GLU* 1.3 66.6 + - - +
230B HIS* 3.7 6.9 + - - +
231B ARG* 3.0 34.1 + - - +
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Residues in contact with GLU 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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176B ILE* 4.4 14.9 - - + +
179B LEU* 3.5 19.3 - - + -
224B ARG* 2.9 35.4 + - + +
225B LEU 3.9 1.6 - - - +
227B ASP* 1.3 82.3 - - - +
229B ALA* 1.3 61.8 + - - +
231B ARG* 3.0 42.7 + - - +
232B ARG* 2.9 45.7 + - - +
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Residues in contact with ALA 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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179B LEU* 3.7 18.5 - - + +
190B LEU* 4.9 0.2 - - + -
225B LEU* 2.9 19.8 + - + +
226B VAL 3.8 2.7 - - - +
228B GLU* 1.3 76.9 - - - +
230B HIS* 1.3 60.3 + - - +
232B ARG* 2.9 11.6 + - - -
233B GLY 3.2 0.2 + - - -
234B ILE* 2.8 48.0 + - + +
236B ILE* 3.9 19.5 - - + -
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Residues in contact with HIS 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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226B VAL* 2.9 35.7 + - + +
227B ASP* 3.7 8.8 + - - +
229B ALA* 1.3 77.1 - - - +
231B ARG* 1.3 58.5 + - - +
233B GLY* 2.8 21.1 + - - -
234B ILE 3.2 20.2 - - - +
235B LYS* 4.1 4.9 - - + -
236B ILE* 4.3 4.4 + - + +
318B GLY* 3.1 26.6 + - - -
320B ASP* 2.8 30.5 + - - -
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Residues in contact with ARG 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ASP* 3.0 18.4 + - - +
228B GLU* 3.0 45.8 + - - +
230B HIS* 1.3 76.0 - - - +
232B ARG* 1.3 80.0 + - + +
233B GLY 3.2 1.7 + - - -
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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