Contacts of the helix formed by residues 215 - 226 (chain B) in PDB entry 2P0R
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 ASN 215 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213B PRO* 2.6 14.1 + - + +
214B GLU* 1.3 78.7 - - + +
216B PHE* 1.3 61.0 + - - -
217B TYR* 3.5 2.0 - - - -
218B GLU* 3.0 35.7 + - - +
219B ILE* 3.5 27.7 + - - +
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Residues in contact with PHE 216 (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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207B PHE* 3.6 49.8 - + + -
209B THR* 4.6 16.6 - - + -
212B ALA* 3.6 21.8 - - + -
213B PRO* 2.9 19.2 + - + +
214B GLU 3.7 0.8 - - - -
215B ASN* 1.3 74.1 - - - +
217B TYR* 1.3 65.6 + - - +
219B ILE* 3.1 9.3 + - + +
220B LEU* 3.1 58.0 + - + +
321B PHE* 3.8 22.9 - + + -
324B PHE* 5.2 0.2 - + - -
325B LYS* 5.0 4.5 - - + -
331B VAL* 3.9 19.5 - - + -
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Residues in contact with TYR 217 (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 ASN 3.5 1.2 - - - -
216B PHE* 1.3 78.8 - - - +
218B GLU* 1.3 58.8 + - + +
220B LEU* 3.5 6.0 + - - +
221B GLU* 3.0 46.2 + - - +
261B ILE* 3.3 23.0 - - + +
262B ASP* 3.0 38.3 + - - -
263B GLN* 3.4 14.0 + - + +
272B GLU* 3.6 45.5 - - + +
273B LEU 3.7 10.1 - - - -
321B PHE* 3.8 46.9 - + + -
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Residues in contact with GLU 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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215B ASN* 3.0 30.3 + - - +
216B PHE 3.2 0.4 - - - -
217B TYR* 1.3 79.5 - - + +
219B ILE* 1.3 59.0 + - - +
221B GLU* 4.2 11.9 - - + +
222B LYS* 2.7 78.7 + - + +
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Residues in contact with ILE 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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205B GLU* 5.0 2.2 - - - +
207B PHE* 3.9 28.5 - - + -
213B PRO* 3.9 26.9 - - + -
215B ASN* 3.5 28.7 + - - +
216B PHE* 3.1 14.1 + - + +
218B GLU* 1.3 77.6 - - - +
220B LEU* 1.3 56.5 + - - +
222B LYS* 3.9 6.8 - - - +
223B ALA* 2.9 30.9 + - + +
226B ARG* 4.3 3.9 + - - +
333B ILE* 4.2 13.7 - - + -
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Residues in contact with LEU 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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216B PHE* 3.1 53.3 + - + +
217B TYR* 3.8 4.3 - - - +
219B ILE* 1.3 73.8 - - - +
221B GLU* 1.3 58.9 + - - +
223B ALA* 3.7 2.0 - - - +
224B LEU* 2.8 32.1 + - - +
230B LEU* 3.6 23.0 - - + +
258B VAL* 6.0 0.4 - - + -
261B ILE* 3.1 22.1 - - + +
274B ILE* 4.6 9.2 - - + -
321B PHE* 4.0 21.3 - - + -
324B PHE* 4.9 2.0 - - + -
331B VAL* 3.8 19.1 - - + -
333B ILE* 3.8 13.0 - - + -
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Residues in contact with GLU 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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217B TYR* 3.0 36.0 + - - +
218B GLU* 3.7 12.4 - - + +
220B LEU* 1.3 73.7 - - - +
222B LYS* 1.3 68.4 + - + +
224B LEU* 3.8 1.7 - - - +
225B LYS* 3.0 27.8 + - + +
261B ILE* 3.4 34.8 - - + +
262B ASP* 5.3 2.3 - - - -
263B GLN 5.8 0.3 + - - -
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Residues in contact with LYS 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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218B GLU* 2.7 60.9 + - + +
219B ILE* 3.9 6.3 - - + +
221B GLU* 1.3 75.3 - - + +
223B ALA* 1.3 57.5 + - - +
225B LYS* 3.8 4.7 - - - +
226B ARG* 2.8 44.1 + - - +
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Residues in contact with ALA 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 ILE* 2.9 23.1 + - + +
220B LEU* 3.7 4.3 - - - +
222B LYS* 1.3 73.4 - - - +
224B LEU* 1.3 62.1 + - - +
226B ARG* 3.4 24.3 + - - +
228B SER* 3.1 28.7 + - - -
230B LEU* 4.1 4.3 - - + -
333B ILE* 3.9 35.4 - - + -
335B ASN* 4.2 2.7 - - - +
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Residues in contact with LEU 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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108B LEU* 4.3 18.1 - - + +
220B LEU 2.8 21.3 + - - +
221B GLU* 3.8 4.0 - - - +
223B ALA* 1.3 70.2 - - - +
225B LYS* 1.3 65.6 + - - +
227B GLY* 3.3 13.3 + - - -
228B SER 4.5 5.1 - - - +
230B LEU* 3.5 22.1 - - + +
258B VAL* 3.4 24.0 - - + +
259B THR 3.8 2.9 - - - +
260B GLY* 3.3 37.2 - - - +
261B ILE* 3.5 15.9 - - + +
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Residues in contact with LYS 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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221B GLU* 3.0 19.8 + - + +
222B LYS* 3.8 5.4 - - - +
224B LEU* 1.3 77.0 - - - +
226B ARG* 1.3 57.9 + - - +
227B GLY* 3.1 6.3 + - - -
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Residues in contact with ARG 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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109B ASN* 4.7 2.1 + - - -
219B ILE* 4.3 4.9 + - - +
222B LYS* 2.8 25.5 + - - +
223B ALA* 3.4 38.3 - - - +
224B LEU 3.3 0.4 - - - -
225B LYS* 1.3 75.0 - - - +
227B GLY* 1.3 57.0 + - - +
228B SER* 4.0 7.0 - - - +
335B ASN* 3.2 24.6 + - - +
336B LEU* 5.6 1.9 - - - +
337B THR* 2.9 51.1 + - - +
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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