Contacts of the helix formed by residues 220 - 234 (chain B) in PDB entry 2R8O
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 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B LYS* 4.6 5.8 + - - +
217B ASP* 3.1 26.5 + - - +
218B GLY 3.5 1.0 - - - -
219B HIS* 1.3 79.1 - - - +
221B ALA* 1.3 65.7 + - - +
222B ALA* 3.7 12.7 + - - +
223B SER* 2.7 35.5 + - - +
224B ILE* 3.0 25.5 + - - +
226B ARG* 4.5 1.6 + - - -
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Residues in contact with ALA 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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4B ARG* 3.6 39.3 - - + +
5B LYS* 5.2 3.3 - - + +
35B ASP* 5.3 4.7 - - + +
38B GLU* 4.6 1.1 - - - +
39B VAL* 3.7 23.0 - - + +
219B HIS 4.1 2.0 + - - -
220B ASP* 1.3 72.7 + - - +
222B ALA* 1.3 57.8 + - - +
224B ILE* 3.3 5.7 + - - +
225B LYS* 2.9 30.9 + - - +
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Residues in contact with ALA 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ASP* 3.2 12.5 + - - +
221B ALA* 1.3 77.3 - - - +
223B SER* 1.3 58.0 + - - +
225B LYS* 3.4 6.8 + - - +
226B ARG* 3.0 44.3 + - + +
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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
----------------------------------------------------------
216B ILE* 4.1 6.0 - - - +
217B ASP* 3.9 26.7 - - - +
220B ASP* 2.7 30.7 + - - +
222B ALA* 1.3 72.0 - - - +
224B ILE* 1.3 66.3 + - - +
226B ARG* 3.3 28.3 + - - +
227B ALA* 3.1 22.7 + - - +
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Residues in contact with ILE 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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35B ASP* 3.8 7.9 - - + +
36B ILE* 3.8 41.1 - - + +
39B VAL* 3.9 19.7 - - + -
181B PHE* 4.6 4.5 - - + -
216B ILE* 4.2 11.7 - - + -
217B ASP 3.7 9.6 - - - +
218B GLY* 3.4 30.7 - - - +
220B ASP 3.0 21.1 + - - +
221B ALA* 3.7 8.1 - - - +
223B SER* 1.3 74.7 - - - +
225B LYS* 1.3 64.2 + - - +
227B ALA* 3.1 4.6 + - - +
228B VAL* 3.0 32.3 + - + +
241B LEU* 5.7 0.9 - - + -
243B CYS* 5.5 2.2 - - - -
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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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4B ARG* 4.7 6.1 - - - +
39B VAL* 3.9 13.4 - - + +
43B ASP* 2.9 38.9 + - - +
44B PHE* 3.7 21.1 - - + -
221B ALA 2.9 18.3 + - - +
222B ALA* 3.8 6.7 - - - +
224B ILE* 1.3 77.2 - - - +
226B ARG* 1.3 63.5 + - + +
228B VAL* 3.3 2.6 + - - +
229B GLU* 3.0 44.8 + - - +
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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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220B ASP* 4.5 2.0 + - - -
222B ALA* 3.0 22.1 + - + +
223B SER* 3.3 38.8 + - - +
224B ILE 3.3 0.2 - - - -
225B LYS* 1.3 76.3 - - + +
227B ALA* 1.3 58.0 + - - +
229B GLU* 3.4 16.3 + - - +
230B GLU* 3.0 29.0 + - - +
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Residues in contact with ALA 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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213B ILE* 3.2 22.7 - - + +
216B ILE* 3.6 33.9 - - + -
223B SER 3.1 12.6 + - - +
224B ILE* 3.1 10.5 + - - +
226B ARG* 1.3 77.1 - - - +
228B VAL* 1.3 62.2 + - - +
230B GLU* 3.2 3.7 + - - -
231B ALA* 3.0 20.4 + - - +
241B LEU* 3.8 10.8 - - + -
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Residues in contact with VAL 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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39B VAL* 5.0 1.6 - - + -
40B LEU* 5.2 2.7 - - + -
44B PHE* 3.7 40.8 - - + -
150B TYR* 4.7 13.0 - - + -
179B ILE* 5.1 2.2 - - + -
181B PHE* 3.7 33.9 - - + -
224B ILE* 3.0 27.7 + - + +
225B LYS 3.8 4.0 - - - +
227B ALA* 1.3 73.1 - - - +
229B GLU* 1.3 57.5 + - - +
231B ALA* 3.2 5.3 + - - +
232B ARG* 2.9 39.1 + - + +
241B LEU* 3.9 5.8 - - + -
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Residues in contact with GLU 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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44B PHE* 3.8 16.1 - - + -
225B LYS* 3.0 49.9 + - - +
226B ARG* 3.6 17.4 - - - +
228B VAL* 1.3 77.4 - - - +
230B GLU* 1.3 60.7 + - - +
232B ARG* 3.3 9.5 + - - +
233B ALA* 3.0 22.5 + - - +
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Residues in contact with GLU 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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211B HIS* 2.8 33.9 + - + +
212B VAL 5.1 0.5 - - - +
213B ILE* 3.6 24.0 - - + +
226B ARG 3.0 14.6 + - - +
227B ALA* 3.5 8.8 - - - +
229B GLU* 1.3 74.8 - - - +
231B ALA* 1.3 63.0 + - - +
233B ALA* 3.1 16.3 + - - +
234B VAL* 3.3 16.2 + - + +
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Residues in contact with ALA 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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176B GLY 4.6 3.1 - - - +
179B ILE* 3.8 20.8 - - + +
211B HIS* 5.1 0.4 - - - -
213B ILE* 4.0 3.8 - - + +
227B ALA 3.0 12.7 + - - +
228B VAL 3.6 8.3 - - - +
230B GLU* 1.3 75.8 - - - +
232B ARG* 1.3 61.8 + - - +
234B VAL* 3.3 21.1 + - - +
239B SER* 3.6 35.6 + - - +
241B LEU* 3.9 14.1 - - + -
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Residues in contact with ARG 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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44B PHE* 3.6 41.4 + - - -
58B ASP* 5.3 0.6 + - - -
148B TYR* 3.4 50.3 + - + +
150B TYR* 3.0 22.5 + - - -
179B ILE* 3.8 17.9 - - + -
228B VAL* 2.9 25.3 + - - +
229B GLU* 3.7 6.5 - - - +
231B ALA* 1.3 76.5 - - - +
233B ALA* 1.3 61.2 + - - +
234B VAL 3.5 2.1 + - - +
235B THR* 4.3 11.1 - - - +
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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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229B GLU 3.0 12.4 + - - +
230B GLU* 3.1 13.2 + - - +
232B ARG* 1.3 77.2 - - - +
234B VAL* 1.3 61.0 + - + +
235B THR* 3.5 11.2 + - - +
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Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLY 3.6 11.6 - - - +
211B HIS* 3.8 42.2 - - + +
230B GLU* 3.3 15.4 + - + +
231B ALA 3.3 15.6 - - - +
232B ARG 3.3 2.7 - - - +
233B ALA* 1.3 77.4 - - + +
235B THR* 1.3 60.2 + - - +
236B ASP* 3.6 20.0 - - - +
237B LYS* 3.8 26.2 - - + +
239B SER* 4.5 2.5 - - - +
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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