Contacts of the helix formed by residues 224 - 236 (chain B) in PDB entry 2POD
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 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A LYS* 5.3 3.4 - - - +
186B ASP 3.5 16.2 + - - -
187B GLY* 2.8 15.7 + - - +
188B TYR* 3.3 47.6 + - + -
222B LEU 4.8 1.8 + - - -
223B TRP* 1.3 78.2 - - - +
225B LEU* 1.3 65.9 + - - +
226B PRO* 3.8 2.9 - - + -
227B PRO* 3.4 4.7 - - - +
228B ALA* 3.2 22.3 + - - +
247B ILE* 4.3 4.0 - - - -
248B ARG* 6.1 0.3 - - - +
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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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224B ASN* 1.3 77.6 - - - +
226B PRO* 1.4 74.8 - - + +
228B ALA* 3.3 3.5 + - - +
229B LEU* 3.1 41.5 + - + +
247B ILE* 4.6 12.9 - - + +
254B SER* 4.2 22.4 - - - +
257B ARG* 3.5 52.7 - - + +
258B TYR* 4.3 15.7 - - + +
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Residues in contact with PRO 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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188B TYR* 5.3 7.2 - - + +
224B ASN* 4.9 2.9 - - + -
225B LEU* 1.4 95.3 - - + +
227B PRO* 1.4 70.5 - - + +
229B LEU* 3.4 10.6 + - + +
230B GLN* 3.1 25.3 + - - +
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Residues in contact with PRO 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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187B GLY 3.3 23.6 - - - +
188B TYR* 3.6 22.2 - - - +
189B TYR* 4.2 0.7 - - - +
190B ILE* 4.0 21.8 - - + +
223B TRP* 3.7 19.3 - - + -
224B ASN 3.4 9.9 - - - +
226B PRO* 1.4 96.4 - - + +
228B ALA* 1.3 52.6 + - - +
230B GLN* 3.2 13.0 + - + +
231B ILE* 2.8 40.7 + - - +
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Residues in contact with ALA 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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219B PHE* 6.0 0.8 - - - -
223B TRP* 4.1 7.9 - - + +
224B ASN 3.2 21.3 + - - +
225B LEU 3.5 4.3 - - - +
227B PRO* 1.3 76.9 - - - +
229B LEU* 1.3 55.8 + - - +
231B ILE* 3.4 6.9 + - - +
232B ALA 2.9 23.4 + - - -
246B PRO* 3.9 20.0 - - + +
247B ILE* 4.0 6.7 - - + -
258B TYR* 3.3 32.4 + - + -
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Residues in contact with LEU 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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225B LEU* 3.1 39.9 + - + +
226B PRO* 3.7 9.9 - - + +
228B ALA* 1.3 74.9 - - - +
230B GLN* 1.3 58.6 + - - +
232B ALA* 3.4 4.9 + - + +
233B GLU* 3.0 30.7 + - - +
257B ARG* 3.6 33.2 - - - +
258B TYR* 3.8 20.6 - - + +
261B ARG* 3.8 40.7 - - + +
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Residues in contact with GLN 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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189B TYR* 5.7 2.8 - - - +
190B ILE* 3.7 29.9 + - + +
192B LYS* 4.5 15.9 + - - +
195B LEU* 3.8 18.2 - - + +
226B PRO* 3.1 12.3 + - - +
227B PRO* 3.3 21.7 - - - +
229B LEU* 1.3 77.3 - - - +
231B ILE* 1.3 60.7 + - - +
233B GLU* 3.7 6.1 + - - +
234B ALA* 3.3 20.8 + - - +
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Residues in contact with ILE 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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178B PHE* 3.6 27.6 - - + -
190B ILE* 4.1 13.5 - - + -
195B LEU* 3.8 22.9 - - + -
219B PHE* 3.6 29.8 - - + -
223B TRP* 3.8 45.3 - - + +
227B PRO 2.8 25.1 + - - +
228B ALA* 3.8 6.1 - - - +
230B GLN* 1.3 71.4 - - - +
232B ALA* 1.3 59.2 + - - +
234B ALA* 3.1 5.4 + - - +
235B LEU* 3.0 28.9 + - + +
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Residues in contact with ALA 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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228B ALA 2.9 14.5 + - - +
229B LEU* 3.7 6.3 - - - +
231B ILE* 1.3 76.0 - - - +
233B GLU* 1.3 61.6 + - - +
235B LEU* 3.4 3.4 + - - +
236B ARG* 3.3 20.1 + - - +
243B HIS* 4.3 11.2 - - + -
258B TYR* 3.4 32.9 + - + +
261B ARG* 4.4 7.8 - - + +
262B SER* 4.1 20.8 - - - +
263B LEU 5.1 1.4 + - - -
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Residues in contact with GLU 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 LEU 3.0 17.2 + - - +
230B GLN* 3.9 7.6 - - - +
232B ALA* 1.3 74.7 - - - +
234B ALA* 1.3 62.3 + - - +
236B ARG* 3.4 45.7 + - - +
237B GLU 4.7 0.5 + - - -
261B ARG* 4.7 7.5 + - - +
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Residues in contact with ALA 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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195B LEU* 4.2 19.1 - - + -
199B LEU* 4.0 32.1 - - + +
230B GLN 3.3 11.0 + - - +
231B ILE 3.1 10.1 + - - +
233B GLU* 1.3 80.8 - - - +
235B LEU* 1.3 60.0 + - - +
236B ARG 3.5 0.5 + - - -
237B GLU* 4.1 11.6 + - - +
238B TYR* 4.1 7.6 - - - -
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Residues in contact with LEU 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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178B PHE* 3.7 13.0 - - + -
199B LEU* 3.9 8.1 - - + -
202B PHE* 3.6 40.4 - - + -
217B VAL* 4.0 9.4 - - + -
219B PHE* 3.7 26.0 - - + -
231B ILE* 3.0 22.1 + - + +
232B ALA* 3.4 6.3 + - - +
233B GLU 3.3 0.2 - - - -
234B ALA* 1.3 74.4 - - - +
236B ARG* 1.3 64.4 + - - +
237B GLU 3.3 1.8 - - - -
238B TYR* 3.1 20.9 + - + +
239B GLU* 3.7 6.4 + - - -
240B THR* 4.3 12.8 + - + +
243B HIS* 3.5 30.5 - - + +
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Residues in contact with ARG 236 (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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232B ALA 3.3 9.3 + - - +
233B GLU* 3.4 38.1 + - - +
234B ALA 3.3 0.4 - - - -
235B LEU* 1.3 76.7 - - - +
237B GLU* 1.3 63.4 + - - +
238B TYR 3.3 0.5 + - - -
239B GLU* 3.4 12.7 + - - +
243B HIS* 6.3 0.2 - - - -
260B GLU 5.2 1.4 + - - -
261B ARG* 2.9 35.8 + - - +
262B SER 4.4 0.4 - - - -
263B LEU* 3.8 57.1 - - + +
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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