Contacts of the helix formed by residues 225 - 239 (chain B) in PDB entry 3DBI
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 THR 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B LYS* 3.7 15.9 + - + +
224B TRP* 1.3 80.2 - - + +
226B PRO* 1.4 73.6 - - + +
227B ALA* 3.7 9.1 + - - +
228B SER* 2.8 38.8 + - - -
229B GLY 3.3 5.0 + - - -
253B MSE 3.3 8.1 - - - +
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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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225B THR* 1.4 88.0 - - + +
227B ALA* 1.3 60.5 - - - +
229B GLY 3.3 1.9 + - - -
230B ALA* 3.3 16.8 + - - +
252B ASP* 3.3 43.7 - - + +
253B MSE 4.5 0.2 - - - -
255B ILE* 5.9 2.9 - - + -
256B GLY* 3.3 18.4 - - - +
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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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225B THR* 3.2 8.8 + - - +
226B PRO* 1.3 78.0 - - - +
228B SER* 1.3 52.3 + - - +
230B ALA* 2.9 10.8 + - - +
231B GLU* 2.7 33.6 + - - +
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Residues in contact with SER 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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187B LEU* 5.0 1.4 - - - +
221B ASN 4.6 7.0 - - - +
222B GLY* 4.1 6.0 - - - -
223B LYS* 3.0 37.9 + - - -
224B TRP 3.7 0.9 + - - -
225B THR* 2.8 32.8 + - - -
227B ALA* 1.3 78.7 - - - +
229B GLY* 1.3 57.9 + - - +
231B GLU* 3.7 19.2 + - - +
232B GLY* 3.4 17.8 + - - -
253B MSE 3.7 5.1 - - - +
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Residues in contact with GLY 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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187B LEU* 3.6 17.7 - - - +
225B THR 3.3 5.9 + - - -
226B PRO 3.3 2.7 + - - -
227B ALA 3.2 0.8 - - - -
228B SER* 1.3 80.3 + - - +
230B ALA* 1.3 58.9 + - - +
232B GLY 3.3 0.5 + - - -
233B VAL 3.1 21.1 + - - -
253B MSE 3.5 27.6 - - - -
257B ALA* 3.7 15.0 - - - -
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PRO 3.3 8.4 + - - +
227B ALA* 2.9 10.5 + - - +
229B GLY* 1.3 73.2 - - - +
231B GLU* 1.3 53.9 + - - +
232B GLY 2.4 18.1 + - - -
233B VAL* 3.2 1.6 + - - +
234B GLU* 2.9 24.3 + - - +
256B GLY* 3.5 19.0 + - - +
259B LYS* 5.9 1.8 - - + -
260B ALA* 3.8 16.2 - - + -
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Residues in contact with GLU 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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221B ASN 5.7 3.7 - - - +
227B ALA 2.7 17.9 + - - +
228B SER* 3.9 18.4 - - - +
229B GLY 3.6 0.4 - - - -
230B ALA* 1.3 71.7 - - - +
232B GLY* 1.3 55.5 + - - +
234B GLU* 3.8 9.6 - - + +
235B MSE 3.3 36.0 + - + +
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Residues in contact with GLY 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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187B LEU* 4.0 18.3 - - - +
220B ALA* 4.3 7.2 - - - +
221B ASN 5.3 2.9 - - - -
228B SER 3.4 9.0 + - - -
229B GLY 3.3 6.2 + - - -
230B ALA 2.4 13.5 + - - -
231B GLU* 1.3 70.0 - - - +
233B VAL* 1.3 64.7 + - - +
234B GLU 3.1 0.9 - - - -
235B MSE 3.2 7.8 + - - +
236B LEU* 3.0 26.7 + - - +
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Residues in contact with VAL 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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187B LEU* 4.4 1.0 - - + +
229B GLY 3.1 9.7 + - - +
230B ALA 4.0 2.9 - - - +
232B GLY* 1.3 77.2 - - - +
234B GLU* 1.3 56.3 + - - +
236B LEU* 3.3 7.4 + - + +
237B LEU* 2.9 44.8 + - + +
243B PHE* 5.4 1.6 - - + -
246B LEU* 3.8 20.2 - - + -
257B ALA* 3.7 34.1 - - + +
260B ALA* 3.8 21.8 - - + +
261B LEU* 3.9 30.1 - - + +
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Residues in contact with GLU 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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230B ALA* 2.9 16.5 + - - +
231B GLU* 3.9 9.9 - - + +
233B VAL* 1.3 74.1 - - - +
235B MSE 1.3 69.0 + - - +
237B LEU* 4.1 4.5 - - - +
238B GLU* 3.3 19.1 + - - +
260B ALA* 3.9 20.4 - - - +
264B ARG* 2.8 49.3 + - - +
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Residues in contact with MSE 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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219B ILE 5.5 0.4 - - - +
220B ALA* 4.4 20.2 - - + -
221B ASN* 4.4 19.3 - - + +
231B GLU* 3.3 30.8 + - + +
232B GLY* 3.2 10.2 + - - +
234B GLU* 1.3 75.3 - - - +
236B LEU* 1.3 56.4 + - - +
238B GLU* 2.5 39.7 + - - +
239B ARG* 3.3 38.7 + - - +
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Residues in contact with LEU 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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185B ALA* 3.9 14.1 - - + -
187B LEU* 3.9 11.2 - - + -
217B LYS 3.4 23.8 - - - +
218B LEU* 3.8 22.0 - - - +
219B ILE 4.2 0.2 - - - +
220B ALA* 4.3 7.6 - - + -
232B GLY 3.0 17.9 + - - +
233B VAL* 3.6 6.1 - - - +
235B MSE 1.3 80.0 - - - +
237B LEU* 1.3 60.6 - - - +
238B GLU 3.3 0.2 + - - -
239B ARG* 3.7 16.4 + - - +
240B GLY 3.5 2.8 + - - -
241B ALA* 3.1 31.2 + - + +
243B PHE* 3.9 17.3 - - + -
246B LEU* 3.8 28.7 - - + -
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Residues in contact with LEU 237 (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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233B VAL* 2.9 34.7 + - + +
234B GLU* 4.2 7.0 - - - +
235B MSE 2.8 1.6 + - - -
236B LEU* 1.3 73.8 - - - +
238B GLU* 1.3 63.0 + - - +
240B GLY* 3.3 12.3 + - - -
241B ALA 4.9 6.7 - - - +
243B PHE* 4.2 23.6 - - + -
261B LEU* 4.8 3.1 - - + -
264B ARG* 3.8 38.6 - - + +
266B VAL* 4.6 17.5 - - + -
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Residues in contact with GLU 238 (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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234B GLU 3.3 11.9 + - - +
235B MSE 2.5 22.0 + - - +
237B LEU* 1.3 70.5 - - - +
239B ARG* 1.3 58.5 + - - +
240B GLY* 3.1 7.6 + - - -
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Residues in contact with ARG 239 (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 GLU 4.2 1.8 + - - -
217B LYS* 3.0 61.7 + - + +
219B ILE 3.1 27.9 + - - -
220B ALA* 4.2 4.6 - - - +
235B MSE 3.3 41.5 + - - +
236B LEU* 3.8 18.8 - - - +
238B GLU* 1.3 80.6 + - - +
240B GLY* 1.3 60.2 + - - +
241B ALA 3.3 1.0 + - - +
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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