Contacts of the helix formed by residues 216 - 231 (chain B) in PDB entry 3BWC
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 216 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211B GLU* 3.5 25.2 - - - +
212B SER 2.7 37.5 + - - +
214B TRP 3.4 0.2 - - - -
215B LEU* 1.3 99.2 - - - +
217B LEU* 1.3 65.4 + - - +
218B GLU* 3.2 13.4 + - - +
219B LEU* 3.6 22.2 + - + +
220B ILE* 3.5 13.0 + - - +
245B TYR* 5.1 0.3 + - - -
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Residues in contact with LEU 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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212B SER 3.5 4.9 + - - -
213B ILE* 3.4 26.1 + - - +
214B TRP 4.5 2.2 + - - +
215B LEU 4.1 0.2 - - - -
216B ASP* 1.3 73.4 - - - +
218B GLU* 1.3 76.3 + - + +
220B ILE* 3.2 14.9 + - - +
221B GLU* 3.3 12.6 + - - +
296B PHE* 3.5 34.3 - - + +
297B ALA* 3.7 14.8 - - + -
299B HIS* 3.7 16.8 + - + +
300B ILE* 3.3 32.2 - - + +
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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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214B TRP 5.5 1.9 - - - +
215B LEU 5.0 1.6 - - - +
216B ASP* 4.2 11.3 - - - +
217B LEU* 1.3 92.4 + - + +
219B LEU* 1.3 60.6 + - - +
221B GLU* 3.5 11.4 + - - +
222B LYS* 3.2 44.9 + - - +
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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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211B GLU* 3.6 31.4 - - + +
216B ASP* 3.6 22.5 + - + +
218B GLU* 1.3 78.2 + - - +
220B ILE* 1.3 58.6 + - - +
222B LYS* 4.1 23.0 - - + +
223B MSE 2.9 47.9 + - + +
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Residues in contact with ILE 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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210B GLY* 6.1 0.4 - - - -
211B GLU* 3.1 41.7 - - + +
212B SER 3.5 20.2 - - - +
213B ILE* 3.7 12.1 - - + +
216B ASP 3.5 10.3 + - - +
217B LEU* 3.2 8.2 + - - +
219B LEU* 1.3 75.5 - - - +
221B GLU* 1.3 59.1 + - - +
223B MSE 3.7 7.1 - - - +
224B SER* 2.8 28.8 + - - -
237B TYR* 3.5 28.9 - - + -
253B LEU* 4.7 7.0 - - + +
300B ILE* 3.4 28.9 - - + -
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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 LEU 3.3 8.8 + - - +
218B GLU* 3.7 12.7 - - - +
219B LEU 3.4 0.2 - - - -
220B ILE* 1.3 75.7 - - - +
222B LYS* 1.3 68.9 + - - +
224B SER* 3.3 6.1 + - - -
225B ARG* 2.5 74.4 + - + +
299B HIS* 3.3 35.3 - - + +
300B ILE* 4.8 7.6 - - + +
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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* 3.2 33.0 + - - +
219B LEU* 3.6 24.9 - - + +
220B ILE 3.3 0.2 - - - -
221B GLU* 1.3 80.6 - - + +
223B MSE 1.3 57.8 + - - +
225B ARG* 3.3 8.5 + - - +
226B PHE* 2.8 33.2 + - - +
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Residues in contact with MSE 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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193B TYR* 5.4 6.5 - - + +
208B ASN* 4.4 12.3 - - - +
209B GLN 4.6 6.1 - - - +
210B GLY* 4.8 5.2 - - - -
211B GLU* 3.9 21.5 - - + +
219B LEU* 2.9 48.1 + - + +
220B ILE* 3.7 5.8 - - - +
222B LYS* 1.3 76.4 - - - +
224B SER* 1.3 57.1 + - - +
226B PHE* 3.8 10.4 - - + +
227B ILE* 3.0 46.0 + - + +
253B LEU* 3.9 20.6 - - + -
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Residues in contact with SER 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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220B ILE 2.8 18.6 + - - -
221B GLU* 3.6 8.3 - - - -
222B LYS 3.2 0.2 - - - -
223B MSE 1.3 78.4 - - - +
225B ARG* 1.3 62.4 + - - +
227B ILE* 3.9 2.9 - - - +
228B ARG* 3.1 40.2 + - - +
235B VAL* 4.0 22.1 + - - +
253B LEU* 4.4 16.0 - - - +
300B ILE* 4.0 18.9 + - - +
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Residues in contact with ARG 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* 2.5 65.6 + - + +
222B LYS* 3.8 6.1 - - - +
224B SER* 1.3 73.9 - - - +
226B PHE* 1.3 62.3 + - - +
228B ARG* 3.1 28.5 + - - +
229B GLU* 2.8 47.3 + - - +
299B HIS* 5.2 3.0 + - - +
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Residues in contact with PHE 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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190B GLU* 3.6 44.0 - - + -
193B TYR* 3.5 36.6 - + + -
222B LYS 2.8 20.0 + - - +
223B MSE 3.8 10.3 - - + +
225B ARG* 1.3 78.1 - - - +
227B ILE* 1.3 64.4 + - + +
229B GLU* 3.5 10.7 + - - +
230B THR* 3.0 41.0 + - - -
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Residues in contact with ILE 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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193B TYR* 4.0 21.1 - - + -
206B CYS* 5.5 1.8 - - - -
208B ASN* 3.3 29.6 - - - +
223B MSE 3.0 28.2 + - + +
224B SER 3.9 4.0 - - - +
226B PHE* 1.3 87.4 - - + +
228B ARG* 1.3 61.8 + - - +
230B THR* 3.4 12.6 - - - -
232B PHE* 3.3 42.4 + - + -
235B VAL* 3.6 22.4 - - + -
253B LEU* 3.9 13.2 - - + -
255B CYS* 4.2 7.4 - - + -
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Residues in contact with ARG 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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224B SER* 3.1 39.5 + - - +
225B ARG* 3.1 41.1 + - - +
227B ILE* 1.3 77.9 - - - +
229B GLU* 1.3 64.1 + - + +
231B GLY* 3.2 12.8 + - - -
232B PHE 3.4 24.8 - - - +
233B ALA 4.3 12.3 - - - +
234B SER* 5.3 1.3 - - - +
235B VAL* 4.3 17.4 + - + +
300B ILE 4.9 5.1 + - - -
302B ASN* 5.1 12.9 - - - +
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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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225B ARG* 2.8 30.0 + - - +
226B PHE* 4.0 10.0 - - + +
228B ARG* 1.3 76.3 + - + +
230B THR* 1.3 64.6 + - - +
231B GLY* 3.4 0.7 + - - -
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Residues in contact with THR 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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190B GLU* 4.7 4.0 + - - +
193B TYR* 3.4 38.3 - - + +
194B LYS* 3.6 26.2 + - + +
197B LEU* 3.6 13.3 - - + +
226B PHE* 3.0 38.7 + - - -
227B ILE* 3.4 14.3 - - - +
228B ARG 3.2 0.4 - - - -
229B GLU* 1.3 78.6 - - - +
231B GLY* 1.3 55.6 + - - +
232B PHE* 4.5 4.0 - - + -
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Residues in contact with GLY 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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197B LEU* 3.6 19.4 - - - +
228B ARG 3.2 4.8 + - - -
229B GLU 3.2 4.5 - - - -
230B THR* 1.3 80.0 - - - +
232B PHE* 1.3 67.7 + - - +
233B ALA* 3.5 3.1 + - - +
257B LYS 4.9 2.8 - - - +
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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