Contacts of the helix formed by residues 217 - 229 (chain B) in PDB entry 3BUW
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 SER 217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B ILE* 3.4 9.7 + - - +
216B SER* 1.3 81.7 - - - +
218B GLY* 1.3 59.5 + - - +
219B LEU 3.6 1.3 + - - -
220B GLU* 3.1 18.0 + - - +
221B ALA* 3.0 24.1 + - - +
262D ALA 4.0 6.1 - - - -
263D VAL 2.5 29.6 + - - -
264D THR* 4.1 0.6 - - - -
265D HIS 3.6 22.9 - - - -
266D PRO* 4.5 3.6 - - - -
343D ARG* 5.1 1.8 - - - +
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Residues in contact with GLY 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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217B SER* 1.3 74.4 - - - +
219B LEU* 1.3 63.0 + - - +
221B ALA* 3.2 9.5 + - - +
222B MET* 3.0 27.8 + - - +
266D PRO 5.9 0.2 + - - -
268D TYR* 5.0 11.1 + - - -
269D MET* 6.2 0.6 - - - +
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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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217B SER* 3.3 6.7 + - - +
218B GLY* 1.3 76.9 - - - +
220B GLU* 1.3 62.5 + - - +
222B MET* 3.3 13.0 + - + +
223B ALA* 3.0 22.5 + - - +
223D ALA* 4.2 20.8 - - + +
226D SER* 3.4 26.2 - - - +
227D THR* 4.0 16.8 - - - +
258D TRP* 4.5 0.2 - - - +
262D ALA* 3.8 33.4 + - + +
263D VAL* 4.0 21.8 - - + +
268D TYR* 4.2 15.1 - - + -
270D ALA* 5.7 6.7 - - + -
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Residues in contact with GLU 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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214B PRO 4.7 1.2 - - - +
215B ILE* 3.9 9.4 - - + -
216B SER* 2.6 44.1 + - - -
217B SER* 3.1 19.9 + - - +
219B LEU* 1.3 76.6 - - - +
221B ALA* 1.3 58.2 + - - +
223B ALA* 3.2 5.0 + - - -
224B LEU* 2.8 25.5 + - - +
255B LEU* 4.4 15.4 - - - +
258B TRP* 3.3 31.4 - - + -
259B ASN* 4.4 13.6 - - - +
263B VAL* 5.7 2.2 - - + -
263D VAL* 4.1 6.4 + - + +
264D THR* 5.9 0.2 - - - -
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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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202B TRP* 3.3 23.4 - - + +
206B ARG* 4.6 17.3 - - + +
215B ILE* 3.8 15.6 - - + +
217B SER 3.0 13.8 + - - +
218B GLY* 3.2 12.1 + - - +
220B GLU* 1.3 77.2 - - - +
222B MET* 1.3 58.4 + - + +
224B LEU* 3.3 5.9 + - - +
225B LYS 2.9 23.9 + - - -
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Residues in contact with MET 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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202B TRP* 5.3 5.4 - - - -
218B GLY 3.0 17.5 + - - +
219B LEU* 3.7 16.8 - - + +
220B GLU 3.2 0.2 - - - -
221B ALA* 1.3 75.0 - - - +
223B ALA* 1.3 65.2 + - - +
225B LYS* 3.4 35.4 + - - +
226B SER* 3.0 23.4 + - - -
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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 LEU 3.0 14.2 + - - +
220B GLU* 3.5 10.3 - - - +
222B MET* 1.3 76.3 - - - +
224B LEU* 1.3 59.8 + - - +
226B SER* 2.6 23.7 + - - -
227B THR* 2.9 15.6 + - - -
258B TRP* 3.4 14.8 - - + -
263B VAL* 4.8 6.5 - - + -
219D LEU* 4.2 24.6 - - + +
223D ALA* 6.3 2.0 - - + -
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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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202B TRP* 4.0 10.8 - - + -
206B ARG* 6.2 0.2 - - - -
209B LEU* 3.9 26.5 - - + -
215B ILE* 4.0 22.7 - - + -
220B GLU 2.8 13.5 + - - +
221B ALA 3.5 8.3 - - - +
222B MET 3.2 0.2 - - - -
223B ALA* 1.3 74.9 - - - +
225B LYS* 1.3 67.1 + - - +
227B THR* 3.0 3.1 + - - -
228B ILE* 3.0 54.6 + - + +
244B PHE* 3.4 24.7 - - + -
255B LEU* 4.2 13.7 - - + -
258B TRP* 3.3 19.9 - - + -
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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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202B TRP* 3.6 58.5 - - + +
221B ALA 2.9 16.2 + - - +
222B MET* 3.7 35.4 - - - +
223B ALA 3.4 0.2 - - - -
224B LEU* 1.3 76.3 - - - +
226B SER* 1.3 59.6 + - - +
228B ILE* 4.7 0.4 - - - +
229B ASP* 2.9 52.4 + - + +
234B ASP* 3.8 22.2 + - - +
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Residues in contact with SER 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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222B MET 3.0 12.7 + - - -
223B ALA* 2.6 24.9 + - - -
225B LYS* 1.3 81.0 - - - +
227B THR* 1.3 58.9 + - - +
229B ASP* 4.3 5.2 + - - +
232B CYS* 6.0 0.2 - - - -
271B PHE* 3.7 27.6 - - - -
219D LEU* 3.5 19.4 - - - +
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Residues in contact with THR 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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223B ALA 2.9 13.2 + - - -
224B LEU 3.0 8.3 + - - -
226B SER* 1.3 82.2 + - - +
228B ILE* 1.3 59.5 + - - +
230B LEU* 3.2 18.4 - - - +
244B PHE* 3.8 17.8 - - + -
247B LEU* 6.3 0.4 - - + -
248B PHE* 3.8 15.5 - - + -
258B TRP* 3.1 26.7 + - + +
268B TYR* 4.0 21.2 + - + +
271B PHE* 5.6 1.8 - - - -
295B LEU* 5.4 5.8 - - + +
219D LEU* 4.0 11.3 - - - +
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Residues in contact with ILE 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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202B TRP* 4.9 1.3 - - + -
205B PHE* 3.8 25.6 - - + -
209B LEU* 5.2 0.9 - - + -
224B LEU* 3.0 39.2 + - + +
225B LYS* 4.5 1.8 - - - +
227B THR* 1.3 72.7 - - - +
229B ASP* 1.3 53.7 + - - +
230B LEU* 2.8 30.6 + - - +
236B ILE* 4.2 23.3 - - + -
240B GLU* 3.6 24.1 - - - +
241B PHE* 4.6 2.2 - - + +
244B PHE* 3.1 49.6 - - + -
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Residues in contact with ASP 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 LYS* 2.9 32.2 + - + +
226B SER* 4.4 5.7 - - - +
227B THR 3.6 0.4 - - - -
228B ILE* 1.3 74.4 - - - +
230B LEU* 1.3 60.3 + - - +
232B CYS* 3.0 34.9 + - - -
233B ASN* 3.1 21.7 + - - +
234B ASP* 2.9 31.4 + - - +
235B TYR 3.5 8.9 - - - +
236B ILE* 4.3 11.8 - - + +
240B GLU* 3.5 5.6 - - - +
271B PHE* 4.3 3.1 - - - -
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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