Contacts of the helix formed by residues 218 - 234 (chain B) in PDB entry 2BKU
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 ARG 218 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B SER* 5.9 0.2 + - - -
178B ASN* 4.5 9.6 + - - +
214B ASN* 3.3 30.5 + - - +
215B ASN* 3.2 19.4 + - - +
216B MET 3.3 2.4 + - - -
217B GLU* 1.3 82.3 - - - +
219B GLU* 1.3 67.8 + - - +
220B GLY* 3.0 2.7 + - - +
221B GLU* 2.9 46.2 + - - +
222B ARG* 2.8 27.8 + - - +
264D GLU* 4.6 17.2 + - - +
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Residues in contact with GLU 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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218B ARG* 1.3 67.7 - - - +
220B GLY* 1.3 56.5 + - - +
222B ARG* 3.8 24.4 - - - +
223B ASN* 2.9 57.9 + - - +
219D GLU* 2.3 45.7 - - - +
261D PRO* 6.3 3.6 - - + +
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Residues in contact with GLY 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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218B ARG* 3.0 3.8 + - - +
219B GLU* 1.3 82.3 - - - +
221B GLU* 1.3 59.9 + - - +
223B ASN* 3.9 3.7 - - - +
224B TYR* 3.3 19.9 + - - +
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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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178B ASN* 3.7 22.1 + - - +
181B LEU* 4.7 9.6 - - + +
182B ILE* 4.8 17.9 - - + -
215B ASN* 2.7 47.4 - - + +
218B ARG* 2.9 40.6 + - + +
220B GLY* 1.3 73.8 - - - +
222B ARG* 1.3 63.2 + - - +
224B TYR* 3.3 8.8 + - - +
225B LEU* 3.1 25.3 + - - +
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Residues in contact with ARG 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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215B ASN 3.9 2.8 + - - -
216B MET* 2.8 61.6 + - + +
217B GLU* 3.8 0.6 - - - +
218B ARG 2.8 38.8 + - - +
219B GLU* 3.8 25.1 - - - +
221B GLU* 1.3 73.5 - - - +
223B ASN* 1.3 55.9 + - - +
225B LEU* 3.5 6.2 + - - +
226B MET* 2.9 42.0 + - + +
258B PHE* 3.4 49.5 + - - +
259B MET* 4.9 0.7 - - - -
261B PRO* 6.4 0.6 - - - +
262B TYR* 2.8 31.6 + - + +
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Residues in contact with ASN 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 GLU* 2.9 48.2 + - - +
220B GLY* 3.9 4.2 - - - +
222B ARG* 1.3 73.4 - - - +
224B TYR* 1.3 66.5 + - - +
226B MET* 3.2 4.8 + - - +
227B GLN* 2.9 25.6 + - - +
262B TYR* 2.6 40.0 + - - -
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Residues in contact with TYR 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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181B LEU* 4.6 5.6 - - + -
182B ILE* 4.4 31.5 - - + +
185B VAL* 3.3 27.0 - - + +
186B GLN* 3.7 20.6 + - - +
189B GLN* 3.3 39.0 + - - -
220B GLY 3.3 11.0 + - - +
221B GLU* 3.6 7.6 - - - +
223B ASN* 1.3 76.6 - - - +
225B LEU* 1.3 67.5 + - - +
227B GLN* 3.0 20.5 + - + +
228B VAL* 3.2 20.1 + - + +
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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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181B LEU* 3.7 30.3 - - + -
185B VAL* 4.1 18.4 - - + -
205B LEU* 4.1 17.9 - - + -
209B LEU* 5.1 0.7 - - + -
212B ILE* 3.8 15.9 - - + -
215B ASN* 6.2 0.7 - - + -
216B MET* 3.9 20.0 - - + +
221B GLU 3.1 14.0 + - - +
222B ARG* 3.6 4.3 - - - +
224B TYR* 1.3 80.2 - - - +
226B MET* 1.3 85.4 + - + +
228B VAL* 3.3 3.3 + - - +
229B VAL* 3.2 31.9 + - + +
251B ILE* 4.1 8.1 - - + -
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Residues in contact with MET 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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216B MET* 5.5 1.8 - - - -
222B ARG* 2.9 28.5 + - + +
223B ASN 3.7 3.6 - - - +
224B TYR 3.2 0.2 - - - -
225B LEU* 1.3 83.6 - - + +
227B GLN* 1.3 64.8 + - - +
229B VAL* 4.2 6.4 - - + +
230B CYS* 3.1 33.1 + - - +
248B LEU* 4.0 20.9 - - + -
251B ILE* 3.3 48.2 - - + -
259B MET* 4.3 14.1 - - - +
262B TYR* 4.1 37.9 - - + -
267B LEU* 5.2 2.7 - - - -
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Residues in contact with GLN 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 ASN 2.9 13.8 + - - +
224B TYR* 3.0 14.8 + - + +
226B MET* 1.3 74.9 - - - +
228B VAL* 1.3 62.1 + - + +
230B CYS* 3.9 4.2 - - - +
231B GLU* 3.1 45.0 + - - +
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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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185B VAL* 3.3 36.6 - - + +
188B ALA* 3.8 13.5 - - + +
189B GLN* 3.5 48.5 - - + +
198B ARG* 5.8 0.2 + - - -
202B LEU* 5.5 0.4 - - + -
224B TYR* 3.2 21.0 + - + +
225B LEU 3.8 2.9 - - - +
226B MET 3.2 0.2 - - - -
227B GLN* 1.3 77.7 - - + +
229B VAL* 1.3 67.8 + - + +
231B GLU* 3.3 7.7 + - - +
232B ALA* 3.0 22.2 + - - +
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Residues in contact with VAL 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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185B VAL* 6.2 0.2 - - + -
202B LEU* 4.8 9.0 - - + -
205B LEU* 3.8 28.3 - - + -
225B LEU* 3.2 24.0 + - + +
226B MET* 4.2 9.4 - - + +
228B VAL* 1.3 77.7 - - + +
230B CYS* 1.3 62.4 + - - +
232B ALA* 3.3 9.2 + - - +
233B THR* 3.3 20.3 + - - +
244B ALA* 3.6 25.8 - - - +
247B CYS* 4.0 13.9 - - + -
248B LEU* 3.9 20.6 - - + -
251B ILE* 4.7 0.4 - - + -
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Residues in contact with CYS 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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226B MET* 3.1 26.6 + - - +
227B GLN* 3.9 5.6 - - - +
229B VAL* 1.3 74.9 - - - +
231B GLU* 1.3 61.8 + - - +
233B THR* 2.3 36.4 + - - -
234B GLN* 3.8 4.0 + - - +
248B LEU* 4.7 6.5 - - - -
262B TYR* 6.0 2.0 - - - -
266B ALA* 5.3 7.9 - - + -
267B LEU* 3.6 38.8 - - - -
270B LEU* 4.3 15.7 - - + +
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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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189B GLN* 6.5 0.9 - - - -
198B ARG* 4.7 9.7 + - - +
227B GLN* 3.1 40.5 + - - +
228B VAL* 3.5 8.5 - - + +
230B CYS* 1.3 75.3 - - - +
232B ALA* 1.3 57.5 + - - +
234B GLN* 3.0 33.4 + - - +
235B ALA* 3.6 0.9 + - - -
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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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188B ALA 5.4 2.7 - - - +
198B ARG* 4.3 16.3 - - - +
202B LEU* 4.2 23.6 - - + -
228B VAL* 3.0 14.5 + - + +
229B VAL 3.5 5.6 - - - +
230B CYS 3.2 0.2 - - - -
231B GLU* 1.3 73.5 - - - +
233B THR* 1.3 64.5 + - - +
235B ALA* 3.2 20.2 + - - +
240B VAL* 3.9 5.4 - - + +
241B GLN* 3.6 11.1 - - - -
244B ALA* 3.5 19.5 - - + -
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Residues in contact with THR 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 VAL 3.3 16.6 + - - +
230B CYS* 2.3 26.2 + - - +
232B ALA* 1.3 75.6 - - - +
234B GLN* 1.3 73.3 + - - +
235B ALA 3.3 0.4 - - - -
241B GLN* 2.7 35.0 + - - +
244B ALA* 3.4 13.4 - - + +
245B PHE* 4.0 27.7 - - + -
248B LEU* 3.7 28.7 - - + -
267B LEU* 5.4 1.8 - - + -
270B LEU* 4.2 4.9 - - - +
274B THR* 5.1 0.5 - - - +
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Residues in contact with GLN 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 CYS 4.0 6.1 - - - +
231B GLU* 3.0 16.9 + - - +
233B THR* 1.3 103.5 + - - +
235B ALA* 1.3 62.9 + - - +
236B GLU* 3.9 2.8 + - - +
241B GLN* 4.2 3.2 + - - +
245B PHE* 5.4 0.4 - - - -
270B LEU* 4.0 37.1 + - + +
274B THR* 4.0 22.7 - - - +
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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