Contacts of the helix formed by residues 218 - 235 (chain B) in PDB entry 6B0Z
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 LYS 218 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B LYS* 1.3 88.2 - - + +
219B TYR* 1.3 63.5 + - - +
221B GLY 4.0 0.2 - - - -
222B ARG* 3.1 23.9 + - - +
143D ASP* 2.8 37.1 + - - +
144D PHE* 3.9 21.1 - - - +
145D VAL* 4.1 14.7 - - + +
178D VAL* 3.8 5.2 - - - +
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Residues in contact with TYR 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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137B ASP* 3.0 36.5 + - - -
182B MET* 4.2 4.4 - - + +
183B TYR 3.1 20.8 + - - -
184B ASN* 3.6 0.9 - - + +
216B LEU* 4.0 6.3 - - + -
218B LYS* 1.3 79.4 - - - +
220B ASP* 1.3 75.2 + - - +
222B ARG* 3.5 8.5 + - - +
223B PHE* 3.4 31.2 - + - -
270B LYS* 3.7 10.1 - - - -
143D ASP* 2.9 20.2 + - + +
144D PHE 5.3 0.2 - - - -
178D VAL* 3.7 36.6 - - + +
179D ALA* 3.8 30.1 - - - -
180D MET* 3.8 26.2 - - + -
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Residues in contact with ASP 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B THR* 3.7 17.7 - - - +
212B LYS* 2.7 32.2 + - - +
213B ASN* 3.8 9.9 - - - +
216B LEU* 2.9 27.6 + - - +
219B TYR* 1.3 74.7 - - - +
221B GLY* 1.3 66.5 + - - +
222B ARG 3.1 2.2 - - - -
223B PHE* 3.2 11.2 + - - +
224B LYS* 3.1 21.0 + - - +
270B LYS* 2.7 37.9 + - - +
271B ASN* 3.8 3.8 + - - -
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Residues in contact with GLY 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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213B ASN* 3.5 15.8 + - - -
216B LEU 3.4 7.7 + - - -
217B LYS 3.3 18.6 + - - -
218B LYS 4.0 0.4 - - - -
219B TYR 3.4 0.4 - - - -
220B ASP* 1.3 77.6 - - - +
222B ARG* 1.3 55.5 + - - +
224B LYS* 3.4 5.5 + - - +
225B ASP* 2.9 40.6 + - - +
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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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186B ASP* 2.8 36.6 + - - +
189B ILE* 4.4 5.4 - - + -
190B GLU* 5.8 0.4 + - - -
218B LYS 3.1 18.8 + - - +
219B TYR 3.6 2.7 - - - +
220B ASP 3.1 0.4 - - - -
221B GLY* 1.3 74.5 - - - +
223B PHE* 1.3 66.3 + - - +
225B ASP* 3.3 16.9 + - - +
226B ILE* 2.9 59.5 + - + +
145D VAL* 4.2 28.9 - - - +
177D GLY 4.8 0.2 + - - -
178D VAL* 3.5 20.2 - - + -
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Residues in contact with PHE 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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133B HIS* 6.4 0.4 - - + -
184B ASN* 3.6 25.4 - - + -
189B ILE* 3.6 43.7 - - + -
192B PHE* 4.3 19.7 - + - -
209B LEU* 4.2 6.3 - - + -
211B THR* 4.3 12.8 - - + -
219B TYR* 3.4 31.2 - + - -
220B ASP 3.2 7.4 + - - +
222B ARG* 1.3 79.0 - - - +
224B LYS* 1.3 63.3 + - - +
226B ILE* 3.8 0.3 - - - -
227B PHE* 2.9 38.9 + + - -
270B LYS* 3.4 41.1 - - + -
178D VAL* 4.7 0.7 - - + -
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Residues in contact with LYS 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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209B LEU* 4.0 11.2 - - - +
211B THR* 5.0 0.7 - - + +
213B ASN* 3.3 32.7 - - - +
220B ASP 3.1 10.6 + - - +
221B GLY* 3.6 7.9 - - - +
223B PHE* 1.3 78.6 - - - +
225B ASP* 1.3 65.7 + - - +
227B PHE* 3.8 1.6 - - - +
228B GLN* 2.9 39.3 + - + +
246B TYR* 4.8 1.2 + - - -
248B HIS* 3.7 45.6 + - + +
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Residues in contact with ASP 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 GLY* 2.9 26.2 + - - +
222B ARG* 3.9 17.1 + - - +
224B LYS* 1.3 85.4 - - - +
226B ILE* 1.3 58.0 + - - +
228B GLN* 3.8 5.5 - - - +
229B GLU* 2.8 33.3 + - - +
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Residues in contact with ILE 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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186B ASP* 3.8 30.5 - - + +
189B ILE* 3.7 36.8 - - + +
190B GLU* 3.8 26.2 - - + +
193B ALA* 4.9 0.7 - - + -
222B ARG* 2.9 46.6 + - + +
223B PHE 3.9 0.2 - - - +
225B ASP* 1.3 74.5 - - - +
227B PHE* 1.3 66.5 + - - +
229B GLU* 4.0 3.7 - - - +
230B ILE* 3.0 36.2 + - + +
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Residues in contact with PHE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ILE* 3.9 16.8 - - + -
192B PHE* 3.7 35.9 - + - -
193B ALA* 3.6 41.7 - - + -
196B SER* 4.4 8.7 - - - -
197B PHE* 3.3 18.4 - + - -
207B LEU* 5.0 1.3 - - + -
209B LEU* 3.6 21.3 - - + -
223B PHE* 2.9 28.2 + + - +
224B LYS 3.8 0.9 - - - +
226B ILE* 1.3 75.3 - - - +
228B GLN* 1.3 57.9 + - - +
230B ILE 3.5 0.2 + - - -
231B TYR* 2.9 25.0 + - - +
246B TYR* 3.4 33.2 - + + +
268B ALA* 4.1 17.5 - - + -
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Residues in contact with GLN 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 LYS* 2.9 27.0 + - + +
225B ASP* 3.8 6.7 - - - +
227B PHE* 1.3 77.9 - - - +
229B GLU* 1.3 57.2 + - - +
231B TYR* 3.3 15.9 + - - +
232B ASP* 2.8 67.3 + - - +
246B TYR* 3.7 19.6 + - - -
247B GLU* 5.6 0.3 - - - -
248B HIS* 4.9 10.7 + - - +
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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 ASP 2.8 21.0 + - - +
226B ILE* 4.1 3.8 - - - +
228B GLN* 1.3 73.2 - - - +
230B ILE* 1.3 64.2 + - + +
232B ASP* 4.6 6.4 - - - +
233B LYS* 3.1 61.9 + - + +
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Residues in contact with ILE 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* 4.1 12.8 - - + -
193B ALA* 3.8 18.2 - - + -
194B HIS* 3.8 26.9 - - + +
197B PHE* 3.5 21.8 - - + -
226B ILE* 3.0 33.4 + - + +
227B PHE 3.9 2.0 - - - +
229B GLU* 1.3 79.7 - - + +
231B TYR* 1.3 55.4 + - - +
234B GLN* 2.8 49.8 + - - +
235B TYR* 3.6 20.6 + - + -
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Residues in contact with TYR 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 PHE* 3.4 30.5 - + + -
227B PHE 2.9 18.5 + - - +
228B GLN* 3.7 8.3 - - - +
230B ILE* 1.3 77.4 - - - +
232B ASP* 1.3 76.0 + - - +
235B TYR* 3.1 10.4 + - + +
236B LYS* 2.8 64.7 + - + +
239B PHE* 3.6 34.8 - + - +
240B GLU* 5.1 3.1 - - - +
244B ILE 4.6 0.5 + - - -
245B TRP* 3.8 5.0 - - - +
246B TYR* 3.4 52.1 + + + -
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Residues in contact with ASP 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 GLN* 2.8 54.3 + - - +
229B GLU* 4.0 7.9 - - - +
231B TYR* 1.3 82.4 - - - +
233B LYS* 1.3 73.8 + - + +
236B LYS* 3.9 29.6 + - + +
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Residues in contact with LYS 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 GLU* 3.1 49.5 + - + +
232B ASP* 1.3 87.1 - - + +
234B GLN* 1.3 71.7 + - + +
235B TYR 3.9 0.2 - - - -
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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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194B HIS* 3.3 24.7 + - - -
229B GLU 5.3 0.2 + - - -
230B ILE* 2.8 36.5 + - - +
233B LYS* 1.3 90.0 - - + +
235B TYR* 1.3 75.5 + - + +
238B GLN* 3.2 17.0 - - - +
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Residues in contact with TYR 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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194B HIS* 2.7 37.5 + + - +
197B PHE* 3.6 32.8 - + + -
198B GLN* 2.9 34.7 + - + -
201B LEU* 3.7 22.9 - - + -
230B ILE* 3.6 19.3 - - + -
231B TYR* 3.1 13.1 + - + +
233B LYS 3.9 0.2 - - - -
234B GLN* 1.3 89.2 - - + +
236B LYS* 1.3 67.2 + - - +
237B SER 3.3 2.5 - - - -
238B GLN* 3.1 16.7 + - - +
239B PHE* 3.0 36.5 + - + -
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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
------------------------------------------------------------
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