Contacts of the helix formed by residues 225 - 234 (chain B) in PDB entry 6ACQ
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 GLY 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213B ASP* 3.1 32.3 - - - -
216B MET* 4.7 0.7 - - - -
217B LYS* 3.9 2.6 - - - +
224B MET* 1.3 73.5 - - - +
226B PRO* 1.3 74.9 - - - +
228B GLU* 3.0 15.3 + - - +
229B LEU* 2.9 23.7 + - - +
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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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194B MET* 4.3 13.7 - - + +
195B ILE* 3.7 26.1 - - + +
198B ALA* 3.7 28.5 - - + -
212B ILE* 3.9 5.8 - - + -
213B ASP* 3.4 7.4 - - - +
216B MET* 3.5 34.5 - - + -
222B HIS* 5.8 1.3 - - - +
224B MET 3.9 1.8 - - - +
225B GLY* 1.3 82.8 - - - +
227B LEU* 1.3 60.2 + - - +
229B LEU* 3.2 10.3 + - + +
230B GLY* 2.8 24.8 + - - -
190C ILE* 4.1 4.5 - - + -
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Residues in contact with LEU 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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195B ILE* 4.4 3.4 - - + +
198B ALA* 3.7 23.6 - - + -
199B VAL* 4.1 17.3 - - + +
202B LEU* 4.5 11.7 - - + -
209B VAL* 3.6 35.9 - - + +
212B ILE* 4.0 22.0 - - + -
213B ASP* 2.9 16.6 + - - +
226B PRO* 1.3 76.2 - - - +
228B GLU* 1.3 62.1 + - - +
230B GLY* 3.1 3.4 + - - -
231B ASP* 3.0 25.5 + - - +
277B PHE* 3.9 36.5 - - + -
278B TYR* 4.4 1.8 - - + -
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Residues in contact with GLU 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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213B ASP* 3.0 13.4 + - - +
217B LYS* 3.5 22.3 + - - -
224B MET* 3.7 23.7 - - - +
225B GLY* 3.0 30.2 + - - +
227B LEU* 1.3 75.5 - - - +
229B LEU* 1.3 59.9 + - - +
231B ASP* 3.4 5.8 - - - +
232B PHE* 2.8 27.9 + - - +
278B TYR* 3.4 29.1 + - + -
280B TYR* 4.3 4.6 + - - +
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Residues in contact with LEU 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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191B LEU* 4.0 30.3 - - + -
194B MET* 5.6 2.5 - - - -
195B ILE* 4.0 17.3 - - + -
224B MET* 3.9 33.0 - - + +
225B GLY 2.9 18.9 + - - +
226B PRO* 3.3 7.6 - - + +
228B GLU* 1.3 77.2 - - - +
230B GLY* 1.3 58.6 + - - +
232B PHE* 3.5 7.3 - - + +
233B ILE* 2.8 46.9 + - + +
222C HIS* 6.2 0.7 - - - +
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Residues in contact with GLY 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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195B ILE* 3.8 19.7 - - - +
226B PRO 2.8 14.4 + - - -
227B LEU 3.1 4.0 + - - -
229B LEU* 1.3 75.3 - - - +
231B ASP* 1.3 51.7 + - - +
233B ILE* 3.9 0.2 - - - -
234B GLY 2.7 40.9 + - - +
235B LEU* 3.5 18.2 - - - -
238B CYS* 4.0 5.6 - - - -
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Residues in contact with ASP 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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227B LEU 3.0 12.1 + - - +
228B GLU 3.4 6.1 - - - +
230B GLY* 1.3 76.1 - - - +
232B PHE* 1.3 59.6 + - - +
234B GLY* 3.8 4.4 + - - -
235B LEU* 3.8 6.1 - - - +
269B LEU 4.1 0.5 - - - +
270B GLY* 3.6 9.7 - - - -
271B ARG* 3.0 25.6 + - - +
272B LYS* 4.7 0.7 + - - +
276B GLY* 3.5 9.2 - - - -
277B PHE* 2.9 32.5 + - - -
278B TYR* 3.0 25.7 + - - -
280B TYR* 2.8 37.2 + - + +
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Residues in contact with PHE 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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224B MET* 3.7 29.4 - - + -
228B GLU 2.8 17.2 + - - +
229B LEU* 3.5 14.8 - - + +
230B GLY 3.1 0.6 - - - -
231B ASP* 1.3 78.3 - - - +
233B ILE* 1.3 69.6 + - + +
234B GLY* 3.2 0.4 - - - -
271B ARG* 3.6 44.1 - - - +
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Residues in contact with ILE 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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191B LEU* 4.7 9.4 - - + -
192B ILE* 4.3 15.3 - - + -
195B ILE* 4.1 14.4 - - + -
229B LEU* 2.8 43.8 + - + +
230B GLY 3.9 2.5 - - - +
232B PHE* 1.3 82.4 - - + +
234B GLY* 1.3 63.7 + - - +
237B ILE* 3.6 37.1 - - + +
238B CYS* 3.9 8.7 - - - -
241B ILE* 5.8 0.2 - - + -
272B LYS* 4.9 2.9 - - - -
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Residues in contact with GLY 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 GLY 2.7 10.0 + - - -
231B ASP 4.2 2.9 - - - -
232B PHE 3.2 2.6 - - - -
233B ILE* 1.3 78.0 - - - +
235B LEU* 1.3 60.9 + - - -
236B ASP* 3.3 13.2 - - - -
237B ILE* 3.1 6.4 + - - +
238B CYS* 3.1 26.2 + - - -
269B LEU 3.5 11.2 - - - -
272B LYS* 4.0 10.3 - - - -
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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