Contacts of the helix formed by residues 208 - 221 (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 SER 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B LEU* 4.3 2.9 - - - -
207B ALA* 1.3 78.1 - - - +
209B VAL* 1.3 64.8 + - - +
210B GLU* 3.6 12.1 + - - +
211B ASP* 3.1 31.6 + - - +
212B ILE* 3.0 22.3 + - - +
178C GLU 4.9 0.6 + - - -
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Residues in contact with VAL 209 (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 LEU* 3.9 20.3 - - + +
208B SER* 1.3 75.6 - - - +
210B GLU* 1.3 72.1 + - - +
212B ILE* 3.3 3.4 + - - +
213B ASP* 3.1 24.1 + - - +
227B LEU* 3.6 27.9 - - + +
263B TYR* 6.0 0.4 - - - +
277B PHE* 4.3 22.4 - - + +
278B TYR* 3.5 36.1 - - + +
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Residues in contact with GLU 210 (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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208B SER* 3.3 10.3 + - - +
209B VAL* 1.3 92.9 + - - +
211B ASP* 1.3 64.8 + - - +
213B ASP* 3.5 1.6 + - - +
214B LYS* 3.0 29.8 + - - +
278B TYR* 4.1 25.3 - - + +
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Residues in contact with ASP 211 (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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207B ALA* 4.3 8.7 - - + -
208B SER* 3.1 28.6 + - - +
210B GLU* 1.3 80.8 - - - +
212B ILE* 1.3 61.4 + - - +
214B LYS* 4.2 10.8 + - - -
215B ALA* 2.9 30.3 + - - +
176C PRO 4.7 1.3 - - - +
177C VAL* 3.6 30.8 - - + +
178C GLU* 3.1 28.6 + - - +
186C VAL* 4.9 0.7 - - - +
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Residues in contact with ILE 212 (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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198B ALA* 4.0 12.6 - - + +
201B ILE* 4.0 12.1 - - + -
202B LEU* 3.8 35.9 - - + +
207B ALA* 3.7 22.9 - - + +
208B SER 3.0 21.4 + - - +
209B VAL 3.7 4.3 - - - +
211B ASP* 1.3 78.6 - - - +
213B ASP* 1.3 62.4 + - - +
215B ALA* 3.3 2.6 + - - +
216B MET* 3.2 24.9 + - - +
226B PRO* 3.9 22.0 - - + -
227B LEU* 4.0 17.3 - - + -
186C VAL* 4.2 12.0 - - + +
190C ILE* 4.6 7.6 - - + -
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Residues in contact with ASP 213 (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 VAL 3.1 11.5 + - - +
210B GLU 4.1 2.2 - - - +
212B ILE* 1.3 75.3 - - - +
214B LYS* 1.3 65.9 + - - +
216B MET 3.6 0.5 + - - -
217B LYS* 3.1 33.2 + - - +
225B GLY* 3.1 25.7 - - - -
226B PRO* 3.2 4.5 - - - +
227B LEU* 2.9 29.4 + - - +
228B GLU* 3.0 27.8 + - - +
278B TYR* 2.5 31.9 + - - +
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Residues in contact with LYS 214 (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 GLU* 3.0 20.2 + - - +
211B ASP* 3.9 13.4 + - - +
213B ASP* 1.3 79.1 - - - +
215B ALA* 1.3 57.9 + - - +
217B LYS* 3.9 8.7 - - - +
218B LEU* 3.0 45.3 + - + +
148C LEU* 4.7 0.7 - - + -
175C ASP* 3.0 41.9 + - - +
176C PRO 4.1 6.9 + - - -
177C VAL* 3.9 21.3 - - + -
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Residues in contact with ALA 215 (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 ASP 2.9 20.2 + - - +
212B ILE 3.7 4.5 - - - +
213B ASP 3.3 0.2 - - - -
214B LYS* 1.3 78.8 - - - +
216B MET* 1.3 56.8 + - - +
219B GLY* 2.8 30.0 + - - -
148C LEU* 3.5 18.8 - - + +
150C GLU* 4.7 0.9 - - - +
177C VAL* 4.4 9.0 - - + -
186C VAL* 3.8 22.4 - - + -
187C VAL* 3.4 16.9 - - + +
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Residues in contact with MET 216 (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* 5.4 1.3 - - - -
212B ILE 3.2 12.3 + - - +
213B ASP 4.1 0.9 - - - +
215B ALA* 1.3 74.3 - - - +
217B LYS* 1.3 61.8 + - - +
220B ALA* 2.9 40.1 + - + +
221B ASN 3.4 1.4 + - - -
222B HIS* 3.5 34.5 + - + +
224B MET 5.0 0.4 - - - +
225B GLY* 4.7 1.6 - - - -
226B PRO* 3.5 37.9 - - + -
186C VAL* 4.2 2.2 - - + +
187C VAL* 4.0 24.9 - - + +
190C ILE* 3.8 42.8 - - + -
191C LEU* 4.3 9.4 - - + -
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Residues in contact with LYS 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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213B ASP* 3.1 28.5 + - - +
214B LYS* 3.9 6.1 - - - +
216B MET* 1.3 76.3 - - - +
218B LEU* 1.3 66.5 + - + +
221B ASN* 2.9 28.6 + - - +
222B HIS 2.9 23.8 + - - +
223B PRO 3.8 16.4 - - - +
224B MET* 3.7 16.8 - - - -
228B GLU* 3.5 20.1 + - - +
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Residues in contact with LEU 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 LYS* 3.0 34.1 + - + +
217B LYS* 1.3 82.9 - - + +
219B GLY* 1.3 64.3 + - - +
220B ALA 3.7 0.2 + - - -
221B ASN* 4.0 4.0 + - - +
146C MET* 3.3 18.7 - - - +
147C LYS* 4.6 14.2 + - + -
148C LEU* 3.6 26.3 + - + +
175C ASP* 3.7 37.5 - - + +
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Residues in contact with GLY 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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215B ALA 2.8 22.1 + - - -
218B LEU* 1.3 75.0 - - - +
220B ALA* 1.3 58.9 + - - +
221B ASN 3.5 0.2 - - - -
140C PHE* 4.4 13.5 - - - -
146C MET* 3.9 15.7 - - - +
148C LEU* 3.4 17.2 - - - +
187C VAL* 4.5 9.9 - - - +
191C LEU* 5.5 1.9 - - - +
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Residues in contact with ALA 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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215B ALA 4.0 0.2 + - - -
216B MET* 2.9 23.5 + - + +
219B GLY* 1.3 76.7 - - - +
221B ASN* 1.3 74.8 + - - +
222B HIS* 3.3 31.0 + - + +
187C VAL* 5.0 1.3 - - + +
191C LEU* 3.8 23.8 - - + -
223C PRO* 4.1 5.5 - - - +
229C LEU* 6.3 0.4 - - + -
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Residues in contact with ASN 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 LYS 2.9 16.8 + - - +
218B LEU 4.0 4.2 + - - +
219B GLY 3.5 2.0 - - - +
220B ALA* 1.3 81.9 - - - +
222B HIS* 1.3 62.0 + - - +
223B PRO* 4.0 1.2 - - - +
146C MET* 6.1 2.2 - - + -
223C PRO* 3.4 38.9 - - + +
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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