Contacts of the helix formed by residues 208 - 220 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A LEU* 4.2 4.0 - - - -
207A ALA* 1.3 75.9 - - - +
209A VAL* 1.3 66.6 + - - +
210A GLU* 3.8 12.8 + - - +
211A ASP* 3.3 29.1 + - - +
212A ILE* 3.0 26.3 + - - +
178F GLU 5.0 0.2 + - - -
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LEU* 3.8 23.2 - - + +
208A SER* 1.3 74.9 - - - +
210A GLU* 1.3 77.3 + - - +
212A ILE* 3.3 2.5 + - - +
213A ASP* 3.0 26.0 + - - +
227A LEU* 3.6 24.4 - - + +
263A TYR* 6.0 0.7 - - - +
277A PHE* 4.1 23.6 - - + +
278A TYR* 3.5 36.3 - - + +
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Residues in contact with GLU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A SER* 3.2 11.1 + - - +
209A VAL* 1.3 97.3 + - - +
211A ASP* 1.3 60.8 + - - +
213A ASP* 3.6 1.7 + - - +
214A LYS* 2.9 29.0 + - - +
278A TYR* 4.2 24.9 - - + -
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Residues in contact with ASP 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ALA* 4.4 7.6 - - + -
208A SER* 3.3 25.2 + - - +
210A GLU* 1.3 80.5 - - - +
212A ILE* 1.3 57.5 + - - +
214A LYS* 3.7 11.4 + - - +
215A ALA* 2.7 36.6 + - - +
176F PRO 4.7 1.6 - - - +
177F VAL* 3.7 32.4 - - + +
178F GLU* 3.2 26.3 + - - +
186F VAL* 5.5 0.9 - - - -
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ALA* 4.0 16.4 - - + +
201A ILE* 4.0 11.4 - - + -
202A LEU* 3.8 38.1 - - + +
207A ALA* 3.7 21.5 - - + +
208A SER 3.0 22.5 + - - +
209A VAL 3.5 3.6 - - - +
211A ASP* 1.3 76.3 - - - +
213A ASP* 1.3 66.6 + - - +
215A ALA* 3.6 2.1 - - - +
216A MET* 3.2 23.6 + - - +
226A PRO* 4.1 20.9 - - + -
227A LEU* 4.1 8.3 - - + -
186F VAL* 4.0 17.7 - - + -
190F ILE* 4.5 2.7 - - + -
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Residues in contact with ASP 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A VAL 3.0 9.4 + - - +
210A GLU* 4.0 2.5 - - - +
212A ILE* 1.3 76.7 - - - +
214A LYS* 1.3 65.6 + - - +
216A MET* 3.3 1.9 + - - +
217A LYS* 3.0 32.8 + - - +
225A GLY* 3.5 19.4 - - - -
226A PRO* 3.1 9.4 - - - +
227A LEU* 2.9 27.9 + - - +
228A GLU* 2.9 30.1 + - - +
278A TYR* 2.6 30.8 + - - +
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Residues in contact with LYS 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A GLU 2.9 19.8 + - - +
211A ASP* 3.7 13.1 + - - +
213A ASP* 1.3 76.0 - - - +
215A ALA* 1.3 63.7 + - - +
216A MET 3.2 0.3 + - - -
217A LYS* 3.2 10.7 + - - +
218A LEU* 2.9 40.8 + - + +
148F LEU* 4.6 0.4 - - + -
175F ASP* 3.0 39.4 + - - +
176F PRO 4.4 4.9 + - - -
177F VAL* 4.0 20.2 - - + -
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Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ASP 2.7 21.9 + - - +
212A ILE 3.6 5.2 - - - +
214A LYS* 1.3 75.0 - - - +
216A MET* 1.3 52.6 + - - +
219A GLY* 2.7 33.3 + - - -
148F LEU* 3.5 19.8 - - + +
150F GLU* 4.6 0.7 - - - +
177F VAL* 4.4 8.7 - - + -
186F VAL* 4.0 17.3 - - + -
187F VAL* 3.3 23.1 - - + +
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Residues in contact with MET 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A MET* 5.2 1.3 - - + -
212A ILE 3.2 15.0 + - - +
213A ASP 3.9 0.9 - - - +
214A LYS 3.1 0.8 - - - -
215A ALA* 1.3 75.7 - - - +
217A LYS* 1.3 65.7 + - - +
220A ALA* 3.1 29.9 + - + +
222A HIS* 3.3 43.3 + - + +
225A GLY* 4.7 1.6 - - - -
226A PRO* 3.7 33.2 - - + -
186F VAL* 4.5 1.8 - - + +
187F VAL* 3.9 31.4 - - - +
190F ILE* 3.7 36.3 - - + -
191F LEU* 4.3 8.3 - - + -
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Residues in contact with LYS 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ASP* 3.0 23.9 + - - +
214A LYS* 3.8 8.1 - - - +
216A MET* 1.3 76.9 - - - +
218A LEU* 1.3 66.7 + - + +
221A ASN* 3.0 28.8 - - - +
222A HIS 3.2 19.4 + - - +
223A PRO 3.8 18.8 - - - +
224A MET 3.9 0.4 - - - -
225A GLY 3.8 11.4 - - - +
228A GLU* 3.5 25.0 + - - +
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LYS* 2.9 38.4 + - + +
217A LYS* 1.3 85.0 - - + +
219A GLY* 1.3 64.9 + - - +
220A ALA 3.4 0.2 - - - -
221A ASN* 4.0 3.8 + - - +
146F MET* 3.4 18.4 - - - +
147F LYS* 4.7 18.8 + - + +
148F LEU* 3.8 27.5 + - + +
175F ASP* 3.7 32.1 - - + +
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Residues in contact with GLY 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ALA 2.7 23.8 + - - -
218A LEU* 1.3 75.4 - - - +
220A ALA* 1.3 58.6 + - - +
140F PHE* 4.4 11.7 - - - -
146F MET* 3.8 16.5 - - - +
148F LEU* 3.6 16.4 - - - +
187F VAL* 4.3 11.8 - - - +
191F LEU* 5.4 1.7 - - - +
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Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ALA 4.0 0.4 + - - -
216A MET* 3.1 22.8 + - + +
219A GLY* 1.3 76.5 - - - +
221A ASN* 1.3 72.7 + - - +
222A HIS* 3.2 21.5 + - + -
187F VAL* 4.9 0.9 - - + -
191F LEU* 3.9 35.7 - - + -
223F PRO* 4.5 4.3 - - - +
229F LEU* 6.1 1.0 - - + +
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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