Contacts of the helix formed by residues 211 - 222 (chain F) in PDB entry 3ECS
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 211 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128F HIS* 3.6 14.4 + - - -
183F VAL* 5.9 2.3 - - - +
210F ILE* 1.3 73.9 - - - +
212F THR* 1.3 61.8 + - - +
213F ASN 3.5 2.2 - - - -
214F GLN* 3.6 8.4 + - - +
215F MSE 3.4 21.3 + - - +
274F ASP* 2.8 9.4 + - - -
181G ALA* 3.1 31.3 + - - -
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Residues in contact with THR 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F HIS* 3.4 12.6 - - - -
195F VAL* 4.2 9.0 - - + +
206F ILE* 4.1 20.6 - - + -
208F ASN* 3.1 23.8 + - + +
209F LYS 2.8 19.2 + - - -
211F GLY* 1.3 77.0 - - - +
213F ASN* 1.3 68.2 + - - +
215F MSE 3.0 7.5 + - - +
216F ALA* 3.0 19.6 + - - +
226F PHE* 4.1 14.7 - - + -
274F ASP* 3.5 7.2 - - - -
276F THR* 3.4 15.3 - - - +
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Residues in contact with ASN 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F THR* 1.3 76.3 - - - +
214F GLN* 1.3 61.7 + - - +
216F ALA* 3.1 7.3 + - - +
217F VAL* 3.0 33.7 + - - +
243F GLN* 4.0 4.9 + - - +
274F ASP* 3.0 27.9 + - + +
275F TYR 3.2 20.6 - - - +
276F THR* 3.4 12.7 + - - -
277F ALA 5.1 0.5 + - - -
280F LEU* 4.2 14.7 - - - +
184G GLY* 3.1 39.7 + - - +
185G TYR 5.0 0.2 - - - +
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Residues in contact with GLN 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F ASP* 4.2 5.1 + - - +
183F VAL* 5.3 3.6 - - + +
211F GLY* 3.6 12.6 + - - +
213F ASN* 1.3 78.8 - - + +
215F MSE 1.3 68.2 + - - +
217F VAL* 3.8 1.9 - - - +
218F CYS* 3.0 30.9 + - - -
274F ASP* 5.4 0.2 - - - +
180G ASP 2.9 19.8 + - - -
181G ALA* 3.3 22.9 - - - +
183G VAL* 2.8 19.3 + - - +
184G GLY* 2.8 28.8 + - - +
214G GLN* 3.5 25.3 - - + +
218G CYS* 3.7 23.1 - - - -
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Residues in contact with MSE 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F LEU* 3.9 17.7 - - + -
127F THR 3.7 17.7 - - - +
128F HIS* 3.7 23.3 - - + +
153F THR* 3.6 31.2 - - + -
183F VAL* 4.0 27.1 - - + -
187F MSE 3.4 11.6 - - + +
193F VAL* 3.8 29.2 - - + -
195F VAL* 4.3 5.2 - - - -
211F GLY 3.4 13.0 + - - +
212F THR* 3.0 10.8 + - - +
214F GLN* 1.3 78.9 - - - +
216F ALA* 1.3 57.0 + - - +
219F ALA* 2.9 25.8 + - - +
226F PHE* 4.2 1.6 - - + -
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Residues in contact with ALA 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F THR 3.0 8.3 + - - +
213F ASN 3.1 9.4 + - - +
215F MSE 1.3 74.5 - - - +
217F VAL* 1.3 66.0 + - - +
219F ALA* 3.2 2.8 + - - +
220F LYS* 2.9 23.2 + - - +
226F PHE* 3.5 34.4 - - + +
276F THR* 3.8 21.1 - - + -
280F LEU* 4.0 17.0 - - + +
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Residues in contact with VAL 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213F ASN* 3.0 28.9 + - - +
214F GLN* 3.4 6.5 + - - +
216F ALA* 1.3 74.5 - - - +
218F CYS* 1.3 64.1 + - - +
220F LYS* 3.2 5.1 - - + +
221F ALA* 3.1 20.3 + - - +
280F LEU* 3.6 28.5 - - + -
217G VAL* 3.7 29.4 - - + +
218G CYS* 4.2 15.9 - - + -
221G ALA* 4.0 20.0 - - + -
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Residues in contact with CYS 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F VAL* 4.8 2.5 - - + -
184F GLY* 3.8 19.5 - - - -
187F MSE 3.7 23.2 - - + +
214F GLN* 3.0 22.0 + - - +
215F MSE 3.6 4.5 - - - +
217F VAL* 1.3 74.5 - - - +
219F ALA* 1.3 66.1 + - - +
220F LYS 3.2 0.2 + - - -
221F ALA* 3.3 10.9 + - - +
222F GLN* 3.5 10.9 + - - +
214G GLN* 3.7 35.2 - - - -
217G VAL* 4.0 20.0 - - - -
218G CYS* 5.4 0.7 - - - -
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Residues in contact with ALA 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F MSE 3.3 23.9 - - + +
193F VAL* 4.1 5.4 - - + -
215F MSE 2.9 17.5 + - - +
216F ALA 3.7 4.0 - - - +
218F CYS* 1.3 76.1 - - - +
220F LYS* 1.3 62.1 + - - +
222F GLN 3.2 2.4 + - - -
223F ASN 3.2 3.1 + - - -
224F LYS* 2.9 45.7 + - + +
226F PHE* 4.1 20.2 - - + -
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Residues in contact with LYS 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216F ALA 2.9 13.1 + - - +
217F VAL* 3.2 11.4 - - + +
218F CYS 3.1 0.2 - - - -
219F ALA* 1.3 78.8 - - - +
221F ALA* 1.3 61.6 + - - +
222F GLN 3.1 1.6 + - - -
223F ASN* 3.2 16.0 + - - +
224F LYS 5.0 1.8 - - - -
279F SER* 3.3 30.9 + - - +
280F LEU* 3.9 22.6 - - + +
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Residues in contact with ALA 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F VAL 3.1 9.3 + - - +
218F CYS 3.3 7.9 + - - +
220F LYS* 1.3 78.3 - - - +
222F GLN* 1.3 64.3 + - + +
223F ASN* 3.5 0.8 + - - -
217G VAL* 4.0 23.3 - - + -
280G LEU* 6.4 0.7 - - + -
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Residues in contact with GLN 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F GLY* 3.9 10.5 + - - -
187F MSE 3.3 30.6 - - - +
188F GLU* 3.4 29.8 - - - +
218F CYS* 3.5 9.9 + - - +
219F ALA 3.2 1.8 + - - -
220F LYS 3.1 0.8 - - - -
221F ALA* 1.3 85.0 - - + +
223F ASN* 1.3 64.4 + - - +
224F LYS* 2.9 36.9 + - + +
213G ASN* 5.5 1.4 - - - +
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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