Contacts of the helix formed by residues 211 - 222 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128D HIS* 3.7 12.9 + - - -
183D VAL* 6.0 1.2 - - - +
210D ILE* 1.3 73.9 - - - +
212D THR* 1.3 65.0 + - - +
213D ASN 3.4 2.0 - - - -
214D GLN* 3.4 9.9 - - - +
215D MSE 3.3 18.4 + - - +
274D ASP* 2.6 9.4 + - - -
181E ALA* 3.0 31.8 + - - -
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Residues in contact with THR 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D HIS* 3.6 9.7 + - - -
195D VAL* 4.1 17.5 - - + -
206D ILE* 4.2 7.0 - - + -
208D ASN* 3.0 29.9 + - + +
209D LYS 2.5 22.2 + - - -
211D GLY* 1.3 74.6 - - - +
213D ASN* 1.3 66.2 + - - +
215D MSE 3.0 17.5 + - + +
216D ALA* 3.1 11.1 + - - +
226D PHE* 4.1 18.8 - - + -
274D ASP* 3.3 8.7 + - - -
276D THR* 3.8 11.9 - - - +
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Residues in contact with ASN 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D THR* 1.3 76.5 - - - +
214D GLN* 1.3 62.8 + - - +
216D ALA* 3.0 5.4 + - - +
217D VAL* 3.0 31.3 + - - +
243D GLN* 4.5 5.0 + - - +
274D ASP* 3.2 18.7 + - + +
275D TYR 3.5 25.1 - - - +
276D THR* 3.3 11.4 + - - -
277D ALA 5.1 0.3 + - - -
280D LEU* 3.8 19.9 - - - +
184E GLY* 3.0 44.3 + - - -
218E CYS* 5.0 0.2 - - - -
222E GLN* 5.6 0.8 + - - -
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Residues in contact with GLN 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D ASP 4.4 4.0 - - - +
183D VAL* 5.1 3.6 - - + +
211D GLY* 3.4 10.3 + - - +
213D ASN* 1.3 79.5 - - - +
215D MSE 1.3 62.6 + - - +
217D VAL* 3.5 2.0 + - - +
218D CYS* 3.1 31.7 + - - -
274D ASP* 4.8 0.6 + - - -
180E ASP 3.0 18.0 + - - +
181E ALA* 3.1 20.1 + - - +
183E VAL* 2.4 45.0 - - + +
184E GLY* 2.8 21.1 - - - +
214E GLN* 3.5 22.8 - - + +
218E CYS* 4.0 17.5 - - - -
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Residues in contact with MSE 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D LEU* 3.8 32.1 - - + -
127D THR* 4.0 2.5 - - - -
128D HIS* 3.7 32.8 - - + +
153D THR* 5.5 0.7 - - - -
183D VAL* 3.9 29.1 - - + +
187D MSE 4.8 1.6 - - - +
193D VAL* 3.0 39.5 - - + -
195D VAL* 3.6 26.0 - - + -
211D GLY 3.3 7.7 + - - +
212D THR* 3.0 12.3 + - + +
214D GLN* 1.3 78.6 - - - +
216D ALA* 1.3 58.6 + - - +
218D CYS* 3.4 2.6 + - - +
219D ALA* 2.8 29.5 + - - +
226D PHE* 3.9 5.4 - - + -
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Residues in contact with ALA 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D THR 3.1 5.2 + - - +
213D ASN 3.0 8.4 + - - +
215D MSE 1.3 74.4 - - - +
217D VAL* 1.3 59.7 + - - +
219D ALA* 3.3 2.3 + - - +
220D LYS* 2.9 30.1 + - - +
226D PHE* 3.5 37.8 - - + -
276D THR* 3.7 22.9 - - + -
280D LEU* 3.9 17.0 - - + +
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Residues in contact with VAL 217 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213D ASN* 3.0 35.4 + - - +
214D GLN 3.8 4.3 - - - +
216D ALA* 1.3 76.1 - - - +
218D CYS* 1.3 61.2 + - - +
220D LYS* 3.8 2.4 - - - +
221D ALA* 3.3 21.1 + - - +
280D LEU* 3.7 28.3 - - + -
217E VAL* 3.9 16.8 - - + +
218E CYS* 4.1 15.7 - - + -
221E ALA* 3.6 31.0 - - + -
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Residues in contact with CYS 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D VAL* 4.5 8.1 - - + -
184D GLY* 4.1 17.5 - - - -
187D MSE 3.7 15.2 - - + +
214D GLN 3.1 25.3 + - - +
215D MSE 3.8 3.8 - - - +
217D VAL* 1.3 75.5 - - - +
219D ALA* 1.3 65.9 + - - +
221D ALA* 3.5 9.9 + - - +
222D GLN* 3.5 11.1 + - - +
214E GLN* 3.9 31.6 - - - -
217E VAL* 4.0 27.4 - - + -
218E CYS* 5.1 3.4 - - - -
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Residues in contact with ALA 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D MSE 3.8 12.8 - - - -
193D VAL* 4.1 21.8 - - + -
215D MSE 2.8 18.4 + - - +
216D ALA* 3.4 9.9 - - - +
218D CYS* 1.3 77.8 - - - +
220D LYS* 1.3 58.6 + - - +
222D GLN* 3.2 3.1 + - - -
223D ASN 3.1 3.6 + - - -
224D LYS* 2.7 44.9 + - + +
226D PHE* 4.2 7.6 - - + -
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Residues in contact with LYS 220 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216D ALA 2.9 16.8 + - - +
217D VAL 3.8 4.7 - - - +
218D CYS 3.3 0.2 - - - -
219D ALA* 1.3 77.2 - - - +
221D ALA* 1.3 57.4 + - - +
223D ASN* 3.0 29.1 + - - +
224D LYS 4.8 2.2 - - - +
279D SER* 3.4 27.2 + - - +
280D LEU* 4.2 22.0 - - + +
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Residues in contact with ALA 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D VAL 3.3 10.9 + - - +
218D CYS 3.7 10.1 - - - +
219D ALA 3.3 0.4 - - - -
220D LYS* 1.3 77.9 - - - +
222D GLN* 1.3 62.8 + - + +
223D ASN 3.3 0.6 + - - -
217E VAL* 3.9 22.0 - - + -
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Residues in contact with GLN 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D GLY 4.0 8.9 + - - -
187D MSE 3.3 30.2 - - + +
188D GLU* 3.6 26.3 + - - +
218D CYS* 3.5 10.5 + - - +
219D ALA 3.2 1.8 + - - -
220D LYS 3.1 0.6 - - - -
221D ALA* 1.3 81.1 - - + +
223D ASN* 1.3 72.0 + - - +
224D LYS* 3.2 33.2 + - + -
213E ASN* 5.7 0.6 - - - +
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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