Contacts of the helix formed by residues 204 - 214 (chain D) in PDB entry 5AYZ
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 204 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202D CYS* 3.6 5.2 - - - +
203D SER* 1.3 81.0 + - - +
205D LEU* 1.3 64.3 + - - +
206D GLN* 3.5 8.0 + - - +
207D GLU* 3.2 25.9 + - - +
208D ALA* 3.2 17.5 + - - +
221D LEU* 5.0 0.2 - - - +
224D PHE* 3.9 10.2 - - - -
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Residues in contact with LEU 205 (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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204D SER* 1.3 71.6 - - - +
206D GLN* 1.3 67.6 + - - +
208D ALA* 3.2 4.6 + - - +
209D VAL* 3.0 33.6 + - + +
224D PHE* 4.2 4.2 - - - -
232D THR* 3.0 63.3 - - + +
235D VAL* 3.9 27.1 - - + -
236D LEU* 4.5 6.3 - - + -
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Residues in contact with GLN 206 (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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204D SER* 3.3 7.8 + - - +
205D LEU* 1.3 81.4 - - - +
207D GLU* 1.3 62.4 + - - +
209D VAL* 3.3 8.9 + - + +
210D GLN* 3.1 44.7 + - + +
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Residues in contact with GLU 207 (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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175D VAL* 4.9 7.4 - - - +
181D VAL* 3.3 35.1 - - + +
201D GLU 4.3 3.4 - - - +
202D CYS* 3.4 14.3 - - + -
203D SER* 2.9 37.1 + - - -
204D SER* 3.2 19.1 + - - +
205D LEU 3.2 0.6 - - - -
206D GLN* 1.3 80.0 - - - +
208D ALA* 1.3 61.7 + - - +
210D GLN* 3.2 13.0 + - - +
211D ALA* 2.9 23.4 + - - +
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Residues in contact with ALA 208 (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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202D CYS* 3.7 12.9 - - - -
204D SER 3.2 8.7 + - - +
205D LEU* 3.2 10.2 + - - +
207D GLU* 1.3 78.1 - - - +
209D VAL* 1.3 57.0 + - - +
211D ALA* 3.3 1.7 + - - +
212D ALA* 2.8 31.4 + - - +
219D VAL* 3.6 16.4 - - + +
221D LEU* 4.0 8.3 - - + -
236D LEU* 3.5 33.4 - - + +
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Residues in contact with VAL 209 (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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205D LEU* 3.0 32.3 + - + +
206D GLN* 3.3 10.1 + - + +
208D ALA* 1.3 74.4 - - - +
210D GLN* 1.3 59.9 + - + +
212D ALA* 3.4 1.0 + - - +
213D GLU* 2.8 48.9 + - - +
235D VAL* 5.2 1.8 - - + -
236D LEU* 4.1 17.7 - - + -
239D GLN* 4.8 15.9 - - - +
240D PHE* 4.1 15.0 - - + -
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Residues in contact with GLN 210 (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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181D VAL* 3.8 26.2 - - + +
182D GLU* 4.6 18.0 - - + +
206D GLN* 3.1 38.7 + - + +
207D GLU* 3.2 16.9 + - - +
209D VAL* 1.3 75.3 - - + +
211D ALA* 1.3 60.8 + - - +
213D GLU* 3.3 10.4 + - - +
214D ALA* 2.9 32.1 + - - +
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Residues in contact with ALA 211 (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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181D VAL* 4.0 6.6 - - + +
185D VAL* 4.4 9.6 - - + +
200D VAL* 3.7 40.2 - - + -
202D CYS* 4.3 5.6 - - - -
207D GLU 2.9 15.8 + - - +
208D ALA 3.7 3.8 - - - +
210D GLN* 1.3 77.0 - - - +
212D ALA* 1.3 62.6 + - - +
214D ALA 3.2 2.3 + - - -
215D GLY 3.1 6.6 + - - -
216D ALA* 3.0 25.0 + - + +
219D VAL* 4.3 3.1 - - + -
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Residues in contact with ALA 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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208D ALA 2.8 21.6 + - - +
209D VAL 3.8 0.2 - - - +
211D ALA* 1.3 71.3 - - - +
213D GLU* 1.3 58.7 + - - +
215D GLY* 3.0 19.9 + - - -
216D ALA* 4.0 8.3 + - - +
219D VAL* 4.5 2.6 - - + +
236D LEU* 4.6 3.8 - - + -
240D PHE* 3.5 46.3 - - + -
243D VAL* 4.4 17.4 - - + +
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Residues in contact with GLU 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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209D VAL* 2.8 39.9 + - - +
210D GLN* 3.9 9.1 - - - +
212D ALA* 1.3 73.9 - - - +
214D ALA* 1.3 58.9 + - - +
215D GLY 3.6 0.3 + - - -
239D GLN* 5.3 3.8 + - - -
240D PHE* 3.5 22.4 - - + -
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Residues in contact with ALA 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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182D GLU* 4.1 18.6 - - + +
185D VAL* 3.2 32.1 - - + +
186D ARG* 4.3 14.9 - - + +
189D ARG* 3.9 16.5 - - - +
210D GLN 2.9 14.7 + - - +
211D ALA 3.6 1.8 - - - +
212D ALA 3.2 0.2 - - - -
213D GLU* 1.3 77.0 - - - +
215D GLY* 1.3 56.8 + - - +
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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