Contacts of the helix formed by residues 202 - 214 (chain D) in PDB entry 1YAA
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 202 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201D THR* 1.3 74.8 - - - +
203D GLU* 1.3 61.8 + - - +
205D TRP* 4.8 0.7 - - - -
206D VAL* 3.5 12.1 + - - +
238D TYR* 3.5 46.0 + - - -
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Residues in contact with GLU 203 (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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201D THR* 3.1 8.4 + - - +
202D SER* 1.3 77.0 - - - +
204D GLN* 1.3 67.8 + - + +
205D TRP 3.2 1.6 - - - -
206D VAL* 3.1 19.5 + - - +
207D GLN* 3.4 18.4 + - - +
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Residues in contact with GLN 204 (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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168D LEU* 3.5 21.6 + - - +
170D LEU* 3.9 33.7 - - + +
199D ASP 4.4 1.2 - - - +
200D PRO* 3.3 15.4 - - + +
201D THR* 3.0 42.9 + - - +
203D GLU* 1.3 77.8 - - + +
205D TRP* 1.3 58.9 + - - +
207D GLN* 3.4 13.5 + - - +
208D ILE* 2.9 31.3 + - - +
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Residues in contact with TRP 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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173D PHE* 5.8 1.6 - + - -
188D LEU* 4.3 26.2 - - + -
189D HIS 3.5 26.2 - - - -
190D SER 3.8 8.2 + - - -
191D CYS* 5.7 0.2 - - - -
199D ASP* 5.3 2.8 - - + +
200D PRO* 3.8 33.9 + - + +
201D THR 3.0 24.4 + - - +
202D SER* 4.0 6.3 - - - +
203D GLU 3.2 0.2 - - - -
204D GLN* 1.3 75.6 - - - +
206D VAL* 1.3 59.3 + - - +
208D ILE* 3.2 25.1 + - + +
209D VAL* 2.9 42.1 + - + +
221D PHE* 4.4 11.9 - + - -
238D TYR* 4.0 22.4 - + + -
239D ALA* 3.3 33.0 - - + +
242D LEU* 3.8 6.1 - - + -
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Residues in contact with VAL 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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202D SER 3.5 15.9 - - - +
203D GLU* 3.1 11.8 + - - +
205D TRP* 1.3 78.0 - - - +
207D GLN* 1.3 59.6 + - + +
209D VAL* 3.5 1.0 + - - +
210D ASP* 3.0 45.7 + - - +
238D TYR* 3.6 15.7 - - - +
242D LEU* 3.8 17.3 - - + -
243D LYS* 6.2 2.9 - - - -
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Residues in contact with GLN 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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170D LEU* 3.6 22.4 - - + +
174D LEU* 3.8 28.6 - - + +
203D GLU* 3.4 16.5 + - - +
204D GLN* 3.7 11.7 - - - +
205D TRP 3.2 0.6 - - - -
206D VAL* 1.3 77.1 - - + +
208D ILE* 1.3 65.1 + - - +
210D ASP* 4.0 4.6 - - - +
211D ALA* 3.1 24.8 + - - +
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Residues in contact with ILE 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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170D LEU* 4.4 15.0 - - + -
173D PHE* 3.9 36.6 - - + -
174D LEU* 4.1 10.3 - - + -
177D ILE* 4.2 5.6 - - + +
188D LEU* 4.7 2.2 - - + -
200D PRO* 3.8 30.1 - - + -
204D GLN 2.9 23.6 - - - +
205D TRP* 3.2 29.8 + - + +
207D GLN* 1.3 76.1 - - - +
209D VAL* 1.3 62.4 + - + +
211D ALA* 3.3 3.3 + - - +
212D ILE* 3.1 39.4 + - + +
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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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188D LEU* 6.3 1.3 - - + -
205D TRP* 2.9 33.4 + - + +
206D VAL* 4.0 3.1 - - - +
208D ILE* 1.3 76.6 - - + +
210D ASP* 1.3 57.9 + - - +
212D ILE* 3.5 8.6 + - + +
213D ALA* 2.9 26.9 + - - +
221D PHE* 5.3 4.5 - - + -
239D ALA 4.8 2.7 - - - +
242D LEU* 3.6 44.9 - - + +
243D LYS* 3.5 33.9 - - + -
244D LEU* 4.3 7.9 - - + +
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Residues in contact with ASP 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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206D VAL* 3.0 34.7 + - - +
207D GLN* 4.0 6.2 - - - +
209D VAL* 1.3 74.7 - - - +
211D ALA* 1.3 60.5 + - - +
213D ALA* 3.8 5.7 - - - +
214D SER* 3.0 28.8 + - - -
243D LYS* 3.8 30.5 + - - +
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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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174D LEU* 4.2 13.5 - - + -
177D ILE* 3.8 13.4 - - + +
178D GLN* 3.7 24.8 + - - +
207D GLN 3.1 18.5 + - - +
208D ILE 3.3 4.2 + - - +
210D ASP* 1.3 74.0 - - - +
212D ILE* 1.3 64.0 + - - +
214D SER* 3.0 21.0 + - - -
215D LYS* 3.3 13.7 + - - +
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Residues in contact with ILE 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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177D ILE* 4.0 24.5 - - + -
186D PHE* 4.4 14.8 - - + -
188D LEU* 4.0 27.6 - - + -
208D ILE* 3.1 30.0 + - + +
209D VAL* 3.8 7.2 - - + +
211D ALA* 1.3 76.1 - - - +
213D ALA* 1.3 63.9 + - - +
215D LYS 3.4 0.9 + - - -
216D ASN 3.1 18.0 + - - -
217D HIS* 3.1 47.0 + - + +
219D ALA* 4.5 14.4 - - + +
244D LEU* 4.4 11.4 - - + -
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Residues in contact with ALA 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 2.9 18.2 + - - +
210D ASP* 3.8 9.0 - - - +
212D ILE* 1.3 79.5 - - - +
214D SER* 1.3 60.1 + - - +
216D ASN* 3.5 5.9 + - - +
243D LYS* 4.3 10.3 - - + +
244D LEU* 3.5 22.4 - - + -
247D VAL* 3.4 31.4 - - + +
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Residues in contact with SER 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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178D GLN* 3.7 16.3 + - - -
182D GLU* 4.6 2.4 - - - +
210D ASP 3.0 15.4 + - - -
211D ALA* 3.0 13.7 + - - -
213D ALA* 1.3 78.3 - - - +
215D LYS* 1.3 62.7 + - - +
216D ASN* 3.3 10.2 + - - -
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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