Contacts of the helix formed by residues 211 - 221 (chain A) in PDB entry 1YDY
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 ASP 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A PRO* 3.4 34.4 - - + +
176A TRP* 3.9 21.0 + - + +
209A CYS* 3.3 4.5 - - - -
210A PHE* 1.3 76.8 - - - +
212A ALA* 1.3 58.3 + - - +
213A ASP* 3.0 14.2 + - - +
214A GLU* 2.9 26.6 + - + +
215A LEU* 3.0 29.8 + - - +
234A GLN* 4.5 0.9 - - - -
244A THR* 4.0 21.0 + - + +
245A GLN 4.4 2.2 - - - +
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Residues in contact with ALA 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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210A PHE 3.2 6.8 + - - +
211A ASP* 1.3 69.1 + - - +
213A ASP* 1.3 67.8 + - - +
215A LEU* 3.2 3.7 + - - +
216A LYS* 3.0 32.9 + - - +
234A GLN* 3.3 27.4 - - - +
244A THR* 5.4 0.8 - - - +
256A TYR* 4.0 28.6 - - + +
260A TRP* 5.6 1.1 - - + -
261A MET* 4.5 3.4 - - + -
273A TYR* 3.6 12.4 - - + +
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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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211A ASP* 3.0 8.7 + - - +
212A ALA* 1.3 78.9 - - - +
214A GLU* 1.3 63.6 + - - +
216A LYS* 3.3 21.3 + - - +
217A ARG* 3.0 22.7 + - - +
246A GLN* 2.8 41.8 + - - +
247A LYS 5.3 0.3 + - - -
256A TYR* 4.6 5.6 - - - -
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Residues in contact with GLU 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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172A ILE* 5.3 1.1 - - + -
175A PRO* 3.6 22.0 - - + +
179A HIS* 3.1 27.4 + - - -
186A ALA* 3.6 20.1 + - + +
209A CYS* 4.4 5.2 - - - -
211A ASP* 2.9 32.5 + - + +
213A ASP* 1.3 78.6 - - - +
215A LEU* 1.3 56.5 + - - +
217A ARG* 2.9 40.3 + - - +
218A ILE* 2.9 36.9 + - + +
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Residues in contact with LEU 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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207A LEU* 4.5 7.0 - - + +
208A GLN 4.9 0.2 - - - -
209A CYS* 3.7 28.5 - - + +
211A ASP 3.0 13.1 + - - +
212A ALA 3.2 6.9 + - - +
214A GLU* 1.3 77.5 - - - +
216A LYS* 1.3 57.0 + - - +
218A ILE* 3.3 16.2 + - + +
219A LYS* 2.8 30.0 + - - +
232A LEU* 4.2 27.5 - - + +
233A VAL 3.6 9.9 - - - +
234A GLN* 3.5 47.3 - - + +
273A TYR* 4.0 16.6 - - + -
274A ALA* 5.2 1.8 - - + -
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Residues in contact with LYS 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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212A ALA* 3.0 22.0 + - - +
213A ASP* 3.6 22.1 + - - +
215A LEU* 1.3 75.8 - - - +
217A ARG* 1.3 54.8 + - - +
219A LYS* 3.3 3.3 + - - -
220A ASN* 2.7 50.6 + - - +
260A TRP* 6.3 1.4 - - - -
273A TYR* 3.7 45.1 - - + -
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Residues in contact with ARG 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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179A HIS* 3.8 14.5 - - - -
184A ASP* 2.8 41.6 + - - -
213A ASP 3.0 13.2 + - - +
214A GLU* 2.9 39.7 + - - +
216A LYS* 1.3 72.9 - - - +
218A ILE* 1.3 61.6 + - - +
221A GLU* 2.8 59.0 + - - +
222A LEU* 3.1 37.8 + - + +
225A LYS* 5.9 0.4 - - - +
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Residues in contact with ILE 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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172A ILE* 3.6 30.7 - - + -
186A ALA* 3.9 19.7 - - + -
190A LEU* 4.2 11.2 - - + -
207A LEU* 4.2 11.7 - - + -
209A CYS* 5.6 0.7 - - + -
214A GLU* 2.9 25.5 + - + +
215A LEU* 3.3 19.5 + - + +
217A ARG* 1.3 76.8 - - - +
219A LYS* 1.3 61.1 + - - +
222A LEU* 4.1 11.9 - - + -
223A GLU* 2.9 56.1 + - + +
232A LEU* 4.2 15.0 - - + -
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Residues in contact with LYS 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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201A LYS* 5.8 4.2 - - - +
215A LEU 2.8 16.9 + - - +
216A LYS* 3.8 4.7 - - - +
218A ILE* 1.3 78.6 - - - +
220A ASN* 1.3 73.7 + - - +
223A GLU* 3.8 14.5 - - - +
224A PRO* 3.4 20.6 - - - +
229A GLU* 5.6 5.9 + - - +
232A LEU* 3.9 12.1 - - + +
272A GLU 3.5 19.3 - - - -
273A TYR* 3.3 35.0 + - + +
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Residues in contact with ASN 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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216A LYS* 2.7 34.3 + - - +
219A LYS* 1.3 99.4 + - - +
221A GLU* 1.3 66.4 + - + +
224A PRO* 3.8 12.3 - - - +
273A TYR* 5.5 1.6 - - - +
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Residues in contact with GLU 221 (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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217A ARG* 2.8 51.1 + - + +
219A LYS 3.5 0.4 - - - -
220A ASN* 1.3 84.5 - - + +
222A LEU* 1.3 71.2 + - + +
223A GLU 3.6 0.7 - - - -
224A PRO* 3.5 4.2 - - - +
225A LYS* 3.4 22.4 + - - +
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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