Contacts of the helix formed by residues 214 - 219 (chain A) in PDB entry 1DY1
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 TRP 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A LEU* 5.1 0.2 - - + -
143A LEU* 5.7 0.4 - - + -
180A PHE* 3.8 34.3 - + - -
188A LEU* 3.3 28.7 - - + -
189A TYR* 2.7 22.0 + + - -
191A ILE* 4.8 0.2 - - + -
192A VAL* 3.7 30.6 - - + +
196A ASP 4.6 2.9 - - - +
197A ARG* 3.3 40.2 + - + +
200A VAL 4.0 1.6 + - - -
202A ILE* 3.9 16.3 - - + +
213A SER* 1.3 73.2 - - - +
215A ASP* 1.3 72.7 + - - +
216A SER 2.9 1.9 + - - -
217A LEU* 2.9 29.0 + - + +
218A PHE* 3.4 35.5 - + - -
305A ILE* 3.8 31.6 - - + -
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Residues in contact with ASP 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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189A TYR* 2.8 36.5 + - - -
197A ARG* 2.9 28.1 + - - +
198A GLY* 3.8 11.5 + - - +
213A SER* 3.5 4.2 - - - +
214A TRP* 1.3 74.6 - - - +
216A SER* 1.3 61.7 + - - +
218A PHE* 3.0 21.5 + - - +
219A SER* 3.5 9.4 + - - -
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Residues in contact with SER 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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211A SER* 3.8 9.2 - - - -
212A PRO* 4.3 12.0 - - - +
213A SER* 2.6 37.4 + - - -
214A TRP 2.9 1.2 + - - -
215A ASP* 1.3 77.4 - - - +
217A LEU* 1.3 58.2 + - - +
219A SER* 2.6 31.5 + - - -
221A SER* 3.1 6.4 + - - -
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Residues in contact with LEU 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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143A LEU* 5.9 1.8 - - + -
180A PHE* 4.5 11.0 - - + -
202A ILE* 5.0 9.2 - - + -
211A SER* 4.1 23.8 - - - +
213A SER 4.3 0.4 - - - +
214A TRP* 2.9 44.9 + - + +
216A SER* 1.3 78.6 - - - +
218A PHE* 1.3 72.7 - - + +
219A SER 3.3 2.8 + - - -
221A SER* 3.5 2.3 + - - -
222A GLN 4.0 3.1 + - - -
223A GLY* 3.0 50.6 + - - +
224A GLN 4.8 3.6 - - - +
225A LEU* 4.6 6.3 - - + -
256A PRO 4.3 0.7 - - - +
288A LEU* 4.1 20.0 - - + -
289A LEU* 3.7 6.9 - - + +
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Residues in contact with PHE 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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180A PHE* 4.9 2.0 - + - -
188A LEU* 4.5 13.0 - - + -
189A TYR* 3.4 28.3 - + + -
214A TRP* 3.4 67.1 - + - -
215A ASP 3.0 9.4 + - - +
217A LEU* 1.3 86.0 - - + +
219A SER* 1.3 58.0 + - - +
220A GLY 3.2 6.0 + - - -
256A PRO 3.5 10.4 - - - +
257A SER* 3.6 29.5 - - - +
258A GLY* 3.6 16.4 - - - -
289A LEU* 3.6 26.2 - - + -
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Residues in contact with SER 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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215A ASP 3.5 5.1 + - - -
216A SER* 2.6 30.2 + - - -
217A LEU 3.3 0.6 - - - -
218A PHE* 1.3 77.0 - - - +
220A GLY* 1.3 57.6 + - - +
221A SER* 2.8 21.3 + - - -
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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