Contacts of the strand formed by residues 211 - 216 (chain A) in PDB entry 2Y05
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 TYR 211 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A THR* 3.8 16.8 - - + +
146A MET* 3.4 32.3 - - + -
170A VAL* 3.7 22.1 - - + +
203A LEU* 2.8 48.4 + - + +
206A ALA* 3.5 16.5 - - - +
207A SER* 3.6 16.1 - - - -
210A GLY* 1.3 74.8 - - - -
212A ASP* 1.3 62.4 + - - +
213A CYS 4.2 5.8 - - - +
226A VAL* 5.3 3.8 - - + -
229A GLN* 3.0 34.0 + - + -
230A MET* 3.5 24.6 - - - +
231A LYS* 2.8 31.0 + - - +
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Residues in contact with ASP 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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142A GLY 4.8 0.3 - - - +
143A GLU* 3.5 24.6 - - + +
144A THR* 2.9 30.9 + - - +
211A TYR* 1.3 73.9 - - - +
213A CYS* 1.3 62.7 + - - +
230A MET* 3.9 1.3 - - - -
231A LYS* 2.9 40.5 + - - +
234A GLY* 3.5 6.1 - - - -
235A ARG* 3.1 41.7 + - - +
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Residues in contact with CYS 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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137A CYS* 4.0 20.0 - - + -
139A VAL* 3.9 19.7 - - + -
143A GLU* 4.6 4.9 - - - -
144A THR 3.3 2.9 + - - +
145A VAL* 3.4 17.7 - - + -
146A MET* 2.8 28.5 + - - +
211A TYR* 3.5 2.8 - - - +
212A ASP* 1.3 89.3 - - - +
214A TYR* 1.3 61.0 + - - +
215A PHE 4.1 0.2 - - - -
230A MET* 3.9 3.4 - - - -
235A ARG* 3.3 39.7 - - - +
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Residues in contact with TYR 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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137A CYS* 3.8 3.2 - - - -
146A MET* 3.3 35.7 - - + -
148A ASN* 2.7 32.1 + - - -
213A CYS* 1.3 74.6 - - - +
215A PHE* 1.3 55.5 + - - +
216A ASP* 3.5 17.6 + - + -
222A PHE* 3.5 5.2 - - - -
223A SER* 2.7 41.6 + - - -
226A VAL* 3.6 24.5 - - + -
227A ILE* 5.2 1.3 - - + -
230A MET* 3.8 18.2 - - + -
235A ARG 3.0 6.3 + - - -
236A ILE* 3.3 31.3 - - + +
237A ALA 2.8 31.7 + - - +
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Residues in contact with PHE 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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128A THR 3.9 9.2 - - - -
129A ALA 3.9 1.6 - - - -
132A GLY* 3.6 13.0 - - - -
133A LEU* 3.6 30.7 - - + -
137A CYS* 4.3 9.8 - - - -
145A VAL* 4.9 3.8 - - + +
146A MET 2.9 11.5 + - - +
147A VAL* 3.6 19.7 - - + +
148A ASN* 3.7 5.0 + - - +
154A VAL* 3.6 21.3 - - + -
158A VAL* 3.3 45.8 - - + -
213A CYS 4.1 0.6 - - - -
214A TYR* 1.3 73.4 - - - +
216A ASP* 1.3 58.9 + - - +
217A ASN* 3.5 31.1 + - - -
237A ALA* 3.9 4.9 - - + -
239A CYS* 3.5 21.1 - - + -
270A PHE* 4.1 1.6 - + - -
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Residues in contact with ASP 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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148A ASN* 3.1 11.9 + - - -
214A TYR* 3.1 24.7 + - + -
215A PHE* 1.3 70.4 - - - +
217A ASN* 1.3 59.5 + - - +
218A VAL 2.8 25.9 + - - -
219A GLY* 2.9 17.0 + - - -
223A SER* 2.8 24.1 + - - -
236A ILE* 4.4 7.3 - - + +
237A ALA 2.9 17.0 + - - +
238A ILE* 4.8 8.6 - - - +
239A CYS* 3.0 28.7 + - - +
240A GLY 3.1 8.7 + - - +
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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