Contacts of the strand formed by residues 211 - 216 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144D THR* 3.6 21.1 - - + +
146D MET* 3.5 25.1 - - + -
170D VAL* 3.6 30.2 - - + +
203D LEU* 2.6 47.3 + - + -
206D ALA* 3.4 17.7 - - - +
207D SER* 3.5 12.0 - - - -
210D GLY* 1.3 75.2 - - - -
212D ASP* 1.3 63.5 + - - +
213D CYS 4.3 5.2 - - - +
226D VAL* 5.3 4.5 - - + -
229D GLN* 2.9 34.2 + - + +
230D MET* 3.6 22.2 - - - +
231D LYS* 2.9 28.6 + - - +
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Residues in contact with ASP 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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143D GLU* 3.6 22.1 - - + +
144D THR* 2.9 32.7 + - - +
211D TYR* 1.3 72.8 - - - +
213D CYS* 1.3 64.1 + - - +
230D MET* 3.9 1.1 - - - -
231D LYS* 2.9 41.5 + - - +
234D GLY* 3.5 6.8 - - - -
235D ARG* 3.1 44.5 + - - +
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Residues in contact with CYS 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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137D CYS* 3.7 25.1 - - + -
139D VAL* 3.9 17.7 - - + -
143D GLU* 4.6 4.5 - - - -
144D THR 3.3 3.1 + - - +
145D VAL* 3.4 16.1 - - + -
146D MET* 2.8 28.5 + - - +
211D TYR* 4.3 2.3 - - - +
212D ASP* 1.3 90.2 - - - +
214D TYR* 1.3 60.5 + - - +
215D PHE 4.1 0.2 - - - -
230D MET* 4.0 4.5 - - - -
235D ARG* 3.3 36.8 - - - +
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Residues in contact with TYR 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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137D CYS* 3.7 3.6 - - - -
146D MET* 3.1 42.8 - - + +
148D ASN* 2.9 21.4 + - - -
213D CYS* 1.3 73.9 - - - +
215D PHE* 1.3 65.0 + - - +
216D ASP* 3.5 19.6 + - + -
222D PHE* 3.5 5.0 - - - -
223D SER* 2.6 41.1 + - - -
226D VAL* 3.6 24.9 - - + -
227D ILE* 5.2 0.9 - - + -
230D MET* 3.8 18.8 - - + +
235D ARG 3.0 6.5 + - - -
236D ILE* 3.4 30.1 - - + +
237D ALA 2.9 27.7 + - - -
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Residues in contact with PHE 215 (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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128D THR 3.9 8.3 - - - -
129D ALA 3.8 2.0 - - - -
132D GLY* 3.7 26.2 - - - -
133D LEU* 3.7 14.6 - - - -
137D CYS* 4.4 7.1 - - - -
145D VAL* 4.9 3.8 - - + +
146D MET 2.9 14.6 + - - +
147D VAL* 3.7 15.5 - - + -
148D ASN* 3.5 12.3 + - - +
154D VAL* 3.6 17.9 - - + -
158D VAL* 3.3 45.8 - - + -
213D CYS 4.1 0.4 - - - -
214D TYR* 1.3 73.7 - - - +
216D ASP* 1.3 59.7 + - - +
217D ASN* 3.3 30.3 - - - -
237D ALA* 4.0 6.5 - - + -
239D CYS* 3.5 21.8 - - + -
270D PHE* 4.2 2.0 - + - -
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Residues in contact with ASP 216 (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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148D ASN* 3.2 3.5 + - - -
214D TYR* 3.0 31.4 + - + -
215D PHE* 1.3 71.7 - - - +
217D ASN* 1.3 60.7 + - - +
218D VAL 3.0 7.8 + - - -
219D GLY* 3.0 27.3 + - - -
223D SER* 2.7 23.7 + - - -
236D ILE* 4.3 8.1 - - + +
237D ALA 3.0 17.2 + - - +
238D ILE* 4.6 9.3 - - - +
239D CYS* 2.9 28.5 + - - +
240D GLY 3.0 8.6 + - - +
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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