Contacts of the strand formed by residues 231 - 236 (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 ASN 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A LYS* 3.5 43.0 - - - +
203A ASP 5.3 0.3 - - - +
205A VAL 4.0 12.4 + - - +
206A TYR* 3.6 36.8 + - + -
207A LEU* 2.9 27.2 + - - +
230A LEU* 1.3 71.6 - - - +
232A LEU* 1.3 60.0 - - - +
275A ASP* 3.4 26.8 + - + +
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Residues in contact with LEU 232 (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* 3.3 31.0 - - + +
215A LEU* 4.2 23.3 - - + +
218A ILE* 4.2 8.7 - - + -
219A LYS* 3.9 22.9 - - + +
223A GLU* 4.0 19.3 - - - +
230A LEU* 3.4 16.8 - - + +
231A ASN* 1.3 77.7 - - - +
233A VAL* 1.3 62.8 + - - +
273A TYR 3.7 23.6 - - - +
274A ALA* 3.7 3.9 - - + -
275A ASP* 2.7 41.1 + - - +
276A GLY 3.1 5.5 + - - +
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TYR* 3.6 25.1 - - - +
206A TYR* 3.9 28.7 - - + -
207A LEU 2.8 12.5 + - - +
208A GLN* 3.3 8.4 - - + -
209A CYS 3.1 26.2 + - - +
215A LEU* 3.6 5.7 - - - +
232A LEU* 1.3 79.2 - - - +
234A GLN* 1.3 62.3 + - - +
235A LEU* 3.4 8.8 + - + -
275A ASP* 5.5 0.4 - - + -
276A GLY* 3.3 11.4 - - - +
277A ILE 3.7 7.9 - - - +
278A GLY* 3.6 27.4 - - - +
309A VAL* 5.3 1.3 - - + -
311A HIS* 4.9 2.9 - - - +
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Residues in contact with GLN 234 (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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209A CYS 3.7 0.8 + - - -
210A PHE 3.0 24.9 + - - -
212A ALA* 3.3 15.3 - - - +
215A LEU* 3.5 11.5 - - + +
232A LEU 4.2 0.6 - - - -
233A VAL* 1.3 69.1 - - - +
235A LEU* 1.3 86.6 + - - +
236A ILE* 3.7 4.1 + - + +
258A TYR* 4.5 0.2 - - - -
261A MET* 3.9 26.1 - - + +
270A VAL* 3.9 25.1 - - + -
273A TYR* 2.6 32.9 + - - +
274A ALA* 4.2 4.4 - - + +
276A GLY 2.9 10.4 + - - +
277A ILE* 3.1 8.1 - - + +
278A GLY 2.8 20.8 + - - -
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Residues in contact with LEU 235 (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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171A GLU* 3.3 41.1 - - + +
208A GLN* 3.3 28.0 - - + +
209A CYS 2.9 25.2 + - - +
210A PHE* 3.4 36.2 - - + +
233A VAL* 4.3 4.3 - - + -
234A GLN* 1.3 92.0 + - - +
236A ILE* 1.3 59.7 + - - +
258A TYR* 3.9 1.9 - - - -
278A GLY* 3.3 24.9 - - - +
313A TYR* 4.7 1.8 - - + -
344A PHE* 4.9 3.4 - - + -
902A GOL 3.5 13.9 - - - +
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Residues in contact with ILE 236 (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* 3.6 2.2 - - - -
234A GLN* 4.0 10.3 - - + +
235A LEU* 1.3 78.3 - - - +
237A ALA* 1.3 65.7 + - - +
258A TYR* 4.3 3.8 - - + -
261A MET* 3.9 27.4 - - + -
262A PHE* 3.9 13.7 - - + -
267A MET* 4.2 16.4 - - + -
277A ILE* 4.1 20.6 - - + -
278A GLY 2.9 9.7 + - - +
279A PRO* 4.1 5.8 - - + -
280A ASP 3.9 1.0 + - - -
283A MET* 3.4 26.5 - - - +
299A MET* 4.1 26.7 - - + -
313A TYR* 2.8 27.2 + - - -
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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