Contacts of the helix formed by residues 258 - 263 (chain B) 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 TYR 258 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B PHE* 2.6 34.2 + + - +
235B LEU 4.0 7.4 - - - -
236B ILE* 4.3 0.4 - - + -
237B ALA* 3.2 55.9 - - + +
238B TYR 5.0 0.9 - - - -
239B THR* 2.9 18.1 + - - +
243B GLU* 4.9 2.2 - - + -
244B THR* 2.7 32.4 + - - +
256B TYR* 3.6 38.3 - + - -
257B ASN* 1.3 70.5 - - - +
259B ASP* 1.3 66.6 + - - +
260B TRP* 3.2 5.6 - - - -
261B MET* 2.9 43.7 + - + +
262B PHE* 3.6 8.6 - - + -
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Residues in contact with ASP 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B THR* 2.8 27.5 + - - +
257B ASN* 2.9 28.4 + - - +
258B TYR* 1.3 77.1 - - - +
260B TRP* 1.3 62.6 + - - +
262B PHE* 3.1 30.3 + - - +
263B LYS* 4.0 19.3 + - - +
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Residues in contact with TRP 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ALA* 5.6 1.1 - - + -
216B LYS* 6.3 1.6 - - - -
256B TYR* 2.8 30.1 + - - -
257B ASN* 3.3 23.7 + - - -
258B TYR 3.0 2.4 + - - -
259B ASP* 1.3 78.0 - - - +
261B MET* 1.3 85.4 + - + +
262B PHE 3.0 2.0 + - - -
263B LYS* 3.1 32.0 + - + +
266B ALA* 3.2 31.9 - - + +
269B GLN* 3.6 36.1 - - + -
270B VAL* 4.0 12.3 - - + -
273B TYR* 5.0 5.8 - + - -
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Residues in contact with MET 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ALA* 4.4 2.0 - - + -
234B GLN* 3.8 33.7 - - + +
236B ILE* 3.9 33.4 - - + -
256B TYR* 3.8 12.8 - - + +
258B TYR* 2.9 36.0 + - + +
260B TRP* 1.3 115.5 - - + +
262B PHE* 1.3 60.3 + - + +
263B LYS 3.4 0.9 - - - +
266B ALA* 3.6 10.2 - - - +
267B MET* 3.5 22.9 - - + +
270B VAL* 4.6 7.4 - - + -
273B TYR* 4.3 3.8 - - - +
299B MET* 3.8 7.8 - - - +
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Residues in contact with PHE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ILE* 3.8 8.7 - - + -
237B ALA 3.7 22.7 - - - -
238B TYR* 4.0 19.7 - + - -
239B THR 5.6 0.2 - - - -
258B TYR* 3.6 17.5 - - + -
259B ASP* 3.1 26.6 + - - +
260B TRP 3.0 1.6 - - - -
261B MET* 1.3 77.3 - - - +
263B LYS* 1.3 62.7 + - + +
264B PRO* 4.2 1.4 - - - +
283B MET* 3.5 43.3 - - + -
299B MET* 3.5 22.2 - - + -
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Residues in contact with LYS 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B ASP* 4.0 16.0 + - - +
260B TRP* 3.1 30.6 + - + +
261B MET 4.4 0.9 - - - +
262B PHE* 1.3 83.5 - - + +
264B PRO* 1.3 82.4 - - + +
265B GLY 3.4 0.5 + - - -
266B ALA* 3.2 16.3 + - + +
302B ASP* 4.5 2.3 - - - +
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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