Contacts of the strand formed by residues 226 - 230 (chain A) in PDB entry 1YNU
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 HIS 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A PHE* 5.6 0.4 - + - -
131A LEU* 4.2 29.5 - - + +
193A LYS* 3.0 20.7 + - - +
194A GLY* 3.0 1.3 - - - -
195A VAL 2.8 26.2 + - - -
220A VAL* 4.2 5.2 - - - +
224A GLY 5.8 0.7 - - - -
225A ILE* 1.3 80.3 - - - +
227A LEU* 1.3 63.4 + - - +
228A ILE* 4.1 1.6 - - + -
263A GLN 4.7 2.2 + - - -
264A ARG* 3.4 31.2 - - + +
266A HIS* 3.0 34.7 - + + -
289A ASP* 5.8 1.6 - - - -
292A VAL* 5.1 8.7 - - + +
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 3.5 22.4 - - + +
197A VAL* 4.1 22.2 - - + -
213A LEU* 5.4 1.3 - - + +
216A LEU* 4.3 27.8 - - + +
217A LEU* 3.8 29.2 - - + +
220A VAL* 4.2 15.5 - - + +
225A ILE 4.2 0.2 + - - -
226A HIS* 1.3 75.0 - - - +
228A ILE* 1.3 68.1 + - - +
229A SER* 5.0 1.1 - - - +
246A VAL* 3.8 20.6 - - + -
264A ARG 2.7 14.1 + - - +
265A VAL* 3.5 6.8 - - + -
266A HIS* 2.8 29.8 + - - +
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Residues in contact with ILE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASN* 4.8 2.7 - - - +
127A PHE* 3.7 39.3 - - + -
128A ILE* 4.9 8.5 - - + -
131A LEU* 3.7 24.2 - - + -
138A VAL* 5.3 3.1 - - + -
194A GLY 6.0 0.2 - - - -
195A VAL 2.8 16.7 + - - +
196A LEU* 3.2 28.7 - - + -
197A VAL* 2.7 36.7 + - - +
226A HIS* 5.1 0.7 - - + -
227A LEU* 1.3 79.4 - - - +
229A SER* 1.3 59.1 + - - +
230A ASP 4.0 0.4 + - - +
266A HIS* 3.6 12.6 - - + +
268A VAL* 4.1 26.0 - - + -
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Residues in contact with SER 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A VAL* 3.4 14.1 - - - +
199A ASN* 3.9 16.8 + - - +
213A LEU* 5.8 1.0 - - - +
227A LEU* 4.1 2.2 - - - -
228A ILE* 1.3 73.6 - - - +
230A ASP* 1.3 58.8 + - - +
231A GLU* 3.2 26.0 + - - +
246A VAL* 3.8 30.3 - - - +
266A HIS 2.9 11.6 + - - -
267A VAL* 3.5 3.2 - - - -
268A VAL 3.0 22.6 + - - -
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Residues in contact with ASP 230 (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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124A ASN* 2.9 30.4 + - - +
148A PHE* 4.2 1.7 - - - -
196A LEU* 4.2 10.7 - - + +
197A VAL 2.7 16.4 + - - +
198A THR* 3.5 14.6 - - - +
199A ASN 3.1 20.9 + - - +
200A PRO 4.4 0.3 - - - +
228A ILE* 4.0 1.2 + - + +
229A SER* 1.3 68.6 - - - +
231A GLU* 1.3 58.0 + - - +
232A ILE* 3.3 30.8 + - - +
268A VAL* 3.8 16.9 - - + +
600A PY4 3.1 23.3 + - + +
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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
------------------------------------------------------------
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