Contacts of the strand formed by residues 226 - 231 (chain A) in PDB entry 1OLY
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 VAL 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ARG* 4.7 21.1 - - - +
172A LEU 3.6 14.1 - - - +
173A HIS* 4.1 20.2 - - + +
174A VAL* 3.4 1.0 - - - +
198A THR* 4.0 1.4 - - - +
199A GLY* 3.4 13.9 - - - +
224A SER* 3.0 23.9 + - - +
225A GLY* 1.3 87.9 - - - +
227A VAL* 1.4 77.9 + - - +
228A THR* 4.2 13.5 - - + -
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A HIS 4.0 0.2 - - - +
171A ARG* 3.6 1.4 - - - -
172A LEU* 2.6 50.3 + - + +
174A VAL* 3.9 6.1 - - + -
198A THR 3.4 10.3 - - - +
199A GLY 4.1 3.1 - - - +
200A LEU* 4.0 17.5 - - + -
221A TYR* 3.4 39.0 - - + -
226A VAL* 1.4 80.9 - - - +
228A THR* 1.3 71.0 + - - +
229A VAL* 3.8 15.9 - - + -
237A TRP* 4.2 14.8 - - + -
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Residues in contact with THR 228 (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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2A GLU* 5.1 6.5 - - - +
170A HIS 3.2 10.3 - - - +
171A ARG* 4.3 17.7 - - + +
196A THR 4.4 0.6 + - - -
197A THR* 3.1 21.9 - - - -
198A THR* 3.1 33.7 + - + +
226A VAL* 4.2 14.6 - - + -
227A VAL* 1.3 78.2 - - - +
229A VAL* 1.3 68.2 + - - +
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Residues in contact with VAL 229 (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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165A LEU* 4.0 26.5 - - + -
168A GLY 3.7 1.4 - - - +
169A LYS* 3.4 1.7 - - - -
170A HIS* 2.6 42.8 + - + +
172A LEU* 4.9 7.4 - - + -
185A LEU* 4.4 10.8 - - + -
195A VAL* 4.2 0.9 - - + -
196A THR 3.4 3.6 - - - -
197A THR* 3.8 20.2 - - + -
200A LEU* 5.7 0.2 - - + -
227A VAL* 3.8 16.4 - - + -
228A THR* 1.3 83.1 - - - +
230A GLU* 1.3 61.0 + - - +
231A THR* 3.4 26.7 - - + -
235A LEU* 4.2 7.6 - - + -
237A TRP* 4.9 0.2 - - + -
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Residues in contact with GLU 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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168A GLY* 3.3 9.6 - - - +
169A LYS* 3.1 46.6 + - + +
194A GLN* 3.5 3.5 - - - +
195A VAL* 3.3 6.8 - - - +
196A THR* 2.9 47.1 + - - +
206A ASN* 5.2 2.9 - - - +
229A VAL* 1.3 72.8 - - - +
231A THR* 1.4 69.7 + - - +
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Residues in contact with THR 231 (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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165A LEU* 4.2 4.7 + - + +
166A GLN 3.8 13.0 + - - -
167A PRO* 3.4 1.0 - - - +
168A GLY 3.0 27.5 + - - +
170A HIS* 5.2 0.8 + - + -
192A CYS* 4.6 0.9 - - - -
194A GLN 3.6 4.9 - - - -
195A VAL* 4.0 9.6 - - + -
229A VAL* 3.4 13.0 - - + -
230A GLU* 1.4 83.6 - - - +
232A ASP* 1.3 61.1 + - - +
233A HIS 2.7 26.1 + - - -
235A LEU* 3.3 39.2 - - + +
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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