Contacts of the strand formed by residues 226 - 231 (chain A) in PDB entry 3V56
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 LEU 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A GLN* 3.5 38.6 - - + +
214A ARG 3.3 6.5 - - - +
215A LYS* 3.8 34.5 - - + +
224A LEU* 3.5 23.5 - - - +
225A SER* 1.3 78.3 - - - +
227A VAL* 1.3 61.7 + - - +
228A THR 4.2 1.0 + - - -
260A GLN* 4.0 20.2 - - + +
222F ASP* 4.7 0.5 - - - +
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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
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213A GLN* 3.1 6.5 - - - -
214A ARG* 2.9 46.8 + - + +
216A LYS* 3.7 31.9 - - + -
224A LEU* 4.3 6.3 - - + +
226A LEU* 1.3 74.6 - - - +
228A THR* 1.3 73.5 + - - +
229A LEU* 3.2 20.1 + - + -
220F PHE 4.3 3.4 - - - +
222F ASP* 3.5 14.1 - - - +
223F GLU* 4.1 32.3 - - + +
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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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211A LEU* 3.7 21.7 - - + +
212A ILE 3.8 2.9 - - - +
213A GLN* 3.4 21.4 + - - -
226A LEU 4.2 0.6 + - - -
227A VAL* 1.3 69.7 - - - +
229A LEU* 1.3 59.1 + - - +
230A PHE 3.7 19.7 - - - +
231A ARG* 4.0 1.6 - - + -
275B ASP* 3.4 20.7 - - - +
221F GLY* 3.4 0.3 - - - -
222F ASP* 2.8 51.9 + - - +
30G ARG* 3.3 19.7 + - - +
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Residues in contact with LEU 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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195A ILE* 4.3 7.6 - - + -
212A ILE* 2.8 20.2 + - + +
214A ARG* 3.9 34.1 - - + +
227A VAL* 3.2 16.1 + - + +
228A THR* 1.3 72.1 - - - +
230A PHE* 1.4 86.1 + - + +
251A ALA* 3.9 30.7 - - + -
253A LEU* 4.3 2.7 - - + -
259A LEU* 4.0 19.3 - - + -
274B GLY 4.5 0.5 - - - +
275B ASP* 3.3 7.8 - - - -
220F PHE* 4.0 18.6 - - + -
221F GLY* 3.2 21.2 - - - +
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Residues in contact with PHE 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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195A ILE* 4.3 15.9 - - + -
210A HIS* 4.1 0.7 - - - +
211A LEU* 3.5 2.4 - - - -
212A ILE* 2.8 53.3 + - + +
228A THR* 3.7 3.4 - - - +
229A LEU* 1.4 110.7 - - + +
231A ARG* 1.3 58.7 + - - +
247A SER* 3.9 22.0 - - - +
248A ALA 4.4 1.1 - - - -
249A GLY* 3.3 47.6 - - - -
250A ILE 3.7 15.9 - - - -
251A ALA* 4.6 2.2 - - + -
148B GLN* 4.4 10.5 - - - -
150B ILE* 6.5 0.7 - - + -
274B GLY 5.6 0.7 - - - -
275B ASP 3.2 6.5 - - - +
278B PHE* 3.9 25.1 - + + -
221F GLY 5.8 2.2 - - - -
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Residues in contact with ARG 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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210A HIS* 3.4 5.4 - - - -
211A LEU* 3.5 26.7 - - + -
228A THR* 4.0 0.7 - - + -
230A PHE* 1.3 75.3 - - - +
232A CYS* 1.4 64.0 + - - +
233A ILE* 3.8 14.9 - - + +
247A SER* 4.6 3.1 - - - -
198B GLN* 2.9 29.0 + - - -
200B LEU* 4.5 4.2 - - - +
271B SER* 4.7 0.6 + - - -
273B ASP* 3.1 30.1 + - - +
275B ASP* 2.8 49.8 + - - +
276B VAL* 3.4 25.3 - - + +
28G LEU* 2.8 32.2 + - + -
29G VAL 4.0 12.1 + - - -
30G ARG* 3.7 20.6 - - - +
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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