Contacts of the strand formed by residues 224 - 229 (chain B) in PDB entry 5E0T
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 THR 224 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LYS* 5.8 8.7 - - + -
139B MET 3.3 15.7 - - - +
141B SER* 3.8 3.4 - - - +
192B GLU* 4.2 25.8 - - + +
194B ALA 5.8 2.0 - - - +
222B SER* 2.9 26.0 + - - -
223B SER* 1.3 91.3 - - - +
225B VAL* 1.3 63.0 + - - +
226B THR* 6.0 0.7 - - - -
238B GLU 4.4 2.1 - - - +
239B TYR* 4.3 5.9 - - - -
240B LYS* 4.8 2.1 + - - +
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Residues in contact with VAL 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B VAL 3.7 1.0 - - - +
138B LYS* 3.5 2.8 - - - +
139B MET* 2.9 44.3 + - + +
141B SER* 3.8 8.3 - - - -
144B PHE* 3.6 32.8 - - + -
224B THR* 1.3 75.3 - - - +
226B THR* 1.3 67.5 + - - +
227B LEU* 4.1 4.9 + - + -
237B VAL* 3.5 29.4 - - + -
238B GLU 3.5 14.4 - - - +
239B TYR* 3.6 25.1 - - + +
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Residues in contact with THR 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B VAL* 3.8 21.1 - - + -
137B VAL 3.3 4.3 - - - +
138B LYS* 3.1 33.8 + - + +
224B THR* 6.0 0.7 - - - -
225B VAL* 1.3 74.6 - - - +
227B LEU* 1.3 63.4 + - - +
228B ILE* 3.8 25.5 - - + +
236B VAL 3.4 3.8 - - - +
237B VAL* 3.6 2.3 - - - -
238B GLU* 3.0 49.7 + - - +
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Residues in contact with LEU 227 (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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135B CYS 3.8 0.5 - - - +
136B VAL* 3.4 5.0 - - - -
137B VAL* 2.7 52.8 + - + +
139B MET* 3.7 28.5 - - + -
144B PHE* 3.8 37.9 - - + -
160B ILE* 5.2 7.6 - - + -
169B PHE* 4.0 15.5 - - + -
225B VAL* 4.4 7.0 - - + -
226B THR* 1.3 75.4 - - - +
228B ILE* 1.3 62.1 + - - +
229B MET* 4.0 8.7 - - + +
235B LEU* 4.5 10.1 - - + -
236B VAL 3.5 2.9 - - - +
237B VAL* 3.9 25.4 - - + -
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Residues in contact with ILE 228 (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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131B GLN* 3.5 31.6 - - + +
133B TYR* 3.8 50.7 - - + +
135B CYS 3.5 4.5 - - - +
136B VAL* 4.6 5.4 - - + -
226B THR* 3.8 16.2 - - + +
227B LEU* 1.3 75.2 - - - +
229B MET* 1.3 63.7 + - - +
230B SER* 4.1 1.9 + - - +
234B PRO 4.4 1.2 - - - +
235B LEU* 3.7 4.3 - - - +
236B VAL* 2.9 49.1 + - + +
238B GLU* 4.1 17.7 - - + +
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Residues in contact with MET 229 (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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134B SER* 3.4 3.0 + - - -
135B CYS* 2.8 42.2 + - + +
137B VAL* 5.5 5.8 - - + -
160B ILE* 3.4 51.1 - - + +
162B CYS* 5.0 10.8 - - + -
167B VAL* 5.5 1.6 - - + -
203B VAL* 3.8 27.9 - - + +
205B LEU* 3.9 12.6 - - + -
207B PHE* 4.3 12.8 - - + -
227B LEU* 4.0 10.7 + - + -
228B ILE* 1.3 75.4 - - - +
230B SER* 1.3 65.2 + - - +
235B LEU* 4.2 16.2 - - + +
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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