Contacts of the strand formed by residues 230 - 236 (chain B) in PDB entry 4LOE
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 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B VAL 3.6 1.2 - - - +
144B GLN* 3.3 2.4 - - - -
145B LEU* 2.7 62.4 + - + +
220B TYR* 4.0 5.7 + - + -
221B GLU* 2.7 37.3 + - + +
222B PRO* 4.0 1.5 - - - +
223B PRO* 3.3 20.7 - - - +
229B CYS* 1.3 71.8 - - - +
231B THR* 1.3 70.8 + - - +
232B ILE* 4.8 4.9 - - + -
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Residues in contact with THR 231 (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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142B PRO* 4.0 14.1 - - + -
143B VAL 3.5 7.6 - - - +
144B GLN* 4.0 16.2 + - + +
229B CYS* 4.0 8.5 + - - -
230B THR* 1.3 79.3 - - - +
232B ILE* 1.3 69.0 + - - +
233B HIS* 3.7 33.5 + - + +
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Residues in contact with ILE 232 (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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141B CYS 3.4 2.8 - - - +
142B PRO* 3.5 1.4 - - - +
143B VAL* 2.8 36.9 + - - +
145B LEU* 3.7 30.7 - - + -
157B VAL* 3.8 7.9 - - + -
197B VAL* 4.0 21.1 - - + -
200B ASN* 6.3 0.2 - - - +
218B VAL* 3.7 26.5 - - + -
230B THR* 4.8 5.4 - - + -
231B THR* 1.3 77.7 - - - +
233B HIS* 1.3 64.0 + - - +
234B TYR* 3.6 46.1 + - + +
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Residues in contact with HIS 233 (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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140B THR* 3.5 29.1 - - + +
141B CYS 3.8 2.9 - - - -
142B PRO* 4.0 11.4 - - + +
197B VAL* 3.5 4.8 - - - +
198B GLU* 3.0 58.6 + - + +
199B GLY* 6.2 1.3 - - - -
231B THR* 3.7 27.3 + - + +
232B ILE* 1.3 73.1 + - - +
234B TYR* 1.3 63.6 + - - +
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Residues in contact with TYR 234 (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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141B CYS* 2.8 41.5 + - + +
143B VAL* 3.7 36.8 - - + -
145B LEU* 6.2 0.2 - - + -
157B VAL* 4.2 11.1 + - - +
158B ARG 4.7 0.2 - - - -
159B ALA* 3.6 31.7 + - + +
195B ILE* 3.6 20.2 - - + -
196B ARG 3.3 2.5 - - - +
197B VAL* 3.5 28.3 - - + -
216B VAL* 4.4 2.4 + - + -
218B VAL* 5.5 0.3 - - - +
232B ILE* 3.6 33.5 - - + +
233B HIS* 1.3 73.4 - - - +
235B ASN* 1.3 65.4 + - - +
236B TYR* 4.2 21.8 - + + -
253B THR* 6.0 0.7 - - + -
255B ILE* 3.8 17.7 - - + +
270B PHE* 5.6 0.9 - + - -
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Residues in contact with ASN 235 (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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138B ALA* 4.0 13.5 + - - +
139B LYS 3.3 17.4 + - - -
194B LEU 3.5 3.1 - - - +
195B ILE* 3.6 3.1 - - - +
196B ARG* 2.9 43.4 + - + +
198B GLU* 2.7 47.5 + - - +
234B TYR* 1.3 83.5 + - - +
236B TYR* 1.3 63.9 + - - +
237B MET* 3.9 21.4 - - - +
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Residues in contact with TYR 236 (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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133B MET* 5.6 2.2 - - + -
135B CYS* 3.9 18.8 - - - -
136B GLN 5.2 1.0 + - - +
137B LEU* 3.7 7.3 - - - +
138B ALA 2.9 25.4 + - - +
139B LYS 4.7 1.8 + - - -
141B CYS* 4.0 15.1 - - + -
194B LEU* 3.5 19.5 - - + -
195B ILE* 3.8 27.9 - - + +
234B TYR* 4.2 20.3 - + + +
235B ASN* 1.3 75.7 - - - +
237B MET* 1.3 60.7 + - - +
238B CYS 3.5 2.4 + - - -
251B ILE* 4.8 1.1 - - + -
253B THR* 2.6 40.1 + - - +
270B PHE* 3.6 10.0 - + - -
272B VAL* 3.5 28.1 - - + +
274B VAL* 3.6 24.6 - - + +
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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