Contacts of the strand formed by residues 234 - 240 (chain B) in PDB entry 5EZD
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 ALA 234 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A PHE* 3.5 13.3 - - - -
166B LYS* 4.0 36.3 - - + +
167B ARG 5.3 1.1 - - - +
221B GLN* 3.6 1.2 - - - -
222B LEU* 2.9 39.6 + - + +
233B THR* 1.3 80.7 + - - +
235B ASN* 1.3 66.8 + - - +
236B VAL* 5.5 2.7 - - + -
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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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263A PHE* 2.9 32.3 - - - -
265A ARG* 3.3 26.7 - - - +
280A TYR* 4.9 2.2 - - - -
282A GLY* 4.0 16.7 + - - +
166B LYS 4.9 1.2 + - - -
167B ARG 4.8 0.2 - - - +
168B GLY* 3.2 19.8 - - - +
169B ILE* 2.9 23.4 + - - +
219B LEU* 4.1 17.4 - - + +
220B PHE 3.7 2.0 - - - -
234B ALA* 1.3 74.0 - - - +
236B VAL* 1.3 65.7 + - - +
237B THR* 4.2 3.4 - - + -
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Residues in contact with VAL 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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169B ILE* 3.6 19.7 - - + +
171B LEU* 4.5 13.9 - - + -
189B TRP* 4.3 17.0 - - + -
220B PHE* 2.9 41.1 + - + -
222B LEU* 3.7 37.7 - - + -
234B ALA* 3.8 3.6 + - + +
235B ASN* 1.3 79.1 - - - +
237B THR* 1.3 71.5 + - - +
238B VAL* 4.2 12.6 - - + -
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Residues in contact with THR 237 (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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169B ILE 2.8 9.8 + - - +
170B ASP* 2.5 40.4 + - + +
171B LEU* 2.9 25.6 + - - +
217B THR* 6.2 1.8 - - - -
218B TYR 3.1 9.4 - - - +
219B LEU* 3.6 27.1 - - + -
235B ASN* 5.2 3.6 - - + -
236B VAL* 1.3 77.3 - - - +
238B VAL* 1.3 64.6 + - - +
239B THR* 5.4 1.3 - - - -
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Residues in contact with VAL 238 (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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171B LEU* 3.4 15.5 - - + +
173B VAL* 3.9 26.9 - - + -
179B LEU* 4.2 15.5 - - + -
181B LEU* 5.2 2.2 - - + -
189B TRP* 5.8 0.2 - - + -
210B LEU* 4.3 9.2 - - + -
213B LEU* 4.4 7.9 - - + -
217B THR* 3.5 2.3 - - - -
218B TYR* 2.8 42.6 + - + +
220B PHE* 4.0 23.6 - - + -
236B VAL* 4.2 12.3 - - + -
237B THR* 1.3 77.4 - - - +
239B THR* 1.3 61.7 + - - +
240B VAL* 4.2 10.3 - - + -
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Residues in contact with THR 239 (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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170B ASP* 3.4 14.9 + - - -
171B LEU 2.8 8.7 + - - -
172B LYS* 3.4 31.5 + - + +
173B VAL* 2.9 27.1 + - - -
216B GLY* 3.5 6.1 - - - +
217B THR* 3.5 26.5 - - + +
237B THR* 4.2 1.4 + - - -
238B VAL* 1.3 71.8 - - - +
240B VAL* 1.3 67.4 + - - +
241B LEU* 3.3 11.3 + - + +
245B GLN* 4.7 14.4 - - - +
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Residues in contact with VAL 240 (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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173B VAL* 3.5 17.7 - - + +
175B PRO* 3.6 40.6 - - + -
213B LEU* 3.9 24.0 - - + -
214B LYS* 3.3 21.8 - - - +
215B GLU* 3.5 17.0 - - - +
216B GLY* 2.8 26.9 + - - +
218B TYR* 4.1 7.0 - - + -
238B VAL* 4.2 7.0 - - + -
239B THR* 1.3 70.5 - - - +
241B LEU* 1.3 64.7 - - - +
242B SER 3.7 0.9 + - - -
245B GLN* 4.4 2.8 - - - +
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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