Contacts of the strand formed by residues 224 - 231 (chain B) in PDB entry 3MY0
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 GLU 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B LEU* 3.5 4.4 - - - -
221B TRP* 2.9 35.6 + - + +
222B HIS 3.1 6.8 + - - +
223B GLY* 1.3 77.6 - - - +
225B SER* 1.3 65.3 + - - +
226B VAL* 5.0 4.0 - - + -
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Residues in contact with SER 225 (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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218B ARG* 4.4 11.8 + - - -
219B GLY 3.4 6.5 - - - -
220B LEU* 3.6 14.8 - - - +
223B GLY 5.2 0.7 + - - -
224B GLU* 1.3 75.6 - - - +
226B VAL* 1.3 65.8 + - - +
278B HIS* 5.0 1.2 - - - -
279B TYR* 3.7 35.2 + - - +
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Residues in contact with VAL 226 (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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202B VAL* 4.1 16.8 - - + -
218B ARG* 3.6 4.7 - - - -
219B GLY* 2.7 50.5 + - - +
221B TRP* 4.4 21.5 - - + -
224B GLU* 4.7 4.7 - - + +
225B SER* 1.3 79.4 - - - +
227B ALA* 1.3 58.0 + - - +
228B VAL* 4.2 5.4 - - + -
260B ILE* 3.6 26.2 - - + -
276B ILE* 3.9 18.6 - - + -
277B THR 3.5 9.2 - - - +
278B HIS* 5.5 0.2 - - - -
279B TYR* 3.4 10.0 - - - +
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Residues in contact with ALA 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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216B VAL* 4.4 13.2 - - + -
217B TRP 3.4 6.7 - - - +
226B VAL* 1.3 73.2 - - - +
228B VAL* 1.3 60.5 + - - +
229B LYS 4.0 1.3 - - - +
257B LEU* 6.1 0.2 - - + -
275B LEU 3.7 1.0 - - - +
276B ILE* 3.3 6.2 - - - +
277B THR* 2.9 39.6 + - - +
278B HIS 3.5 18.6 - - - +
279B TYR* 3.6 16.6 - - + +
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Residues in contact with VAL 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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202B VAL* 3.8 29.2 - - + -
204B LEU* 4.1 13.2 - - + -
215B GLU 3.8 0.2 - - - +
216B VAL* 3.5 2.7 - - - -
217B TRP* 2.9 44.1 + - + +
219B GLY* 4.8 3.4 - - - -
226B VAL* 4.2 7.9 - - + -
227B ALA* 1.3 76.8 - - - +
229B LYS* 1.3 61.1 + - - +
230B ILE* 3.6 11.8 + - + -
274B TRP* 3.7 39.3 - - + -
275B LEU 3.5 3.6 - - - +
276B ILE* 4.0 14.6 - - + -
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Residues in contact with LYS 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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213B TYR* 3.7 37.0 - - + +
215B GLU 3.4 10.8 - - - +
216B VAL* 3.9 18.6 - - + +
227B ALA* 4.0 1.6 - - - +
228B VAL* 1.3 70.3 - - - +
230B ILE* 1.3 64.9 + - - +
231B PHE* 3.6 46.0 - - + -
235B ASP* 5.0 1.6 + - - -
242B GLU* 4.7 3.9 + - - +
274B TRP* 3.5 2.8 - - - -
275B LEU* 2.8 43.6 + - + +
277B THR* 6.3 0.9 - - + -
348B ASP* 4.4 24.2 + - - +
369B ARG* 5.6 1.4 - - - +
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Residues in contact with ILE 230 (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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204B LEU* 4.1 17.5 - - + -
214B GLY* 3.4 1.0 - - - -
215B GLU* 2.8 44.0 + - + +
217B TRP* 3.8 29.6 - - + +
228B VAL* 4.3 9.6 - - + +
229B LYS* 1.3 74.4 - - - +
231B PHE* 1.3 68.6 + - - +
272B GLN* 3.7 36.6 - - + +
273B LEU 3.6 3.4 - - - -
274B TRP* 3.6 29.8 - - + +
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Residues in contact with PHE 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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213B TYR 3.6 7.4 - - - -
214B GLY* 4.2 0.4 - - - -
229B LYS* 3.6 45.5 - - + -
230B ILE* 1.3 82.1 - - - +
232B SER* 1.3 67.6 + - - +
233B SER 4.1 0.2 + - - -
235B ASP* 3.6 26.9 - - - +
238B SER* 3.9 11.2 - - - -
239B TRP* 3.5 38.8 - + + -
242B GLU* 3.7 18.6 - - - -
272B GLN* 5.4 3.8 - - - +
273B LEU* 3.1 34.4 + - + +
275B LEU* 3.8 24.9 - - + -
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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