Contacts of the strand formed by residues 224 - 231 (chain B) in PDB entry 3EWJ
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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222B LYS 3.7 1.0 - - - -
223B ASN* 1.3 92.5 + - - +
225B CYS* 1.3 62.7 + - - +
226B LYS* 3.5 20.8 + - + -
263B ARG* 2.9 25.8 + - - +
276B GLY 3.5 2.0 - - - -
278B GLN* 3.4 34.3 - - + +
469B CYS 4.5 0.3 - - - +
470B PHE* 3.3 8.3 - - - -
471B GLN* 2.8 38.8 + - - +
472B GLU 4.3 0.9 - - - -
473B ARG* 3.6 10.0 + - - +
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Residues in contact with CYS 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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224B THR* 1.3 72.5 - - - +
226B LYS* 1.3 65.7 + - - +
227B LEU* 3.6 3.9 + - - +
276B GLY 2.8 16.3 + - - +
277B ILE* 3.4 7.5 - - + +
278B GLN 3.3 17.3 + - - -
333B CYS* 2.0 50.0 - - - -
334B LEU* 3.6 29.2 - - - -
364B VAL* 4.1 2.5 - - - -
411B PHE* 3.8 17.5 - - + -
470B PHE* 3.8 8.2 - - + -
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Residues in contact with LYS 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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224B THR* 3.5 21.0 + - + +
225B CYS* 1.3 71.6 - - - +
227B LEU* 1.3 60.3 + - - +
278B GLN* 3.4 30.0 - - + +
279B ILE 5.5 0.2 - - - +
280B GLU* 3.8 36.3 + - + +
332B VAL* 4.0 4.0 - - + +
333B CYS* 3.2 31.4 + - + +
334B LEU 3.3 9.0 + - - +
469B CYS 5.4 0.2 + - - -
471B GLN* 2.7 42.5 + - - +
472B GLU 3.1 27.2 + - - -
473B ARG 4.2 5.3 + - - -
474B SER 4.7 6.9 + - - -
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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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225B CYS* 3.8 18.6 - - - +
226B LYS* 1.3 76.0 - - - +
228B LEU* 1.3 61.4 + - - +
229B VAL* 4.1 15.9 - - + -
255B ILE* 3.8 41.7 - - + -
277B ILE* 4.2 18.2 - - + -
278B GLN 2.8 18.6 + - - +
279B ILE* 3.8 2.4 - - + -
280B GLU* 2.8 29.9 + - - +
281B GLN 3.3 6.9 + - - +
332B VAL* 4.7 1.8 - - - -
334B LEU* 3.3 32.8 - - + +
336B HIS* 5.6 5.8 - - + +
407B LEU* 4.6 9.9 - - + -
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Residues in contact with LEU 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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227B LEU* 1.3 73.5 - - - +
229B VAL* 1.3 64.2 + - - +
230B VAL* 4.1 7.2 - - + -
281B GLN* 3.5 33.9 - - + +
283B ARG* 3.9 16.2 - - + -
325B ILE* 3.6 35.7 - - + -
328B GLU* 3.8 26.0 - - + +
332B VAL* 3.7 23.9 - - + +
334B LEU 2.9 8.3 + - - +
335B ALA* 4.2 10.5 - - + -
336B HIS* 2.9 27.4 + - - +
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Residues in contact with VAL 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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227B LEU* 4.1 20.9 - - + -
228B LEU* 1.3 77.7 - - - +
230B VAL* 1.3 63.2 + - - +
251B LEU* 3.6 36.1 - - + -
255B ILE* 4.3 7.2 - - + -
279B ILE* 4.0 24.0 - - + -
281B GLN 2.8 13.8 + - - +
282B ILE* 3.3 11.9 - - + +
283B ARG* 2.8 27.0 + - - +
336B HIS* 3.6 4.7 - - + +
338B PHE* 3.7 22.0 - - + -
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Residues in contact with VAL 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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228B LEU* 4.1 14.1 - - + +
229B VAL* 1.3 81.5 - - - +
231B ALA* 1.3 62.2 + - - +
283B ARG* 3.4 17.9 - - + +
285B LEU* 4.1 13.0 - - + -
298B TYR* 3.5 32.1 - - + +
321B PHE* 4.0 16.6 - - + -
325B ILE* 4.0 24.0 - - + -
336B HIS 2.9 13.1 + - - +
337B LEU* 3.5 2.7 - - + +
338B PHE* 2.7 34.9 + - - +
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Residues in contact with ALA 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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230B VAL* 1.3 75.2 - - - +
232B ASP* 1.3 63.2 + - - +
235B PHE* 3.9 11.2 - - + -
236B TYR 4.9 0.2 - - - +
247B THR* 3.7 30.1 - - + -
251B LEU* 3.8 15.4 - - + +
283B ARG 2.9 10.6 + - - +
284B ILE* 4.5 6.4 - - + +
285B LEU* 2.9 29.1 + - - +
338B PHE* 3.6 6.7 - - - -
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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