Contacts of the strand formed by residues 387 - 393 (chain B) in PDB entry 4EEM
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 TYR 387 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B LEU* 4.2 12.8 - - + +
164B GLY* 3.3 13.5 - - - -
165B GLY 3.4 3.6 - - - +
188B GLN* 3.6 21.5 + - - -
191B LEU* 3.9 11.4 - - + +
195B LEU* 3.5 28.0 - - + -
211B ILE* 3.7 22.7 - - + +
213B VAL* 3.5 20.2 - - + -
382B GLN 4.0 0.2 - - - +
384B TYR* 2.7 72.4 + + + +
386B LEU* 1.3 86.1 - - + +
388B THR* 1.3 63.5 + - - +
389B GLN* 3.7 22.6 + - + -
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Residues in contact with THR 388 (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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164B GLY* 3.2 18.9 + - - -
211B ILE 2.9 12.3 + - - -
212B TYR* 3.4 18.8 - - + +
213B VAL* 2.8 26.9 + - - +
381B VAL* 4.1 17.7 - - + -
382B GLN 3.4 10.3 - - - +
383B ARG* 3.0 34.1 + - - +
387B TYR* 1.3 72.8 - - - +
389B GLN* 1.3 61.9 + - - +
390B ILE* 4.0 14.5 + - + +
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Residues in contact with GLN 389 (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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184B PHE* 4.2 11.1 - - - -
188B GLN* 4.7 4.3 - - - +
191B LEU* 4.7 0.3 - - - +
213B VAL* 3.2 21.1 - - + +
215B ASN* 3.8 33.9 - - + +
380B ASP 4.0 0.7 - - - +
381B VAL* 3.5 2.4 - - - -
382B GLN* 2.9 57.7 + - - +
384B TYR* 4.1 13.0 + - + -
387B TYR* 3.7 30.5 + - + -
388B THR* 1.3 71.9 - - - +
390B ILE* 1.3 62.5 + - - +
391B THR* 4.0 4.3 + - - +
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Residues in contact with ILE 390 (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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212B TYR* 4.1 24.5 - - + -
213B VAL 2.8 9.5 + - - +
214B ILE* 3.5 18.6 - - + +
215B ASN 2.8 26.3 + - - +
230B VAL* 4.8 3.8 - - + -
234B GLU* 3.5 36.6 - - + +
378B VAL* 4.1 27.4 - - + -
380B ASP 3.5 9.4 - - - +
381B VAL* 4.5 12.8 - - + -
388B THR* 4.1 12.6 - - + +
389B GLN* 1.3 75.8 - - - +
391B THR* 1.3 64.4 + - - +
392B VAL* 3.8 6.0 + - + -
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Residues in contact with THR 391 (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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215B ASN* 2.7 39.6 + - - +
217B ALA* 3.9 22.7 - - + -
378B VAL* 3.7 2.9 - - - +
379B LEU* 2.9 31.4 + - + -
380B ASP* 3.0 24.8 + - - +
382B GLN* 4.5 6.4 + - - -
389B GLN* 4.0 9.4 + - - +
390B ILE* 1.3 71.4 - - - +
392B VAL* 1.3 63.6 + - - +
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Residues in contact with VAL 392 (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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214B ILE* 3.8 16.2 - - + -
215B ASN 2.8 19.1 + - - +
216B GLN* 3.8 2.3 - - - +
217B ALA* 2.9 24.8 + - - -
227B LEU* 3.7 23.6 - - + -
230B VAL* 4.4 8.7 - - + -
376B TYR* 3.5 42.4 - - + -
377B GLN 3.5 8.3 - - - +
378B VAL* 4.2 2.7 - - - +
379B LEU* 4.9 0.2 - - - -
390B ILE* 4.4 4.7 - - + +
391B THR* 1.3 78.4 - - - +
393B ASP* 1.3 64.5 + - - +
394B ILE* 3.5 11.6 + - + +
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Residues in contact with ASP 393 (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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217B ALA* 4.2 9.5 - - + +
376B TYR* 3.4 4.9 - - - +
377B GLN* 2.7 51.8 + - + +
379B LEU* 4.4 18.4 - - + +
392B VAL* 1.3 71.8 - - - +
394B ILE* 1.3 58.9 + - - +
395B GLY* 3.1 19.9 + - - -
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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