Contacts of the strand formed by residues 388 - 393 (chain A) 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 THR 388 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLY* 3.1 21.5 + - - -
211A ILE 3.2 11.0 + - - -
212A TYR* 3.5 22.6 - - + -
213A VAL* 2.9 24.8 + - - +
381A VAL* 4.1 13.7 - - + -
382A GLN 3.4 10.8 - - - +
383A ARG* 3.0 38.6 + - - +
387A TYR* 1.3 74.8 - - - +
389A GLN* 1.3 59.7 + - - +
390A ILE* 4.2 9.3 - - + +
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Residues in contact with GLN 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A PHE* 4.3 10.6 - - - -
188A GLN* 4.9 2.9 - - - +
191A LEU* 5.1 0.3 - - - +
213A VAL* 3.4 16.5 - - + +
215A ASN* 3.5 38.1 - - + +
380A ASP 3.7 1.7 - - - +
381A VAL* 3.4 4.0 - - - +
382A GLN* 2.8 45.5 + - + +
384A TYR* 4.1 19.6 + - + -
387A TYR* 3.9 30.9 + - + -
388A THR* 1.3 72.7 - - - +
390A ILE* 1.3 62.7 + - - +
391A THR* 3.7 8.5 + - - +
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Residues in contact with ILE 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A TYR* 4.2 18.4 - - + -
213A VAL 2.9 9.8 + - - +
214A ILE* 3.6 21.5 - - + +
215A ASN* 2.7 32.4 + - - +
230A VAL* 4.8 4.3 - - + -
234A GLU* 3.6 33.7 - - + +
378A VAL* 4.1 31.2 - - + -
380A ASP 3.5 2.7 - - - +
381A VAL* 4.5 12.6 - - + -
388A THR* 4.2 13.2 - - + +
389A GLN* 1.3 76.3 - - - +
391A THR* 1.3 59.7 + - - +
392A VAL* 3.8 6.9 + - + -
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Residues in contact with THR 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ASN* 2.9 34.0 + - - +
217A ALA* 4.0 20.2 - - + -
378A VAL* 3.6 3.1 - - - +
379A LEU* 2.8 33.8 + - + -
380A ASP* 2.7 34.1 + - + +
382A GLN* 6.1 0.2 - - - +
389A GLN* 3.7 13.7 + - - +
390A ILE* 1.3 72.6 - - - +
392A VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ILE* 3.7 31.0 - - + -
215A ASN 2.9 13.0 + - - +
216A GLN* 3.7 2.8 - - - +
217A ALA* 2.8 25.6 + - - -
227A LEU* 4.0 13.0 - - + -
230A VAL* 4.2 9.9 - - + -
376A TYR* 3.6 38.4 - - + -
377A GLN 3.5 12.8 - - - +
378A VAL* 4.1 3.4 - - + +
379A LEU* 4.2 0.4 - - - +
390A ILE* 4.3 4.3 - - + +
391A THR* 1.3 78.6 - - - +
393A ASP* 1.3 62.9 + - - +
394A ILE* 3.6 9.1 + - + +
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Residues in contact with ASP 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ALA* 4.3 10.2 - - + +
376A TYR* 3.5 5.0 - - - +
377A GLN* 2.8 44.3 + - + +
379A LEU* 4.3 20.4 - - + +
392A VAL* 1.3 69.9 - - - +
394A ILE* 1.3 59.8 + - - +
395A GLY* 3.0 21.1 + - - -
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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