Contacts of the strand formed by residues 353 - 357 (chain A) in PDB entry 3EDY
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 353 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A HIS 2.8 14.5 + - - -
320A VAL* 3.5 12.3 - - + +
321A HIS 2.9 27.5 + - - +
351A GLY 3.9 0.4 + - - -
352A LEU* 1.3 70.5 - - - +
354A LEU* 1.3 63.7 + - - +
355A LEU* 3.8 22.0 - - + +
386A THR* 4.8 4.0 - - - +
485A LEU* 4.0 19.7 - - + -
489A ASN* 4.7 2.9 + - - -
500A LEU* 4.2 6.3 - - + +
501A GLY 2.6 35.4 + - - +
502A PHE* 5.0 1.3 - - - +
503A LEU* 4.7 9.0 - - + +
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TRP* 4.4 19.3 - - + -
311A LEU* 4.7 5.8 - - + -
321A HIS* 3.6 24.5 - - + -
323A VAL* 5.1 0.7 - - + -
344A LEU* 3.5 33.9 - - + +
347A ALA* 3.9 22.0 - - + -
352A LEU* 3.8 27.3 + - + +
353A THR* 1.3 77.5 - - - +
355A LEU* 1.3 60.9 + - - +
356A PHE* 4.5 5.6 - - + -
384A TYR 5.3 2.5 - - - +
385A VAL* 3.8 16.0 - - + +
386A THR* 3.1 26.0 + - - -
502A PHE* 5.9 0.4 - - - +
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Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A VAL* 3.8 24.7 - - + -
321A HIS 3.0 17.3 + - - +
322A THR* 4.2 2.2 - - + -
323A VAL* 2.8 36.2 + - - +
353A THR* 3.8 17.0 - - + +
354A LEU* 1.3 75.4 - - - +
356A PHE* 1.3 57.6 + - - +
386A THR* 3.1 19.7 - - + +
388A VAL* 3.8 21.1 - - + -
478A THR* 4.1 14.6 - - + +
481A PHE* 4.0 7.4 - - + -
482A GLY* 3.9 26.0 - - - +
485A LEU* 4.0 16.4 - - + -
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Residues in contact with PHE 356 (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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304A PHE* 3.7 24.0 - + - -
307A TRP* 4.4 3.6 - + - -
323A VAL* 3.3 48.0 - - + -
325A TYR* 3.7 20.4 - - + -
344A LEU* 4.3 8.5 - - + -
354A LEU* 4.5 7.6 - - + -
355A LEU* 1.3 76.6 - - - +
357A ALA* 1.3 66.4 + - - +
379A PRO* 3.6 29.6 - - + -
380A ALA* 4.6 8.7 - - - +
385A VAL* 3.8 39.7 - - + -
386A THR 3.0 6.1 + - - -
387A THR* 3.2 5.0 - - - +
388A VAL 2.8 26.6 + - - -
478A THR* 4.0 4.3 - - - -
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Residues in contact with ALA 357 (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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323A VAL 3.2 12.1 + - - +
324A SER* 4.5 11.9 - - - +
325A TYR 4.9 8.7 - - - +
356A PHE* 1.3 75.4 - - - +
358A SER* 1.3 63.9 + - - +
359A GLY* 3.3 2.1 + - - +
380A ALA* 3.9 9.9 - - - +
388A VAL 3.8 1.8 - - - -
474A THR* 3.3 26.5 - - - +
475A SER* 3.9 7.4 - - - +
478A THR* 3.1 22.8 + - - +
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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