Contacts of the strand formed by residues 421 - 426 (chain A) in PDB entry 1OEY
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 CYS 421 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A THR* 3.4 23.1 - - - +
355A LYS* 3.7 35.9 - - - -
363A VAL* 6.1 0.2 - - - -
416A GLN 4.4 0.9 - - - +
417A VAL* 3.4 5.9 - - - +
418A LYS* 2.8 38.9 + - - +
419A ASN 3.9 4.7 - - - +
420A TYR* 1.3 80.2 - - - +
422A LEU* 1.3 66.1 + - - +
423A THR* 4.0 9.2 + - - -
291J GLU* 5.0 6.7 - - - +
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Residues in contact with LEU 422 (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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352A TYR* 6.0 0.4 - - - -
353A THR 3.0 7.2 + - - +
354A LEU* 3.4 26.3 - - + +
355A LYS 2.8 26.3 + - - +
394A TYR* 5.2 2.7 - - + -
410A MSE 3.8 23.8 - - + -
413A ALA* 3.3 27.6 - - + +
414A TRP* 3.7 30.3 - - + -
416A GLN* 4.7 13.2 - - + +
417A VAL* 3.9 14.0 - - + +
421A CYS* 1.3 71.7 - - - +
423A THR* 1.3 72.5 + - - +
424A LEU* 4.2 14.6 - - + -
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Residues in contact with THR 423 (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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355A LYS* 3.2 19.2 - - + +
357A HIS* 3.6 34.5 - - + +
394A TYR* 4.5 4.5 - - - +
395A ARG 5.1 0.5 + - - -
416A GLN 5.6 1.2 + - - -
421A CYS* 4.0 15.4 + - - -
422A LEU* 1.3 79.4 - - - +
424A LEU* 1.3 70.5 + - - +
425A TRP* 3.8 28.6 - - + -
291J GLU* 4.7 3.5 + - - -
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Residues in contact with LEU 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LEU* 4.3 18.2 - - + -
355A LYS 2.8 9.2 + - - +
356A VAL* 3.3 8.2 - - + -
357A HIS* 2.8 27.6 + - - +
375A VAL* 3.9 29.4 - - + -
379A VAL* 4.8 2.5 - - + -
392A LEU* 4.2 15.9 - - + -
393A SER 3.4 14.6 - - - +
394A TYR* 3.9 14.4 - - + -
405A LEU* 3.9 22.0 - - + -
413A ALA* 5.2 0.4 - - + -
422A LEU* 4.2 20.0 - - + -
423A THR* 1.3 81.1 - - - +
425A TRP* 1.3 72.6 + - - +
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Residues in contact with TRP 425 (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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357A HIS* 3.4 35.2 - + + +
391A LYS 3.7 0.7 - - - +
392A LEU* 3.2 8.8 - - - +
393A SER* 2.9 42.0 + - - +
395A ARG* 3.4 35.9 - - + -
402A LEU* 3.6 38.4 - - + -
423A THR* 3.8 29.2 - - + -
424A LEU* 1.3 77.8 - - - +
426A CYS* 1.3 61.3 + - - +
337J THR 3.0 29.6 + - - -
338J MSE 4.0 2.7 - - - -
339J PRO* 3.7 29.8 - - + -
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Residues in contact with CYS 426 (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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356A VAL* 3.9 14.8 - - + +
357A HIS 2.9 16.5 + - - +
358A TYR* 3.6 20.5 - - + -
383A LEU* 3.8 20.2 - - + -
385A LEU* 4.0 16.8 - - - -
390A THR* 4.3 4.5 - - - -
391A LYS 3.5 14.8 - - - -
392A LEU* 3.8 21.3 - - + -
425A TRP* 1.3 73.0 - - - +
427A GLU* 1.3 72.2 + - - +
428A ASN 3.3 6.2 + - - +
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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