Contacts of the strand formed by residues 421 - 426 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B THR* 3.2 26.7 - - - +
355B LYS* 3.8 35.7 - - - -
363B VAL* 5.8 0.9 - - - -
416B GLN 4.5 0.9 - - - +
417B VAL* 3.5 6.9 - - - +
418B LYS* 3.1 25.3 + - + +
419B ASN 2.9 12.0 + - - +
420B TYR* 1.3 79.5 - - - +
422B LEU* 1.3 65.9 + - - +
423B THR* 3.9 8.4 + - - -
291K GLU* 5.6 3.1 - - - -
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Residues in contact with LEU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B TYR* 6.0 0.6 - - - -
353B THR 3.0 7.0 + - - +
354B LEU* 3.4 26.9 - - + +
355B LYS 2.9 24.4 + - - +
394B TYR* 4.9 3.1 - - + -
410B MSE 3.9 23.3 - - + -
413B ALA* 3.3 25.8 - - + +
414B TRP* 3.7 37.2 - - + -
416B GLN* 4.8 11.9 - - + +
417B VAL* 4.3 8.4 - - + +
421B CYS* 1.3 72.3 - - - +
423B THR* 1.3 72.8 + - - +
424B LEU* 4.1 14.6 - - + -
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Residues in contact with THR 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B LYS* 3.3 19.6 - - + +
357B HIS* 3.7 26.0 - - + +
394B TYR* 4.1 5.0 - - - +
395B ARG* 4.6 5.0 + - - +
416B GLN 5.6 0.8 + - - -
421B CYS* 3.9 14.5 + - - -
422B LEU* 1.3 81.6 - - - +
424B LEU* 1.3 71.1 + - - +
425B TRP* 3.6 35.6 - - + -
291K GLU* 4.8 4.5 + - - -
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Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B LEU* 4.1 19.3 - - + -
355B LYS 2.8 10.0 + - - +
356B VAL* 3.4 11.6 - - + -
357B HIS* 2.9 26.7 + - - +
375B VAL* 3.9 27.8 - - + -
379B VAL* 4.9 0.4 - - + -
392B LEU* 4.4 17.7 - - + -
393B SER 3.2 14.4 - - - +
394B TYR* 3.9 13.9 - - + -
405B LEU* 4.2 23.6 - - + -
413B ALA* 5.2 0.2 - - + -
422B LEU* 4.1 20.2 - - + -
423B THR* 1.3 81.9 - - - +
425B TRP* 1.3 69.6 + - - +
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Residues in contact with TRP 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B HIS* 3.4 36.9 - + + +
391B LYS 3.6 1.2 - - - +
392B LEU* 3.3 9.2 - - - -
393B SER* 2.9 39.4 + - - +
394B TYR* 4.2 0.2 - - - -
395B ARG* 3.5 63.0 - - + -
402B LEU* 3.5 29.4 - - + -
423B THR* 3.6 30.1 - - + -
424B LEU* 1.3 77.6 - - - +
426B CYS* 1.3 62.0 + - - +
427B GLU* 5.4 4.4 - - + +
337K THR 3.0 29.8 + - - -
338K MSE 4.8 1.6 - - - -
339K PRO* 3.8 23.1 - - + -
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Residues in contact with CYS 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B VAL* 3.9 14.7 - - + +
357B HIS 2.9 15.7 + - - +
358B TYR* 3.8 29.8 - - + -
383B LEU* 4.0 18.4 - - + -
385B LEU* 4.5 4.3 - - - -
389B HIS 4.2 17.5 - - - -
390B THR* 4.2 12.3 - - - -
391B LYS 3.6 4.0 - - - -
392B LEU* 3.8 19.3 - - + -
425B TRP* 1.3 74.8 - - - +
427B GLU* 1.3 64.9 + - - +
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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
------------------------------------------------------------
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