Contacts of the strand formed by residues 424 - 429 (chain B) in PDB entry 4OE4
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 LEU 424 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417B ASP 5.1 0.2 - - - -
418B ALA* 3.7 29.9 - - + +
421B ASP* 2.9 25.6 + - + +
422B PRO* 4.1 4.9 - - - +
423B GLU* 1.3 86.3 - - - +
425B GLU* 1.3 63.6 + - - +
445B ILE* 4.0 12.6 - - + -
446B LYS 3.3 10.8 - - - +
447B ALA* 4.0 9.2 - - + -
452B HIS* 3.4 41.7 - - + +
454B TYR* 3.5 41.5 - - + -
465B THR* 5.1 0.4 - - + -
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Residues in contact with GLU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ALA 5.2 0.7 - - - -
424B LEU* 1.3 75.3 - - - +
426B ILE* 1.3 67.9 + - - +
427B LEU* 3.3 26.2 + - + +
445B ILE* 4.2 1.3 - - - -
446B LYS* 2.9 56.6 + - + +
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Residues in contact with ILE 426 (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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415B ILE* 3.6 34.3 - - + +
418B ALA* 3.9 21.9 + - + +
419B LYS* 3.8 26.5 - - + -
424B LEU 4.4 0.2 - - - -
425B GLU* 1.3 75.5 - - - +
427B LEU* 1.3 63.5 + - - +
428B TYR* 3.7 25.1 - - - +
429B GLY 4.3 7.6 - - - +
430B GLY* 5.2 1.6 - - - -
443B THR* 4.1 9.4 - - + -
444B VAL 3.8 6.1 - - - +
445B ILE* 4.3 9.6 - - + +
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Residues in contact with LEU 427 (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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368B LEU* 3.7 29.8 - - + -
372B PHE* 3.5 29.4 - - + -
425B GLU* 3.6 44.6 - - - +
426B ILE* 1.3 73.6 - - - +
428B TYR* 1.3 63.2 + - - +
444B VAL* 2.8 14.0 + - + +
446B LYS* 3.8 26.7 - - + +
466B VAL* 4.3 9.2 - - + -
468B GLU* 4.8 0.4 - - - +
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Residues in contact with TYR 428 (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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372B PHE* 3.6 52.0 - + + -
375B LEU* 3.4 35.7 + - + +
376B GLN* 3.3 27.9 + - + +
426B ILE* 3.4 5.6 - - - +
427B LEU* 1.3 83.3 - - - +
429B GLY* 1.3 68.1 + - - +
442B PRO* 3.6 26.2 - - + +
443B THR* 3.2 6.9 - - - +
444B VAL* 2.9 30.6 + - + -
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Residues in contact with GLY 429 (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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426B ILE* 4.3 7.1 - - - +
428B TYR* 1.3 83.8 - - - +
430B GLY* 1.3 64.4 + - - -
431B GLN* 3.2 7.1 + - - -
442B PRO 3.3 14.8 - - - -
443B THR* 4.3 0.7 - - - -
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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