Contacts of the strand formed by residues 456 - 462 (chain B) in PDB entry 3UO8
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 456 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B VAL 3.7 4.7 + - - +
407B TYR* 3.6 42.5 - - + -
408B GLY 2.9 26.7 + - - +
454B THR* 3.3 1.7 - - - -
455B GLY* 1.3 80.7 - - - +
457B ASN* 1.3 67.9 + - - +
458B VAL* 3.7 27.4 - - + -
485B ASN* 3.4 19.7 - - - +
487B VAL* 4.6 4.3 - - + -
525B ILE* 4.8 6.3 - - + -
554B LEU* 3.8 34.8 - - + -
558B ARG* 4.3 11.4 - - + -
559B ALA 5.0 0.2 - - - +
560B LEU* 4.6 11.0 - - + -
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Residues in contact with ASN 457 (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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408B GLY 3.5 3.6 - - - -
446B LEU* 4.0 10.5 - - + -
449B MET* 3.2 32.3 - - + +
450B GLN* 4.3 11.1 - - - +
454B THR* 2.7 30.3 + - - -
456B LEU* 1.3 70.3 - - - +
458B VAL* 1.3 63.3 + - - +
459B PHE* 3.9 14.7 - - + -
485B ASN* 2.9 37.7 + - - +
486B ILE* 3.4 9.7 - - + +
487B VAL 2.8 27.5 + - - +
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Residues in contact with VAL 458 (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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408B GLY 2.9 11.0 + - - +
409B LEU* 3.1 21.3 - - + -
410B LEU 2.8 31.7 + - - +
449B MET* 5.2 0.3 - - - +
456B LEU* 3.7 30.7 - - + -
457B ASN* 1.3 77.5 - - - +
459B PHE* 1.3 61.5 + - - +
460B LEU* 3.8 28.9 - - + -
487B VAL* 3.2 16.4 - - + +
525B ILE* 4.6 16.8 - - + -
560B LEU* 4.5 10.3 - - + -
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Residues in contact with PHE 459 (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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410B LEU* 3.5 28.3 - - + +
442B VAL* 3.6 24.2 - - + -
445B ILE* 4.4 2.5 - - + -
446B LEU* 3.5 43.1 - - + -
449B MET* 3.4 32.1 - - + -
457B ASN* 3.9 15.5 - - + -
458B VAL* 1.3 74.0 - - - +
460B LEU* 1.3 63.5 + - - +
461B LEU* 3.9 8.3 - - + -
486B ILE* 4.8 0.7 - - + -
487B VAL 2.9 8.9 + - - -
488B PHE* 3.3 41.1 - + + +
489B GLY 2.8 27.0 + - - +
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Residues in contact with LEU 460 (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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369B LEU* 4.7 6.7 - - + -
409B LEU* 4.2 26.9 - - + -
410B LEU 2.9 12.5 + - - +
411B TYR* 3.3 22.0 - - + -
412B TYR 3.1 25.1 + - - -
458B VAL* 3.8 17.7 - - + -
459B PHE* 1.3 80.4 - - - +
461B LEU* 1.3 61.4 + - - +
462B ASP 3.9 0.4 - - - -
489B GLY* 3.2 19.7 - - - +
511B PHE* 4.1 9.4 - - + -
515B LEU* 4.2 22.7 - - + -
519B LEU* 5.1 5.8 - - + -
525B ILE* 5.6 3.1 - - + -
529B LEU* 4.3 18.8 - - + -
560B LEU* 5.9 1.1 - - + -
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Residues in contact with LEU 461 (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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410B LEU* 4.5 11.0 - - + -
412B TYR* 4.0 18.2 - - + -
423B SER* 4.1 10.1 - - - -
425B MET* 4.5 3.4 - - - -
442B VAL* 3.8 32.8 - - + -
459B PHE* 4.4 11.0 - - + -
460B LEU* 1.3 77.9 - - - +
462B ASP* 1.3 59.9 + - - +
463B MET* 3.4 22.8 + - + +
465B ARG* 6.0 0.3 - - - -
488B PHE* 4.1 16.8 - - + -
489B GLY 2.9 9.5 + - - +
490B TYR* 3.7 35.5 - - + +
491B ALA 2.9 25.7 + - - -
511B PHE* 5.1 0.9 - - - -
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Residues in contact with ASP 462 (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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365B ASP* 4.0 9.5 - - - +
411B TYR* 2.6 34.1 + - + +
412B TYR 2.7 18.2 + - - +
413B ALA* 3.5 5.3 - - - -
414B GLY 3.3 19.4 + - - +
460B LEU 3.8 0.2 + - - -
461B LEU* 1.3 69.3 - - - +
463B MET* 1.3 60.6 + - - +
491B ALA* 3.5 15.2 - - - +
498B ALA* 4.3 6.7 - - - +
499B PHE 5.2 4.7 - - - +
509B GLY* 5.6 1.7 - - - -
510B ILE 5.6 0.5 + - - -
511B PHE* 3.4 31.8 + - + +
512B MET 4.1 2.8 + - - -
546B GLN* 5.1 0.2 + - - -
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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