Contacts of the strand formed by residues 456 - 462 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406C VAL 3.5 4.5 + - - +
407C TYR* 3.6 42.8 - - + -
408C GLY 2.9 26.4 + - - +
454C THR* 3.4 2.2 - - - -
455C GLY* 1.3 81.0 - - - +
457C ASN* 1.3 67.4 + - - +
458C VAL* 3.7 27.4 - - + -
485C ASN 3.5 18.6 - - - +
487C VAL* 4.6 4.3 - - + -
525C ILE* 4.8 6.3 - - + -
554C LEU* 3.8 32.1 - - + -
558C ARG* 4.3 11.7 - - + -
559C ALA 5.0 0.4 - - - +
560C LEU* 4.6 11.4 - - + -
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Residues in contact with ASN 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C GLY 3.5 3.6 - - - -
446C LEU* 4.1 11.0 - - + -
449C MET* 3.4 23.5 - - + +
450C GLN* 4.1 13.9 - - - +
454C THR* 2.6 28.9 + - - -
456C LEU* 1.3 71.9 - - - +
458C VAL* 1.3 62.2 + - - +
459C PHE* 3.9 18.1 - - + -
485C ASN* 2.8 37.0 + - - +
486C ILE* 3.4 12.3 - - + +
487C VAL 2.8 27.0 + - - +
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Residues in contact with VAL 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C GLY 2.9 10.0 + - - +
409C LEU* 3.2 27.6 - - + -
410C LEU 2.9 25.8 + - - -
449C MET* 5.2 0.3 - - - +
456C LEU* 3.7 31.6 - - + -
457C ASN* 1.3 78.5 - - - +
459C PHE* 1.3 68.9 + - - +
460C LEU* 3.9 22.2 - - + -
487C VAL* 3.2 16.2 - - + +
525C ILE* 4.7 15.3 - - + -
560C LEU* 4.5 10.5 - - + -
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Residues in contact with PHE 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410C LEU* 3.5 28.7 - - + +
442C VAL* 3.5 25.4 - - + -
445C ILE* 4.4 2.9 - - + -
446C LEU* 3.5 41.7 - - + -
449C MET* 3.3 33.0 - - + -
457C ASN* 3.9 15.0 - - + -
458C VAL* 1.3 77.5 - - - +
460C LEU* 1.3 63.4 + - - +
461C LEU* 3.9 9.2 - - + -
486C ILE* 4.7 0.4 - - + -
487C VAL 2.9 7.4 + - - -
488C PHE* 3.3 39.4 - + + +
489C GLY 2.8 27.0 + - - +
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Residues in contact with LEU 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369C LEU* 4.7 6.3 - - + -
409C LEU* 4.0 27.6 - - + -
410C LEU 2.8 11.4 + - - +
411C TYR* 3.3 22.8 - - + -
412C TYR 3.0 24.8 + - - -
458C VAL* 3.9 16.8 - - + -
459C PHE* 1.3 80.2 - - - +
461C LEU* 1.3 61.5 + - - +
462C ASP 3.9 0.2 - - - -
489C GLY* 3.3 20.6 - - - +
511C PHE* 4.1 11.4 - - + -
515C LEU* 4.1 22.4 - - + -
519C LEU* 5.3 5.2 - - + -
525C ILE* 5.6 3.1 - - + -
529C LEU* 4.2 20.2 - - + -
560C LEU* 5.8 0.9 - - + -
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Residues in contact with LEU 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410C LEU* 4.5 7.4 - - + -
412C TYR* 4.0 18.6 - - + -
423C SER* 4.2 9.0 - - - -
425C MET* 4.5 3.8 - - - -
442C VAL* 3.8 40.8 - - + -
459C PHE* 4.3 16.2 - - + -
460C LEU* 1.3 77.9 - - - +
462C ASP* 1.3 59.3 + - - +
463C MET* 3.4 22.3 + - + +
465C ARG* 6.0 0.5 - - - -
488C PHE* 4.0 8.3 - - + -
489C GLY 3.0 10.2 + - - +
490C TYR* 3.7 36.0 - - + +
491C ALA* 3.0 24.3 + - - -
511C PHE* 5.1 0.9 - - - -
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Residues in contact with ASP 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365C ASP* 3.8 10.7 - - - +
411C TYR* 2.7 33.3 + - + +
412C TYR 2.7 18.4 + - - +
413C ALA* 3.4 4.7 - - - +
414C GLY 3.3 21.3 + - - +
460C LEU 3.7 0.4 + - - -
461C LEU* 1.3 69.8 - - - +
463C MET* 1.3 60.0 + - - +
491C ALA* 3.5 15.0 - - - +
498C ALA* 4.3 6.8 - - - +
499C PHE 5.1 4.9 - - - +
509C GLY* 5.4 1.8 - - - -
510C ILE 5.7 0.2 + - - -
511C PHE* 3.5 30.1 + - + +
512C MET 4.2 3.1 + - - -
546C GLN* 5.2 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