Contacts of the strand formed by residues 343 - 349 (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 LYS 343 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340C ALA* 3.7 15.5 - - + -
342C ASP* 1.3 94.4 + - - +
344C VAL* 1.3 57.8 + - - +
376C LEU 2.7 30.0 + - - -
377C ASP* 4.1 5.3 + - - +
378C PHE* 3.3 28.3 - - + -
379C LYS* 2.8 29.5 + - - +
407C TYR* 3.5 15.7 - - + -
560C LEU 2.9 22.2 + - - +
561C THR* 3.8 5.9 + - - +
562C ASP 2.8 29.8 + - - +
563C PRO* 5.0 0.4 - - - +
564C ILE* 3.8 21.0 - - + +
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Residues in contact with VAL 344 (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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342C ASP* 4.4 9.0 - - - +
343C LYS* 1.3 79.6 - - - +
345C ALA* 1.3 63.2 + - - +
378C PHE* 3.5 4.7 - - - -
379C LYS* 3.4 7.4 - - + +
398C PHE* 3.7 16.0 - - + -
401C LEU* 3.9 36.3 - - + +
402C LEU* 4.0 7.6 - - + -
406C VAL* 3.8 20.4 - - + -
407C TYR 2.9 8.6 + - - +
408C GLY* 3.4 3.5 - - - -
409C LEU 3.0 22.5 + - - -
580C TRP* 3.7 26.0 - - + -
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Residues in contact with ALA 345 (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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344C VAL* 1.3 76.7 - - - +
346C LEU* 1.3 59.8 + - - +
347C LEU* 4.0 7.2 - - + -
373C LEU* 3.9 27.8 - - + -
378C PHE* 4.0 11.6 - - + -
379C LYS 2.9 9.2 + - - +
380C VAL* 3.5 9.4 - - + -
381C VAL 2.9 25.5 + - - -
398C PHE* 4.0 4.5 - - - -
409C LEU* 3.1 16.2 - - + +
580C TRP* 3.7 4.9 - - - -
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Residues in contact with LEU 346 (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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345C ALA* 1.3 72.9 - - - +
347C LEU* 1.3 63.1 + - - +
348C ILE* 3.9 21.8 - - + -
381C VAL* 3.5 30.5 - - + +
383C LEU* 4.1 15.3 - - + -
394C ALA* 3.9 29.6 - - + +
395C VAL* 3.9 12.6 - - + +
398C PHE* 3.8 24.6 - - + -
409C LEU 3.0 5.9 + - - -
410C LEU* 3.3 26.5 - - + +
411C TYR 3.0 23.4 + - - -
580C TRP* 5.1 2.0 - - + -
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Residues in contact with LEU 347 (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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345C ALA* 4.0 11.4 - - + -
346C LEU* 1.3 82.1 - - - +
348C ILE* 1.3 63.4 + - - +
349C GLY 4.3 0.2 - - - -
366C VAL* 3.7 19.2 - - + +
369C LEU* 3.9 13.2 - - + +
370C THR* 3.1 45.1 - - - +
373C LEU* 3.8 21.5 - - + -
380C VAL* 4.2 5.8 - - + -
381C VAL 2.9 11.8 + - - +
382C SER* 3.4 2.4 - - - -
383C LEU* 2.9 27.6 + - - +
409C LEU* 4.2 1.3 - - + -
411C TYR* 3.4 28.7 - - + +
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Residues in contact with ILE 348 (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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346C LEU* 3.9 32.1 - - + -
347C LEU* 1.3 78.5 - - - +
349C GLY* 1.3 61.1 + - - +
350C ASN* 3.8 21.5 - - - +
366C VAL* 3.9 6.2 - - - +
383C LEU* 3.3 5.2 - - + +
386C LEU* 3.8 30.7 - - + -
391C MET* 4.3 23.8 - - + +
394C ALA* 4.7 3.8 - - + -
395C VAL* 5.1 3.1 - - + -
410C LEU* 4.7 7.0 - - + -
411C TYR 2.9 7.8 + - - +
412C TYR* 3.4 27.0 - - + -
413C ALA 2.9 24.8 + - - +
425C MET* 5.9 2.2 - - + -
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Residues in contact with GLY 349 (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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348C ILE* 1.3 74.4 - - - +
350C ASN* 1.3 62.3 + - - -
362C PRO* 4.0 9.2 - - - -
366C VAL* 3.7 17.0 - - - +
383C LEU 2.9 11.5 + - - -
384C LEU* 3.2 18.5 - - - +
385C ASP 2.8 22.9 + - - -
413C ALA 3.2 7.0 - - - -
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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