Contacts of the strand formed by residues 342 - 348 (chain C) in PDB entry 3IXK
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 GLN 342 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A VAL* 3.8 14.6 - - + +
342A GLN* 5.2 0.2 - - + -
421A PRO* 4.0 9.9 - - + -
237C TRP* 3.8 22.4 - - - -
238C TYR 5.5 0.2 + - - -
337C GLY* 2.8 32.1 + - - -
338C GLU* 2.8 26.7 + - - +
339C VAL* 3.0 36.9 + - + +
340C THR 4.0 1.3 - - - +
341C ASN* 1.3 78.6 - - - +
343C SER* 1.3 85.5 + - - +
344C PHE* 4.0 1.8 - - - +
421C PRO* 3.8 19.1 - - + -
422C PHE 3.3 3.8 - - - +
427C MET* 2.9 12.7 - - - +
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Residues in contact with SER 343 (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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252C VAL* 4.1 9.4 - - - -
334C TYR* 4.3 5.9 - - - -
335C LEU 3.4 15.0 - - - -
337C GLY 3.9 0.7 - - - +
342C GLN* 1.3 86.2 + - - +
344C PHE* 1.3 62.2 + - - +
421C PRO* 3.6 0.3 - - - +
422C PHE* 2.7 48.2 + - - +
424C THR* 2.7 20.4 + - - -
427C MET* 3.2 17.2 - - - +
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Residues in contact with PHE 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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237C TRP* 3.7 50.9 - + + -
238C TYR 3.3 32.1 - - - -
239C THR* 4.0 3.4 - - - -
334C TYR* 3.1 8.4 - - - +
335C LEU* 2.9 59.8 + - + -
336C MET 3.8 12.3 - - - -
337C GLY* 4.3 0.2 - - - -
342C GLN* 4.2 7.9 - - - -
343C SER* 1.3 77.1 - - - +
345C ARG* 1.3 68.6 + - - +
346C ILE* 4.1 14.6 - - + -
402C PHE* 4.3 6.1 - + + -
418C VAL* 4.1 5.6 - - + -
419C GLU 3.3 14.1 - - - +
420C GLY* 4.2 1.1 - - - -
422C PHE* 4.0 4.7 - - - -
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Residues in contact with ARG 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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255C GLU* 3.9 10.1 + - - -
332C SER* 4.1 9.8 + - - -
333C LEU 3.1 10.1 - - - +
334C TYR* 3.0 48.6 + - + -
344C PHE* 1.3 75.6 - - - +
346C ILE* 1.3 64.2 + - - +
347C THR* 4.2 10.4 + - - +
417C ALA 3.8 1.1 - - - +
418C VAL* 3.3 7.6 - - - +
419C GLU* 2.4 69.7 + - + +
422C PHE* 3.8 25.5 - - + -
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Residues in contact with ILE 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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331C ILE 3.5 0.9 - - - +
332C SER* 3.1 3.1 - - - -
333C LEU* 2.8 58.4 + - + +
335C LEU* 4.1 7.4 - - + -
344C PHE* 4.1 12.1 - - + -
345C ARG* 1.3 76.7 - - - +
347C THR* 1.3 62.5 + - - +
348C ILE* 4.1 1.1 + - + -
381C MET* 3.8 29.4 - - + -
385C ILE* 4.0 18.2 - - + -
389C PHE* 3.6 18.2 - - + -
402C PHE* 4.0 36.1 - - + -
417C ALA 3.5 2.9 - - - -
418C VAL* 4.3 6.5 - - + -
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Residues in contact with THR 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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330C VAL* 3.6 32.3 - - + -
331C ILE 3.0 13.2 - - - +
332C SER* 2.8 20.1 + - - +
345C ARG* 4.2 14.2 + - - +
346C ILE* 1.3 74.8 - - - +
348C ILE* 1.3 63.0 + - - +
349C LEU* 5.1 2.9 - - + -
389C PHE* 3.8 2.4 - - - -
415C THR 4.6 2.9 - - - +
416C ALA* 3.3 10.0 - - - +
417C ALA* 3.1 42.7 + - + +
419C GLU* 4.6 1.0 + - - -
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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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282C LEU* 4.8 4.3 - - + -
330C VAL* 3.6 5.2 - - - +
331C ILE* 2.9 43.4 + - + +
346C ILE* 4.1 1.1 + - + -
347C THR* 1.3 73.5 - - - +
349C LEU* 1.3 63.5 + - - +
352C GLN* 3.6 19.1 - - + +
353C TYR* 3.9 23.8 - - + -
384C VAL* 3.9 33.7 - - + +
385C ILE* 4.1 23.3 - - + +
388C GLY* 5.2 0.2 - - - -
389C PHE* 3.7 29.8 - - + -
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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