Contacts of the strand formed by residues 399 - 405 (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 ARG 399 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238C TYR* 3.5 46.5 + - + -
239C THR 3.4 16.2 - - - +
240C PRO* 4.4 1.6 - - + -
241C ILE* 3.6 7.4 - - - +
338C GLU* 2.7 43.5 + - + +
394C ASP* 2.8 62.4 + - + +
397C ARG* 3.5 50.4 - - - +
398C LYS* 1.3 81.6 - - - +
400C ILE* 1.3 65.8 + - - +
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Residues in contact with ILE 400 (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 3.6 0.9 - - - +
238C TYR* 3.2 5.5 - - - -
239C THR* 2.9 42.8 + - + +
241C ILE* 3.8 17.5 - - + -
247C TYR* 4.0 27.8 - - + -
249C VAL* 4.0 20.9 - - + -
275C VAL* 4.3 8.5 - - + -
391C VAL* 3.8 18.8 - - + -
392C VAL 3.2 10.1 - - - +
393C PHE* 4.3 13.9 - - + -
399C ARG* 1.3 79.2 - - - +
401C GLY* 1.3 61.5 + - - +
402C PHE* 3.5 26.1 - - + -
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Residues in contact with GLY 401 (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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236C LEU* 4.2 6.3 - - - -
237C TRP 3.2 7.6 - - - -
238C TYR* 3.4 22.5 - - - -
390C TYR 4.2 1.1 - - - -
391C VAL* 3.2 10.0 - - - +
392C VAL* 2.7 41.4 + - - -
400C ILE* 1.3 72.6 - - - +
402C PHE* 1.3 64.6 + - - -
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Residues in contact with PHE 402 (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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235C SER 3.8 0.2 - - - +
236C LEU* 3.6 2.7 - - - +
237C TRP 2.9 33.0 + - - +
239C THR* 4.3 7.4 - - + -
249C VAL* 5.7 0.4 - - + -
275C VAL* 4.4 13.7 - - + -
335C LEU* 3.7 22.0 - - + -
344C PHE* 4.3 4.5 - + + -
346C ILE* 4.0 38.8 - - + -
381C MET* 4.0 22.2 - - + -
385C ILE* 4.6 8.1 - - + -
386C MET* 6.1 0.7 - - + -
389C PHE* 4.2 16.4 - + + -
390C TYR 3.4 4.3 - - - -
391C VAL* 4.1 17.9 - - + -
400C ILE* 3.5 31.0 - - + -
401C GLY* 1.3 76.2 - - - -
403C ALA* 1.3 61.5 + - - +
418C VAL* 3.7 14.5 - - + +
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Residues in contact with ALA 403 (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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232C TYR* 3.5 36.1 - - + -
233C THR 4.0 1.3 - - - +
235C SER 3.8 12.8 - - - +
236C LEU* 3.7 14.6 - - + -
389C PHE* 3.2 5.9 - - - +
390C TYR* 2.8 32.1 + - + +
402C PHE* 1.3 75.3 - - - +
404C VAL* 1.3 61.8 + - - +
405C SER 3.1 0.2 + - - -
418C VAL* 3.7 9.0 - - - -
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Residues in contact with VAL 404 (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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232C TYR* 3.3 3.6 - - - +
233C THR* 3.0 57.8 + - - +
234C GLY* 5.0 2.0 - - - -
235C SER 5.2 0.2 + - - -
388C GLY 4.1 6.1 - - - +
389C PHE* 4.1 3.4 - - + -
403C ALA* 1.3 72.9 - - - +
405C SER* 1.3 63.0 + - - +
408C HIS* 5.1 6.7 - - + +
416C ALA 3.6 11.7 - - - +
417C ALA* 3.5 16.8 - - - +
418C VAL* 3.2 33.6 - - + +
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Residues in contact with SER 405 (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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201C GLN* 3.3 22.2 + - - +
202C LEU 5.1 0.6 + - - -
231C LEU 3.9 3.1 - - - -
233C THR* 5.1 2.1 + - - -
387C GLU 4.3 2.6 + - - -
388C GLY 3.1 25.5 + - - -
389C PHE 3.6 15.3 - - - -
390C TYR* 3.8 6.1 - - - +
403C ALA 3.1 1.6 + - - -
404C VAL* 1.3 73.6 - - - +
406C ALA* 1.3 64.6 + - - +
407C CYS* 3.1 16.2 + - - -
408C HIS* 3.3 26.5 - - - -
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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