Contacts of the strand formed by residues 408 - 412 (chain C) in PDB entry 4J2X
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 408 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381C PRO* 3.6 24.2 - - + -
403C ASN 4.2 1.1 - - - +
404C PHE* 3.8 10.1 - - + -
405C THR* 3.4 37.8 - - + +
406C PRO 3.2 5.2 - - - +
407C ASN* 1.3 79.0 - - - +
409C ARG* 1.3 70.2 + - - +
419C THR* 3.7 16.7 - - - +
427C MET* 4.6 12.9 - - + +
454C LEU* 4.5 9.9 - - + -
455C VAL 3.3 19.3 - - - +
456C ARG* 4.0 7.4 - - + +
462C TYR* 3.7 36.1 - - + -
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Residues in contact with ARG 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ARG* 3.6 29.2 - - - +
406C PRO 3.0 26.6 + - - -
407C ASN* 3.5 7.8 - - - +
408C LEU* 1.3 76.0 + - - +
410C VAL* 1.3 60.6 + - - +
411C TRP* 3.4 11.6 - - - +
416C GLU* 4.1 29.4 + - + +
417C ALA 4.4 4.5 - - - +
419C THR* 3.6 19.1 - - - +
454C LEU* 3.7 4.2 - - - -
455C VAL* 2.9 33.5 + - + +
456C ARG 6.4 0.2 - - - -
457C ASN* 3.3 26.5 + - - +
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Residues in contact with VAL 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C LEU* 5.4 0.2 - - + -
399C LEU* 3.6 27.1 - - + -
409C ARG* 1.3 71.0 - - - +
411C TRP* 1.3 59.4 + - - +
412C PHE* 3.8 18.4 - - + -
417C ALA* 2.7 35.1 + - + +
419C THR* 2.9 29.9 + - + +
427C MET* 3.9 1.1 - - + -
429C CYS* 3.8 15.3 - - + -
452C VAL* 3.8 27.4 - - + -
453C THR 3.5 5.4 - - - +
454C LEU* 3.8 14.1 - - + -
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Residues in contact with TRP 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LEU* 3.6 39.9 - - + -
58C THR 4.2 6.5 - - - -
59C ARG* 4.3 8.7 - - + -
62C MET* 3.7 42.2 - - + -
409C ARG* 3.4 20.4 + - - +
410C VAL* 1.3 78.0 - - - +
412C PHE* 1.3 62.0 + - - +
413C GLY 3.6 6.6 + - - +
414C ASP 3.5 28.7 - - - -
415C VAL 3.4 2.7 - - - -
416C GLU* 3.4 46.1 + - + +
451C PRO 3.1 6.8 - - - +
452C VAL* 3.5 2.8 - - - -
453C THR* 2.7 37.6 + - - +
455C VAL* 3.4 25.4 - - + +
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Residues in contact with PHE 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C LEU* 3.7 16.8 - - + -
410C VAL* 3.8 8.3 - - + -
411C TRP* 1.3 72.8 - - - +
413C GLY* 1.3 64.0 + - - +
414C ASP 3.2 0.5 + - - -
415C VAL* 2.8 21.6 + - - +
417C ALA* 3.7 20.6 - - + -
429C CYS* 3.6 33.2 - - - -
430C VAL 4.5 0.2 - - - -
431C VAL* 4.1 11.9 - - + -
432C PRO* 3.6 30.3 - - + -
437C PHE* 3.3 29.5 - - + -
450C VAL* 4.0 5.6 - - + -
451C PRO 3.4 5.4 - - - -
452C VAL* 4.7 4.7 - - + -
468C PHE* 3.8 42.6 - + + -
470C TYR* 4.3 1.1 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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