Contacts of the helix formed by residues 412 - 422 (chain C) in PDB entry 1O04
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 THR 412 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410C PHE* 3.4 11.4 - - - -
411C LYS* 1.3 103.5 - - + +
413C ILE* 1.3 64.5 + - - +
414C GLU* 3.5 16.2 + - - +
415C GLU* 3.0 28.6 + - - +
416C VAL 3.0 18.5 + - - -
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Residues in contact with ILE 413 (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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278C MET* 4.1 18.2 - - + +
410C PHE* 4.6 0.8 - - - -
412C THR* 1.3 74.3 - - - +
414C GLU* 1.3 85.3 + - - +
416C VAL* 3.4 7.1 - - + +
417C VAL* 3.2 23.0 + - - +
438C LYS* 3.9 31.9 - - + -
441C TYR* 3.7 35.4 - - + -
442C LEU* 3.8 28.3 - - + -
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Residues in contact with GLU 414 (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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412C THR* 3.5 19.0 - - - +
413C ILE* 1.3 92.3 - - - +
415C GLU* 1.3 66.4 + - - +
417C VAL* 3.4 11.8 + - - +
418C GLY* 3.5 8.7 + - - -
441C TYR* 3.6 23.8 + - - +
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Residues in contact with GLU 415 (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 PHE* 3.7 8.3 - - - +
411C LYS* 2.7 34.8 + - - +
412C THR* 3.0 24.5 + - + +
414C GLU* 1.3 77.4 - - - +
416C VAL* 1.3 62.0 + - - +
418C GLY* 3.3 4.0 + - - -
419C ARG* 2.9 57.5 + - + +
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Residues in contact with VAL 416 (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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276C ILE* 4.1 26.2 - - + -
278C MET* 4.9 0.2 - - - -
309C PHE* 3.8 31.6 - - + -
410C PHE* 3.5 46.2 - - + -
412C THR 3.0 6.6 + - - +
413C ILE* 3.4 16.6 - - + +
414C GLU 3.3 0.2 - - - -
415C GLU* 1.3 74.7 - - - +
417C VAL* 1.3 63.1 + - - +
419C ARG* 4.4 4.3 - - - +
420C ALA* 2.8 33.9 + - - +
442C LEU* 4.3 7.4 - - + -
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Residues in contact with VAL 417 (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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413C ILE 3.2 11.9 + - - +
414C GLU* 3.7 9.0 - - - +
415C GLU 3.2 0.4 - - - -
416C VAL* 1.3 76.3 - - - +
418C GLY* 1.3 63.7 + - - +
420C ALA* 3.8 4.0 - - - +
421C ASN* 3.0 42.9 + - - +
441C TYR* 3.6 18.4 - - + +
442C LEU* 3.4 29.6 - - + -
445C ALA* 4.0 20.6 - - + -
446C LEU* 5.0 4.7 - - + -
72D LEU* 5.4 4.0 - - + -
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Residues in contact with GLY 418 (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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414C GLU 3.5 5.3 + - - -
415C GLU* 3.3 6.7 + - - -
417C VAL* 1.3 82.4 - - - +
419C ARG* 1.3 57.4 + - - +
421C ASN* 3.4 4.8 + - - +
422C ASN* 3.0 30.0 + - - +
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Residues in contact with ARG 419 (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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307C ARG* 3.0 15.4 + - - -
309C PHE* 3.7 26.0 - - + -
389C VAL 4.7 3.4 + - - -
390C GLN* 5.0 5.7 + - - -
391C ASP* 2.8 46.7 + - - +
408C LEU* 3.8 12.7 - - - +
409C LYS 2.8 29.1 + - - -
410C PHE* 3.6 6.9 - - - +
415C GLU* 2.9 49.6 + - + +
416C VAL* 3.9 3.6 - - - +
418C GLY* 1.3 74.6 - - - +
420C ALA* 1.3 64.4 + - - +
422C ASN* 3.2 16.9 + - - +
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Residues in contact with ALA 420 (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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274C PRO* 3.7 22.4 - - + +
276C ILE* 4.1 7.0 - - + -
307C ARG* 2.9 30.3 + - - +
309C PHE* 4.2 7.3 - - + -
416C VAL 2.8 22.1 + - - +
417C VAL 3.8 0.9 - - - +
419C ARG* 1.3 72.2 - - - +
421C ASN* 1.3 61.5 + - - +
422C ASN 3.5 0.2 + - - -
423C SER* 4.4 1.7 - - - -
446C LEU* 3.6 28.0 - - + -
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Residues in contact with ASN 421 (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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417C VAL* 3.0 31.6 + - - +
418C GLY* 4.1 4.7 - - - +
420C ALA* 1.3 76.7 - - - +
422C ASN* 1.3 57.1 + - - +
423C SER* 2.9 8.1 + - - +
445C ALA 3.0 23.8 + - - -
446C LEU* 3.6 8.9 - - - +
447C GLN* 2.9 53.6 + - - +
469C LYS* 2.8 27.6 + - - +
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Residues in contact with ASN 422 (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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307C ARG* 4.4 4.2 + - - -
391C ASP* 5.8 6.0 + - - +
418C GLY 3.0 18.1 + - - +
419C ARG* 3.2 14.7 + - - +
420C ALA 3.3 0.2 - - - -
421C ASN* 1.3 72.4 - - - +
423C SER* 1.3 59.4 + - - +
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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