Contacts of the helix formed by residues 465 - 472 (chain C) in PDB entry 1OVM
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 TYR 465 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410C ILE* 5.0 2.7 - - + -
436C GLY* 3.7 19.5 + - - -
439C GLN* 5.2 1.4 + - - -
440C LEU* 5.7 2.3 - - + +
464C GLY* 1.3 74.0 - - - -
466C THR* 1.3 64.3 + - - +
467C VAL 3.3 1.8 - - - -
468C GLU* 3.2 12.8 + - + +
469C ARG* 3.0 25.0 + - - +
478C TYR 3.8 6.7 - - - -
479C ASN* 3.2 24.9 + - - +
480C ASP 4.3 2.0 + - - -
481C ILE* 3.3 28.6 - - + +
600C TPP 3.2 48.7 - - + -
26D VAL* 4.9 4.3 - - - +
27D PRO* 3.3 38.4 - - + +
49D CYS 4.3 13.3 + - - -
50D ALA* 5.3 3.1 + - - -
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Residues in contact with THR 466 (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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385C THR* 3.4 8.0 - - - +
462C ASN* 3.0 43.5 - - + +
464C GLY 4.1 0.9 - - - +
465C TYR* 1.3 72.4 - - - +
467C VAL* 1.3 56.3 + - - -
469C ARG* 3.1 11.7 + - - +
470C ALA* 2.8 30.1 + - - +
531C PRO 4.5 1.3 - - - +
532C LYS 3.0 28.3 - - - +
533C ALA* 5.0 0.4 - - - -
534C ASP 4.0 1.0 + - - +
535C ILE* 3.1 25.5 - - - +
600C TPP 2.6 19.7 + - - -
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Residues in contact with VAL 467 (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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384C GLY* 3.3 22.0 - - - -
388C PHE* 4.8 1.8 - - + -
466C THR* 1.3 76.9 + - - +
468C GLU* 1.3 69.2 + - - +
470C ALA* 3.2 8.7 + - - +
471C ILE* 3.0 28.7 + - + +
539C LEU* 3.2 42.2 - - + -
543C THR* 3.7 1.1 + - - +
600C TPP 3.2 54.4 + - - +
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Residues in contact with GLU 468 (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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465C TYR* 3.2 24.1 + - + +
467C VAL* 1.3 77.8 - - - +
469C ARG* 1.3 57.6 + - - +
471C ILE* 2.9 21.7 + - - +
472C HIS 2.8 33.1 + - - +
479C ASN* 3.0 22.9 - - - +
600C TPP 3.8 37.4 + - + +
27D PRO* 5.2 1.1 - - + -
28D GLY* 3.3 15.6 + - - -
29D ASP* 3.2 26.0 + - - +
32D LEU* 3.9 11.8 - - + +
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Residues in contact with ARG 469 (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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462C ASN 4.0 3.6 + - - -
463C GLU 3.3 20.2 + - - -
464C GLY* 4.2 4.9 - - - -
465C TYR 3.0 12.8 + - - +
466C THR* 3.4 9.3 - - - +
468C GLU* 1.3 77.7 - - - +
470C ALA* 1.3 62.1 + - - +
471C ILE 3.3 0.7 + - - -
472C HIS* 3.5 6.6 + - - -
474C ALA* 3.2 52.7 + - + +
476C GLN 5.0 0.4 + - - -
479C ASN* 3.2 37.3 + - + +
480C ASP* 2.3 33.1 + - - -
532C LYS* 2.9 55.0 + - - +
533C ALA* 6.1 1.8 - - - +
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Residues in contact with ALA 470 (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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466C THR 2.8 13.7 + - - +
467C VAL* 3.4 8.1 - - - +
468C GLU 3.1 0.2 - - - -
469C ARG* 1.3 76.9 - - - +
471C ILE* 1.3 60.5 + - - +
535C ILE* 4.2 22.0 - - + -
539C LEU* 5.5 0.4 - - + -
543C THR* 3.2 37.5 - - + +
547C GLU* 5.7 0.2 - - - +
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Residues in contact with ILE 471 (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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467C VAL* 3.0 16.9 + - + +
468C GLU* 2.9 29.2 + - - +
470C ALA* 1.3 81.6 - - - +
472C HIS* 1.3 59.1 + - + +
543C THR* 3.4 19.7 - - - +
546C LEU* 3.4 33.2 - - + -
547C GLU* 2.8 39.6 - - + +
550C ASN* 4.0 23.3 - - - +
29D ASP* 4.6 11.4 - - + +
32D LEU* 4.0 12.3 - - + -
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Residues in contact with HIS 472 (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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468C GLU 2.8 22.2 + - - +
469C ARG 3.5 3.0 + - - -
471C ILE* 1.3 78.6 - - + +
473C GLY* 1.3 80.0 + - - +
474C ALA 3.5 2.0 - - - -
478C TYR* 3.2 12.2 + - - -
479C ASN* 3.3 8.5 + - - -
547C GLU* 3.0 30.7 - - - +
550C ASN* 5.6 0.7 - - - +
32D LEU* 4.1 25.0 - - + +
33D GLN* 4.0 23.6 + - + -
36D ASP* 2.7 38.9 + - - -
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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