Contacts of the helix formed by residues 461 - 468 (chain C) in PDB entry 1MPX
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 ASP 461 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458C ASP* 3.0 34.6 + - + +
459C PHE 4.1 0.8 - - - +
460C ALA* 1.3 74.1 - - - +
462C ARG* 1.3 62.6 + - - +
463C ALA* 3.2 20.3 + - - +
464C MSE 3.1 30.5 + - + +
465C TRP* 3.2 12.8 + - - +
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Residues in contact with ARG 462 (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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218C VAL* 5.4 4.9 - - - +
309C GLU* 4.4 8.1 + - - -
459C PHE 3.4 21.2 + - - -
460C ALA* 2.9 20.4 + - - +
461C ASP* 1.3 71.8 + - - +
463C ALA* 1.3 59.9 + - - +
465C TRP* 3.8 29.5 - - - +
466C THR* 2.8 43.9 + - + +
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Residues in contact with ALA 463 (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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461C ASP* 3.2 13.9 + - - +
462C ARG* 1.3 78.2 - - - +
464C MSE 1.3 56.3 + - - +
466C THR* 3.4 4.7 + - - -
467C THR* 2.6 40.4 + - + +
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Residues in contact with MSE 464 (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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452C PHE* 4.0 10.8 - - + -
453C VAL* 3.9 32.1 - - + -
454C PRO 5.9 0.9 - - - +
457C VAL* 3.8 20.6 - - + -
458C ASP 3.0 37.7 - - - +
459C PHE* 3.8 15.7 - - + -
461C ASP* 3.1 26.6 + - + +
463C ALA* 1.3 79.6 - - - +
465C TRP* 1.3 74.3 + - + +
467C THR* 3.4 4.9 + - - -
468C TRP* 3.0 22.0 + - - +
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Residues in contact with TRP 465 (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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216C ARG* 3.9 13.0 - - - -
218C VAL* 3.8 27.7 - - + +
308C GLN* 3.2 47.0 - - + +
309C GLU* 3.0 27.7 + - + -
452C PHE* 4.1 15.9 - + - -
459C PHE* 4.3 12.6 - + - +
461C ASP 3.2 12.0 + - - +
462C ARG* 3.8 30.7 - - - +
464C MSE 1.3 87.4 - - + +
466C THR* 1.3 62.3 - - + +
467C THR 3.4 0.2 + - - -
468C TRP* 3.4 44.2 - + - -
595C LEU* 3.7 31.2 - - + -
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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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306C TRP 5.3 0.5 - - - +
308C GLN* 3.8 18.1 - - - +
339C ARG* 3.1 60.6 - - - +
340C HIS 5.5 0.2 - - - +
350C LEU* 3.6 4.2 - - - +
462C ARG* 2.8 35.1 + - + +
463C ALA* 3.4 8.1 + - - -
465C TRP* 1.3 80.2 - - + +
467C THR* 1.3 65.7 + - - +
468C TRP 3.7 0.2 - - - -
469C LEU* 5.3 1.4 + - - +
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Residues in contact with THR 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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350C LEU* 4.0 8.3 - - + -
351C GLY* 3.8 34.3 - - - +
463C ALA* 2.6 26.0 + - + +
464C MSE 3.4 5.4 + - - -
465C TRP 3.2 0.6 - - - -
466C THR* 1.3 85.9 - - - +
468C TRP* 1.3 64.2 + - - +
469C LEU 3.3 3.1 - - - -
470C VAL* 3.3 20.1 + - - +
471C HIS* 3.3 16.6 + - - +
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Residues in contact with TRP 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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216C ARG* 5.6 2.0 - - - -
308C GLN* 3.8 18.5 + - + +
452C PHE* 3.4 37.4 - + + +
453C VAL* 3.4 24.5 - - + +
464C MSE 3.0 13.3 + - - +
465C TRP* 3.4 46.4 + + - -
466C THR 3.7 1.4 - - - -
467C THR* 1.3 77.8 - - - +
469C LEU* 1.3 88.8 + - + +
470C VAL 3.3 1.0 + - - -
471C HIS* 3.3 19.2 + - - +
473C GLN* 4.4 9.2 + - - -
542C LEU* 3.9 27.3 - - + +
592C LEU* 4.1 15.5 - - + -
595C LEU* 3.3 26.0 - - + +
596C TYR* 5.2 1.8 - + - -
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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