Contacts of the helix formed by residues 461 - 468 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458A ASP* 3.0 34.9 + - + +
459A PHE 4.4 1.2 - - - +
460A ALA* 1.3 74.7 - - - +
462A ARG* 1.3 62.6 + - - +
463A ALA* 3.0 24.4 + - - +
464A MSE 3.2 27.5 + - + +
465A TRP* 3.3 12.8 + - - +
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Residues in contact with ARG 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A VAL* 5.1 6.9 - - - +
309A GLU* 4.4 7.3 + - - -
459A PHE 3.6 19.2 + - - -
460A ALA* 2.9 17.0 + - - +
461A ASP* 1.3 72.7 + - - +
463A ALA* 1.3 60.5 + - - +
465A TRP* 3.5 36.1 - - - +
466A THR* 2.9 43.8 + - + +
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Residues in contact with ALA 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A ASP* 3.0 12.7 + - - +
462A ARG* 1.3 79.8 - - - +
464A MSE 1.3 53.9 + - - +
466A THR* 3.8 5.2 - - - -
467A THR* 2.6 40.0 + - + +
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Residues in contact with MSE 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A PHE* 4.0 11.2 - - - -
453A VAL* 3.9 32.1 - - + -
454A PRO 5.9 1.1 - - - +
457A VAL* 3.7 21.3 - - + -
458A ASP* 3.0 38.4 - - + +
459A PHE* 3.9 16.4 - - + -
461A ASP* 3.2 27.3 + - + +
463A ALA* 1.3 80.6 - - - +
465A TRP* 1.3 67.9 + - + +
467A THR* 3.4 4.0 + - - -
468A TRP* 3.0 27.4 + - - +
471A HIS* 6.5 0.4 - - + -
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Residues in contact with TRP 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ARG* 3.8 8.5 - - - -
218A VAL* 3.8 29.5 - - + +
308A GLN* 3.3 52.4 - - + +
309A GLU* 3.0 25.0 + - + -
452A PHE* 4.0 15.0 - + - -
459A PHE* 4.6 5.6 - + + +
461A ASP 3.3 9.8 + - - +
462A ARG* 3.4 42.2 + - - +
464A MSE 1.3 88.3 - - + +
466A THR* 1.3 63.3 + - + +
467A THR 3.3 0.9 + - - -
468A TRP* 3.4 44.2 - + - -
595A LEU* 3.7 31.9 - - + -
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Residues in contact with THR 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A TRP 5.3 0.3 - - - +
308A GLN* 3.8 18.7 - - - +
339A ARG* 3.1 60.3 - - - +
350A LEU* 3.6 5.3 - - - +
462A ARG* 2.9 34.5 + - + +
463A ALA* 3.4 9.0 + - - -
465A TRP* 1.3 80.4 - - + +
467A THR* 1.3 66.3 + - - +
469A LEU* 5.4 1.3 + - - +
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Residues in contact with THR 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A LEU* 4.0 8.7 - - + -
351A GLY* 3.8 32.5 - - - +
463A ALA* 2.6 26.5 + - + +
464A MSE 3.6 4.2 + - - -
465A TRP 3.2 0.4 - - - -
466A THR* 1.3 88.4 + - - +
468A TRP* 1.3 64.2 + - - +
469A LEU 3.3 3.1 - - - -
470A VAL* 3.2 20.9 + - - +
471A HIS* 3.4 16.0 + - - +
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Residues in contact with TRP 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ARG* 5.7 2.0 - - - -
308A GLN* 3.9 15.6 + - + +
452A PHE* 3.4 40.3 - + + +
453A VAL* 3.4 23.9 - - + +
464A MSE 3.0 13.5 + - - +
465A TRP* 3.4 51.7 + + - -
466A THR 3.7 0.4 - - - -
467A THR* 1.3 77.4 - - - +
469A LEU* 1.3 91.4 + - + +
471A HIS* 3.3 21.1 + - - +
473A GLN* 4.4 9.6 + - - -
542A LEU* 3.8 28.4 - - + +
592A LEU* 4.2 15.0 - - + -
595A LEU* 3.4 22.0 - - + +
596A TYR* 5.3 1.3 - + - -
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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