Contacts of the helix formed by residues 461 - 468 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458B ASP* 3.0 33.8 + - + +
459B PHE 4.1 0.4 - - - +
460B ALA* 1.3 72.6 - - - +
462B ARG* 1.3 63.1 + - - +
463B ALA* 3.1 21.1 + - - +
464B MSE 3.2 30.2 + - + +
465B TRP* 3.3 12.1 + - - +
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Residues in contact with ARG 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B VAL* 5.3 5.7 - - - +
309B GLU* 4.4 7.3 + - - -
459B PHE 3.4 20.8 + - - -
460B ALA* 2.9 19.6 + - - +
461B ASP* 1.3 72.9 + - - +
463B ALA* 1.3 61.0 + - - +
465B TRP* 3.4 32.2 + - - +
466B THR* 2.9 42.1 + - + +
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Residues in contact with ALA 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B ASP* 3.1 13.7 + - - +
462B ARG* 1.3 78.2 - - - +
464B MSE 1.3 55.1 + - - +
466B THR* 3.4 6.2 + - - -
467B THR* 2.7 38.5 + - + +
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Residues in contact with MSE 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B PHE* 4.0 11.7 - - - -
453B VAL* 3.9 34.1 - - + -
454B PRO 5.9 0.4 - - - +
457B VAL* 3.9 15.7 - - + -
458B ASP 3.0 38.8 - - - +
459B PHE* 3.8 17.0 - - + +
461B ASP* 3.2 25.2 + - + +
463B ALA* 1.3 79.1 - - - +
465B TRP* 1.3 73.5 + - + +
467B THR* 3.4 4.6 + - - -
468B TRP* 3.0 22.3 + - - +
471B HIS* 6.6 0.2 - - + -
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Residues in contact with TRP 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ARG* 3.8 15.3 - - - -
218B VAL* 3.8 25.9 - - + +
308B GLN* 3.4 46.6 - - + +
309B GLU* 3.0 24.3 + - + -
452B PHE* 4.0 15.9 - + - -
459B PHE* 4.4 6.5 - + - +
461B ASP 3.3 9.3 + - - +
462B ARG* 3.4 42.5 + - - +
464B MSE 1.3 88.0 - - + +
466B THR* 1.3 64.6 + - + +
467B THR 3.3 0.9 + - - -
468B TRP* 3.4 48.0 - + - -
595B LEU* 3.6 31.9 - - + -
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Residues in contact with THR 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B TRP 5.2 0.3 - - - +
308B GLN* 3.7 18.4 - - - +
339B ARG* 3.1 62.4 - - - +
350B LEU* 3.8 3.7 - - - +
462B ARG* 2.9 34.6 + - + +
463B ALA* 3.4 9.0 + - - -
465B TRP* 1.3 78.9 - - + +
467B THR* 1.3 67.7 + - - +
468B TRP 3.6 0.4 - - - -
469B LEU* 5.3 1.7 + - - +
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Residues in contact with THR 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B LEU* 4.1 9.2 - - + -
351B GLY* 3.8 33.7 - - - +
463B ALA* 2.7 25.8 + - + +
464B MSE 3.6 4.5 + - - -
465B TRP 3.2 0.6 - - - -
466B THR* 1.3 87.1 - - - +
468B TRP* 1.3 62.8 + - - +
469B LEU 3.3 2.7 - - - -
470B VAL* 3.2 22.8 + - - +
471B HIS* 3.4 12.7 + - - +
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Residues in contact with TRP 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ARG* 5.7 1.6 - - - -
308B GLN* 3.8 18.0 + - + +
452B PHE* 3.5 37.2 - + + +
453B VAL* 3.4 23.3 - - + -
464B MSE 3.0 13.1 + - - +
465B TRP* 3.4 48.5 + + - -
466B THR 3.6 0.4 - - - -
467B THR* 1.3 78.3 - - - +
469B LEU* 1.3 89.3 + - + +
470B VAL 3.3 0.9 + - - -
471B HIS* 3.3 20.0 + - - +
473B GLN* 4.4 9.6 + - - -
518B LYS* 6.5 0.2 - - - -
539B PRO* 5.2 0.2 - - - +
542B LEU* 3.8 28.0 - - + -
592B LEU* 4.1 15.7 - - + -
595B LEU* 3.3 26.5 - - + -
596B 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