Contacts of the helix formed by residues 486 - 495 (chain A) in PDB entry 1PRH
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 GLU 486 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ARG* 5.5 5.1 + - - +
438A ARG* 6.2 2.0 - - - +
484A GLU* 3.5 8.1 + - - +
485A LYS* 1.3 83.1 - - - +
487A MET* 1.3 65.6 + - + +
489A ALA* 3.1 9.2 + - - +
490A GLU* 3.2 13.2 + - - +
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Residues in contact with MET 487 (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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181A PHE* 3.5 34.5 - - + +
436A GLY 4.3 16.8 - - - +
437A GLY* 5.7 1.8 - - - -
438A ARG* 3.3 37.7 - - + +
482A THR* 4.7 11.4 - - + -
484A GLU* 3.0 37.0 + - + +
486A GLU* 1.3 71.8 - - + +
488A ALA* 1.3 54.4 + - - +
490A GLU* 3.0 5.9 + - - +
491A LEU* 2.8 38.6 + - + +
509A LEU* 4.6 15.0 - - + +
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Residues in contact with ALA 488 (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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478A PHE* 3.5 11.2 - - + +
479A GLN* 3.7 27.1 - - + +
482A THR* 3.3 27.6 - - - +
484A GLU* 2.8 20.7 + - - +
485A LYS 3.8 3.1 - - - +
487A MET* 1.3 76.3 - - - +
489A ALA* 1.3 51.8 + - - +
491A LEU* 3.2 3.6 + - - +
492A GLU* 2.8 36.0 + - - +
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Residues in contact with ALA 489 (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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479A GLN* 5.3 5.3 - - - +
485A LYS 2.9 20.7 + - - +
486A GLU* 3.4 5.6 - - - +
488A ALA* 1.3 76.9 - - - +
490A GLU* 1.3 57.3 + - - +
492A GLU* 3.3 11.1 + - - +
493A GLU* 3.0 25.3 + - - +
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Residues in contact with GLU 490 (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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176A PHE* 4.1 11.1 - - - -
180A ARG* 2.8 57.3 + - - +
181A PHE* 4.0 15.1 - - + -
438A ARG* 5.9 0.5 + - - -
486A GLU* 3.2 8.6 + - - +
487A MET* 3.0 9.8 + - - +
489A ALA* 1.3 75.8 - - - +
491A LEU* 1.3 55.4 + - - +
493A GLU* 3.1 26.3 + - - +
494A LEU* 2.8 40.1 + - + +
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Residues in contact with LEU 491 (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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177A LEU* 4.7 4.5 - - + -
181A PHE* 3.5 30.9 - - + -
478A PHE* 3.6 27.8 - - + -
481A LEU* 4.6 5.4 - - + -
482A THR* 3.8 25.4 - - + -
487A MET* 2.8 16.4 + - + +
488A ALA 3.2 4.7 - - - +
490A GLU* 1.3 75.5 - - - +
492A GLU* 1.3 57.6 + - - +
494A LEU* 3.1 5.0 + - + +
495A TYR* 2.8 50.2 + - + +
501A LEU* 4.8 1.1 - - + -
509A LEU* 3.9 28.7 - - + -
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Residues in contact with GLU 492 (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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168A LYS* 4.9 0.3 + - - -
477A SER* 5.3 5.2 - - - -
478A PHE* 3.6 34.9 + - + +
479A GLN* 5.9 3.1 - - - +
488A ALA 2.8 14.3 + - - +
489A ALA* 3.3 12.9 - - - +
491A LEU* 1.3 75.1 - - - +
493A GLU* 1.3 57.7 + - - +
496A GLY* 2.9 37.8 + - - +
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Residues in contact with GLU 493 (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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168A LYS* 3.4 21.9 + - - +
489A ALA 3.0 12.7 + - - +
490A GLU* 3.2 31.0 - - - +
492A GLU* 1.3 77.1 - - - +
494A LEU* 1.3 61.9 + - + +
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Residues in contact with LEU 494 (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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168A LYS* 3.6 15.2 - - - +
172A PRO* 3.6 40.0 - - + +
173A ASP 5.4 0.2 - - - +
176A PHE* 3.8 36.3 - - + -
177A LEU* 5.2 6.1 - - + -
181A PHE* 4.0 24.7 - - + -
490A GLU* 2.8 24.7 + - + +
491A LEU* 3.1 5.1 + - + +
493A GLU* 1.3 84.3 - - + +
495A TYR* 1.3 66.1 + - + +
496A GLY 3.6 0.2 + - - -
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Residues in contact with TYR 495 (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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167A GLY* 3.9 3.3 - - - -
168A LYS* 3.4 22.3 + - - +
171A LEU* 4.5 8.3 - - + +
172A PRO* 3.6 26.5 - - + -
177A LEU* 3.3 36.2 - - + +
478A PHE* 3.5 26.5 - + + -
491A LEU* 2.8 19.6 + - + -
494A LEU* 1.3 75.3 - - + +
496A GLY* 1.3 57.4 + - - +
497A ASP 3.1 11.5 + - - +
500A ALA* 3.5 21.1 - - + +
501A LEU* 3.6 29.2 - - + -
502A GLU* 3.0 45.4 + - + +
505A PRO* 3.9 6.0 - - + +
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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