Contacts of the helix formed by residues 447 - 455 (chain J) in PDB entry 6NR8
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 PRO 447 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411J GLY 4.8 4.3 - - - +
414J GLU* 4.4 2.9 - - + -
415J MET* 3.8 27.6 - - + -
443J LEU 3.6 5.2 - - - +
444J ARG* 3.3 18.6 - - - +
446J LEU* 1.3 96.2 - - + +
448J THR* 1.3 61.5 + - - +
450J ILE* 3.4 11.5 - - + +
451J ALA* 3.1 26.3 + - - +
461J LEU* 3.6 15.8 - - + +
462J VAL* 3.7 15.9 - - + -
478J LEU* 4.0 11.4 - - + -
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Residues in contact with THR 448 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444J ARG 3.3 19.1 - - - +
445J MET* 2.3 36.7 + - + +
447J PRO* 1.3 78.4 - - - +
449J ILE* 1.3 65.1 + - - +
450J ILE 3.1 1.5 + - - -
451J ALA 3.6 1.0 + - - -
452J ASP* 3.3 12.5 - - - +
458J SER* 3.0 36.2 + - - +
462J VAL* 3.7 15.0 - - + -
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Residues in contact with ILE 449 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J LYS* 3.4 51.6 + - + +
43J LEU* 3.8 18.2 - - + -
104J VAL* 3.7 20.4 - - + -
108J GLU* 3.7 9.0 - - + +
445J MET* 3.4 13.7 - - + +
446J LEU* 3.2 31.9 - - + +
448J THR* 1.3 77.6 - - - +
450J ILE* 1.3 51.7 + - + +
452J ASP* 2.9 16.3 - - - +
453J ASN* 2.4 30.0 + - - -
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Residues in contact with ILE 450 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J LEU 3.3 25.4 - - - +
44J GLY* 4.0 5.4 - - - -
45J PRO* 3.6 25.6 - - + -
46J LYS 3.6 16.2 - - - +
47J GLY 4.6 0.2 - - - +
410J GLY 5.6 1.8 - - - +
446J LEU* 3.7 8.3 - - + +
447J PRO* 3.4 23.6 - - + +
449J ILE* 1.3 82.4 - - + +
451J ALA* 1.3 67.5 + - - +
452J ASP 3.3 2.0 - - - -
453J ASN* 3.1 17.9 + - + +
454J ALA* 3.1 21.9 + - + +
461J LEU* 5.0 0.2 - - + -
478J LEU* 4.3 17.0 - - + -
480J MET* 4.4 12.1 - - + +
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Residues in contact with ALA 451 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447J PRO 3.1 16.0 + - - +
448J THR 3.6 0.6 + - - -
450J ILE* 1.3 78.5 - - - +
452J ASP* 1.3 50.5 + - - +
454J ALA 3.4 0.9 + - - -
455J GLY 2.7 12.0 + - - -
456J TYR* 2.5 47.0 + - + +
457J ASP 4.3 0.2 - - - -
458J SER* 3.3 25.4 - - - +
461J LEU* 3.7 17.0 - - + -
480J MET* 4.0 10.5 - - - -
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Residues in contact with ASP 452 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J LYS* 4.5 14.4 + - - -
448J THR 3.7 11.3 + - - +
449J ILE* 2.9 27.3 - - - +
451J ALA* 1.3 73.1 - - - +
453J ASN* 1.3 71.4 + - - +
455J GLY 3.2 5.2 + - - -
456J TYR 3.7 2.4 + - - -
458J SER* 4.0 3.5 + - - +
129L HIS* 3.4 37.1 + - + +
131L THR* 3.0 19.4 + - - +
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Residues in contact with ASN 453 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J LYS 3.5 13.5 + - - -
41J SER* 3.5 14.6 + - - +
43J LEU 4.0 0.4 + - - -
47J GLY* 3.3 29.0 - - - +
48J MET* 3.6 25.3 - - - +
449J ILE 2.4 28.2 + - - -
450J ILE* 3.1 25.2 + - + +
452J ASP* 1.3 88.7 + - - +
454J ALA* 1.3 56.9 + - - +
131L THR* 3.1 26.0 + - - +
132L ILE* 4.7 1.6 - - - +
135L GLU* 5.2 2.3 - - - +
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Residues in contact with ALA 454 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450J ILE* 3.1 7.2 + - + +
453J ASN* 1.3 76.7 - - - +
455J GLY* 1.3 60.4 + - - +
456J TYR 3.5 0.8 + - - -
480J MET* 3.4 55.0 - - + +
483J GLY* 4.1 13.2 - - - +
132L ILE* 3.3 15.4 - - - +
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Residues in contact with GLY 455 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469E ASN* 5.7 2.6 + - - -
472E GLN* 4.8 10.7 - - - +
451J ALA 2.7 8.9 + - - -
452J ASP 3.2 6.4 + - - -
454J ALA* 1.3 78.9 - - - +
456J TYR* 1.3 58.7 + - - -
457J ASP 4.0 0.3 + - - -
129L HIS* 3.5 34.8 + - - -
132L ILE* 3.7 9.9 - - - -
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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