Contacts of the helix formed by residues 45 - 52 (chain N) in PDB entry 6PSU
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 45 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272I ARG* 6.3 0.9 - - - +
672J LEU* 6.1 4.5 - - + -
43N PRO* 3.5 12.3 - - + +
44N ILE* 1.3 85.8 - - + +
46N GLU* 1.3 61.9 + - - +
47N ALA* 3.0 13.1 + - + +
48N ARG* 3.0 23.5 + - + +
49N ARG* 3.1 5.5 + - - +
58N CYS* 5.4 5.4 - - + -
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Residues in contact with GLU 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N ILE 3.6 0.4 + - - -
45N PRO* 1.3 68.8 - - - +
47N ALA* 1.3 59.7 + - - +
48N ARG 3.4 0.2 - - - -
49N ARG* 3.2 43.3 + - + +
50N LYS* 2.9 29.0 + - + +
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Residues in contact with ALA 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667J GLN* 6.1 1.3 - - - +
672J LEU* 3.2 27.1 - - + -
45N PRO* 3.0 5.0 + - + +
46N GLU* 1.3 75.1 - - - +
48N ARG* 1.3 60.7 + - - +
50N LYS* 2.9 21.1 + - - +
51N ILE* 3.0 19.2 + - + +
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Residues in contact with ARG 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672J LEU* 2.6 42.7 + - + +
673J VAL* 3.8 9.4 - - - +
674J THR* 4.6 3.8 + - - +
677J GLU* 5.4 2.2 - - - +
44N ILE* 5.2 7.9 - - + +
45N PRO* 3.0 19.0 + - + +
47N ALA* 1.3 77.8 - - - +
49N ARG* 1.3 61.1 + - - +
50N LYS 3.3 0.5 + - - -
51N ILE* 3.3 25.1 + - + +
52N PHE* 3.7 18.0 + - - +
55N VAL* 3.4 28.7 - - + +
57N LEU 3.5 13.7 + - - -
58N CYS* 4.8 2.2 - - - +
59N VAL* 3.1 37.2 - - - +
62N GLN* 2.2 40.8 + - - +
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Residues in contact with ARG 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N PRO* 3.1 43.4 - - + +
35N TYR* 3.2 36.1 + - - +
44N ILE* 2.9 51.8 - - + +
45N PRO 3.1 7.0 - - - +
46N GLU* 3.2 41.9 + - + +
47N ALA 3.1 0.6 - - - -
48N ARG* 1.3 77.2 - - - +
50N LYS* 1.3 61.3 + - - +
52N PHE 4.0 10.6 - - - +
53N PRO* 4.2 9.2 - - - +
55N VAL* 5.5 2.0 - - - -
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Residues in contact with LYS 50 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46N GLU* 2.9 17.9 + - + +
47N ALA* 2.9 8.2 + - - +
49N ARG* 1.3 80.1 - - - +
51N ILE* 1.3 71.1 + - + +
53N PRO* 3.8 11.1 - - - +
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Residues in contact with ILE 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664J ILE* 5.3 8.7 - - + -
667J GLN* 3.0 45.1 - - - +
672J LEU* 4.5 4.7 - - + +
673J VAL* 3.3 34.1 - - + -
681J LYS* 4.8 16.5 + - - +
27N ILE* 5.9 0.2 - - - +
47N ALA 3.0 13.5 + - - +
48N ARG* 3.3 23.1 - - - +
50N LYS* 1.3 80.7 - - + +
52N PHE* 1.3 78.8 + - + +
53N PRO* 3.0 12.5 - - - +
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Residues in contact with PHE 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664J ILE* 5.5 1.3 - - + -
673J VAL* 3.3 33.4 - - + -
677J GLU* 3.5 39.5 - - + -
678J ARG* 5.7 0.2 - - - -
681J LYS* 4.2 26.2 - - + -
27N ILE* 3.4 38.8 - - + -
28N ASN* 5.2 3.6 - - + +
48N ARG* 3.7 12.8 + - - +
49N ARG* 4.0 5.5 - - - +
51N ILE* 1.3 92.0 - - + +
53N PRO* 1.3 61.5 - - - +
54N GLY 3.0 5.1 + - - -
55N VAL* 2.9 40.0 + - + +
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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