Contacts of the helix formed by residues 51 - 60 (chain N) in PDB entry 2FBW
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 PHE 51 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50N LEU* 1.3 74.1 - - - +
52N PRO* 1.3 80.6 - - + +
53N THR* 3.3 36.3 - - + -
54N ARG* 2.9 46.9 + - + +
162N TYR* 3.4 34.8 - + - -
174N VAL* 3.7 24.5 - - + +
175N GLU* 4.7 8.5 + - - +
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Residues in contact with PRO 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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26N ALA* 3.5 36.9 - - + +
31N LEU* 4.3 11.0 - - + -
48N THR* 4.6 3.8 - - + -
50N LEU 3.9 3.4 - - - +
51N PHE* 1.3 104.5 - - + -
53N THR* 1.3 56.6 + - - +
55N SER* 2.6 32.8 + - - +
158N LEU* 3.4 5.9 - - - +
162N TYR* 3.8 29.6 - - + -
172N TYR* 4.8 7.6 - - + -
174N VAL* 4.3 11.9 - - + -
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Residues in contact with THR 53 (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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51N PHE* 3.1 21.9 + - + -
52N PRO* 1.3 73.5 - - - +
54N ARG* 1.3 69.5 + - - +
55N SER 3.4 0.4 - - - -
58N VAL* 3.3 24.9 - - - +
158N LEU* 3.4 11.2 - - + +
159N HIS* 3.6 41.0 + - + +
162N TYR* 3.8 39.0 - - + -
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Residues in contact with ARG 54 (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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50N LEU* 4.0 23.5 - - + +
51N PHE* 2.9 43.9 + - + +
53N THR* 1.3 90.7 + - - +
55N SER* 1.3 65.8 + - - +
56N HIS* 3.8 0.5 + - - -
58N VAL* 4.2 5.8 - - - +
159N HIS* 6.1 1.4 - - - -
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Residues in contact with SER 55 (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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26N ALA* 3.2 16.5 + - - +
27N GLY* 3.8 20.0 - - - -
48N THR* 5.0 1.6 + - - -
50N LEU* 4.1 16.3 - - - +
51N PHE 4.1 1.4 + - - -
52N PRO* 2.6 24.5 + - - +
53N THR 3.4 1.0 - - - -
54N ARG* 1.3 77.4 - - - +
56N HIS* 1.3 67.2 + - - +
57N THR* 3.1 2.0 - - - -
58N VAL* 2.9 25.1 + - - +
158N LEU* 4.2 4.5 - - - -
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Residues in contact with HIS 56 (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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50N LEU* 5.3 1.4 - - - +
54N ARG 4.6 0.2 - - - -
55N SER* 1.3 73.6 - - - +
57N THR* 1.3 65.4 + - - +
58N VAL* 4.9 0.9 - - - -
59N ALA* 2.7 35.9 + - + +
60N ALA* 3.8 2.6 + - + +
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Residues in contact with THR 57 (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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27N GLY* 4.0 4.9 - - - -
28N GLY* 3.1 26.8 + - - +
55N SER* 3.1 0.8 + - - -
56N HIS* 1.3 76.5 - - - +
58N VAL* 1.3 62.3 + - - +
60N ALA* 3.0 19.1 + - + +
154N GLY* 3.2 13.8 - - - +
157N LEU* 3.9 24.0 - - + -
158N LEU* 3.9 25.6 - - + -
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Residues in contact with VAL 58 (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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53N THR 3.3 24.9 - - - +
54N ARG* 4.2 6.5 - - - +
55N SER 2.9 22.0 + - - +
56N HIS* 2.9 1.3 + - - +
57N THR* 1.3 77.9 - - - +
59N ALA* 1.3 64.8 + - + +
60N ALA 3.3 0.7 - - - +
154N GLY 3.9 7.6 - - - -
155N HIS* 3.2 41.3 + - - +
158N LEU* 3.5 10.6 - - + +
159N HIS* 4.0 17.5 - - + +
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Residues in contact with ALA 59 (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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56N HIS* 2.7 33.6 + - + +
58N VAL* 1.3 84.3 - - + +
60N ALA* 1.3 62.5 + - - -
61N GLN* 3.4 17.8 + - - +
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Residues in contact with ALA 60 (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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56N HIS* 3.8 2.3 + - + +
57N THR* 3.0 21.9 + - + +
58N VAL 4.3 0.3 - - - +
59N ALA* 1.3 81.2 - - - +
61N GLN* 1.3 58.0 + - - +
152N ARG* 3.7 4.7 - - - -
153N THR* 3.5 2.6 + - - -
154N GLY* 2.7 32.7 + - - +
155N HIS 3.7 1.7 + - - -
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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