Contacts of the helix formed by residues 46 - 59 (chain N) in PDB entry 5FLX
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 THR 46 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9261 A 5.0 0.7 - - - +
44N GLY 3.8 2.1 + - - -
45N LEU* 1.3 72.2 - - - +
47N PRO* 1.3 63.2 - - + -
48N SER* 3.5 20.6 - - - +
49N GLN* 2.7 30.7 + - + -
50N ILE* 2.5 33.4 + - - +
86N GLU* 3.7 20.4 - - + -
89N TYR* 5.9 2.3 - - - -
90N HIS* 4.1 23.5 - - + +
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Residues in contact with PRO 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10171 U 4.1 1.2 + - - -
10181 U 4.4 8.7 - - - +
10191 C 5.9 0.7 - - - +
37N ILE* 6.4 0.4 - - + -
45N LEU 3.6 5.8 - - - +
46N THR* 1.3 86.5 - - + +
48N SER* 1.3 56.5 + - - +
50N ILE* 3.5 18.4 - - + +
51N GLY* 2.9 24.8 + - - -
71N ILE* 4.0 24.6 - - + +
72N LEU* 6.2 6.1 - - + -
75N LEU* 4.4 22.7 - - + -
82N PRO* 4.8 9.0 - - + -
86N GLU* 3.2 30.1 - - + +
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Residues in contact with SER 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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9251 G 3.7 7.5 + - - -
9261 A 3.7 30.4 + - - +
10171 U 2.8 20.6 + - - +
10181 U 3.1 39.4 + - - -
46N THR* 3.1 12.5 - - - +
47N PRO* 1.3 77.6 - - - +
49N GLN* 1.3 61.5 + - - +
52N VAL* 3.3 13.7 + - - +
86N GLU* 5.1 5.5 - - - +
90N HIS* 5.6 0.3 + - - -
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Residues in contact with GLN 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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9261 A 3.8 16.1 + - - +
9271 C 3.4 35.0 + - - -
45N LEU* 4.2 18.0 - - + +
46N THR* 2.7 37.7 + - - +
48N SER* 1.3 71.1 - - - +
50N ILE* 1.3 59.2 + - - +
51N GLY 3.2 0.4 - - - -
52N VAL* 2.9 11.4 + - + +
53N ILE* 2.9 36.6 + - + +
90N HIS* 6.3 1.0 - - - -
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Residues in contact with ILE 50 (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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37N ILE* 3.6 40.2 - - + +
40N LEU* 4.8 4.7 - - + -
41N ALA* 4.5 18.4 - - + +
45N LEU* 3.3 38.1 - - + +
46N THR 2.5 15.6 + - - +
47N PRO* 3.2 24.9 + - + +
49N GLN* 1.3 73.2 - - - +
51N GLY* 1.3 57.8 + - - +
53N ILE* 4.4 6.1 - - - +
54N LEU* 2.9 46.0 + - + +
71N ILE* 5.4 2.0 - - + -
75N LEU* 6.4 2.5 - - + -
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Residues in contact with GLY 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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10171 U 3.5 30.0 - - - +
10181 U 5.2 2.2 - - - -
47N PRO 2.9 13.2 + - - -
48N SER 3.7 0.2 + - - -
49N GLN 3.2 0.2 - - - -
50N ILE* 1.3 76.7 - - - +
52N VAL* 1.3 49.4 + - - +
54N LEU* 4.9 3.1 - - - -
55N ARG* 2.5 39.4 + - - +
63N VAL* 6.0 4.9 - - - -
71N ILE* 5.1 4.0 - - - +
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Residues in contact with VAL 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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9261 A 5.2 3.1 - - + +
9271 C 4.8 17.3 - - - +
10171 U 4.4 6.5 - - - +
48N SER 3.3 16.8 + - - +
49N GLN* 2.9 13.8 + - + +
51N GLY* 1.3 77.0 - - - +
53N ILE* 1.3 63.5 + - + +
55N ARG* 3.3 36.6 - - - +
56N ASP* 2.9 38.7 + - - +
51b GLN* 4.3 9.9 - - + +
52b THR* 4.3 16.4 - - + -
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Residues in contact with ILE 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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40N LEU* 3.5 30.1 - - + -
45N LEU* 4.2 18.4 - - + -
49N GLN* 2.9 21.2 + - + +
50N ILE 3.2 3.5 + - - +
52N VAL* 1.3 78.6 - - + +
54N LEU* 1.3 65.5 + - - +
55N ARG 3.0 1.1 + - - -
56N ASP* 3.2 1.1 + - - -
57N SER* 2.9 38.4 + - - -
52b THR* 4.4 22.9 - - + +
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Residues in contact with LEU 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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33N VAL* 4.1 28.3 - - + +
36N GLN* 4.4 11.0 - - + -
37N ILE* 4.1 33.0 - - + +
40N LEU* 3.5 25.8 - - + -
50N ILE* 2.9 35.2 + - + +
51N GLY* 4.7 3.1 - - - +
53N ILE* 1.3 74.2 - - - +
55N ARG* 1.3 63.8 + - - +
58N HIS* 3.6 32.5 + - + +
60N VAL* 3.7 12.2 + - + +
63N VAL* 4.6 18.2 - - + -
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Residues in contact with ARG 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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10151 U 4.2 13.8 + - - +
10161 U 4.2 10.5 - - - +
10171 U 2.7 54.5 + - - -
51N GLY 2.5 26.9 + - - +
52N VAL* 3.3 29.7 - - - +
53N ILE 3.0 0.4 - - - -
54N LEU* 1.3 77.3 - - - +
56N ASP* 1.3 70.8 + - - +
59N GLY* 3.1 21.1 + - - -
60N VAL 3.2 14.0 - - - +
61N ALA* 5.2 0.4 - - - -
62N GLN 6.0 0.2 - - - +
47b PHE* 3.0 37.3 - - + -
49b HIS 5.5 2.8 + - - -
51b GLN* 2.7 44.8 + - - +
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Residues in contact with ASP 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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52N VAL* 2.9 24.2 + - - +
53N ILE 4.4 0.2 - - - +
55N ARG* 1.3 91.0 + - - +
57N SER* 1.3 60.6 + - - +
59N GLY* 3.6 0.9 + - - -
45b THR 2.9 24.4 - - - +
46b VAL* 4.3 4.3 - - - -
47b PHE* 3.3 19.0 - - - -
49b HIS 4.5 0.2 - - - +
50b ALA* 3.8 17.0 - - + -
51b GLN 3.1 20.4 + - - -
52b THR* 3.3 27.9 + - + +
54b VAL* 4.2 17.3 - - + +
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Residues in contact with SER 57 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53N ILE* 2.9 26.9 + - - -
56N ASP* 1.3 82.0 - - - +
58N HIS* 1.3 74.2 + - - +
59N GLY 3.6 0.2 + - - -
44b THR* 4.6 6.8 - - - +
45b THR* 3.6 12.1 + - - +
54b VAL* 5.1 11.0 - - - -
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Residues in contact with HIS 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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26N LEU* 3.6 19.0 - - + +
28N LEU* 5.3 12.0 - - + +
36N GLN* 3.2 49.4 + - + +
40N LEU* 6.0 2.5 - - + +
53N ILE 5.5 0.2 - - - -
54N LEU* 3.6 30.6 + - + +
57N SER* 1.3 85.8 + - - +
59N GLY* 1.3 59.7 + - - +
60N VAL* 3.1 18.0 + - + +
45b THR* 3.0 13.9 + - - -
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Residues in contact with GLY 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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25N TRP* 5.5 1.2 + - - -
26N LEU* 3.8 9.7 - - - +
55N ARG 3.1 14.0 + - - -
56N ASP 3.6 1.2 + - - -
57N SER 3.3 2.0 - - - -
58N HIS* 1.3 78.2 - - - +
60N VAL* 1.3 62.4 + - - +
61N ALA 3.5 0.9 + - - -
32b PHE* 3.4 26.5 - - - -
45b THR* 3.2 24.0 + - - -
47b PHE* 4.3 7.6 - - - -
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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