Contacts of the strand formed by residues 52 - 58 (chain R) in PDB entry 5EF3
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 52 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23R GLY* 3.9 12.1 - - - -
24R LEU 3.4 3.4 - - - -
26R ARG* 3.4 2.6 + - - -
33R HIS* 2.6 23.6 + - - -
47R GLN 4.5 2.7 - - - +
48R PHE* 3.6 6.4 - - + -
49R THR* 3.0 36.6 + - - +
51R HIS* 1.3 77.5 - - - +
53R SER* 1.3 56.6 + - - +
54R ALA 3.5 23.1 - - - +
55R ILE* 3.9 18.2 - - + -
101S TRP* 2.8 30.0 + - + +
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Residues in contact with SER 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47Q GLN* 3.0 35.2 + - - +
49Q THR* 3.6 22.4 - - - -
24R LEU 3.4 4.6 + - - -
25R THR 3.8 0.3 + - - -
26R ARG* 3.3 29.2 + - - +
48R PHE* 3.8 7.1 - - - -
52R THR* 1.3 71.2 - - - +
54R ALA* 1.3 60.4 + - - +
101R TRP* 2.8 34.4 + - - +
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Residues in contact with ALA 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Q LEU* 4.3 10.8 - - + -
45Q ILE 3.0 13.0 - - - +
46Q ALA* 3.9 16.2 - - + -
24R LEU* 2.9 44.1 + - + -
48R PHE* 3.8 2.1 - - - -
52R THR* 3.5 7.6 - - - +
53R SER* 1.3 80.7 + - - +
55R ILE* 1.3 62.2 + - - +
101R TRP* 4.0 15.0 - - + -
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Residues in contact with ILE 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43Q VAL 3.8 0.7 - - - +
44Q LEU* 3.4 4.3 - - - -
45Q ILE* 2.7 48.5 + - + +
10R VAL* 3.9 23.3 - - + -
12R ILE* 4.6 2.0 - - + -
21R VAL* 3.7 29.2 - - + -
22R ILE 3.4 7.4 - - - +
46R ALA* 4.4 9.4 - - + +
47R GLN 4.5 2.9 - - - +
48R PHE* 3.9 22.4 - - + -
52R THR* 3.9 13.2 - - + -
54R ALA* 1.3 79.3 - - - +
56R LYS* 1.3 65.6 + - - +
57R VAL* 4.3 8.1 - - + -
101S TRP* 3.9 18.8 - - + -
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Residues in contact with LYS 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Q GLU* 2.8 21.6 + - + +
37Q LYS 3.9 1.2 + - - -
38Q LEU* 3.9 18.6 - - + -
42Q GLU* 3.6 22.2 + - + -
43Q VAL 3.4 9.6 - - - +
44Q LEU* 4.0 4.7 - - + -
21R VAL* 3.7 0.7 - - - -
22R ILE* 2.8 47.3 + - + +
24R LEU* 3.9 14.2 - - + +
32R PHE* 4.5 9.6 - - + -
55R ILE* 1.3 74.6 - - - +
57R VAL* 1.4 69.9 + - - +
58R ARG* 2.9 25.8 - - + +
132W A 3.6 8.7 - - - +
133W G 2.7 30.5 + - - -
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Residues in contact with VAL 57 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42Q GLU* 3.8 8.8 - - - +
43Q VAL* 2.9 31.2 + - + +
45Q ILE* 4.6 7.4 - - + -
12R ILE* 4.1 27.1 - - + -
19R VAL* 4.1 10.5 - - + -
20R ASN 3.4 8.3 - - - +
21R VAL* 4.7 3.1 - - + -
55R ILE* 4.3 9.2 - - + -
56R LYS* 1.4 76.9 - - - +
58R ARG* 1.3 64.2 + - - +
61R ALA* 4.1 15.7 - - + -
63R ILE* 4.1 20.9 - - + -
72R SER* 3.7 23.7 - - - +
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Residues in contact with ARG 58 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42Q GLU* 2.8 31.2 + - + +
18R GLY 4.6 0.9 - - - +
19R VAL* 3.4 5.9 - - - +
20R ASN* 3.0 43.7 + - + +
22R ILE* 4.2 23.0 - - + +
32R PHE* 4.1 3.2 - - - -
56R LYS* 2.9 34.4 - - + +
57R VAL* 1.3 74.0 - - - +
59R GLY* 1.3 64.1 + - - +
131W G 5.6 4.2 - - - +
132W A 4.7 3.2 + - - +
133W G 3.2 12.5 + - - -
134W U 3.1 32.9 + - - +
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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