Contacts of the helix formed by residues 47 - 55 (chain E) in PDB entry 3L3T
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 47 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E TRP* 3.5 9.9 - - - +
45E PHE* 4.0 2.1 - - - +
46E ASP* 1.3 96.1 - - + +
48E GLU* 1.3 66.9 + - - +
49E GLU* 3.5 20.5 - - + +
50E TYR* 3.2 25.7 + - - +
51E CYS* 3.2 18.2 + - - +
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Residues in contact with GLU 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E TRP* 3.5 55.3 - - + +
29E LYS* 5.6 4.2 - - - +
30E CYS* 4.5 11.6 + - + +
47E THR* 1.3 72.0 - - - +
49E GLU* 1.3 76.6 + - - +
51E CYS* 2.9 15.1 + - - +
52E MET* 2.9 25.8 + - + +
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Residues in contact with GLU 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E THR* 3.5 23.5 - - + +
48E GLU* 1.3 84.4 + - - +
50E TYR* 1.3 58.0 + - - +
52E MET* 3.3 6.8 + - - +
53E ALA* 2.8 28.6 + - - +
59E ILE* 5.2 1.4 - - - +
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Residues in contact with TYR 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E PHE* 3.6 35.4 - + + -
46E ASP* 5.0 6.7 - - + -
47E THR* 3.2 21.9 + - - +
48E GLU 3.2 0.8 - - - -
49E GLU* 1.3 77.2 - - + +
51E CYS* 1.3 64.9 + - - +
53E ALA* 3.2 11.2 + - + +
54E VAL* 3.1 42.5 + - + +
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Residues in contact with CYS 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E TRP* 4.1 4.5 - - + -
22E TYR* 3.6 4.0 - - - -
23E PHE* 3.6 20.2 - - - -
30E CYS* 2.0 43.7 - - + -
45E PHE* 3.4 40.7 - - + +
47E THR 3.2 10.6 + - - +
48E GLU 2.9 7.9 + - - +
50E TYR* 1.3 76.6 - - - +
52E MET* 1.3 56.9 + - - +
54E VAL* 3.2 2.1 + - - +
55E CYS* 2.8 33.8 + - - +
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Residues in contact with MET 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E PHE* 4.4 6.5 - - + -
28E GLY 5.0 0.7 - - - +
29E LYS* 4.0 13.7 - - + -
30E CYS* 3.7 36.8 - - + +
48E GLU* 2.9 22.4 + - + +
49E GLU* 3.8 9.0 - - - +
51E CYS* 1.3 76.2 - - - +
53E ALA* 1.3 60.2 + - - +
55E CYS 2.8 23.5 - - - +
56E GLY 4.1 0.7 - - - +
57E SER* 3.4 29.4 - - - +
59E ILE* 4.1 15.4 - - + +
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Residues in contact with ALA 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E GLU 2.8 15.4 + - - +
50E TYR* 3.3 22.0 - - + +
52E MET* 1.3 80.5 - - - +
54E VAL* 1.3 62.8 + - + +
59E ILE* 3.3 39.3 - - + +
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Residues in contact with VAL 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 5.3 4.3 - - + -
5E CYS* 4.0 8.5 - - - -
45E PHE* 4.0 19.5 - - + -
50E TYR* 3.1 44.6 + - + +
51E CYS 4.0 2.5 - - - +
53E ALA* 1.3 78.1 - - + +
55E CYS* 1.3 69.7 + - - +
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Residues in contact with CYS 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E CYS* 2.0 50.0 - - - -
23E PHE* 3.5 30.5 - - + -
45E PHE* 3.9 27.1 - - - -
51E CYS 2.8 11.4 + - - +
52E MET* 2.8 26.0 - - - +
53E ALA 4.6 0.2 - - - -
54E VAL* 1.3 80.3 - - - +
56E GLY* 1.3 70.0 + - - +
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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