Contacts of the helix formed by residues 44 - 50 (chain E) in PDB entry 3LNX
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 GLY 44 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E ASN* 4.1 9.9 - - - -
19E GLY* 4.6 9.6 - - - -
41E ILE* 2.9 19.3 + - - -
42E PRO 3.0 2.3 + - - -
43E GLN* 1.3 79.5 - - - +
45E ALA* 1.3 65.4 - - - -
46E ALA 3.5 2.5 - - - -
47E GLU* 3.3 2.5 + - - +
48E SER* 3.0 26.7 + - - -
103E SCN 4.9 0.4 - - - -
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Residues in contact with ALA 45 (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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11E LEU* 3.9 8.4 - - + +
12E ALA 3.1 28.3 - - - +
13E LYS* 4.3 0.2 - - - -
14E ASN* 3.8 21.9 - - + +
17E SER 3.9 4.9 + - - +
18E LEU 3.6 13.7 + - - +
19E GLY* 4.4 1.8 - - - -
44E GLY* 1.3 71.0 - - - -
46E ALA* 1.3 65.5 + - - +
48E SER* 3.2 3.1 + - - -
49E ASP* 2.9 24.4 + - - +
103E SCN 4.1 12.1 - - - +
82F GLY* 5.0 1.8 - - - -
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Residues in contact with ALA 46 (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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11E LEU* 4.1 17.0 - - + +
18E LEU 3.1 17.4 + - - +
19E GLY* 4.0 4.2 - - - +
20E ILE* 3.5 25.8 - - + -
40E VAL* 4.6 5.4 - - + -
44E GLY 3.5 0.4 - - - -
45E ALA* 1.3 78.6 - - - +
47E GLU* 1.3 57.6 + - - +
49E ASP* 3.4 2.5 + - - +
50E GLY* 2.9 25.6 + - - -
51E ARG 4.2 2.6 + - - -
52E ILE* 4.4 21.3 + - + +
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Residues in contact with GLU 47 (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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19E GLY 5.2 0.6 + - - -
40E VAL* 4.6 21.4 - - + +
41E ILE 3.9 13.0 + - - +
42E PRO* 3.5 16.5 - - - +
43E GLN* 2.7 31.9 + - - +
44E GLY 3.3 7.2 + - - +
45E ALA 3.2 1.0 - - - -
46E ALA* 1.3 75.8 - - - +
48E SER* 1.3 66.0 + - - +
50E GLY* 3.3 13.3 + - - -
52E ILE 5.6 1.3 - - - -
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Residues in contact with SER 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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43E GLN* 4.3 9.0 + - - -
44E GLY 3.0 17.9 + - - -
45E ALA 3.7 3.4 - - - -
47E GLU* 1.3 77.9 + - - +
49E ASP* 1.3 62.0 + - - +
50E GLY* 4.4 0.5 - - - -
103E SCN 3.6 33.5 - - - -
80F ASN 4.1 4.5 - - - +
81F THR* 3.4 21.3 + - - +
82F GLY* 3.9 5.8 - - - -
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Residues in contact with ASP 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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9E VAL* 4.7 3.2 - - - +
10E GLU 4.9 0.5 - - - +
11E LEU* 3.8 21.9 - - + +
45E ALA 2.9 17.1 + - - +
46E ALA* 3.7 4.2 - - - +
48E SER* 1.3 78.5 - - - +
50E GLY* 1.3 57.9 + - - +
51E ARG* 2.9 58.9 + - - +
52E ILE* 4.8 2.9 + - - +
62F ASN* 3.8 18.4 + - - +
80F ASN 4.9 2.6 - - - +
81F THR* 4.8 2.3 - - - -
82F GLY* 3.8 14.7 + - - +
84F VAL 4.2 9.4 - - - +
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Residues in contact with GLY 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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46E ALA 2.9 11.7 + - - -
47E GLU* 3.7 12.3 - - - -
48E SER 3.3 1.7 - - - -
49E ASP* 1.3 76.6 - - - +
51E ARG* 1.3 59.3 + - - +
52E ILE 3.6 3.4 - - - -
53E HIS* 3.2 24.4 + - - -
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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