Contacts of the helix formed by residues 46 - 54 (chain D) in PDB entry 1E3S
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 GLU 46 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D ALA* 4.1 11.9 - - - +
45D SER* 1.3 73.4 - - - +
47D GLY* 1.3 63.2 + - - +
48D GLU 3.3 2.4 + - - -
49D THR* 3.3 28.0 + - - +
50D GLU* 3.1 38.5 + - + +
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Residues in contact with GLY 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ALA* 3.6 16.9 - - - +
39D LEU* 4.1 4.7 - - - +
45D SER* 3.3 9.7 + - - -
46D GLU* 1.3 77.6 - - - +
48D GLU* 1.3 63.4 + - - +
50D GLU* 3.3 2.7 + - - +
51D ALA* 3.0 25.3 + - - +
60D PHE* 3.7 29.3 - - - +
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Residues in contact with GLU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D SER 5.0 1.2 + - - -
46D GLU 3.3 0.6 - - - -
47D GLY* 1.3 74.5 - - - +
49D THR* 1.3 67.6 + - + +
51D ALA* 3.4 3.1 + - - +
52D LYS* 3.1 23.6 + - + +
60D PHE* 3.5 35.9 + - + +
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Residues in contact with THR 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D GLU* 3.3 30.1 + - - +
48D GLU* 1.3 76.7 - - + +
50D GLU* 1.3 67.8 + - - +
52D LYS* 3.4 11.5 + - - +
53D LYS* 3.1 35.4 + - - +
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Residues in contact with GLU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ALA* 4.0 14.3 - - - +
24D LEU* 3.8 42.2 - - + +
28D LYS* 4.5 5.9 + - - -
39D LEU* 4.3 8.1 - - + -
46D GLU* 3.1 32.1 + - + +
47D GLY* 3.9 3.6 - - - +
49D THR* 1.3 77.8 + - - +
51D ALA* 1.3 58.1 + - - +
53D LYS* 3.3 33.6 + - - +
54D LEU* 3.0 31.8 + - - +
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Residues in contact with ALA 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU* 4.0 3.5 - - + +
47D GLY 3.0 17.3 + - - +
48D GLU* 3.8 5.2 - - - +
50D GLU* 1.3 78.1 - - - +
52D LYS* 1.3 59.5 + - - +
54D LEU* 3.5 1.7 + - - -
55D GLY 3.3 15.8 + - - +
58D CYS* 3.2 43.6 - - - +
59D ILE* 3.7 3.8 - - - -
60D PHE* 3.7 25.6 - - + +
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Residues in contact with LYS 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D GLU* 3.1 19.3 + - + +
49D THR* 3.7 11.7 - - - +
50D GLU 3.3 0.2 - - - -
51D ALA* 1.3 75.4 - - - +
53D LYS* 1.3 65.8 + - + +
55D GLY* 3.1 14.9 + - - -
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Residues in contact with LYS 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D LYS* 5.1 9.9 - - - +
49D THR* 3.1 26.6 + - - +
50D GLU* 3.3 33.7 + - - +
52D LYS* 1.3 77.8 - - + +
54D LEU* 1.3 62.6 + - + +
55D GLY* 3.6 0.7 + - - -
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU* 4.9 8.3 - - + -
27D ALA* 4.1 11.9 - - + +
28D LYS* 3.9 51.6 - - + +
31D VAL* 3.9 27.3 - - + +
32D GLY 5.8 0.4 - - - +
39D LEU* 5.5 0.7 - - + -
50D GLU 3.0 16.9 + - - +
51D ALA 4.0 0.4 - - - +
52D LYS 3.2 0.8 - - - -
53D LYS* 1.3 80.5 - - + +
55D GLY* 1.3 56.7 + - - +
57D ASN 5.0 0.5 + - - -
58D CYS* 3.7 33.6 + - + +
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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