Contacts of the helix formed by residues 42 - 50 (chain E) in PDB entry 3ECS
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 ILE 42 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40E GLU 4.4 2.0 - - - +
41E THR* 1.3 82.2 + - - +
43E GLN* 1.3 56.2 + - - +
44E GLY* 2.8 17.7 - - - +
45E LEU* 2.7 61.9 + - + +
46E ARG* 3.4 3.6 + - - +
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Residues in contact with GLN 43 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E THR 3.0 6.1 + - - -
42E ILE* 1.3 71.3 - - - +
44E GLY* 1.3 61.2 + - - +
46E ARG* 3.1 24.5 - - - +
47E ALA* 3.5 13.4 + - - +
88E LYS* 2.9 39.7 + - + +
90E LYS* 5.6 7.1 - - - +
93E MSE 5.6 6.0 - - - +
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Residues in contact with GLY 44 (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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42E ILE* 2.7 12.8 + - - +
43E GLN* 1.3 76.1 - - - +
45E LEU* 1.3 49.6 + - - -
46E ARG 2.8 5.6 + - - -
47E ALA* 3.2 5.5 + - - +
48E ASN* 2.8 38.8 + - - +
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Residues in contact with LEU 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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40E GLU 5.6 3.4 - - - +
41E THR* 3.0 27.1 - - - +
42E ILE* 2.7 42.1 + - + +
44E GLY* 1.3 69.4 - - - -
46E ARG* 1.3 55.4 + - - +
48E ASN* 3.5 22.2 - - - +
49E LEU* 2.7 61.1 + - + +
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Residues in contact with ARG 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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33E PHE* 4.4 5.7 - - - -
34E LEU* 4.7 13.9 - - + +
37E ASP* 2.9 36.4 + - - -
40E GLU* 2.9 26.7 - - - +
42E ILE 3.4 2.4 + - - +
43E GLN* 3.1 29.1 + - - +
44E GLY 2.8 1.4 + - - -
45E LEU* 1.3 79.2 + - - +
47E ALA* 1.3 57.4 + - - +
48E ASN 2.6 14.6 + - - -
49E LEU* 4.7 4.4 - - - +
50E THR* 3.1 39.6 + - + +
88E LYS* 4.0 9.6 - - - +
91E LYS* 3.3 31.1 - - - +
93E MSE 4.6 25.6 - - + -
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Residues in contact with ALA 47 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43E GLN* 3.5 12.9 + - - +
44E GLY* 3.2 7.2 + - - +
46E ARG* 1.3 79.6 - - - +
48E ASN* 1.3 55.4 + - - +
50E THR* 3.9 8.3 + - - -
51E SER* 3.1 17.0 + - - -
73E LEU* 4.7 9.2 - - + +
93E MSE 6.0 4.5 - - + -
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Residues in contact with ASN 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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44E GLY 2.8 18.0 + - - +
45E LEU* 3.5 17.4 - - - +
46E ARG 2.6 6.3 + - - -
47E ALA* 1.3 72.8 - - - +
49E LEU* 1.3 85.8 + - - +
50E THR 3.1 1.1 - - - -
51E SER* 2.8 11.0 + - - -
52E ALA* 2.6 44.5 + - - +
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Residues in contact with LEU 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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33E PHE* 3.6 19.7 - - + -
37E ASP* 3.7 22.2 - - - +
40E GLU 5.8 0.7 - - - +
45E LEU* 2.7 52.1 + - + +
46E ARG* 4.4 2.9 - - - +
48E ASN* 1.3 95.1 - - - +
50E THR* 1.3 55.9 + - - +
52E ALA* 2.9 18.7 + - + -
53E ILE* 2.8 29.8 + - + +
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Residues in contact with THR 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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30E LEU* 5.2 9.0 - - + +
33E PHE* 3.9 23.3 - - + -
34E LEU* 5.2 12.8 - - + -
46E ARG* 3.1 28.9 + - + +
47E ALA* 3.9 5.2 - - - -
49E LEU* 1.3 77.9 - - - +
51E SER* 1.3 61.7 + - - -
53E ILE* 2.8 27.0 - - + +
54E GLU* 2.9 22.5 + - - +
73E LEU* 3.8 18.0 - - - +
76E ILE* 6.1 4.5 - - + -
93E MSE 6.4 1.8 - - + -
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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