Contacts of the helix formed by residues 40 - 50 (chain E) in PDB entry 1Z6Z
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 ASN 40 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ASN* 5.9 4.4 - - - +
13E SER* 4.3 2.3 - - - -
14E ARG* 6.0 5.4 - - + +
38E ALA* 3.5 0.8 - - - +
39E ARG* 1.3 73.1 - - - +
41E ASP* 1.3 62.2 + - - +
42E GLU* 3.2 21.9 + - - +
43E ALA* 3.3 24.9 + - + +
44E LEU* 3.2 26.2 + - - +
805E NAP 3.1 18.5 + - - +
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Residues in contact with ASP 41 (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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39E ARG 3.1 7.0 + - - +
40E ASN* 1.3 69.1 + - - +
42E GLU* 1.3 61.6 + - - +
44E LEU* 3.1 7.4 + - - +
45E ARG* 2.9 33.4 + - - +
62E ARG* 2.9 29.7 + - - -
64E PRO* 3.5 32.9 - - + +
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Residues in contact with GLU 42 (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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14B ARG* 5.8 11.0 - - - +
40E ASN* 3.2 10.0 + - - +
41E ASP* 1.3 79.1 - - - +
43E ALA* 1.3 55.9 + - - +
45E ARG* 3.4 8.1 + - - +
46E GLN* 3.0 28.8 + - - +
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Residues in contact with ALA 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASN* 6.3 0.9 - - - +
13E SER* 3.8 30.7 - - - +
14E ARG* 5.8 1.8 - - + -
18E ARG* 5.2 1.9 - - - -
40E ASN* 3.3 28.9 + - - +
42E GLU* 1.3 75.5 - - - +
44E LEU* 1.3 59.2 + - - +
46E GLN* 3.5 9.3 + - - +
47E LEU* 3.0 27.7 + - - +
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Residues in contact with LEU 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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12E ALA* 4.0 22.4 - - + -
13E SER 4.2 4.9 - - - +
36E LEU* 4.0 23.0 - - + +
37E SER 4.0 4.0 - - - -
38E ALA* 3.9 42.6 - - + +
40E ASN 3.2 16.9 + - - +
41E ASP* 3.1 10.6 + - - +
43E ALA* 1.3 74.3 - - - +
45E ARG* 1.3 58.5 + - - +
47E LEU* 3.3 7.6 + - + +
48E GLU* 2.9 24.4 + - - +
62E ARG* 3.5 21.2 - - + +
63E VAL 4.1 3.4 - - - +
64E PRO* 4.0 23.6 - - + -
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Residues in contact with ARG 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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41E ASP* 2.9 25.1 + - - +
42E GLU* 3.6 7.9 - - - +
44E LEU* 1.3 73.3 - - - +
46E GLN* 1.3 64.2 + - - +
48E GLU* 3.3 3.8 + - - +
49E ALA* 3.1 23.2 + - - +
62E ARG* 3.5 35.9 - - - +
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Residues in contact with GLN 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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40B ASN* 5.8 5.2 - - - -
42E GLU 3.0 16.9 + - - +
43E ALA* 3.7 9.2 - - - +
44E LEU 3.3 0.2 - - - -
45E ARG* 1.3 76.6 - - - +
47E LEU* 1.3 60.6 + - - +
49E ALA* 3.7 7.4 + - + +
50E GLU* 3.4 36.9 + - - +
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Residues in contact with LEU 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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12E ALA* 4.7 7.6 - - + +
18E ARG* 4.0 26.2 - - - +
21E ALA* 3.8 24.9 - - + -
22E PRO* 4.2 16.6 - - + -
36E LEU* 4.1 21.1 - - + -
43E ALA 3.0 18.4 + - - +
44E LEU* 3.5 7.4 - - + +
45E ARG 3.2 0.2 - - - -
46E GLN* 1.3 74.9 - - - +
48E GLU* 1.3 66.4 + - - +
50E GLU* 3.0 26.5 + - + +
51E LEU* 3.4 19.4 - - + +
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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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36E LEU* 5.0 1.1 - - + +
44E LEU 2.9 15.8 + - - +
45E ARG* 3.3 5.9 + - - +
47E LEU* 1.3 75.6 - - - +
49E ALA* 1.3 62.4 + - - +
51E LEU* 3.1 28.4 + - - +
60E VAL* 3.8 43.4 - - + +
62E ARG* 2.7 40.2 + - + +
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Residues in contact with ALA 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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45E ARG 3.1 12.7 + - - +
46E GLN* 3.7 12.6 - - - +
47E LEU 3.2 0.2 - - - -
48E GLU* 1.3 73.1 - - - +
50E GLU* 1.3 57.3 + - + +
51E LEU 3.0 15.1 + - - -
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Residues in contact with GLU 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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18E ARG* 5.0 5.5 - - - -
22E PRO* 5.3 8.9 - - + +
46E GLN* 3.4 30.2 + - - +
47E LEU* 3.0 25.6 + - + +
49E ALA* 1.3 75.2 - - + +
51E LEU* 1.3 65.3 + - + +
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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