Contacts of the helix formed by residues 30 - 36 (chain E) in PDB entry 1AW8
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 GLN 30 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28E ILE 3.1 4.1 + - - -
29E ASP* 1.3 74.2 + - - +
31E ASP* 1.3 59.6 + - - +
33E LEU* 3.3 17.1 + - - +
34E ASP* 3.0 39.6 + - - +
38E ILE 5.4 0.2 - - - +
40E GLU* 5.5 2.5 + - - +
61E ALA* 3.2 26.2 - - - +
62E ALA 3.0 18.1 + - - +
64E ARG* 3.6 42.2 - - + +
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Residues in contact with ASP 31 (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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29E ASP* 2.9 15.7 + - - +
30E GLN* 1.3 77.2 - - - +
32E PHE* 1.3 69.0 - - + +
34E ASP* 3.6 4.5 + - - +
35E ALA* 3.2 23.0 + - - +
64E ARG* 2.8 41.6 + - - +
65E GLY* 3.3 24.1 + - - -
114E MET* 4.3 12.4 - - + +
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Residues in contact with PHE 32 (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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10D LEU* 3.5 24.9 - - + +
13D VAL* 4.9 1.3 - - + -
28E ILE* 3.7 9.6 - - + -
29E ASP* 2.8 33.5 + - + +
31E ASP* 1.3 83.7 - - + +
33E LEU* 1.3 64.9 - - - +
35E ALA* 3.3 5.8 + - - +
36E ALA* 3.0 19.4 + - - +
67E ARG* 3.9 26.9 - - + -
69E ILE* 4.0 23.1 - - + -
108E PHE* 3.6 29.6 - + - -
112E ASN* 3.6 32.1 - - + -
114E MET* 4.4 13.0 - - + -
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Residues in contact with LEU 33 (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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10D LEU* 5.4 0.4 - - + -
28E ILE* 3.8 33.2 - - + +
29E ASP 3.3 8.0 + - - +
30E GLN* 3.3 18.1 + - - +
32E PHE* 1.3 79.1 - - - +
34E ASP* 1.3 57.2 + - - +
36E ALA 3.4 0.3 + - - -
37E GLY* 2.9 26.2 + - - -
38E ILE* 3.0 54.7 + - + +
39E LEU 5.1 0.2 - - - -
40E GLU* 5.0 10.3 - - + +
59E ALA* 4.3 5.2 - - + -
60E ILE 4.1 4.5 - - - +
61E ALA* 3.7 37.9 - - + +
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Residues in contact with ASP 34 (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 GLN* 3.0 34.2 + - - +
31E ASP* 3.7 7.0 - - - +
32E PHE 3.3 0.2 - - - -
33E LEU* 1.3 76.1 - - - +
35E ALA* 1.3 61.2 + - - +
37E GLY* 3.3 11.5 + - - -
64E ARG* 2.9 34.7 + - - -
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Residues in contact with ALA 35 (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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31E ASP 3.2 14.4 + - - +
32E PHE 3.3 5.1 + - - +
34E ASP* 1.3 80.6 - - - +
36E ALA* 1.3 57.3 + - - +
37E GLY 3.6 0.3 + - - -
104E ASN* 3.7 15.6 - - - +
105E VAL 5.1 1.4 + - - -
106E ALA* 4.2 12.1 - - + +
114E MET* 3.8 26.0 - - + -
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Residues in contact with ALA 36 (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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7D GLN* 3.0 17.7 - - - +
8D GLY* 3.5 4.9 - - - -
9D LYS 4.0 16.6 - - - +
10D LEU* 3.6 28.0 - - + -
32E PHE 3.0 9.3 + - - +
35E ALA* 1.3 75.5 - - - +
37E GLY* 1.3 57.1 + - - +
38E ILE* 3.3 20.6 + - + +
104E ASN* 3.5 21.1 - - - +
106E ALA* 4.9 1.1 - - + -
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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