Contacts of the helix formed by residues 21 - 34 (chain A) in PDB entry 1WIZ
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 ASP 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A SER* 3.2 3.1 + - - -
20A PRO* 1.3 91.1 - - - +
22A ILE* 1.3 65.4 + - - +
23A TYR* 2.9 4.6 + - - -
24A GLN* 3.0 16.9 + - + +
25A GLN* 2.8 37.5 + - + +
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Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 4.2 12.3 - - + -
19A SER 2.9 21.8 + - - +
21A ASP* 1.3 78.5 - - - +
23A TYR* 1.3 91.0 + - + +
25A GLN* 3.2 11.9 - - - +
26A VAL* 3.0 29.2 + - + +
62A PRO* 4.5 4.0 - - + -
73A LEU* 3.9 20.4 - - + +
76A MET* 4.1 7.6 - - + -
77A GLN* 3.3 54.1 - - + +
80A LEU* 3.9 10.1 - - + -
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Residues in contact with TYR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PRO 3.2 28.5 - - - -
21A ASP* 4.5 0.9 - - - -
22A ILE* 1.3 89.0 - - + +
24A GLN* 1.3 66.7 + - - +
25A GLN 3.0 1.0 + - - -
26A VAL* 3.0 14.0 + - - +
27A ARG* 3.1 19.1 + - - +
55A ILE* 3.3 29.6 - - + -
56A LEU* 3.6 11.3 - - + +
59A GLU* 2.6 69.8 + - + +
60A GLU 2.4 29.6 + - - -
61A ASP* 2.9 9.9 + - - -
62A PRO* 3.4 7.5 - - + +
73A LEU* 5.0 3.6 - - + -
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Residues in contact with GLN 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASP* 3.0 18.1 + - + +
23A TYR* 1.3 78.0 - - - +
25A GLN* 1.3 57.5 + - + +
27A ARG* 3.7 27.8 - - + +
28A ASP* 2.8 38.1 + - + +
59A GLU* 4.4 0.4 + - - -
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Residues in contact with GLN 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A SER* 3.2 32.3 + - - -
21A ASP* 2.8 30.1 + - + +
22A ILE* 3.2 9.4 - - - +
24A GLN* 1.3 74.2 - - + +
26A VAL* 1.3 55.8 + - - +
28A ASP* 3.1 7.6 + - - +
29A GLU* 2.6 39.8 + - - +
77A GLN* 2.8 24.2 + - - +
80A LEU* 3.6 19.3 - - + +
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Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ILE* 3.2 16.2 - - + +
23A TYR* 3.0 6.6 + - - +
25A GLN* 1.3 74.8 - - - +
27A ARG* 1.3 55.9 + - - +
29A GLU* 2.7 10.1 + - - +
30A LEU* 2.7 52.8 + - + +
40A PHE* 3.5 36.6 - - + -
52A LEU* 4.1 15.3 - - + -
56A LEU* 4.0 9.9 - - + -
76A MET* 4.2 17.7 - - - -
80A LEU* 3.9 11.7 - - + -
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Residues in contact with ARG 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR 3.1 21.6 + - - +
24A GLN* 3.7 26.3 - - + +
26A VAL* 1.3 77.0 - - - +
28A ASP* 1.3 59.3 + - - +
30A LEU* 3.3 11.9 + - + +
31A LYS* 2.9 29.0 + - - +
37A GLN* 5.5 2.0 - - - +
56A LEU* 3.8 34.5 + - + +
59A GLU* 3.3 22.1 + - - -
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Residues in contact with ASP 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLN* 2.8 27.8 + - + +
25A GLN* 3.3 5.8 - - - +
27A ARG* 1.3 73.4 - - - +
29A GLU* 1.3 55.0 + - - +
31A LYS* 3.0 20.1 + - - +
32A ARG* 2.7 53.2 + - - +
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLN* 2.6 18.0 + - - +
26A VAL 2.7 10.1 + - - +
28A ASP* 1.3 70.8 - - - +
30A LEU* 1.3 52.2 + - - +
32A ARG* 2.8 25.5 + - - +
33A ALA* 2.7 35.8 + - - +
40A PHE* 3.9 4.3 - - + -
80A LEU* 3.2 33.3 - - + +
87A ARG* 2.5 54.6 + - - +
91A TYR* 3.3 16.6 - - - +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 2.7 36.8 + - + +
27A ARG* 3.6 9.6 - - - +
29A GLU* 1.3 67.5 - - - +
31A LYS* 1.3 55.1 + - - +
32A ARG 2.9 4.5 - - - -
34A SER* 2.4 38.8 + - - -
35A VAL* 3.2 28.4 + - + +
37A GLN* 3.3 41.1 - - + +
40A PHE* 3.0 47.3 - - + -
56A LEU* 4.7 0.4 - - + -
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ARG 2.9 17.7 + - - +
28A ASP* 3.0 18.8 + - - +
30A LEU* 1.3 75.5 - - - +
32A ARG* 1.3 59.1 + - - +
34A SER* 4.0 7.0 + - - +
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Residues in contact with ARG 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ASP* 2.7 26.0 + - - +
29A GLU* 2.8 35.8 + - - +
31A LYS* 1.3 80.0 - - - +
33A ALA* 1.3 58.3 + - - +
34A SER* 3.1 5.8 + - - -
84A GLU* 3.3 32.3 + - - -
87A ARG* 3.9 14.4 - - - +
88A ASP* 5.6 0.3 - - - +
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLU 2.7 11.6 + - - +
32A ARG* 1.3 72.8 - - + +
34A SER* 1.3 71.1 + - - +
35A VAL* 2.9 27.6 + - + +
87A ARG* 5.1 2.5 - - - +
88A ASP* 4.8 12.3 - - - +
91A TYR* 2.9 33.6 - - + +
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Residues in contact with SER 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU 2.4 20.7 + - - -
31A LYS* 4.6 6.1 - - - +
32A ARG 3.1 5.5 - - - -
33A ALA* 1.3 76.0 - - - +
35A VAL* 1.3 59.4 + - - +
95A ARG* 4.3 14.7 + - - -
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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