Contacts of the helix formed by residues 33 - 45 (chain A) in PDB entry 2DHY
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 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ASN 3.7 3.9 + - - +
32A MET* 1.3 78.6 - - - +
34A TYR* 1.3 58.5 + - - +
35A ASP* 2.9 10.6 - - + +
36A ILE* 2.5 50.4 + - + +
37A ILE* 2.8 15.4 + - - +
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Residues in contact with TYR 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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18A PHE* 5.1 1.7 - - - -
19A ASN* 5.6 2.3 + - - -
22A MET* 2.9 47.6 - - + +
26A LYS* 3.6 30.7 - - + +
32A MET 4.2 1.4 + - - -
33A ASP* 1.3 72.2 - - - +
35A ASP* 1.3 61.5 + - - +
37A ILE* 4.2 6.1 - - - +
38A GLU* 3.2 47.0 + - - +
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Residues in contact with ASP 35 (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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33A ASP* 2.9 9.7 - - + +
34A TYR* 1.3 80.7 - - - +
36A ILE* 1.3 63.5 + - + +
38A GLU* 4.1 1.8 - - - +
39A CYS* 2.8 43.8 + - - +
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Residues in contact with ILE 36 (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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32A MET* 4.5 7.2 - - + -
33A ASP* 2.5 34.5 + - + +
35A ASP* 1.3 76.5 - - + +
37A ILE* 1.3 69.6 + - - +
39A CYS* 2.7 23.6 + - + +
40A VAL* 2.8 16.7 + - + +
55A LEU* 4.1 9.0 - - + -
58A MET* 4.1 29.4 - - + -
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Residues in contact with ILE 37 (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 MET* 3.9 16.2 - - + -
25A PHE* 3.3 46.0 - - + -
26A LYS* 4.0 28.3 - - + +
29A PHE 4.2 3.8 - - - +
32A MET* 3.6 31.2 - - + -
33A ASP 2.8 21.4 + - - +
34A TYR* 4.1 4.5 - - - +
36A ILE* 1.3 77.6 - - - +
38A GLU* 1.3 65.4 + - - +
40A VAL* 3.0 6.2 + - - +
41A LEU* 3.0 19.4 + - + +
51A THR* 3.9 1.2 - - - +
55A LEU* 3.8 21.1 - - + -
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Residues in contact with GLU 38 (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 PHE* 3.0 28.6 - - + -
22A MET* 2.9 43.5 - - + +
34A TYR* 3.2 27.7 + - - +
35A ASP* 4.1 2.7 - - - +
36A ILE 3.2 0.6 - - - -
37A ILE* 1.3 76.4 - - - +
39A CYS* 1.3 69.4 + - - +
41A LEU* 2.7 22.6 + - - +
42A ARG* 2.7 43.4 + - - +
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Residues in contact with CYS 39 (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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35A ASP* 2.8 29.4 + - - +
36A ILE* 2.7 25.6 + - + +
38A GLU* 1.3 72.1 - - - +
40A VAL* 1.3 50.6 + - + +
42A ARG* 3.3 5.5 + - - +
43A ALA* 2.5 40.8 + - + +
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Residues in contact with VAL 40 (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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36A ILE* 2.8 15.8 + - + +
37A ILE 3.3 4.9 - - - +
39A CYS* 1.3 73.8 - - + +
41A LEU* 1.3 58.2 + - - +
43A ALA* 3.8 4.3 - - - -
44A ASN* 2.5 63.8 + - - +
51A THR* 3.7 15.9 - - + +
54A GLN* 3.2 33.4 - - + +
55A LEU* 3.7 23.8 - - + -
58A MET* 3.9 15.7 - - + -
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Residues in contact with LEU 41 (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 PHE* 3.9 33.2 - - + -
21A ALA* 4.7 7.9 - - + -
22A MET* 4.1 8.1 - - + -
25A PHE* 3.2 38.4 - - + -
37A ILE* 3.0 8.3 + - + +
38A GLU* 2.7 25.6 + - - +
40A VAL* 1.3 71.7 - - - +
42A ARG* 1.3 50.2 + - + +
44A ASN* 3.6 1.4 - - - +
45A SER 2.7 11.6 + - - -
46A GLY* 2.6 35.1 + - - +
47A ALA 4.6 11.7 - - - +
48A VAL* 4.9 2.2 - - + -
51A THR* 3.4 23.5 - - + +
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Residues in contact with ARG 42 (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 PHE* 5.2 4.0 - - - -
38A GLU* 2.7 48.3 + - + +
39A CYS* 3.7 5.2 - - - +
41A LEU* 1.3 72.2 - - + +
43A ALA* 1.3 61.1 + - - +
44A ASN 3.0 1.3 - - - -
45A SER* 2.6 27.9 + - - +
46A GLY 4.6 0.7 - - - +
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Residues in contact with ALA 43 (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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39A CYS* 2.5 27.4 + - + +
40A VAL* 3.5 7.6 - - + +
42A ARG* 1.3 73.5 - - - +
44A ASN* 1.3 63.2 + - - +
45A SER* 5.0 0.7 - - - -
54A GLN* 5.6 2.0 - - - +
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Residues in contact with ASN 44 (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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40A VAL* 2.5 55.4 + - - +
41A LEU 4.0 0.4 - - - +
43A ALA* 1.3 77.1 - - - +
45A SER* 1.3 71.9 + - - +
47A ALA* 4.4 7.7 - - + +
50A ALA* 3.2 30.1 - - + +
51A THR* 4.0 11.7 - - - +
54A GLN* 3.6 19.5 + - - +
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Residues in contact with SER 45 (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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41A LEU 2.7 5.9 + - - -
42A ARG* 2.6 22.9 + - - +
43A ALA 5.0 0.7 - - - -
44A ASN* 1.3 80.2 - - - +
46A GLY* 1.3 72.0 + - - +
47A ALA* 3.9 1.7 - - - +
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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