Contacts of the helix formed by residues 29 - 37 (chain A) in PDB entry 1DV0
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 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A TYR* 2.8 10.1 + - - -
26A CYS 3.4 16.7 + - - +
27A GLU* 2.7 32.8 + - - +
28A LYS* 1.4 72.8 - - - +
30A GLU* 1.4 59.5 + - - +
31A ASN* 4.8 4.9 + - - +
32A LEU* 3.6 22.7 + - + +
33A ALA* 2.7 38.3 + - - +
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Residues in contact with GLU 30 (chain A).
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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4A GLU* 4.8 7.4 - - - +
5A ALA* 5.1 6.8 - - + +
8A ARG* 3.8 32.2 + - - -
9A LEU* 5.0 2.6 - - + +
23A TYR* 3.1 23.4 + - + +
29A ASN* 1.4 74.3 + - - +
31A ASN* 1.3 66.7 - - - +
33A ALA* 3.6 1.9 - - - +
34A ALA* 3.0 29.5 + - - +
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Residues in contact with ASN 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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29A ASN* 4.7 4.2 + - - +
30A GLU* 1.3 83.9 - - - +
32A LEU* 1.3 64.8 + - + +
34A ALA* 3.2 16.8 + - - +
35A ASN* 3.3 18.8 + - - +
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Residues in contact with LEU 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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26A CYS* 3.0 52.9 - - + +
27A GLU* 5.7 0.2 - - + -
29A ASN* 3.6 22.4 + - + +
30A GLU 3.4 0.2 - - - -
31A ASN* 1.3 81.0 - - + +
33A ALA* 1.4 59.9 + - - +
35A ASN* 3.1 14.7 + - + +
36A PHE 2.8 22.0 + - - -
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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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9A LEU* 3.7 8.1 - - + -
22A ALA 3.7 19.1 - - - +
23A TYR* 3.2 26.7 - - + -
26A CYS* 4.0 1.3 - - + -
29A ASN 2.7 24.9 + - - +
30A GLU 3.6 2.5 - - - +
32A LEU* 1.4 75.0 - - - +
34A ALA* 1.3 52.7 + - - +
35A ASN 2.9 4.3 - - - -
36A PHE* 3.0 1.1 + - - +
37A LEU* 2.8 43.0 + - + +
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Residues in contact with ALA 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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9A LEU* 4.7 2.6 - - + +
12A LEU* 5.2 9.0 - - + -
30A GLU 3.0 17.4 + - - +
31A ASN* 3.2 10.0 + - - +
33A ALA* 1.3 73.6 - - - +
35A ASN* 1.3 59.7 + - - +
37A LEU* 4.3 4.0 - - - +
38A LEU* 3.1 43.2 - - + +
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Residues in contact with ASN 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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31A ASN* 3.3 14.9 + - - +
32A LEU* 3.2 21.1 - - + +
33A ALA 2.9 0.2 - - - -
34A ALA* 1.3 81.6 + - - +
36A PHE* 1.3 57.6 + - - +
37A LEU 3.2 1.1 - - - -
39A SER* 2.8 56.5 + - - -
40A GLN* 3.3 4.5 + - - +
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Residues in contact with PHE 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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21A GLN 4.5 3.8 - - - -
22A ALA* 3.8 35.3 - - + +
25A ALA* 4.5 18.6 - - + -
26A CYS* 3.9 17.3 - - + -
32A LEU 2.8 14.5 + - - +
33A ALA 3.0 4.2 + - - +
35A ASN* 1.3 77.5 - - - +
37A LEU* 1.3 59.9 + - - +
40A GLN* 2.9 56.9 - - + +
43A ASP* 5.1 7.9 - - - -
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Residues in contact with LEU 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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9A LEU* 3.2 42.4 - - + +
12A LEU* 5.1 1.6 - - + -
14A PHE* 3.5 37.9 - - + -
18A LEU* 3.0 41.0 - - + +
19A VAL* 4.5 2.0 - - - -
22A ALA* 3.6 21.3 - - + -
33A ALA* 2.8 24.9 + - + +
34A ALA* 4.3 0.9 - - - +
36A PHE* 1.3 81.5 - - - +
38A LEU* 1.3 73.4 + - + +
39A SER 3.6 0.4 - - - -
40A GLN 4.5 1.5 + - - -
41A ASN* 4.8 10.1 + - - -
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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