Contacts of the helix formed by residues 35 - 40 (chain A) in PDB entry 2A0Y
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 LEU 35 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A CYS* 3.9 3.5 - - + +
32A GLY* 3.5 21.0 + - - +
33A SER 3.0 18.8 - - - +
34A GLY* 1.3 96.0 - - - +
36A GLY* 1.3 60.5 + - - +
37A GLY 2.9 12.7 + - - +
38A LEU* 2.9 35.7 + - + +
114A THR* 3.0 35.0 - - - +
115A ASN* 3.8 15.0 - - - +
116A ALA* 5.9 0.2 - - + -
238A PHE* 5.4 0.4 - - + -
240A LEU* 3.9 17.7 - - + -
264A GLY* 4.9 0.4 - - - +
268A ALA* 6.3 2.0 - - - +
271A LEU* 3.5 31.9 - - + -
272A GLU* 6.3 0.2 - - - -
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Residues in contact with GLY 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A CYS* 3.9 12.4 - - - +
32A GLY 4.1 2.8 + - - -
34A GLY* 3.7 1.2 - - - +
35A LEU* 1.3 78.2 - - - +
37A GLY* 1.3 62.9 + - - +
38A LEU* 3.1 2.8 + - - +
39A THR* 3.1 25.3 + - - +
82A GLN* 3.8 30.7 - - - +
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Residues in contact with GLY 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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34A GLY 5.4 0.2 - - - -
35A LEU 2.9 4.0 + - - -
36A GLY* 1.3 72.2 - - - +
38A LEU* 1.3 52.3 + - - +
39A THR* 2.7 18.5 + - - -
40A ASP* 2.7 34.9 + - - +
272A GLU* 3.4 21.1 - - - +
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Residues in contact with LEU 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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29A ILE* 4.3 9.4 - - + -
31A CYS* 3.8 21.8 - - + -
35A LEU* 2.9 30.5 + - + +
36A GLY 3.1 0.6 + - - -
37A GLY* 1.3 73.7 - - - +
39A THR* 1.3 61.7 + - - +
40A ASP 3.2 0.8 + - - -
41A LYS* 3.6 16.6 + - - +
42A LEU* 4.3 2.9 + - - +
73A LEU* 4.7 5.5 - - + +
80A MET* 3.4 28.8 - - + +
114A THR* 4.9 6.5 - - + +
271A LEU* 4.1 10.1 - - + +
272A GLU* 3.4 48.4 + - + +
275A VAL* 4.4 20.9 - - + -
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Residues in contact with THR 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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31A CYS* 5.3 1.1 - - - -
36A GLY 3.1 19.5 + - - +
37A GLY* 2.7 8.0 + - - +
38A LEU* 1.3 73.3 - - - +
40A ASP* 1.3 74.8 + - - +
41A LYS 3.5 0.3 + - - -
42A LEU* 3.5 16.2 + - - +
45A ALA* 5.1 3.3 - - - +
47A ILE* 5.8 0.7 - - - +
69A VAL* 3.2 35.5 - - - +
80A MET* 3.9 16.0 - - - -
82A GLN* 3.8 22.9 - - - +
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Residues in contact with ASP 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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37A GLY* 2.7 30.3 + - - +
39A THR* 1.3 87.5 - - - +
41A LYS* 1.3 59.5 + - + +
42A LEU 3.2 11.7 + - - +
272A GLU* 4.5 4.6 - - - +
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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