Contacts of the helix formed by residues 19 - 22 (chain A) in PDB entry 4AR3
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 PRO 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ALA 3.5 13.0 - - - +
18A ASP* 1.3 91.1 + - - +
20A ASP* 1.3 67.4 + - - +
21A ASN 3.2 1.2 + - - -
22A GLY* 3.2 9.5 + - - -
23A ILE 2.5 24.8 + - - +
24A SER* 3.8 7.0 - - - +
25A PRO* 4.9 0.7 - - + -
1062A D3O 3.8 9.0 - - - +
2009A DOD 3.5 4.7 - - - +
2052A DOD 3.9 12.1 - - - +
2056A DOD 3.2 16.0 + - - +
2108A DOD 3.4 3.8 + - - -
2109A DOD 3.7 17.5 - - - +
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Residues in contact with ASP 20 (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 ASP 3.2 1.2 + - - -
19A PRO* 1.3 74.5 - - - +
21A ASN* 1.3 71.9 + - - +
22A GLY 3.5 0.4 + - - -
2009A DOD 3.3 10.2 + - - +
2034A DOD 3.0 20.7 + - - +
2043A DOD 3.5 6.9 + - - +
2055A DOD 2.5 22.2 + - - -
2056A DOD 3.1 3.3 + - - -
2108A DOD 2.5 27.3 + - - -
2139A DOD 2.9 19.7 + - - +
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Residues in contact with ASN 21 (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 ASP* 2.9 39.6 + - - +
20A ASP* 1.3 91.5 + - - +
22A GLY* 1.3 55.0 + - - +
23A ILE* 3.1 4.1 - - - -
39A PRO* 3.7 5.9 - - - +
2006A DOD 3.4 6.9 + - - +
2022A DOD 4.6 0.9 - - - -
2026A DOD 4.5 0.2 - - - +
2027A DOD 2.7 23.3 + - - +
2030A DOD 1.8 40.1 + - - +
2072A DOD 3.5 13.9 + - - -
2104A DOD 2.9 3.3 + - - -
2154A DOD 3.6 6.8 + - - -
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Residues in contact with GLY 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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19A PRO* 3.2 9.1 + - - -
20A ASP 3.5 0.8 - - - -
21A ASN* 1.3 75.2 - - - +
23A ILE* 1.3 65.1 + - - +
24A SER 4.1 1.1 + - - -
2010A DOD 4.2 0.7 + - - -
2022A DOD 3.6 19.0 + - - -
2029A DOD 3.8 1.6 + - - -
2103A DOD 2.7 17.8 + - - -
2104A DOD 3.9 4.7 - - - -
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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