Contacts of the helix formed by residues 20 - 25 (chain A) in PDB entry 1IR1
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 TYR 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LYS 3.6 4.8 + - - -
19A ASP* 1.3 72.3 - - - +
21A LYS* 1.3 58.2 + - - +
23A THR* 3.1 4.4 + - - -
24A TYR* 2.8 37.7 + + + +
52A GLU* 2.9 25.0 + - + +
55A ALA* 3.6 22.0 - - + +
56A ALA* 3.5 25.6 - - + +
59A ALA* 3.4 26.9 - - + -
60A GLU* 2.7 33.2 + - + +
65A THR 3.4 21.1 - - - -
66A TRP* 3.6 17.9 - - - +
127A PHE* 3.8 12.7 - + - -
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Residues in contact with LYS 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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19A ASP* 3.8 24.7 - - + -
20A TYR* 1.3 77.6 - - - +
22A LEU* 1.3 70.6 + - + +
23A THR 3.2 0.5 + - - -
25A TYR* 3.4 38.8 + - + +
49A PRO* 4.3 25.3 - - - +
51A GLU* 4.1 20.2 + - + +
52A GLU* 3.0 24.8 + - - +
55A ALA* 3.4 14.3 - - + +
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Residues in contact with LEU 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 LYS* 4.0 35.0 - - + +
19A ASP* 3.6 24.0 - - + +
20A TYR 3.1 0.8 + - - -
21A LYS* 1.3 87.7 - - + +
23A THR* 1.3 62.9 + - - +
25A TYR 5.5 0.4 - - - +
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Residues in contact with THR 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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18A LYS* 3.7 22.3 + - - -
19A ASP 4.5 1.2 + - - -
20A TYR* 3.1 3.3 + - - -
22A LEU* 1.3 82.2 + - - +
24A TYR* 1.3 87.0 + - + +
25A TYR 3.6 1.7 + - - -
26A THR* 4.1 5.5 - - - +
77A LEU* 4.7 12.1 - - + -
81A LYS* 2.8 49.1 + - + +
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Residues in contact with TYR 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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20A TYR* 2.8 26.5 + + - +
23A THR* 1.3 97.3 - - + +
25A TYR* 1.3 56.7 + - - +
26A THR* 3.8 2.7 - - - -
55A ALA* 3.5 21.2 - - + +
58A ALA* 4.4 0.9 - - + -
59A ALA* 3.4 37.7 - - + +
62A SER* 4.1 1.6 - - - -
63A THR* 2.9 28.6 + - - -
64A GLY* 3.2 18.4 + - - -
72A ASP* 5.4 0.3 + - - -
77A LEU* 3.9 13.2 - - - +
81A LYS* 3.6 16.4 - - + -
82A GLY 3.2 22.4 - - - +
83A ARG* 3.7 3.2 - - - -
84A CYS* 3.0 29.3 + - - +
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Residues in contact with TYR 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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21A LYS* 3.4 36.7 + - + +
22A LEU 5.5 0.5 - - - +
23A THR 3.6 0.9 - - - +
24A TYR* 1.3 75.9 - - - +
26A THR* 1.3 64.3 + - - +
27A PRO* 3.5 40.3 - - + +
51A GLU* 3.8 34.5 + - + +
55A ALA* 4.3 4.7 - - + -
84A CYS* 3.5 25.6 - - + -
86A HIS* 5.1 3.5 - - - -
87A ILE* 3.7 30.1 + - + +
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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