Contacts of the helix formed by residues 20 - 25 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C LYS 3.5 4.4 + - - -
19C ASP* 1.3 73.3 - - - +
21C LYS* 1.3 60.3 + - - +
22C LEU 3.0 1.0 + - - -
23C THR* 3.0 3.5 + - - -
24C TYR* 2.8 35.7 + + + -
52C GLU* 2.9 24.7 + - - +
55C ALA* 3.6 21.1 - - + +
56C ALA* 3.6 25.6 - - + +
59C ALA* 3.5 28.0 - - + -
60C GLU* 2.6 33.5 + - + +
65C THR 3.4 20.4 - - - -
66C TRP* 3.6 17.5 - - + +
127C PHE* 3.8 12.1 - + - -
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Residues in contact with LYS 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ASP* 3.3 23.5 + - + -
20C TYR* 1.3 77.5 - - - +
22C LEU* 1.3 77.4 + - + +
23C THR 3.1 0.9 + - - -
25C TYR* 3.4 39.1 + - + +
49C PRO* 6.1 2.9 - - + -
51C GLU* 4.0 22.4 - - + +
52C GLU* 3.0 24.5 + - + +
55C ALA* 3.4 14.5 - - + +
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LYS* 3.8 37.6 + - + +
19C ASP* 3.5 18.8 - - + +
20C TYR 3.0 1.2 + - - -
21C LYS* 1.3 104.5 - - + +
23C THR* 1.3 63.7 + - - +
25C TYR 5.5 0.4 - - - +
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Residues in contact with THR 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LYS* 3.4 24.9 + - - +
19C ASP 4.5 1.2 + - - -
20C TYR* 3.0 2.5 + - - -
22C LEU* 1.3 81.5 + - - +
24C TYR* 1.3 84.2 + - + +
25C TYR 3.6 1.6 - - - -
26C THR* 4.1 5.9 - - - +
77C LEU* 4.4 14.6 - - + -
81C LYS* 2.8 49.9 + - + +
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Residues in contact with TYR 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C TYR* 2.8 25.6 + + - +
23C THR* 1.3 97.1 - - + +
25C TYR* 1.3 57.1 + - - +
26C THR* 3.8 2.5 - - - -
55C ALA* 3.5 21.9 - - + +
58C ALA* 4.2 2.7 - - + +
59C ALA* 3.4 40.6 - - + +
62C SER* 4.0 2.2 - - - -
63C THR* 2.9 27.9 + - - -
64C GLY* 3.2 16.2 + - - -
72C ASP* 5.3 0.9 + - - -
77C LEU* 4.1 11.5 - - + +
81C LYS* 3.7 16.4 - - + -
82C GLY 3.2 22.2 - - - -
83C ARG* 3.6 3.1 - - - +
84C CYS* 2.9 29.3 + - - +
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Residues in contact with TYR 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LYS* 3.4 36.9 + - + +
22C LEU 5.5 0.5 - - - +
23C THR 5.1 0.3 - - - -
24C TYR* 1.3 77.3 - - - +
26C THR* 1.3 62.1 + - - +
27C PRO* 3.5 38.4 - - + +
51C GLU* 3.7 33.3 + - + +
55C ALA* 4.2 5.4 - - + -
84C CYS* 3.4 25.8 - - + -
86C HIS* 5.1 3.9 - - - -
87C ILE* 3.7 31.5 + - + +
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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