Contacts of the strand formed by residues 28 - 33 (chain R) in PDB entry 1ILL
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 28 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16R TRP* 3.8 25.1 - - + -
18R MET* 3.8 25.4 - - + +
26R THR* 3.4 20.4 - - + +
27R GLU* 1.3 79.5 - - - +
29R ARG* 1.4 66.0 + - - +
49R ASN* 3.9 26.4 + - - +
51R GLY* 3.2 27.6 - - - +
53R GLY* 3.5 31.2 - - - +
54R CYS* 3.6 4.9 - - + +
74R TRP 3.5 3.4 - - - +
75R ALA* 4.9 1.6 - - - -
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Residues in contact with ARG 29 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16R TRP* 3.3 15.7 - - - -
27R GLU* 5.8 0.9 - - - -
28R LEU* 1.4 79.3 - - - +
30R LEU* 1.3 60.3 + - - +
31R LEU* 3.2 36.2 - - + +
41R ALA* 4.9 3.2 - - - +
43R THR* 5.8 4.0 - - + -
47R GLU* 3.6 11.0 + - - +
74R TRP* 3.2 59.3 + - + +
77R GLN* 2.6 52.5 + - + +
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Residues in contact with LEU 30 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R CYS* 5.6 0.4 - - + -
16R TRP* 3.0 33.2 - - + +
29R ARG* 1.3 75.3 - - - +
31R LEU* 1.3 72.5 + - - +
32R TYR* 3.4 24.7 - - + -
43R THR* 4.0 2.3 - - - +
44R CYS* 2.8 29.8 + - - +
47R GLU* 2.8 16.7 + - - +
54R CYS* 3.8 5.6 - - - -
56R CYS* 3.3 38.6 - - + -
71R LEU* 3.6 26.9 - - + -
72R ASP 3.3 16.8 - - - +
73R LEU* 4.1 1.3 - - - -
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Residues in contact with LEU 31 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R ARG* 3.2 44.0 - - + +
30R LEU* 1.3 86.8 - - - +
32R TYR* 1.4 69.8 + - - +
41R ALA* 3.5 39.7 - - + +
42R HIS 3.2 9.9 - - - +
43R THR* 3.8 24.5 - - + +
44R CYS 4.0 1.6 - - - +
72R ASP* 2.9 31.1 + - - +
74R TRP* 3.4 21.8 - - + +
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Residues in contact with TYR 32 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13R THR* 5.1 1.6 - - - -
14R CYS* 3.2 29.8 + - - -
30R LEU* 3.4 21.5 - - + -
31R LEU* 1.4 79.6 - - - +
33R GLN* 1.3 67.9 + - - +
37R LEU* 5.0 0.2 - - - +
40R GLU 4.0 1.0 - - - +
41R ALA* 3.3 8.6 - - - -
42R HIS* 3.0 39.4 + - + +
44R CYS* 5.2 2.7 - - + -
56R CYS* 4.3 7.5 - - - -
58R LEU* 3.6 42.6 - - + +
62R ASP* 5.0 7.0 - - + +
69R TYR* 3.5 45.3 + + + -
70R THR 3.2 22.4 - - - -
71R LEU* 3.8 14.4 - - + -
72R ASP* 4.7 0.9 - - - +
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Residues in contact with GLN 33 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884 ARG* 5.1 0.3 + - - -
32R TYR* 1.3 85.1 - - - +
34R LEU* 1.3 77.4 + - - +
37R LEU* 2.8 28.5 + - + +
38R LEU* 2.7 34.9 + - - +
41R ALA* 4.9 8.1 - - + +
62R ASP 5.5 2.0 - - - +
69R TYR* 4.3 2.9 - - - +
70R THR* 2.8 32.1 + - - +
72R ASP* 3.6 8.2 - - + +
82R LYS* 2.5 41.6 + - - +
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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