Contacts of the strand formed by residues 53 - 58 (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 GLY 53 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16R TRP 3.6 11.0 - - - -
17R LYS* 4.1 2.7 - - - -
28R LEU* 3.5 10.0 - - - +
49R ASN* 3.7 7.6 - - - +
50R GLY* 3.4 24.6 + - - -
51R GLY 3.1 1.4 - - - +
52R ALA* 1.3 81.3 - - - +
54R CYS* 1.3 60.6 + - - -
55R VAL* 5.4 2.7 - - - +
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Residues in contact with CYS 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15R GLU* 3.8 1.6 - - - -
16R TRP* 3.1 70.9 + - + +
28R LEU* 3.6 9.5 - - + +
29R ARG 4.8 0.2 - - - -
30R LEU* 3.8 7.9 - - - -
47R GLU* 3.4 35.2 - - - +
48R ASN 4.1 4.0 - - - -
49R ASN* 4.3 1.8 - - - +
53R GLY* 1.3 75.7 - - - -
55R VAL* 1.3 72.2 + - - +
56R CYS* 3.8 7.2 - - - -
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Residues in contact with VAL 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R CYS 4.0 4.9 - - - +
15R GLU* 4.1 18.2 - - + -
47R GLU* 3.6 1.4 - - - +
48R ASN* 2.7 62.6 + - + +
49R ASN* 4.7 2.0 - - - +
53R GLY 5.4 2.7 - - - +
54R CYS* 1.3 79.2 - - - +
56R CYS* 1.3 59.2 + - - +
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Residues in contact with CYS 56 (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* 2.9 25.4 + - - -
14R CYS* 3.3 23.6 + - - +
16R TRP* 5.2 0.2 - - - +
30R LEU* 3.3 33.4 - - + -
32R TYR* 4.3 8.5 - - - -
44R CYS* 2.0 47.3 - - - -
47R GLU* 3.7 11.9 - - + +
54R CYS* 3.8 4.5 - - - -
55R VAL* 1.3 74.9 - - - +
57R HIS* 1.4 59.0 + - - +
58R LEU* 5.3 0.7 - - - -
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Residues in contact with HIS 57 (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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11R ILE* 3.7 21.5 - - + -
12R SER 2.9 22.5 + - - -
13R THR* 4.7 5.3 - - - +
44R CYS* 3.0 17.9 - - - -
45R ILE 3.4 2.1 + - - -
46R PRO* 3.2 57.5 + - + +
56R CYS* 1.4 73.7 - - - +
58R LEU* 1.4 77.0 + - - +
59R LEU* 3.5 19.3 - - + +
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Residues in contact with LEU 58 (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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11R ILE* 4.0 1.0 - - - -
12R SER* 3.3 29.5 + - - +
13R THR* 5.5 0.9 - - - -
32R TYR* 3.6 41.3 - - + +
42R HIS* 4.8 5.2 - - + +
44R CYS* 5.1 5.4 - - - -
45R ILE* 4.9 1.8 - - + -
56R CYS* 5.3 0.7 - - - -
57R HIS* 1.4 83.2 + - - +
59R LEU* 1.4 65.4 + - - +
62R ASP* 3.4 40.8 - - + +
63R VAL* 3.8 15.9 - - + -
69R TYR* 3.4 39.0 - - + -
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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