Contacts of the strand formed by residues 24 - 29 (chain F) in PDB entry 2Z3R
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 ARG 24 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E HIS* 3.6 47.4 + - - -
21E ILE* 5.6 4.2 - - - +
22E ASP* 5.3 5.5 + - - -
53E GLU* 3.3 27.3 + - - +
54E SER 5.8 0.2 + - - -
17F LYS* 6.0 0.2 - - - +
22F TYR 3.8 9.2 - - - +
23F SER* 1.3 74.8 + - - +
25F GLU* 1.3 73.8 + - - +
26F ARG* 5.2 1.6 - - - +
42F LEU* 3.1 40.6 - - + +
43F THR 3.5 4.7 - - - -
44F GLU* 3.0 31.4 + - + +
57G ALA* 5.7 0.2 - - - +
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Residues in contact with GLU 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ILE* 4.1 10.8 - - + -
15F TRP 3.6 8.7 - - - +
16F VAL* 3.9 5.4 - - + -
17F LYS* 3.0 38.2 + - - +
18F SER* 2.9 28.5 + - - +
23F SER* 3.9 3.8 + - - -
24F ARG* 1.3 82.6 - - - +
26F ARG* 1.3 70.6 + - - +
42F LEU* 3.5 3.2 - - - +
43F THR* 2.8 45.0 + - + -
56F TRP* 3.6 25.4 - - + -
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Residues in contact with ARG 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ASP* 2.8 37.0 + - - -
23E ALA* 3.5 16.0 - - - +
53E GLU* 2.8 42.0 + - - -
13F ASP 4.3 0.2 - - - +
14F ILE* 3.4 21.6 - - - +
15F TRP 4.8 2.5 + - - +
24F ARG* 5.2 1.2 - - - +
25F GLU* 1.3 85.0 + - - +
27F TYR* 1.3 65.1 + - - +
28F ILE* 3.9 14.5 + - + +
41F SER* 3.0 31.2 + - - +
42F LEU* 3.6 18.5 - - + +
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Residues in contact with TYR 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F PRO* 3.3 15.2 - - + +
7F MET* 2.6 40.4 + - + +
8F SER* 4.6 0.7 - - - -
9F VAL* 3.7 28.5 - - + -
12F ALA* 4.4 4.0 - - + -
13F ASP* 3.4 12.1 - - - -
14F ILE* 3.7 33.2 - - + -
26F ARG* 1.3 74.4 - - - +
28F ILE* 1.3 63.5 + - - +
29F CYS 4.3 0.2 + - - -
41F SER* 3.1 31.1 + - - +
43F THR* 3.6 27.2 + - + -
56F TRP* 5.2 1.0 - - - +
57F THR 5.3 0.3 + - - -
59F PRO* 3.6 30.3 - - + -
61F LEU* 3.5 22.8 - - + +
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Residues in contact with ILE 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ALA* 3.8 2.9 - - - -
13F ASP* 2.7 36.0 + - + +
14F ILE* 6.4 0.4 - - - -
26F ARG* 4.3 14.1 - - + +
27F TYR* 1.3 81.6 - - - +
29F CYS* 1.3 76.5 + - - +
30F ASN* 4.2 1.4 + - - -
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Residues in contact with CYS 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F HIS 3.6 4.5 - - - -
27F TYR 4.2 0.4 + - - -
28F ILE* 1.3 88.7 - - - +
30F ASN* 1.3 65.3 - - - +
33F PHE 3.9 20.9 - - - +
34F LYS* 4.1 2.5 - - - -
35F ARG* 3.4 29.8 - - - +
61F LEU* 4.0 7.6 - - - -
63F CYS* 2.1 49.6 - - + -
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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