Contacts of the strand formed by residues 25 - 31 (chain A) in PDB entry 2EDW
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 THR 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ALA* 5.1 2.3 - - - +
24A ALA* 1.3 80.5 + - - +
26A ALA* 1.3 69.2 + - - +
27A VAL* 3.6 8.8 - - - +
65A GLN* 3.2 37.0 - - + +
66A ILE 3.5 5.2 - - - +
67A ARG* 3.9 27.4 - - + +
69A LEU* 3.9 1.1 - - - -
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Residues in contact with ALA 26 (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 GLN* 3.6 25.8 - - + -
20A ALA* 4.9 3.6 - - + -
25A THR* 1.3 75.1 - - - +
27A VAL* 1.3 68.5 + - - +
28A LEU* 5.7 0.4 - - + -
64A LEU 4.2 1.3 - - - -
65A GLN* 3.2 21.0 - - - +
66A ILE* 3.5 26.1 + - + -
69A LEU* 3.3 31.5 - - + +
90A LEU* 4.3 2.0 - - + -
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Residues in contact with VAL 27 (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 GLN* 2.8 31.4 + - - +
25A THR 3.6 9.9 - - - +
26A ALA* 1.3 82.2 - - - +
28A LEU* 1.3 61.0 + - - +
29A GLN* 3.7 33.8 + - + +
63A GLU* 4.3 13.0 - - + +
64A LEU 3.4 3.6 - - - -
65A GLN* 3.8 17.0 - - + +
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Residues in contact with LEU 28 (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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15A VAL* 4.0 13.7 - - + -
16A LYS 4.3 0.7 - - - +
18A GLN* 3.7 28.3 - - + +
26A ALA* 5.7 0.2 - - + -
27A VAL* 1.3 72.2 - - - +
29A GLN* 1.3 60.9 + - - +
40A TRP* 2.9 38.5 - - + -
63A GLU* 3.2 0.7 - - - -
64A LEU* 2.9 53.6 + - + +
66A ILE* 4.4 6.5 - - + -
77A TYR* 3.8 33.0 - - + +
88A ALA* 3.7 30.3 - - + +
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Residues in contact with GLN 29 (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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15A VAL* 2.7 32.0 - - - +
16A LYS 4.8 0.5 + - - -
27A VAL* 3.7 23.3 + - + +
28A LEU* 1.3 76.6 - - - +
30A CYS* 1.3 58.4 + - - +
61A LYS* 5.0 15.5 + - - +
62A CYS 3.4 14.8 - - - +
63A GLU* 3.4 24.4 + - + -
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Residues in contact with CYS 30 (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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11A PHE* 3.4 35.2 - - + -
13A GLU* 3.8 13.7 - - - +
14A ASP 5.6 0.2 - - - -
15A VAL* 3.4 19.3 - - + +
29A GLN* 1.3 74.6 - - - +
31A GLU* 1.3 65.6 + - - +
32A LEU* 4.7 0.2 - - - -
40A TRP* 4.7 1.1 - - + -
61A LYS* 3.3 14.9 + - - +
62A CYS* 3.0 49.6 + - - +
79A CYS* 4.5 6.1 - - - -
86A THR* 4.8 1.8 - - + -
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Residues in contact with GLU 31 (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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11A PHE* 3.6 8.5 - - - -
12A ILE* 3.2 35.1 + - + +
13A GLU* 2.8 55.3 + - + +
30A CYS* 1.3 78.4 - - - +
32A LEU* 1.3 72.6 + - - +
60A THR* 3.7 12.1 + - - +
61A LYS* 3.4 30.3 + - + +
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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