Contacts of the strand formed by residues 25 - 32 (chain B) in PDB entry 2CKE
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 ALA 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B SER 2.6 33.7 - - - +
22B GLY* 3.5 5.0 + - - +
23B GLN 3.8 0.6 - - - -
24B PHE* 1.3 81.6 - - - +
26B ILE* 1.3 63.3 + - - +
27B VAL* 4.2 2.0 - - + -
42B LYS* 3.8 33.2 - - + -
43B PHE 3.3 10.5 - - - +
44B ILE* 4.3 7.6 - - + -
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Residues in contact with ILE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLU* 4.0 23.6 - - - +
20B GLY 4.0 8.1 - - - +
21B SER* 5.4 4.5 - - - -
22B GLY* 6.1 0.9 - - - -
25B ALA* 1.3 78.1 - - - +
27B VAL* 1.3 62.0 + - - +
28B LYS* 4.1 28.0 - - + -
42B LYS* 4.5 0.2 - - - -
43B PHE* 2.7 50.3 + - + +
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLU* 3.7 5.2 - - - +
19B LEU* 2.9 29.2 + - + -
20B GLY 3.2 13.9 + - - +
21B SER 5.6 0.9 - - - +
25B ALA* 5.4 2.2 - - + +
26B ILE* 1.3 76.1 - - - +
28B LYS* 1.3 67.5 + - - +
40B ALA* 4.2 8.5 - - + -
41B ALA 3.2 10.1 - - - +
42B LYS* 4.0 24.2 - - + -
1302B IQU 3.4 67.8 - - + +
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.8 26.9 - - + +
16B GLY 3.9 10.5 - - - +
17B GLU 3.5 8.7 - - - +
18B GLU* 4.4 11.4 - - - +
19B LEU* 4.3 5.8 - - - +
26B ILE* 4.1 25.4 - - + -
27B VAL* 1.3 78.4 - - - +
29B LYS* 1.3 60.5 + - - +
40B ALA* 3.4 5.0 - - - +
41B ALA* 2.7 44.3 + - + +
43B PHE* 4.2 24.6 - - + -
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Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 4.0 0.2 - - - -
16B GLY* 2.6 36.4 + - - -
17B GLU* 2.9 46.9 + - + +
19B LEU* 3.6 17.4 - - + +
28B LYS* 1.3 74.5 - - - +
30B CYS* 1.3 62.3 + - - +
38B GLU* 3.3 37.8 + - - -
39B TYR 3.7 10.1 - - - +
95B LEU* 4.1 17.3 - - + -
97B SER* 5.6 1.5 + - - -
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Residues in contact with CYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B TYR* 4.1 22.4 - - + -
14B ASP 3.2 16.8 - - - +
15B ILE* 4.3 11.2 - - + -
16B GLY* 5.3 0.2 - - - -
29B LYS* 1.3 78.9 - - - +
31B ARG* 1.3 58.7 + - - +
38B GLU* 3.4 7.2 - - - +
39B TYR* 2.7 63.8 + - - +
40B ALA 4.2 0.4 - - - -
41B ALA* 3.7 25.8 - - + -
92B ILE* 4.5 4.3 - - - -
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Residues in contact with ARG 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B TYR* 3.5 4.0 - - - -
14B ASP* 3.2 38.1 + - + +
30B CYS* 1.3 78.6 - - - +
32B GLU* 1.3 69.1 + - - +
33B LYS* 3.1 5.7 + - - +
36B GLY* 3.4 35.9 + - - +
37B LEU 3.5 5.4 - - - +
38B GLU* 2.8 38.3 + - + +
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Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PHE* 4.2 8.1 - - + +
13B TYR* 3.5 41.4 + - + -
31B ARG* 1.3 69.3 - - - +
33B LYS* 1.3 59.0 + - - +
34B SER* 3.3 23.3 + - - +
35B THR* 3.8 18.2 + - - +
36B GLY* 2.7 34.7 + - - -
37B LEU 3.1 11.0 + - - +
39B TYR* 3.8 4.6 + - + -
80B HIS* 2.6 31.8 + - - -
81B ASP* 5.1 2.8 - - - +
83B TYR* 5.4 1.9 + - - -
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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