Contacts of the strand formed by residues 43 - 48 (chain E) in PDB entry 1TKK
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 VAL 43 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35E ARG* 3.8 24.7 - - + -
36E ILE 3.4 6.5 - - - +
37E THR* 4.2 14.8 - - + +
38E TYR* 4.5 0.7 - - - -
41E GLY 3.7 10.3 + - - +
42E ALA* 1.3 80.0 - - - +
44E GLY* 1.3 71.0 + - - +
45E TRP* 3.6 35.8 + - + +
113E GLN* 3.2 20.9 + - - +
354E ILE 5.4 0.5 - - - +
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Residues in contact with GLY 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E ARG* 3.3 5.9 - - - -
36E ILE 2.9 34.7 + - - -
38E TYR* 3.7 6.7 - - - -
43E VAL* 1.3 75.0 - - - +
45E TRP* 1.3 61.2 + - - -
106E ALA* 3.5 25.6 - - - +
109E ASP* 3.4 11.2 - - - -
110E GLY 4.3 1.3 - - - -
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Residues in contact with TRP 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ILE* 4.1 13.9 - - + -
34E VAL 3.4 4.3 - - - -
35E ARG* 3.8 33.0 - - + -
43E VAL* 3.6 34.5 + - + +
44E GLY* 1.3 75.0 - - - -
46E GLY* 1.3 58.8 + - - +
105E MET 3.2 7.4 - - - +
106E ALA* 3.1 19.8 + - - +
109E ASP* 3.0 19.6 + - - +
302E LEU* 3.7 17.7 - - + -
333E PHE* 3.7 29.6 - + - -
352E LEU* 3.4 10.2 - - - +
354E ILE* 3.6 32.9 + - + -
355E ILE 3.9 6.1 + - - -
356E GLY* 3.9 28.9 - - - -
357E ALA* 4.3 4.9 - - + -
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Residues in contact with GLY 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ILE* 3.5 2.1 - - - -
34E VAL* 2.9 32.7 + - - +
45E TRP* 1.3 76.1 - - - +
47E GLU* 1.3 61.3 + - - +
102E ALA 3.6 19.1 - - - -
105E MET* 3.6 10.8 - - - -
106E ALA* 3.9 1.8 - - - +
302E LEU* 3.2 16.4 - - - +
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Residues in contact with GLU 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E SER* 2.5 30.7 + - - +
32E VAL 3.3 9.2 - - - +
33E ILE* 4.4 5.2 - - + -
46E GLY* 1.3 75.8 - - - +
48E ALA* 1.3 66.2 + - - +
49E PRO* 4.5 4.0 - - + -
102E ALA* 3.4 9.8 - - - +
105E MET* 3.4 10.4 - - - +
270E MET* 3.0 22.0 - - - +
299E GLU* 3.4 10.6 - - - +
300E THR* 2.5 49.5 + - - +
302E LEU* 3.5 12.9 - - + +
303E GLY* 3.1 24.6 + - - +
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Residues in contact with ALA 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E SER* 3.7 2.9 - - - -
32E VAL* 2.9 36.7 + - + +
47E GLU* 1.3 77.6 - - - +
49E PRO* 1.3 67.7 - - - +
50E PRO 4.2 0.3 - - - -
62E ILE* 3.9 21.7 - - + +
98E SER 3.4 29.2 - - - +
102E ALA* 3.8 7.6 - - + -
270E MET* 3.8 6.3 - - - -
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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