Contacts of the helix formed by residues 44 - 49 (chain D) in PDB entry 5BXD
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 SER 44 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D ALA 3.3 16.4 + - - -
29D ASN* 3.9 11.7 + - - -
30D ALA 3.5 15.3 - - - -
32D VAL* 4.0 3.4 - - - -
43D SER* 1.3 81.8 + - - +
45D LEU* 1.3 59.2 + - - +
46D ALA* 3.7 4.3 + - - +
47D THR* 3.0 11.3 + - - -
48D LEU* 2.9 33.6 + - - +
76E PHE* 4.5 2.7 - - - -
78E ASP* 2.6 24.1 + - - +
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Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D SER* 5.6 3.6 - - - +
27D ASN 4.2 20.6 - - - +
28D ALA* 3.4 14.7 + - + +
30D ALA 4.5 0.6 + - - -
32D VAL* 4.0 20.2 - - + +
44D SER* 1.3 73.9 - - - +
46D ALA* 1.3 55.6 + - - +
48D LEU* 4.3 3.4 - - + +
49D THR* 2.6 44.2 + - + +
60D PHE* 3.5 42.6 - - + +
75D TYR* 6.4 0.2 - - + -
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Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ALA* 2.9 29.3 + - + +
29D ASN* 4.0 11.9 - - - +
44D SER* 3.2 6.0 - - - +
45D LEU* 1.3 78.9 - - - +
47D THR* 1.3 59.0 + - - +
49D THR* 4.3 1.9 + - - -
50D LYS* 3.5 27.3 + - - +
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Residues in contact with THR 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D SER* 3.4 16.4 - - - +
44D SER* 3.0 3.0 + - - -
46D ALA* 1.3 76.6 - - - +
48D LEU* 1.3 65.8 + - - +
49D THR 3.2 1.6 - - - -
50D LYS* 3.1 22.4 + - - +
88D LEU* 3.9 8.5 - - + -
91D LEU* 3.5 32.9 - - + +
92D ARG* 3.6 28.6 - - + +
78E ASP* 2.6 29.1 + - - -
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Residues in contact with LEU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D VAL* 3.9 16.2 - - + -
34D ILE* 3.7 33.9 - - + -
43D SER* 4.1 6.7 - - - +
44D SER 2.9 27.2 + - - +
45D LEU* 4.3 4.0 - - + +
47D THR* 1.3 74.2 - - - +
49D THR* 1.3 59.0 + - - +
50D LYS 3.5 0.4 + - - -
51D TYR 5.1 0.7 + - - -
56D ILE* 3.5 17.4 - - + +
57D GLY* 3.3 19.8 + - - -
60D PHE* 3.8 42.4 - - + -
84D PHE* 4.6 3.4 - - + -
88D LEU* 3.9 22.0 - - + -
91D LEU* 4.2 11.2 - - + +
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Residues in contact with THR 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LEU* 2.6 30.9 + - + +
46D ALA* 4.4 2.3 + - - -
48D LEU* 1.3 79.7 - - - +
50D LYS* 1.3 65.0 + - - +
51D TYR 3.2 4.3 + - - -
52D PRO* 3.7 15.1 - - - +
57D GLY* 3.9 14.4 - - - +
60D PHE* 3.7 36.1 - - + +
61D ASP* 3.9 11.0 - - + -
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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