Contacts of the helix formed by residues 44 - 49 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASN 3.8 10.5 - - - -
30A ALA* 3.8 12.7 - - - +
31A PRO 3.5 17.0 - - - -
33A HIS* 4.5 1.3 - - - -
43A SER* 1.3 84.7 + - - +
45A LEU* 1.3 65.3 + - - +
46A ALA* 3.9 5.0 + - - +
47A THR* 3.2 15.1 + - - -
48A LEU* 3.1 27.8 + - - +
76B PHE* 4.5 7.0 - - - -
78B ASP* 2.9 16.9 + - - +
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Residues in contact with LEU 45 (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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29A ASN* 3.3 22.0 + - - +
31A PRO* 5.6 0.7 - - + -
33A HIS* 3.8 28.6 - - + +
44A SER* 1.3 74.7 - - - +
46A ALA* 1.3 51.8 - - - +
48A LEU* 4.4 4.0 - - + +
49A THR* 2.5 45.5 + - + +
60A PHE* 3.6 41.1 - - + +
75A TYR* 4.0 20.9 - - + +
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Residues in contact with ALA 46 (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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29A ASN* 2.8 30.2 + - + +
30A ALA* 4.8 5.2 - - + +
44A SER* 3.2 6.9 - - - +
45A LEU* 1.3 77.8 - - - +
47A THR* 1.3 60.7 + - - +
49A THR* 3.9 4.9 + - - -
50A LYS* 3.4 21.0 + - - +
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Residues in contact with THR 47 (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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43A SER* 3.5 15.3 - - - +
44A SER* 3.2 5.8 + - - -
46A ALA* 1.3 79.4 - - - +
48A LEU* 1.3 60.9 + - - +
50A LYS* 3.2 21.0 - - - +
88A LEU* 4.3 5.2 - - + -
91A LEU* 3.7 36.5 - - + +
92A ARG* 4.1 20.8 - - + +
78B ASP* 2.7 29.5 + - - +
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Residues in contact with LEU 48 (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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33A HIS* 5.4 7.2 - - + +
35A ASP* 5.3 3.4 - - + +
43A SER* 4.1 14.6 - - - +
44A SER 3.1 22.9 + - - +
45A LEU* 4.1 7.6 - - + +
47A THR* 1.3 77.2 - - - +
49A THR* 1.3 59.7 + - - +
50A LYS 3.3 1.4 + - - -
51A TYR 4.9 0.7 + - - -
56A ILE* 3.5 14.0 - - + +
57A GLY* 3.5 19.1 + - - -
60A PHE* 3.6 55.0 - - + -
84A PHE* 4.8 10.5 - - + -
88A LEU* 3.9 25.6 - - + -
91A LEU* 4.3 12.2 - - + +
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Residues in contact with THR 49 (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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45A LEU* 2.5 32.5 + - + +
46A ALA* 3.9 4.9 + - - -
48A LEU* 1.3 78.1 - - - +
50A LYS* 1.3 65.4 + - - +
51A TYR* 3.2 4.8 + - - -
52A PRO* 3.9 14.5 - - - +
57A GLY* 4.0 7.4 - - - +
60A PHE* 3.6 37.0 - - + +
61A ASP* 3.7 17.0 - - + +
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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