Contacts of the strand formed by residues 46 - 50 (chain B) in PDB entry 2LDX
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 GLU 46 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LYS* 3.0 46.2 + - + +
22B ILE 2.9 23.2 + - - -
44B ALA* 3.6 4.7 - - - +
45B ASP* 1.3 83.1 + - - +
47B LEU* 1.3 64.0 + - - +
75B LYS* 2.5 64.5 + - + +
77B VAL* 2.9 25.7 - - + +
84B VAL 4.9 0.3 - - - +
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Residues in contact with LEU 47 (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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22B ILE* 3.0 22.0 - - + +
24B VAL* 5.0 8.1 - - + -
35B ALA* 4.6 8.1 - - + +
38B ILE* 3.4 35.2 - - + -
39B LEU* 4.3 22.0 - - + -
44B ALA* 4.6 5.2 - - + +
46B GLU* 1.3 76.1 - - - +
48B ALA* 1.3 60.6 + - - +
49B LEU* 3.6 28.3 - - + -
64B LEU* 5.1 2.7 - - + -
73B THR* 4.6 6.5 + - - +
75B LYS 3.1 7.7 + - - +
76B ILE* 3.3 16.9 - - + -
77B VAL 3.1 20.9 + - - +
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LYS* 3.8 9.2 - - - -
22B ILE 2.9 5.1 + - - -
23B THR* 2.9 42.0 - - + +
24B VAL 3.0 3.6 + - - -
46B GLU 4.1 0.4 - - - -
47B LEU* 1.3 73.9 - - - +
49B LEU* 1.3 61.6 + - - +
50B VAL* 4.0 1.1 - - + -
77B VAL* 3.2 24.2 - - + +
84B VAL* 3.3 27.6 - - + +
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Residues in contact with LEU 49 (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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24B VAL* 3.6 14.8 - - + +
27B VAL* 4.5 18.2 - - + -
32B MET* 5.1 2.9 - - + -
35B ALA* 5.2 6.3 - - + -
47B LEU* 3.6 26.2 - - + +
48B ALA* 1.3 74.4 - - - +
50B VAL* 1.3 62.2 + - - +
51B ASP 4.0 0.2 - - - -
57B LEU* 3.4 30.9 - - + +
61B ALA* 3.4 15.3 - - + -
64B LEU* 4.1 22.0 - - + -
76B ILE* 4.7 6.7 - - + -
77B VAL 2.7 28.1 + - - +
78B PHE* 2.9 39.1 - - + +
79B GLY 3.4 3.3 + - - -
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Residues in contact with VAL 50 (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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23B THR* 4.2 15.9 - - + -
24B VAL 3.1 7.1 + - - -
25B VAL* 3.1 17.6 - - + +
26B GLY 2.6 29.5 + - - -
48B ALA 4.0 1.0 + - - +
49B LEU* 1.3 74.1 - - - +
51B ASP* 1.3 60.3 + - - +
57B LEU* 5.0 0.2 - - - -
79B GLY 3.5 8.7 - - - +
80B LYS 4.8 0.9 - - - +
81B ASP 3.8 26.7 - - - +
82B TYR* 3.5 40.6 - - + +
84B VAL* 4.5 16.6 - - + +
85B SER* 4.6 6.1 - - - +
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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