Contacts of the strand formed by residues 48 - 53 (chain B) in PDB entry 1ADI
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 48 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B VAL* 3.3 9.2 - - - +
45B ILE 3.0 32.7 + - - +
46B ASN 4.7 1.1 - - - +
47B GLY* 1.3 79.6 - - - +
49B LYS* 1.3 70.7 + - - +
50B THR* 3.4 5.0 + - - -
89B ARG* 2.8 50.0 + - - -
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Residues in contact with LYS 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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42B THR* 4.7 19.7 - - + -
43B LEU 3.5 7.0 - - - -
44B VAL* 4.6 8.7 - - + +
48B GLU* 1.3 76.2 - - - +
50B THR* 1.3 68.8 + - - +
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Residues in contact with THR 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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41B HIS 3.7 0.5 - - - +
42B THR* 5.1 1.4 - - - +
43B LEU* 2.8 36.1 + - - +
45B ILE* 4.4 14.3 - - + +
48B GLU* 3.4 9.1 + - - -
49B LYS* 1.3 82.8 + - - +
51B VAL* 1.3 64.9 + - - +
52B LEU* 3.5 8.8 + - + +
85B GLU* 3.1 31.9 - - + +
89B ARG* 2.9 36.1 + - - +
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Residues in contact with VAL 51 (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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40B GLY* 4.9 2.7 - - - -
41B HIS 3.2 8.3 - - - +
42B THR* 3.2 38.8 - - + +
50B THR* 1.3 72.0 - - - +
52B LEU* 1.3 65.2 + - - +
53B HIS* 3.3 34.9 + - + +
81B LYS* 4.8 2.4 + - - -
82B GLU* 4.5 2.3 - - - +
85B GLU* 4.6 4.9 - - - +
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Residues in contact with LEU 52 (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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39B ALA* 4.8 1.9 - - - +
40B GLY 4.2 0.5 + - - -
41B HIS* 3.0 38.9 + - + +
43B LEU* 4.7 18.8 - - + -
50B THR* 3.5 11.8 + - + +
51B VAL* 1.3 72.8 - - - +
53B HIS* 1.3 62.2 + - - +
54B LEU 3.6 0.2 - - - -
55B ILE* 3.6 24.2 - - + +
56B PRO 4.6 0.9 - - - +
57B SER* 4.9 2.2 - - - +
59B ILE* 4.1 14.8 - - + -
60B LEU* 5.8 0.2 - - + -
82B GLU* 3.3 28.0 - - + +
85B GLU* 4.3 10.3 - - - +
86B LEU* 3.5 42.0 - - + -
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Residues in contact with HIS 53 (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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36B GLY 3.6 2.4 - - - +
37B HIS* 3.2 34.8 + - + +
38B ASN* 3.3 9.6 + - - -
39B ALA* 3.5 15.2 + - - +
40B GLY* 3.6 28.1 + - - +
51B VAL* 3.3 38.3 + - + +
52B LEU* 1.3 73.0 - - - +
54B LEU* 1.3 59.1 + - - +
81B LYS* 4.0 16.2 - - - +
82B GLU* 3.1 11.3 + - - +
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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