Contacts of the helix formed by residues 47 - 53 (chain B) in PDB entry 1R2B
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 LYS 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU* 4.0 27.1 - - + -
33B ASP* 2.9 41.7 + - + +
34B VAL* 3.5 16.6 - - + +
45B ALA 4.0 0.6 + - - -
46B HIS* 1.3 71.8 - - - +
48B THR* 1.3 52.5 + - - +
50B LEU* 3.1 10.9 + - - +
51B MET* 2.7 41.2 + - - +
61B PHE* 3.6 31.3 - - + -
67B ARG* 2.8 27.4 + - - +
68B ASN* 3.6 9.5 + - - +
69B LEU 2.9 27.0 + - - -
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Residues in contact with THR 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.8 21.6 - - + +
25A LEU* 4.0 7.4 - - + +
31A LEU* 3.9 22.4 - - + +
46A HIS* 3.9 32.5 - - + +
48A THR* 4.3 12.3 + - - +
33B ASP* 5.3 2.4 + - - +
46B HIS* 4.1 7.3 - - - +
47B LYS* 1.3 75.6 - - - +
49B VAL* 1.3 67.0 + - - +
51B MET* 3.3 8.7 + - - +
52B ALA* 2.9 28.8 + - - +
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Residues in contact with VAL 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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18A VAL* 5.4 4.7 - - + -
22A LEU* 5.0 4.7 - - + -
48A THR* 6.6 0.2 - - - -
19B LEU* 5.4 4.9 - - + -
22B LEU* 4.3 23.3 - - + -
46B HIS* 3.1 18.5 + - + +
48B THR* 1.3 82.1 + - - +
50B LEU* 1.3 67.0 + - - +
52B ALA* 3.2 13.6 + - - +
53B CYS* 3.2 27.6 + - - -
90B MET* 4.6 8.1 - - + +
91B TYR* 3.5 53.6 - - + +
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Residues in contact with LEU 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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34B VAL* 4.1 12.6 - - + -
36B ILE* 4.1 27.8 - - + -
45B ALA* 4.0 18.2 - - + -
46B HIS 3.1 14.3 + - - +
47B LYS* 3.5 5.2 - - - +
49B VAL* 1.3 76.6 - - - +
51B MET* 1.3 58.0 + - - +
53B CYS* 3.8 0.5 - - - +
54B SER* 2.8 35.2 + - - -
57B PHE* 3.6 30.1 - - + +
61B PHE* 4.1 10.1 - - + -
83B PHE* 5.5 0.9 - - + -
87B LEU* 4.1 18.2 - - + -
90B MET* 3.6 26.0 - - + -
91B TYR* 5.0 2.5 - - + -
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Residues in contact with MET 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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25A LEU* 4.3 10.3 - - + -
30A ILE* 3.8 24.5 - - + -
31A LEU* 3.8 23.8 - - - -
47B LYS 2.7 22.8 + - - +
48B THR* 3.6 7.0 - - - +
50B LEU* 1.3 71.8 - - - +
52B ALA* 1.3 65.7 + - - +
53B CYS 3.3 0.2 + - - -
54B SER 3.5 2.8 - - - +
57B PHE 3.7 13.9 - - - +
58B TYR* 3.5 49.2 - - + +
61B PHE* 3.7 28.7 - - + +
62B THR* 4.3 3.1 - - - +
1426D HIS* 2.9 22.9 + - - -
1428D ILE* 3.7 5.2 - - - +
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Residues in contact with ALA 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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18A VAL* 4.2 25.4 - - + +
21A ASN* 2.7 48.3 + - + +
22A LEU* 4.4 6.7 - - + -
25A LEU* 4.9 0.9 - - + +
48B THR 2.9 16.8 + - - +
49B VAL* 3.2 7.6 + - - +
51B MET* 1.3 76.2 - - - +
53B CYS* 1.3 58.7 + - - +
1425D ILE* 3.5 4.9 - - - +
1426D HIS* 2.9 9.7 + - - -
1428D ILE* 4.1 3.1 - - - -
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Residues in contact with CYS 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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14A HIS* 3.9 10.3 - - - -
18A VAL* 3.8 28.3 - - - -
49B VAL* 3.2 18.8 + - - +
52B ALA* 1.3 78.6 - - - +
54B SER* 1.3 58.1 + - - +
55B GLY 4.3 0.2 + - - -
90B MET* 3.8 42.8 - - + -
113B GLN 4.5 1.7 - - - +
114B MET* 3.7 19.1 - - + +
1425D ILE* 3.7 22.8 - - + +
1426D HIS* 3.8 8.4 + - - -
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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