Contacts of the helix formed by residues 47 - 53 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ASP* 3.0 49.6 + - - +
34A VAL* 3.7 13.5 - - + -
45A ALA 4.1 0.2 - - - -
46A HIS* 1.3 69.9 - - - +
48A THR* 1.3 53.2 + - - +
50A LEU* 3.1 3.8 + - - +
51A MET* 2.7 40.4 + - - +
61A PHE* 3.8 39.9 - - + -
67A ARG* 2.9 22.4 + - - +
68A ASN* 4.2 4.6 - - - +
69A LEU 2.8 29.9 + - - -
70A SER* 4.8 0.2 - - - +
31B LEU* 3.7 25.6 - - + -
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Residues in contact with THR 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASP* 5.2 1.8 + - - +
46A HIS* 4.0 11.8 - - - +
47A LYS* 1.3 75.8 - - - +
49A VAL* 1.3 60.5 + - - +
51A MET* 3.7 2.4 - - - +
52A ALA* 2.9 28.4 + - - +
22B LEU* 3.9 19.6 - - - +
25B LEU* 4.2 11.1 - - + +
31B LEU* 3.8 26.7 - - + +
33B ASP* 6.1 0.7 - - - +
46B HIS* 3.6 33.4 - - + +
48B THR* 4.3 12.6 + - - +
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Residues in contact with VAL 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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19A LEU* 5.3 3.8 - - + -
22A LEU* 4.2 24.5 - - + -
46A HIS* 3.1 16.7 + - + +
48A THR* 1.3 77.2 + - - +
50A LEU* 1.3 68.3 + - - +
52A ALA* 3.1 6.1 + - - +
53A CYS* 3.0 27.6 + - - -
90A MET* 4.4 20.9 - - + +
91A TYR* 3.6 50.9 - - + +
18B VAL* 5.5 4.9 - - + -
22B LEU* 4.9 4.7 - - + -
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Residues in contact with LEU 50 (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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34A VAL* 4.0 15.3 - - + -
36A ILE* 4.0 28.7 - - + -
45A ALA* 4.2 7.9 - - + -
46A HIS 3.0 15.0 + - - +
47A LYS 3.4 6.3 - - - +
49A VAL* 1.3 78.3 - - - +
51A MET* 1.3 57.5 + - - +
53A CYS* 3.3 1.2 + - - +
54A SER* 2.8 34.1 + - - -
57A PHE* 3.7 28.4 - - + +
61A PHE* 3.9 18.8 - - + -
83A PHE* 5.5 1.6 - - + -
87A LEU* 3.9 19.7 - - + -
90A MET* 3.7 25.1 - - + -
91A TYR* 5.2 2.0 - - + -
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Residues in contact with MET 51 (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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47A LYS 2.7 18.6 + - - +
48A THR* 3.7 5.4 - - - +
50A LEU* 1.3 71.7 - - - +
52A ALA* 1.3 65.0 + - - +
53A CYS 3.2 0.3 + - - -
54A SER 3.5 5.5 - - - +
57A PHE 3.6 7.9 - - - +
58A TYR* 3.6 42.3 - - + +
61A PHE* 3.6 27.4 - - + +
62A THR* 4.2 10.8 - - - +
25B LEU* 3.9 11.2 - - + -
30B ILE* 3.9 22.0 - - + -
31B LEU* 3.0 35.2 - - - -
1426C HIS* 3.1 20.3 + - - -
1428C ILE* 4.0 4.7 - - + +
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Residues in contact with ALA 52 (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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48A THR 2.9 18.6 + - - +
49A VAL* 3.1 8.7 + - - +
51A MET* 1.3 76.2 - - - +
53A CYS* 1.3 60.9 + - - +
18B VAL* 4.2 20.0 - - + +
21B ASN* 2.8 47.7 + - + +
22B LEU* 4.4 8.7 - - + -
25B LEU* 5.5 0.9 - - + -
1425C ILE* 3.2 8.0 - - - +
1426C HIS* 3.2 6.1 + - - -
1428C ILE* 4.1 4.7 - - - +
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Residues in contact with CYS 53 (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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49A VAL* 3.0 18.0 + - - +
52A ALA* 1.3 79.5 - - - +
54A SER* 1.3 58.5 + - - +
55A GLY 4.3 0.2 + - - -
90A MET* 3.5 45.3 - - + -
113A GLN 4.8 0.2 - - - +
114A MET* 3.4 22.1 - - + +
14B HIS* 3.8 11.9 - - - -
18B VAL* 3.8 29.8 - - - -
1425C ILE* 3.7 20.9 - - + +
1426C HIS* 4.1 5.9 + - - -
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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