Contacts of the helix formed by residues 46 - 58 (chain A) in PDB entry 1RRM
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 GLY 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A VAL 3.2 10.6 + - - -
44A GLN 3.1 6.6 + - - -
45A CYS* 1.3 78.8 - - - +
47A VAL* 1.3 64.0 + - - +
48A VAL 3.4 2.2 - - - -
49A ALA* 3.4 15.4 + - - +
50A LYS* 3.3 27.2 + - - +
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Residues in contact with VAL 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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42A LEU* 3.0 29.0 + - + +
45A CYS* 4.2 16.4 - - + +
46A GLY* 1.3 75.5 - - - +
48A VAL* 1.3 67.5 + - - +
50A LYS* 3.1 32.8 + - + +
51A VAL 3.8 0.3 + - - -
95A ILE* 4.3 3.4 - - + -
140A THR* 3.8 20.6 - - + -
181A MSE 3.5 43.1 - - + +
184A GLY* 6.1 3.4 - - - -
389A APR 4.7 6.7 - - + +
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Residues in contact with VAL 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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36A ILE* 4.4 4.3 - - + -
38A THR* 3.6 33.0 - - + +
42A LEU* 3.2 23.1 + - + +
43A VAL* 3.8 13.2 - - + -
46A GLY 3.4 0.2 - - - -
47A VAL* 1.3 74.8 - - - +
49A ALA* 1.3 58.1 + - - +
51A VAL* 3.0 19.6 + - - +
52A THR* 3.0 20.2 + - + +
64A ILE* 3.6 30.5 - - + -
95A ILE* 4.3 23.3 - - + -
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Residues in contact with ALA 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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43A VAL 5.6 1.3 + - - +
46A GLY* 3.4 18.2 + - - +
47A VAL 3.2 0.4 - - - -
48A VAL* 1.3 75.9 - - - +
50A LYS* 1.3 66.0 + - - +
52A THR* 3.4 11.4 - - - +
53A ASP* 2.9 42.5 + - - +
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Residues in contact with LYS 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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19A VAL* 5.9 2.0 - - + -
45A CYS 5.8 1.1 - - - -
46A GLY 3.3 16.3 + - - +
47A VAL* 3.1 23.5 + - + +
49A ALA* 1.3 78.4 - - - +
51A VAL* 1.3 59.2 + - - +
53A ASP* 4.5 4.1 - - - +
54A LYS* 3.4 33.3 + - - +
180A ASP* 4.2 21.4 + - + +
181A MSE 3.9 24.9 - - - -
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Residues in contact with VAL 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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19A VAL* 5.0 8.3 - - + -
22A LEU* 4.6 11.9 - - + -
36A ILE* 5.0 1.8 - - + -
48A VAL 3.0 7.9 + - - +
50A LYS* 1.3 77.4 - - - +
52A THR* 1.3 67.7 + - + +
53A ASP 3.2 1.6 - - - -
54A LYS* 3.0 10.9 + - + +
55A MSE 3.0 38.5 + - + +
93A ILE* 5.0 2.2 - - + -
95A ILE* 3.8 23.6 - - + -
138A ILE* 4.1 19.5 - - + -
181A MSE 3.5 33.2 - - + -
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Residues in contact with THR 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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36A ILE* 3.4 31.4 - - + -
48A VAL* 3.0 16.6 + - + +
49A ALA* 3.4 17.3 - - - +
51A VAL* 1.3 74.2 - - - +
53A ASP* 1.3 63.3 + - - +
55A MSE 3.2 8.6 + - - +
56A ASP* 2.8 36.1 + - - +
62A TRP* 3.5 40.0 - - + -
64A ILE* 4.2 0.4 - - + -
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Residues in contact with ASP 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 ALA* 2.9 34.8 + - - +
50A LYS* 4.5 4.7 - - - +
52A THR* 1.3 81.3 + - - +
54A LYS* 1.3 62.7 + - + +
56A ASP* 3.4 11.9 + - - +
57A ALA* 3.1 23.9 + - - +
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Residues in contact with LYS 54 (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 VAL* 3.9 39.0 - - + +
20A GLY* 4.2 13.8 - - - +
22A LEU* 6.2 1.1 - - + -
23A THR* 3.6 14.1 - - + +
50A LYS* 3.4 20.6 - - - +
51A VAL* 3.0 10.1 + - - +
53A ASP* 1.3 76.3 - - + +
55A MSE 1.3 66.7 + - - +
57A ALA* 3.4 8.3 + - - +
58A ALA* 3.0 23.9 + - - +
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Residues in contact with MSE 55 (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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22A LEU* 4.0 17.5 - - + -
23A THR* 4.0 9.0 - - + -
34A ALA* 4.1 0.7 - - + -
36A ILE* 4.4 6.1 - - - -
51A VAL* 3.0 28.9 + - - +
52A THR* 3.6 8.5 - - - +
54A LYS* 1.3 77.5 - - + +
56A ASP* 1.3 62.4 + - - +
58A ALA* 3.1 2.4 + - - +
59A GLY 2.9 5.0 + - - -
60A LEU* 2.9 42.0 + - + +
61A ALA 3.8 20.2 - - - +
62A TRP* 4.0 26.7 - - + -
91A TYR* 3.4 26.0 - - - +
93A ILE* 3.7 24.2 - - + -
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Residues in contact with ASP 56 (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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52A THR* 2.8 26.8 + - - +
53A ASP* 3.7 11.9 - - - +
55A MSE 1.3 72.3 - - - +
57A ALA* 1.3 63.2 + - - +
59A GLY* 3.0 14.5 + - - -
60A LEU 4.5 2.8 - - - +
62A TRP* 2.7 37.0 + - - -
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Residues in contact with ALA 57 (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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53A ASP 3.1 17.0 + - - +
54A LYS* 3.7 6.7 - - - +
56A ASP* 1.3 77.2 - - - +
58A ALA* 1.3 59.2 + - - +
59A GLY 3.6 0.3 + - - -
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Residues in contact with ALA 58 (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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23A THR* 3.6 30.1 - - + +
27A LYS* 3.3 35.4 + - - +
54A LYS 3.0 16.7 + - - +
55A MSE 3.1 3.1 + - - +
57A ALA* 1.3 76.7 - - - +
59A GLY* 1.3 61.4 + - - +
60A LEU* 3.3 4.0 + - + +
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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