Contacts of the helix formed by residues 59 - 71 (chain A) in PDB entry 1RIO
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 ASN 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ALA 3.7 1.4 + - - +
58A LEU* 1.3 74.8 - - - +
60A ALA* 1.3 63.2 + - - +
61A TYR* 4.1 9.1 - - - +
62A ASN* 2.7 51.9 + - - +
63A ALA* 2.9 21.1 + - - +
81A ILE* 4.4 5.2 - - - -
18T G 3.3 40.6 + - - +
19T G 4.6 3.2 + - - -
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Residues in contact with ALA 60 (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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59A ASN* 1.3 74.0 - - - +
61A TYR* 1.3 57.5 + - - +
63A ALA* 3.3 1.4 + - - +
64A ALA* 2.9 30.5 + - - +
81A ILE* 3.7 15.2 - - - +
84A GLU* 3.8 32.0 + - - +
85A ILE* 4.0 5.2 - - + +
88A MSE 5.2 2.7 - - - -
88B MSE 3.0 31.0 - - + +
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Residues in contact with TYR 61 (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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41A MSE 5.9 0.9 - - - -
59A ASN* 3.3 10.5 + - - +
60A ALA* 1.3 79.6 - - - +
62A ASN* 1.3 76.6 + - - +
64A ALA* 3.2 4.6 + - + +
65A LEU* 3.0 55.1 + - + +
84B GLU* 4.1 27.4 - - + +
87B GLU* 6.6 0.4 - - + -
88B MSE 3.7 21.9 - - + -
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Residues in contact with ASN 62 (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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41A MSE 3.6 25.7 - - + +
43A MSE 5.5 1.7 - - - +
51A LEU* 4.3 21.6 - - + +
58A LEU* 4.4 5.2 - - + -
59A ASN* 2.7 33.1 + - - +
61A TYR* 1.3 86.2 - - - +
63A ALA* 1.3 59.7 + - - +
65A LEU* 3.7 5.4 - - - +
66A LEU* 2.9 29.6 + - - +
18T G 5.1 1.4 - - - +
19T G 2.9 29.3 + - - -
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Residues in contact with ALA 63 (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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58A LEU* 4.2 7.4 - - + +
59A ASN 2.9 18.6 + - - +
60A ALA 3.8 4.0 - - - +
62A ASN* 1.3 78.9 - - - +
64A ALA* 1.3 64.2 + - - +
66A LEU 3.2 0.5 + - - -
67A ALA* 2.9 20.8 + - - +
74A VAL* 4.1 8.1 - - + -
77A PHE* 3.4 32.3 - - + -
81A ILE* 3.9 26.2 - - + -
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Residues in contact with ALA 64 (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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60A ALA 2.9 17.8 + - - +
61A TYR* 3.2 4.2 + - + +
63A ALA* 1.3 76.3 - - - +
65A LEU* 1.3 62.7 + - + +
67A ALA* 3.3 1.9 + - - +
68A LYS* 2.9 31.4 + - - +
74A VAL* 4.0 4.2 - - - +
85A ILE* 4.4 2.5 - - + -
87B GLU 5.1 0.7 - - - +
88B MSE 3.9 35.7 - - + +
91B ALA* 3.9 16.5 - - + +
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Residues in contact with LEU 65 (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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40A LYS 5.6 3.1 - - - +
41A MSE 4.2 44.0 - - + +
61A TYR* 3.0 53.3 + - + +
62A ASN* 3.7 9.0 - - - +
63A ALA 3.2 0.2 - - - -
64A ALA* 1.3 74.2 - - - +
66A LEU* 1.3 66.7 + - - +
68A LYS* 3.2 12.0 + - + +
69A ILE* 2.9 34.0 + - + +
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Residues in contact with LEU 66 (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* 3.7 38.6 - - + -
37A VAL* 3.7 17.9 - - + -
41A MSE 3.6 32.3 - - + -
48A VAL* 5.6 0.2 - - + -
51A LEU* 4.4 7.6 - - + -
52A PHE* 4.1 17.5 - - + -
58A LEU* 3.9 14.6 - - + -
62A ASN 2.9 21.9 + - - +
63A ALA 3.7 2.9 - - - +
65A LEU* 1.3 76.8 - - - +
67A ALA* 1.3 63.8 - - - +
69A ILE* 3.1 6.0 + - + +
70A LEU* 2.9 35.6 + - + +
77A PHE* 4.2 3.1 - - + -
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Residues in contact with ALA 67 (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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63A ALA 2.9 16.4 + - - +
64A ALA 3.6 4.3 - - - +
65A LEU 3.1 0.2 - - - -
66A LEU* 1.3 78.3 - - - +
68A LYS* 1.3 58.4 + - - +
71A LYS* 2.9 25.6 + - - -
72A VAL* 3.1 36.8 + - - +
74A VAL* 3.8 26.0 - - + +
77A PHE* 4.0 8.5 - - + -
91B ALA* 4.2 5.6 - - + -
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Residues in contact with LYS 68 (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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64A ALA* 2.9 20.5 + - - +
65A LEU* 3.2 12.3 + - + +
67A ALA* 1.3 78.6 - - - +
69A ILE* 1.3 62.1 + - + +
71A LYS* 3.4 25.1 + - - +
87B GLU* 3.2 40.9 + - - +
90B GLU* 3.4 27.2 + - - -
91B ALA* 4.2 15.9 - - + +
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Residues in contact with ILE 69 (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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30A LEU* 3.7 12.6 - - - +
32A LEU* 3.5 32.4 - - + +
37A VAL* 4.2 15.3 - - + +
40A LYS* 3.4 43.7 - - + +
41A MSE 4.4 13.5 - - + -
65A LEU* 2.9 34.1 + - + +
66A LEU* 3.1 8.9 + - + +
68A LYS* 1.3 76.9 - - + +
70A LEU* 1.3 67.6 + - + +
71A LYS* 3.3 10.2 + - - +
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Residues in contact with LEU 70 (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* 3.8 28.5 - - + +
22A ILE* 4.0 20.6 - - + +
23A TYR* 4.1 32.1 - - + +
26A LYS* 3.4 22.8 + - + -
30A LEU* 3.8 8.7 - - + +
32A LEU* 3.4 27.1 - - + -
37A VAL* 5.5 0.9 - - + -
52A PHE* 5.3 1.8 - - + -
66A LEU* 2.9 24.7 + - + +
69A ILE* 1.3 80.2 - - + +
71A LYS* 1.3 72.2 + - - +
72A VAL* 3.4 14.6 + - + +
77A PHE* 5.6 0.2 - - + -
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Residues in contact with LYS 71 (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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26A LYS* 3.3 13.8 + - - +
30A LEU* 4.3 19.1 - - + -
67A ALA 2.9 9.5 + - - -
68A LYS* 3.4 19.0 + - - +
69A ILE* 3.3 11.1 - - - +
70A LEU* 1.3 80.4 - - - +
72A VAL* 1.3 63.1 + - - +
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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