Contacts of the helix formed by residues 61 - 73 (chain A) in PDB entry 2AAO
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 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A LEU* 1.3 76.7 - - - +
62A GLU* 1.3 66.7 + - - +
63A SER* 4.1 10.1 - - - +
64A GLU* 2.9 44.5 + - + +
65A ILE* 2.9 12.0 + - - +
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Residues in contact with GLU 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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46A PHE* 4.1 9.3 - - + -
50A LYS* 2.3 52.9 + - + +
60A LEU 3.8 0.6 + - - -
61A LYS* 1.3 72.7 - - - +
63A SER* 1.3 57.7 + - - +
65A ILE* 3.2 10.8 + - + +
66A LEU* 3.0 28.1 + - - +
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Residues in contact with SER 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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61A LYS* 4.1 9.2 - - - +
62A GLU* 1.3 77.9 - - - +
64A GLU* 1.3 68.1 + - - +
66A LEU* 3.4 8.9 + - - +
67A ASP* 3.0 34.5 + - - +
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Residues in contact with GLU 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 LEU* 3.6 27.5 - - + +
61A LYS* 2.9 51.4 + - + +
63A SER* 1.3 79.4 - - - +
65A ILE* 1.3 61.5 + - - +
67A ASP* 3.3 11.4 + - - +
68A LEU* 3.0 28.1 + - - +
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Residues in contact with ILE 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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46A PHE* 3.7 14.1 - - + -
49A LEU* 3.7 28.7 - - + +
50A LYS* 4.0 31.9 - - + +
53A LEU* 3.8 22.0 - - + -
59A ASN* 5.7 1.3 - - - +
60A LEU* 3.6 31.9 - - + +
61A LYS 2.9 15.5 + - - +
62A GLU* 3.5 11.9 - - + +
64A GLU* 1.3 76.8 - - - +
66A LEU* 1.3 56.7 + - - +
68A LEU* 3.2 7.1 + - - +
69A MSE 2.9 27.2 + - - +
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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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46A PHE* 3.5 38.5 - - + -
62A GLU 3.0 12.9 + - - +
63A SER* 3.8 8.3 - - - +
65A ILE* 1.3 77.5 - - - +
67A ASP* 1.3 64.0 + - - +
69A MSE 3.2 3.5 + - + +
70A GLN* 2.9 54.7 + - + +
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Residues in contact with ASP 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 SER* 3.0 22.0 + - - +
64A GLU* 3.5 13.1 - - - +
66A LEU* 1.3 78.9 - - - +
68A LEU* 1.3 59.7 + - - +
70A GLN* 4.0 5.4 - - - +
71A ALA* 3.1 25.5 + - - +
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Residues in contact with LEU 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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49A LEU* 4.4 9.9 - - + -
53A LEU* 4.0 28.9 - - + -
60A LEU* 4.9 4.5 - - + -
64A GLU 3.0 14.2 + - - +
65A ILE* 3.5 8.1 - - - +
67A ASP* 1.3 73.0 - - - +
69A MSE 1.3 62.1 + - - +
71A ALA* 3.3 5.8 + - + -
72A ALA* 2.9 31.1 + - + +
88A ALA* 4.1 25.4 - - + +
91A HIS* 6.3 1.1 - - + -
92A LEU* 3.3 37.7 - - + -
95A ILE* 4.5 8.3 - - + -
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Residues in contact with MSE 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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44A ILE 4.0 3.8 - - - +
45A THR 4.2 2.7 - - - -
46A PHE* 3.7 39.7 - - + +
49A LEU* 3.9 17.3 - - + -
65A ILE 2.9 16.5 + - - +
66A LEU* 3.4 9.2 - - + +
68A LEU* 1.3 76.6 - - - +
70A GLN* 1.3 72.4 + - - +
72A ALA* 4.7 0.4 - - - -
73A ASP* 3.0 36.1 + - + +
78A GLY* 3.1 38.8 - - - +
79A THR* 3.7 16.2 - - - -
80A ILE* 3.5 24.4 - - + +
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Residues in contact with GLN 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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66A LEU* 2.9 37.4 + - + +
67A ASP* 4.0 5.4 - - - +
69A MSE 1.3 97.8 - - - +
71A ALA* 1.3 62.6 + - - +
72A ALA 3.6 0.2 + - - -
73A ASP* 3.7 21.4 + - - +
74A VAL* 5.5 0.3 - - - -
76A ASN* 5.6 1.7 - - - +
78A GLY* 5.9 1.6 - - - -
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Residues in contact with ALA 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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67A ASP 3.1 17.7 + - - +
68A LEU* 3.8 7.0 - - + +
70A GLN* 1.3 78.1 - - - +
72A ALA* 1.3 61.5 + - - +
73A ASP 3.5 0.2 + - - -
74A VAL* 3.7 15.8 + - - +
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Residues in contact with ALA 72 (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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68A LEU* 2.9 20.8 + - + +
71A ALA* 1.3 77.4 - - - +
73A ASP* 1.3 57.8 + - - +
74A VAL* 3.0 12.8 + - - +
80A ILE* 3.5 22.0 - - + -
84A GLU* 3.2 25.5 - - - +
88A ALA* 3.7 31.0 - - + +
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Residues in contact with ASP 73 (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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69A MSE 3.0 21.2 + - + +
70A GLN* 3.7 18.1 + - - +
71A ALA 3.4 1.2 - - - -
72A ALA* 1.3 72.5 - - - +
74A VAL* 1.3 57.3 + - - +
75A ASP* 2.8 10.6 - - - +
76A ASN* 3.1 23.4 + - - +
77A SER* 2.9 8.2 + - - -
78A GLY* 2.7 30.9 + - - -
79A THR 3.5 5.2 - - - -
80A ILE* 3.7 11.0 - - + -
84A GLU* 3.6 3.6 - - - -
294A CA 2.3 30.2 - - - -
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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