Contacts of the helix formed by residues 59 - 68 (chain A) in PDB entry 2MXY
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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12A ARG* 5.2 1.6 - - - +
16A SER* 3.2 20.4 - - - -
57A TYR* 3.4 2.5 - - - +
58A VAL* 1.3 88.9 - - + +
60A GLU* 1.3 61.3 + - - +
61A ARG* 2.9 14.2 + - + +
62A ASN* 2.8 58.5 + - - +
63A ALA 3.6 5.0 + - - -
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Residues in contact with GLU 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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12A ARG 5.1 1.0 + - - -
15A ASN* 3.2 45.9 - - - +
16A SER* 3.8 2.0 - - - +
59A ASN* 1.3 72.6 - - - +
61A ARG* 1.3 67.4 + - - +
63A ALA* 2.9 12.1 + - - +
64A ARG* 2.8 54.2 + - + +
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Residues in contact with ARG 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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59A ASN* 2.9 14.1 + - + +
60A GLU* 1.3 81.4 - - - +
62A ASN* 1.3 70.7 + - - +
64A ARG* 3.5 9.6 + - - +
65A ALA* 3.2 24.4 + - - +
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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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40A TYR 3.8 7.1 - - - +
41A GLY* 2.9 27.3 - - - -
42A LYS* 2.9 14.6 + - - +
57A TYR* 3.1 41.7 - - + -
58A VAL* 4.9 1.6 + - - +
59A ASN* 2.8 44.6 + - - +
61A ARG* 1.3 83.8 - - - +
63A ALA* 1.3 62.2 + - - +
65A ALA* 3.3 15.1 + - - +
66A ALA 3.4 2.6 + - - -
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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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15A ASN 3.6 19.5 - - - +
16A SER* 4.0 11.0 - - - -
17A ARG 3.8 20.0 - - - +
18A VAL* 4.1 1.8 - - + -
57A TYR* 3.4 12.4 - - + -
59A ASN 3.6 0.6 + - - -
60A GLU 2.9 10.3 + - - +
62A ASN* 1.3 76.5 - - - +
64A ARG* 1.3 59.1 + - - +
65A ALA 3.2 0.2 + - - -
66A ALA* 3.3 1.9 + - - +
67A VAL* 2.8 36.0 + - - +
84A LEU* 3.9 8.7 - - + -
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Residues in contact with ARG 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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15A ASN* 5.2 1.0 - - - +
60A GLU* 2.8 47.0 + - + +
61A ARG* 3.8 9.2 - - - +
63A ALA* 1.3 75.1 - - - +
65A ALA* 1.3 62.7 + - - +
67A VAL* 4.0 8.7 - - - +
68A ALA* 3.2 26.7 + - - +
84A LEU* 3.6 26.2 - - - +
87A GLU* 2.7 44.0 + - - -
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Residues in contact with ALA 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 TYR* 3.4 38.3 - - + +
61A ARG* 3.2 19.6 + - - +
62A ASN* 3.3 11.7 - - - +
63A ALA 3.1 0.6 - - - -
64A ARG* 1.3 78.5 - - - +
66A ALA* 1.3 58.2 + - - +
68A ALA 3.9 0.5 - - - -
69A GLY* 2.9 23.7 + - - -
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Residues in contact with ALA 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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18A VAL* 4.7 2.2 - - + -
37A PHE* 3.7 19.7 - - + -
40A TYR* 3.8 17.9 - - + -
57A TYR* 3.1 35.7 - - + +
62A ASN 3.4 0.6 + - - -
63A ALA 3.3 2.2 + - - +
65A ALA* 1.3 75.8 - - - +
67A VAL* 1.3 62.4 + - - +
68A ALA 3.1 2.0 - - - -
69A GLY 3.9 1.1 - - - +
70A GLU* 2.9 29.9 + - + +
71A ASP 3.7 1.4 + - - -
82A ILE* 4.0 4.3 - - - +
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Residues in contact with VAL 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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18A VAL* 3.8 19.5 - - + -
63A ALA 2.8 21.6 + - - +
64A ARG* 4.4 7.2 - - - +
66A ALA* 1.3 76.3 - - - +
68A ALA* 1.3 57.6 + - + +
71A ASP* 3.1 23.4 - - - +
82A ILE* 3.8 8.0 - - + +
83A ASN* 3.5 43.3 - - - +
84A LEU* 3.7 22.4 - - + +
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Residues in contact with ALA 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 ARG 3.2 17.9 + - - +
65A ALA 3.9 0.4 - - - +
67A VAL* 1.3 79.6 - - + +
69A GLY* 1.3 58.3 + - - +
70A GLU 3.6 0.9 - - - -
71A ASP* 4.6 5.5 + - - +
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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