Contacts of the helix formed by residues 66 - 76 (chain A) in PDB entry 2DNM
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 ARG 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ASP* 3.3 28.7 + - - +
65A ARG* 1.3 83.1 - - - +
67A ASP* 1.3 71.5 + - - +
68A ALA 3.1 0.9 - - - -
69A GLN* 2.8 19.7 + - - +
70A ASP* 3.0 20.5 + - - +
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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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37A TYR* 3.2 21.7 - - - +
38A GLY* 3.7 29.9 - - - +
62A PHE* 4.4 7.4 - - + -
63A HIS* 5.9 0.5 - - - +
64A ASP* 3.7 25.3 + - + +
66A ARG* 1.3 78.9 - - - +
68A ALA* 1.3 64.2 + - - +
70A ASP* 2.9 19.6 + - - +
71A ALA* 2.9 14.9 + - - +
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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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14A ILE* 4.1 21.5 - - + -
16A LEU* 3.6 18.2 - - + +
62A PHE* 3.6 36.7 - - + -
64A ASP 4.3 6.8 + - - +
65A ARG 4.9 3.1 - - - +
66A ARG 3.1 1.6 + - - +
67A ASP* 1.3 77.1 - - - +
69A GLN* 1.3 58.8 + - + +
71A ALA 3.4 0.2 + - - -
72A GLU* 2.8 32.9 + - - +
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Residues in contact with GLN 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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65A ARG* 3.5 18.7 + - - +
66A ARG* 2.8 16.4 + - - +
68A ALA* 1.3 75.0 - - + +
70A ASP* 1.3 63.5 + - - +
72A GLU* 3.5 18.8 - - - +
73A ALA* 3.4 19.1 + - - +
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Residues in contact with ASP 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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37A TYR* 5.2 11.7 - - + -
66A ARG* 3.0 23.3 + - - +
67A ASP* 2.9 12.7 + - - +
69A GLN* 1.3 74.5 - - - +
71A ALA* 1.3 62.4 + - - +
72A GLU 3.0 2.3 + - - -
73A ALA* 3.1 4.9 + - - +
74A ALA* 2.8 32.7 + - + +
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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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34A PHE* 3.6 32.8 - - + -
37A TYR* 4.0 23.4 - - + -
62A PHE* 4.6 7.0 - - + -
67A ASP 2.9 16.2 + - - +
68A ALA 4.0 3.1 - - - +
70A ASP* 1.3 73.4 - - - +
72A GLU* 1.3 57.1 + - - +
74A ALA* 4.3 6.7 - - - -
75A MET* 2.9 39.2 + - + +
87A VAL* 4.3 0.2 - - - +
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Residues in contact with GLU 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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16A LEU* 4.2 12.3 - - + +
68A ALA 2.8 17.4 + - - +
69A GLN* 3.5 22.2 - - - +
71A ALA* 1.3 76.7 - - - +
73A ALA* 1.3 61.3 + - - +
76A ASP* 2.8 35.5 + - + +
87A VAL* 3.1 18.5 - - - +
88A GLN* 4.0 16.5 - - + +
89A VAL* 4.3 17.0 - - - +
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Residues in contact with ALA 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 GLN 3.4 8.0 + - - +
70A ASP* 3.1 6.7 + - - +
72A GLU* 1.3 79.4 - - + +
74A ALA* 1.3 68.7 + - - +
76A ASP* 2.9 21.5 - - - +
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Residues in contact with ALA 74 (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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37A TYR* 4.4 21.1 - - + +
70A ASP* 2.8 24.8 + - + +
71A ALA* 4.1 4.7 - - - +
73A ALA* 1.3 74.7 - - - +
75A MET* 1.3 66.4 + - - +
76A ASP 3.9 1.0 - - - +
77A GLY 5.0 1.9 - - - +
78A ALA* 4.7 4.5 - - - +
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Residues in contact with MET 75 (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* 6.0 0.2 - - + -
33A VAL* 3.0 44.6 - - + +
34A PHE* 3.5 21.3 - - - -
37A TYR* 4.7 12.1 - - + +
71A ALA* 2.9 33.0 + - + +
74A ALA* 1.3 76.8 - - - +
76A ASP* 1.3 69.3 + - - +
77A GLY 2.8 4.2 + - - -
78A ALA* 3.1 22.0 + - - +
80A LEU* 4.3 22.9 - - + -
85A LEU* 4.9 4.4 - - + +
87A VAL* 3.6 26.0 - - + -
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Residues in contact with ASP 76 (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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72A GLU* 2.8 22.6 + - + +
73A ALA* 2.9 19.2 - - - +
74A ALA 3.9 0.7 - - - +
75A MET* 1.3 74.8 - - - +
77A GLY* 1.3 65.5 + - - +
84A GLU* 5.2 3.6 - - - +
85A LEU 4.0 11.1 - - - +
86A ARG* 5.1 2.2 - - - +
87A VAL* 3.3 17.2 - - - +
88A GLN* 3.3 32.0 + - + +
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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