Contacts of the helix formed by residues 72 - 87 (chain E) in PDB entry 2AMT
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 ASP 72 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ILE* 6.2 1.1 - - + -
35E SER* 6.3 0.2 - - - -
36E ASP* 3.5 20.9 - - + +
70E GLY 3.5 4.7 + - - +
71E ALA* 1.3 76.0 - - - +
73E SER* 1.3 63.2 + - - +
74E ARG* 3.0 15.0 + - - +
75E GLU* 2.9 53.6 + - - +
76E LEU* 3.3 12.9 + - - +
78E ARG* 5.3 1.3 + - - -
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Residues in contact with SER 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E SER* 4.8 0.9 - - - -
36E ASP* 2.6 27.1 + - - -
38E ASP* 3.2 21.5 - - - +
41E LEU* 3.8 14.2 - - - +
42E HIS* 2.7 32.0 + - - -
45E THR* 4.8 1.7 + - - -
57E ILE* 5.8 0.2 - - - +
72E ASP* 1.3 75.0 - - - +
74E ARG* 1.3 57.7 + - - +
76E LEU* 3.5 11.2 + - - +
77E LEU* 2.8 28.9 + - - +
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Residues in contact with ARG 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ILE* 6.2 0.7 - - + -
22E GLY* 4.1 19.7 + - - -
41E LEU* 3.6 19.7 - - + -
72E ASP* 3.0 11.9 + - - +
73E SER* 1.3 75.0 - - - +
75E GLU* 1.3 60.8 + - - +
77E LEU* 3.6 4.4 - - - +
78E ARG* 2.9 51.8 + - - +
115E PHE* 3.2 52.8 + - - +
118E GLU* 3.9 11.3 + - - +
119E ASP* 2.8 39.6 + - - +
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Residues in contact with GLU 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E PHE* 5.2 4.3 - - + -
70E GLY 4.5 1.2 - - - +
71E ALA* 3.3 17.1 - - + +
72E ASP* 2.9 46.3 + - - +
74E ARG* 1.3 74.6 - - - +
76E LEU* 1.3 59.2 + - - +
78E ARG* 3.4 25.1 + - - +
79E GLU* 3.0 29.1 + - - +
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Residues in contact with LEU 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E SER* 5.3 3.4 - - - -
42E HIS* 4.7 3.4 - - - +
45E THR* 4.8 2.0 - - - -
57E ILE* 4.3 10.8 - - + -
61E PHE* 3.7 41.0 - - + -
68E PHE* 3.9 18.2 - - + +
71E ALA* 3.9 27.1 - - + +
72E ASP 3.3 15.6 + - - +
73E SER* 3.7 13.7 - - - +
75E GLU* 1.3 75.0 - - - +
77E LEU* 1.3 58.9 + - - +
79E GLU* 3.5 0.8 + - - -
80E ALA* 2.9 31.7 + - - +
5901E 1AA 3.5 33.2 - - + -
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Residues in contact with LEU 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LEU* 3.8 27.1 - - + +
44E LEU* 3.9 18.8 - - + -
45E THR* 3.4 24.8 + - + +
48E LEU* 3.8 28.9 - - + +
73E SER 2.8 18.9 + - - +
74E ARG 3.6 3.4 - - - +
75E GLU 3.4 0.2 - - - -
76E LEU* 1.3 77.3 - - - +
78E ARG* 1.3 57.1 + - - +
80E ALA* 3.8 3.4 - - + +
81E TRP* 2.9 30.1 + - - +
116E ILE* 4.8 6.3 - - + -
119E ASP* 3.8 29.2 - - + +
120E LEU* 4.1 10.1 - - + -
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Residues in contact with ARG 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E ASP* 4.7 1.2 + - - -
74E ARG* 2.9 38.2 + - - +
75E GLU* 3.4 37.0 + - - +
76E LEU 3.3 0.2 - - - -
77E LEU* 1.3 72.5 - - - +
79E GLU* 1.3 55.6 + - - +
81E TRP* 3.4 8.4 + - - +
82E ARG* 2.8 33.7 + - - +
119E ASP* 2.7 64.5 + - + +
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Residues in contact with GLU 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E PHE* 3.5 26.9 - - + -
68E PHE* 3.7 21.1 - - + -
75E GLU 3.0 18.1 + - - +
76E LEU 3.9 3.1 - - - +
77E LEU 3.4 0.2 - - - -
78E ARG* 1.3 73.7 - - - +
80E ALA* 1.3 64.2 + - - +
82E ARG* 2.8 42.4 + - - +
83E ARG* 2.8 51.1 + - - +
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Residues in contact with ALA 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E THR* 3.6 25.1 - - + -
48E LEU* 6.3 1.1 - - + -
49E LEU* 3.8 19.8 - - + +
60E LEU* 4.0 15.9 - - + -
61E PHE* 4.1 1.7 - - + -
76E LEU 2.9 18.6 + - - +
77E LEU* 3.8 2.7 - - + +
79E GLU* 1.3 76.0 - - - +
81E TRP* 1.3 57.1 + - - +
83E ARG* 3.3 3.9 + - - +
84E ILE* 2.9 36.7 + - + +
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Residues in contact with TRP 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E LEU* 4.3 4.7 - - + +
77E LEU 2.9 19.1 + - - +
78E ARG* 3.6 7.2 - - - +
80E ALA* 1.3 74.7 - - - +
82E ARG* 1.3 58.9 + - - +
84E ILE* 3.8 23.1 - - + +
85E GLN* 2.9 73.4 + - + +
89E TYR 4.6 0.2 - - - -
90E THR* 3.7 8.7 - - - -
91E LEU* 3.4 45.1 - - + -
119E ASP 3.6 18.4 - - - -
120E LEU* 2.9 47.0 + - + -
121E GLY* 5.0 0.6 - - - -
154E LEU* 3.6 22.9 - - + -
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Residues in contact with ARG 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E ARG 2.8 17.5 + - - +
79E GLU* 2.8 48.2 + - - +
81E TRP* 1.3 74.5 - - - +
83E ARG* 1.3 73.8 + - - +
85E GLN* 3.5 13.9 + - - +
86E ALA* 3.1 32.1 + - - +
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Residues in contact with ARG 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E LEU* 4.1 17.4 - - + +
60E LEU* 3.5 47.5 + - + +
61E PHE* 3.8 15.4 - - - -
68E PHE* 3.9 14.1 - - - -
79E GLU* 2.8 37.0 + - - +
80E ALA* 3.6 7.4 - - - +
82E ARG* 1.3 90.9 - - - +
84E ILE* 1.3 62.5 + - - +
86E ALA* 3.3 9.3 + - - +
87E LYS* 3.2 20.8 + - - +
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Residues in contact with ILE 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E LEU* 3.6 41.1 - - + -
49E LEU* 3.7 9.9 - - + +
52E ALA* 3.8 8.5 - - + -
54E LEU* 3.8 21.5 - - + -
80E ALA* 2.9 27.0 + - + +
81E TRP* 3.3 24.2 + - + +
83E ARG* 1.3 76.0 - - - +
85E GLN* 1.3 57.9 + - - +
87E LYS* 3.1 15.2 + - - +
89E TYR* 3.3 36.6 + - + +
154E LEU* 3.7 15.9 - - + -
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Residues in contact with GLN 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E TRP* 2.9 61.8 + - + +
82E ARG* 3.8 11.4 - - - +
84E ILE* 1.3 75.8 - - - +
86E ALA* 1.3 58.4 + - - +
88E GLY* 2.9 19.9 + - - -
89E TYR 3.6 20.9 + - - +
90E THR* 5.6 3.6 - - - +
120E LEU 4.9 0.2 - - - +
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Residues in contact with ALA 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E ARG* 3.1 22.2 + - - +
83E ARG* 3.5 13.5 - - - +
84E ILE 3.3 0.2 - - - -
85E GLN* 1.3 75.8 - - - +
87E LYS* 1.3 58.0 + - - +
88E GLY* 3.2 1.9 + - - -
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Residues in contact with LYS 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ALA 3.1 26.9 + - - +
53E ALA 4.5 3.3 + - - -
54E LEU* 3.7 28.5 - - + -
83E ARG 3.2 9.1 + - - +
84E ILE* 3.1 13.3 + - - +
86E ALA* 1.3 76.7 - - - +
88E GLY* 1.3 59.2 + - - +
89E TYR* 3.7 22.7 + - + -
156E LYS 5.1 1.2 - - - +
125F ASP* 2.8 36.3 + - - -
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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