Contacts of the helix formed by residues 58 - 73 (chain E) in PDB entry 2I5B
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 58 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56E PRO 4.1 2.2 + - - -
57E ILE* 1.3 74.2 - - - +
59E THR* 1.3 56.3 + - - +
60E ASP* 4.3 8.3 - - + +
61E THR* 2.8 41.2 + - - +
62E ILE 3.1 8.7 + - - -
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Residues in contact with THR 59 (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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57E ILE 3.3 4.9 + - - -
58E ASP* 1.3 70.1 - - - +
60E ASP* 1.3 57.9 + - - +
62E ILE* 3.3 10.0 + - - +
63E ARG* 2.9 44.9 + - - +
85E THR* 5.8 0.5 - - - +
87E ASP* 4.5 30.8 + - + +
88E ILE* 4.9 7.0 - - + +
91E LEU* 4.0 18.3 - - + +
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Residues in contact with ASP 60 (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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58E ASP* 3.0 6.1 + - + +
59E THR* 1.3 79.0 - - - +
61E THR* 1.3 59.0 + - - +
63E ARG* 2.7 36.5 + - - +
64E ALA* 2.9 28.4 + - - +
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Residues in contact with THR 61 (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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57E ILE* 3.6 19.9 - - + +
58E ASP* 2.8 28.2 + - - +
60E ASP* 1.3 69.8 - - - +
62E ILE* 1.3 66.6 + - - +
64E ALA* 3.3 7.8 + - + +
65E GLN* 3.1 37.0 + - + +
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Residues in contact with ILE 62 (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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9E ILE* 4.7 6.1 - - + -
37E ALA* 4.8 4.0 - - + -
38E LEU 3.6 14.6 - - - +
39E THR* 3.8 30.3 - - + -
57E ILE* 3.5 23.1 - - + +
58E ASP 3.5 9.9 - - - +
59E THR* 3.5 9.0 - - - +
61E THR* 1.3 75.0 - - - +
63E ARG* 1.3 63.0 + - - +
65E GLN* 3.2 11.0 + - - +
66E LEU* 3.0 32.5 + - + +
88E ILE* 3.7 32.8 - - + -
91E LEU* 3.7 16.8 - - + -
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Residues in contact with ARG 63 (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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59E THR* 2.9 33.4 + - - +
60E ASP* 2.7 42.0 + - - +
62E ILE* 1.3 75.2 - - - +
64E ALA* 1.3 56.8 + - - +
66E LEU* 3.3 8.0 + - - +
67E ALA* 2.9 28.6 + - + +
91E LEU* 3.8 32.4 - - + +
94E LYS* 5.5 8.7 - - - +
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Residues in contact with ALA 64 (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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60E ASP 2.9 17.1 + - - +
61E THR* 3.3 8.7 + - + +
63E ARG* 1.3 73.7 - - - +
65E GLN* 1.3 65.4 + - - +
67E ALA* 3.2 8.7 + - - +
68E THR* 2.9 26.7 + - - +
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Residues in contact with GLN 65 (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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36E THR 3.6 8.4 - - - +
37E ALA* 3.6 12.3 - - - -
38E LEU* 2.7 57.2 + - - +
57E ILE* 4.7 1.6 - - - +
61E THR* 3.1 35.7 + - + +
62E ILE* 3.5 10.9 - - - +
64E ALA* 1.3 76.1 - - + +
66E LEU* 1.3 62.7 + - - +
68E THR* 3.4 10.5 + - - +
69E ILE* 3.0 29.5 + - + +
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Residues in contact with LEU 66 (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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7E LEU* 4.2 15.3 - - + -
9E ILE* 3.5 38.1 - - + -
37E ALA* 3.7 13.9 - - + -
62E ILE* 3.0 23.4 + - + +
63E ARG* 3.5 8.1 - - - +
64E ALA 3.2 0.2 - - - -
65E GLN* 1.3 74.7 - - - +
67E ALA* 1.3 54.4 + - - +
69E ILE* 4.5 2.5 - - - +
70E THR* 2.7 44.0 + - + -
91E LEU* 4.0 26.0 - - + +
92E ALA* 5.2 0.4 - - - -
95E THR* 3.5 35.0 - - + +
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Residues in contact with ALA 67 (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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63E ARG* 2.9 15.6 + - + +
64E ALA* 3.2 13.4 + - - +
66E LEU* 1.3 74.7 - - - +
68E THR* 1.3 58.7 + - - +
70E THR* 4.3 2.5 - - - -
71E ASP* 2.8 50.8 + - + +
72E GLY 3.4 0.2 + - - -
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Residues in contact with THR 68 (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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64E ALA 2.9 18.6 - - - +
65E GLN* 3.4 14.8 - - - +
67E ALA* 1.3 75.5 - - - +
69E ILE* 1.3 64.3 + - + +
72E GLY* 3.1 24.0 + - - +
73E ILE* 3.3 16.9 + - - +
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Residues in contact with ILE 69 (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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7E LEU* 3.9 29.6 - - + -
35E MET* 3.8 31.9 - - + -
36E THR 3.4 34.5 - - - +
37E ALA* 4.0 1.6 - - + +
65E GLN* 3.0 25.3 + - + +
66E LEU* 4.0 2.7 - - - +
68E THR* 1.3 80.7 - - + +
70E THR* 1.3 54.8 + - + +
73E ILE* 2.5 38.8 + - + +
74E GLY* 4.2 2.4 - - - -
75E VAL* 3.9 22.2 - - + -
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Residues in contact with THR 70 (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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7E LEU* 3.9 28.5 - - + -
66E LEU* 2.7 32.4 + - + +
67E ALA* 4.3 0.5 - - - -
69E ILE* 1.3 73.5 - - + +
71E ASP* 1.3 65.5 + - - +
73E ILE 3.1 10.3 - - - +
74E GLY* 4.5 5.3 - - - -
75E VAL* 5.2 3.8 - - + -
95E THR* 4.1 14.1 - - + +
99E LYS* 3.6 34.5 + - - +
101E LEU* 4.1 21.8 - - + +
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Residues in contact with ASP 71 (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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67E ALA* 2.8 34.9 + - + +
70E THR* 1.3 79.0 + - - +
72E GLY* 1.3 57.9 + - - +
73E ILE 3.6 1.4 - - - +
99E LYS* 3.0 40.1 + - - +
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Residues in contact with GLY 72 (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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67E ALA 3.4 0.8 + - - -
68E THR* 3.1 16.9 + - - -
71E ASP* 1.3 80.7 - - - +
73E ILE* 1.3 66.8 + - - +
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Residues in contact with ILE 73 (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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5E LYS* 3.8 18.8 - - + +
33E TYR* 5.9 2.5 - - + -
35E MET* 3.8 28.9 - - + -
68E THR* 3.3 23.8 + - - +
69E ILE* 2.5 23.6 - - + +
70E THR 3.1 13.5 - - - +
71E ASP 4.0 1.0 - - - -
72E GLY* 1.3 79.2 - - - +
74E GLY* 1.3 70.3 + - - +
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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