Contacts of the helix formed by residues 66 - 81 (chain E) in PDB entry 2BM9
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 66 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56E TYR* 3.7 21.9 - - + +
64E LEU 3.9 0.8 - - - -
65E LYS* 1.3 76.5 - - - +
67E PRO* 1.3 68.7 - - + +
68E ASP* 2.7 25.6 + - - +
69E THR* 2.9 33.4 + - - -
70E GLN 3.0 3.6 + - - -
221E SER* 4.4 1.7 + - - -
222E SER* 4.4 10.1 + - - -
223E GLN* 3.0 25.8 + - - +
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Residues in contact with PRO 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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67D PRO* 3.4 38.1 - - + +
68D ASP* 4.2 7.4 - - - +
71D ALA* 3.9 14.8 - - + -
56E TYR* 3.3 49.4 - - + +
65E LYS 3.5 1.1 - - - +
66E ASP* 1.3 84.4 - - + -
68E ASP* 1.3 61.9 + - - +
70E GLN* 3.3 18.7 - - + +
71E ALA* 3.0 22.0 + - - +
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Residues in contact with ASP 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D TYR* 4.7 9.7 + - - -
67D PRO* 4.4 11.0 - - - +
68D ASP* 4.2 17.7 - - - +
66E ASP* 2.7 18.6 + - - +
67E PRO* 1.3 73.5 - - - +
69E THR* 1.3 65.3 + - - +
71E ALA* 3.0 15.7 + - - +
72E VAL* 3.2 17.8 + - - +
220E ALA 4.3 4.6 - - - +
221E SER* 4.4 12.1 - - - -
222E SER 5.7 0.7 - - - +
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Residues in contact with THR 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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65E LYS* 3.8 27.6 - - + -
66E ASP* 2.9 9.1 + - - -
68E ASP* 1.3 77.9 - - - +
70E GLN* 1.3 61.3 + - - +
72E VAL* 3.3 4.2 + - - +
73E TYR* 3.2 32.8 + - + -
186E GLU* 4.6 0.4 - - - +
221E SER* 2.5 29.5 + - - -
223E GLN* 2.5 32.3 + - + +
224E LEU* 4.2 14.6 - - + -
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Residues in contact with GLN 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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71D ALA* 6.3 0.2 - - - +
56E TYR* 5.1 3.4 - - - +
57E GLN 4.6 6.1 + - - -
58E TRP* 5.1 7.6 - - - -
63E MET* 3.7 42.3 - - + +
65E LYS* 3.6 21.0 + - + +
66E ASP 3.0 5.1 + - - -
67E PRO* 3.3 24.5 - - + +
69E THR* 1.3 77.7 - - - +
71E ALA* 1.3 62.5 + - - +
74E HIS* 3.2 22.2 + - - +
98E TRP* 3.6 35.3 + - + -
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Residues in contact with ALA 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D TYR* 4.2 15.9 - - + -
67D PRO* 4.0 21.8 - - + -
70D GLN* 5.5 6.1 - - - +
67E PRO 3.0 13.3 + - - +
68E ASP 3.0 9.6 + - - +
70E GLN* 1.3 75.4 - - - +
72E VAL* 1.3 61.1 + - + +
74E HIS* 3.6 8.5 + - - +
75E ASP* 3.3 27.6 + - - +
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Residues in contact with VAL 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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68E ASP 3.2 10.7 + - - +
69E THR 3.4 6.7 - - - +
70E GLN 3.2 0.4 - - - -
71E ALA* 1.3 72.3 - - - +
73E TYR* 1.3 63.9 + - - +
74E HIS 3.0 1.1 - - - -
75E ASP* 2.9 12.1 + - - +
76E MET* 2.8 27.8 + - + +
217E TYR* 4.0 30.1 - - + +
220E ALA* 3.2 39.9 - - + +
221E SER* 4.0 7.9 - - - -
224E LEU* 3.3 26.0 - - + -
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Residues in contact with TYR 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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65E LYS* 3.6 21.1 - - + -
69E THR* 3.2 22.1 + - + +
72E VAL* 1.3 78.7 - - - +
74E HIS* 1.3 52.8 + - - +
76E MET* 3.3 20.1 - - + +
77E LEU* 2.6 43.6 + - + +
98E TRP* 3.7 20.2 - + + -
99E PHE* 3.8 22.2 - + + -
156E ILE* 4.8 2.0 - - + -
158E ILE* 3.3 26.3 - - + +
184E ILE* 3.2 41.9 - - + +
186E GLU* 2.6 30.8 + - - -
224E LEU* 4.2 10.5 - - + -
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Residues in contact with HIS 74 (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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57D GLN* 3.5 36.9 + - - -
58D TRP* 3.5 32.4 - + - -
59D ARG* 3.4 20.9 + - - +
70E GLN 3.2 16.8 + - - +
71E ALA* 3.6 9.6 + - - +
72E VAL 3.0 0.2 - - - -
73E TYR* 1.3 76.0 - - - +
75E ASP* 1.3 75.7 + - - +
77E LEU* 3.2 2.0 + - - -
78E TRP* 2.9 20.8 + - + +
98E TRP* 4.7 0.6 - - - -
102E LEU* 4.1 23.8 - - + -
106E MET* 3.4 29.6 - - + +
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Residues in contact with ASP 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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24D TYR* 4.6 6.8 + - - -
27D PRO* 5.9 3.0 - - - +
50D TYR* 5.5 3.1 + - - -
55D PRO* 4.9 5.2 - - - +
56D TYR* 5.7 3.6 - - - -
57D GLN* 2.9 41.2 + - - +
71E ALA 3.3 12.9 + - - +
72E VAL* 2.9 10.2 + - - +
74E HIS* 1.3 83.7 + - - +
76E MET* 1.3 61.8 + - - +
78E TRP* 3.2 3.1 + - - +
79E GLU* 3.1 20.1 + - - +
217E TYR* 3.5 25.8 + - + +
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Residues in contact with MET 76 (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 VAL* 2.8 15.3 + - + +
73E TYR* 3.3 28.5 - - + +
74E HIS 3.1 0.2 - - - -
75E ASP* 1.3 77.8 - - - +
77E LEU* 1.3 61.4 + - + +
79E GLU* 3.5 1.6 + - - +
80E LEU* 3.2 25.1 + - - +
156E ILE* 4.5 14.6 - - + -
182E TYR* 3.5 44.1 + - + +
184E ILE* 3.5 22.9 - - + -
217E TYR* 3.6 35.4 + - + -
224E LEU* 5.6 0.4 - - + -
228E VAL* 3.7 16.8 - - + -
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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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73E TYR* 2.6 33.4 + - + +
74E HIS 3.2 5.1 + - - +
76E MET* 1.3 75.7 - - + +
78E TRP* 1.3 58.4 + - - +
81E ARG* 3.1 27.4 + - - -
82E PRO* 3.7 10.4 - - + +
85E ILE* 4.1 16.2 - - + -
99E PHE* 4.1 25.1 - - + -
102E LEU* 4.1 29.6 - - + -
103E THR* 3.8 29.2 - - + +
106E MET* 3.8 11.2 - - + -
108E ILE* 3.9 6.5 - - + +
156E ILE* 4.4 15.3 - - + -
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Residues in contact with TRP 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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24D TYR* 5.0 6.0 - + - -
57D GLN* 3.7 26.9 - - - +
59D ARG* 3.7 34.5 - - + -
60D GLY* 3.6 19.9 - - - -
74E HIS 2.9 16.4 + - - +
75E ASP 3.2 5.4 + - - +
77E LEU* 1.3 78.4 - - - +
79E GLU* 1.3 66.0 + - - +
81E ARG* 3.6 32.7 - - - +
106E MET* 3.7 42.1 - - + +
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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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34D ARG* 3.0 41.1 + - - -
75E ASP 3.1 14.6 + - - +
76E MET 4.0 2.0 - - - +
77E LEU 3.4 0.2 - - - -
78E TRP* 1.3 83.6 - - - +
80E LEU* 1.3 62.3 + - + +
81E ARG* 4.2 4.0 - - - +
182E TYR* 4.3 4.4 + - - +
217E TYR* 2.7 30.5 + - - +
230E ARG* 5.6 0.7 - - - -
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Residues in contact with LEU 80 (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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76E MET 3.2 15.0 + - - +
79E GLU* 1.3 81.8 - - + +
81E ARG* 1.3 73.5 + - - +
82E PRO* 4.0 9.9 - - + -
154E PRO* 3.2 40.8 - - + +
155E LEU 4.3 5.4 - - - +
156E ILE* 3.7 28.9 - - + -
180E GLY* 4.4 11.4 - - - +
182E TYR* 4.0 27.6 - - + +
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Residues in contact with ARG 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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77E LEU 3.1 6.8 + - - +
78E TRP* 3.6 34.5 - - - +
79E GLU 4.2 3.8 - - - +
80E LEU* 1.3 83.2 - - - +
82E PRO* 1.3 74.0 - - - +
83E ARG* 3.9 6.9 - - - -
106E MET 3.5 14.6 + - - -
107E GLY* 3.6 16.4 + - - -
108E ILE* 3.3 46.3 - - + +
154E PRO* 3.4 12.5 - - - +
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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