Contacts of the helix formed by residues 76 - 99 (chain E) in PDB entry 5BOU
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 LEU 76 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D PHE* 3.8 31.4 - - + -
11D GLY 5.4 4.5 - - - +
12D ARG* 6.3 1.3 - - - -
13D LEU* 4.4 16.8 - - + +
113D LEU* 5.3 4.0 - - + -
153D SER* 5.7 7.9 - - - +
155D THR* 6.2 0.2 - - - +
27E ALA* 5.1 5.3 - - + +
75E GLY* 1.3 68.3 - - - -
77E ALA* 1.3 65.1 + - - +
78E PRO* 3.4 9.2 - - + -
79E ASP* 3.3 32.9 + - + +
80E ALA 3.4 7.8 + - - -
125E ARG* 4.2 6.5 - - - +
128E GLY* 2.8 21.6 + - - +
129E VAL* 3.4 10.9 - - - +
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Residues in contact with ALA 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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155D THR* 4.9 3.4 - - - +
59E GLN* 3.4 29.4 - - + +
60E LYS 5.8 1.1 - - - +
73E LEU* 4.2 24.6 - - + +
75E GLY 3.2 6.1 + - - +
76E LEU* 1.3 68.4 - - - +
78E PRO* 1.3 74.6 - - + +
80E ALA* 3.2 5.2 + - - +
81E ARG* 3.1 20.5 + - - +
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Residues in contact with PRO 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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109D CYS 5.9 0.9 - - - +
113D LEU* 3.6 21.8 - - + -
153D SER 3.4 23.8 - - - +
154D GLY* 3.8 21.8 - - - +
155D THR* 4.2 9.0 - - - +
76E LEU* 3.5 12.3 - - + -
77E ALA* 1.3 94.6 - - + +
79E ASP* 1.3 56.4 + - - +
81E ARG* 3.3 12.0 + - + +
82E VAL* 3.1 30.9 + - - +
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Residues in contact with ASP 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D LEU* 3.9 6.9 - - - +
76E LEU* 3.3 17.3 + - + +
77E ALA 3.2 0.6 - - - -
78E PRO* 1.3 75.2 - - - +
80E ALA* 1.3 60.3 - - - +
82E VAL* 3.3 9.7 + - - +
83E LEU* 3.0 32.6 + - - +
125E ARG* 2.8 37.6 + - - -
127E TYR* 3.4 16.5 - - + -
128E GLY* 2.7 27.5 + - - +
129E VAL* 3.8 14.1 - - + -
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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
----------------------------------------------------------
63E ILE* 4.4 4.5 - - + -
73E LEU* 3.7 39.9 - - + -
76E LEU 3.4 3.3 + - - +
77E ALA 3.2 10.2 + - - +
79E ASP* 1.3 74.9 - - - +
81E ARG* 1.3 53.6 + - - +
83E LEU* 3.8 1.9 - - - +
84E SER* 2.7 41.8 + - - -
129E VAL* 3.8 16.7 - - + +
131E LEU* 4.1 10.1 - - + +
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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
----------------------------------------------------------
106D GLN* 3.3 43.9 + - - +
107D SER* 5.8 0.2 - - - +
110D ASP* 2.8 40.8 + - - +
63E ILE* 4.7 5.6 - - + +
77E ALA 3.1 12.0 + - - +
78E PRO* 3.4 15.3 - - + +
80E ALA* 1.3 77.0 - - - +
82E VAL* 1.3 57.9 + - + +
84E SER* 3.1 7.3 + - - +
85E ASN* 3.0 36.2 + - + +
88E ARG* 5.1 10.7 - - - +
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Residues in contact with VAL 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 PRO 3.1 15.7 + - - +
79E ASP* 3.6 11.7 - - - +
81E ARG* 1.3 77.9 - - + +
83E LEU* 1.3 58.5 + - - +
85E ASN* 3.5 6.9 + - - +
86E TYR* 3.1 25.1 + - - +
114E LYS* 4.9 8.9 - - - +
127E TYR* 4.0 26.7 - - + +
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Residues in contact with LEU 83 (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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79E ASP 3.0 19.5 + - - +
80E ALA 4.1 1.6 - - - +
82E VAL* 1.3 74.2 - - - +
84E SER* 1.3 60.7 + - - +
86E TYR* 3.4 6.3 + - - +
87E LEU* 3.0 25.9 + - - +
111E LEU* 4.0 21.9 - - + +
114E LYS* 3.9 27.6 - - + -
115E ALA 5.4 0.2 - - - +
127E TYR* 3.9 33.4 - - + -
129E VAL* 3.8 22.7 - - + -
131E LEU* 3.9 17.3 - - + -
146E PHE* 3.8 26.5 - - + -
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Residues in contact with SER 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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63E ILE* 3.7 32.2 - - - +
65E CYS* 4.2 1.8 - - - -
71E LEU* 4.0 21.3 - - - +
80E ALA 2.7 27.0 + - - -
81E ARG* 3.1 11.8 + - - -
83E LEU* 1.3 70.2 - - - +
85E ASN* 1.3 63.1 + - - +
87E LEU* 3.2 7.9 + - - +
88E ARG* 2.9 37.1 + - - +
131E LEU* 5.5 0.6 - - - +
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Residues in contact with ASN 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 ARG* 3.0 26.1 + - + +
82E VAL* 3.5 7.5 - - - +
84E SER* 1.3 77.7 + - - +
86E TYR* 1.3 61.4 + - - +
88E ARG* 3.3 20.4 + - - +
89E GLN* 3.0 47.9 + - - +
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Residues in contact with TYR 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 VAL 3.1 14.0 + - - +
83E LEU 3.5 10.5 - - - +
85E ASN* 1.3 76.3 + - - +
87E LEU* 1.3 60.1 + - + +
89E GLN* 3.3 19.3 + - - +
90E GLN* 3.0 64.3 + - + +
110E LEU* 3.9 40.6 + - + +
111E LEU* 4.7 10.3 - - + -
114E LYS* 3.6 42.4 - - + +
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Residues in contact with LEU 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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65E CYS* 3.9 23.3 - - + -
69E MET* 4.4 16.2 - - - -
71E LEU* 4.3 10.8 - - + -
83E LEU 3.0 12.2 + - - +
84E SER 3.2 7.4 + - - +
86E TYR* 1.3 75.0 - - + +
88E ARG* 1.3 61.2 + - - +
90E GLN* 4.4 5.2 - - + +
91E CYS* 2.9 37.0 + - - -
102E LEU* 4.5 7.2 - - + -
107E ALA* 3.6 35.9 - - + +
110E LEU* 5.6 2.2 - - + -
111E LEU* 3.7 32.1 - - + -
131E LEU* 6.1 0.2 - - + -
133E ILE* 4.5 9.6 - - + -
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Residues in contact with ARG 88 (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 ILE* 3.5 21.9 - - - +
64E LYS* 2.8 28.5 + - - +
65E CYS* 3.5 29.6 + - - +
81E ARG* 5.1 10.7 - - - +
84E SER* 2.9 19.4 + - - +
85E ASN* 3.4 23.1 - - - +
87E LEU* 1.3 77.1 - - - +
89E GLN* 1.3 57.4 + - + +
91E CYS* 3.6 2.4 + - - +
92E ASN* 3.0 29.7 + - - +
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Residues in contact with GLN 89 (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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85E ASN* 3.0 37.0 + - - +
86E TYR* 3.5 22.5 - - - +
87E LEU 3.2 0.2 - - - -
88E ARG* 1.3 78.0 - - + +
90E GLN* 1.3 57.7 + - - +
92E ASN* 3.2 6.9 + - - +
93E TYR* 2.8 35.0 + - - +
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Residues in contact with GLN 90 (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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86E TYR* 3.0 62.8 + - + +
87E LEU* 3.3 6.9 + - + +
89E GLN* 1.3 76.6 + - - +
91E CYS* 1.3 67.1 + - - +
93E TYR* 3.4 17.8 + - - +
94E SER* 3.1 23.4 + - - -
102E LEU* 4.0 9.3 - - + +
106E ARG* 5.1 6.4 + - - -
110E LEU* 4.0 30.8 - - + +
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Residues in contact with CYS 91 (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 CYS* 4.4 6.5 - - - +
66E ASP* 3.6 36.1 - - + +
68E HIS* 4.5 1.1 - - - -
69E MET* 4.0 26.0 - - - -
87E LEU* 2.9 26.6 + - - +
88E ARG 3.7 4.7 - - - +
90E GLN* 1.3 75.3 - - - +
92E ASN* 1.3 61.2 + - - +
94E SER* 3.5 4.0 + - - -
95E SER* 3.2 25.6 + - - -
102E LEU* 3.8 28.9 + - + +
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Residues in contact with ASN 92 (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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66E ASP* 5.6 0.9 - - - -
88E ARG 3.0 19.8 + - - +
89E GLN* 3.4 8.3 - - - +
90E GLN 3.1 0.2 - - - -
91E CYS* 1.3 74.9 - - - +
93E TYR* 1.3 60.0 + - - +
95E SER* 3.3 7.8 + - - -
96E LEU* 2.9 60.4 + - + +
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Residues in contact with TYR 93 (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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89E GLN 2.8 19.7 + - - +
90E GLN* 3.7 20.2 - - - +
92E ASN* 1.3 72.0 - - - +
94E SER* 1.3 61.7 + - - +
96E LEU* 4.8 5.4 - - - -
97E VAL* 2.9 66.9 + - + +
98E PHE* 4.2 18.5 - + - -
106E ARG* 5.9 4.9 - - - -
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Residues in contact with SER 94 (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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90E GLN 3.1 10.3 + - - -
91E CYS 3.6 8.5 - - - -
93E TYR* 1.3 82.7 - - - +
95E SER* 1.3 57.3 + - - +
98E PHE* 3.1 35.6 + - - +
100E ARG* 2.7 44.3 + - - +
102E LEU* 3.9 26.5 + - - +
106E ARG* 5.1 5.5 + - - -
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Residues in contact with SER 95 (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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66E ASP* 4.3 9.5 + - - -
91E CYS 3.2 14.9 + - - -
92E ASN* 3.8 11.7 - - - -
94E SER* 1.3 78.6 - - - +
96E LEU* 1.3 62.6 + - - +
99E ASN* 3.1 27.6 + - - +
100E ARG 3.6 17.1 + - - +
101E LYS* 4.6 8.0 - - - +
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Residues in contact with LEU 96 (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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92E ASN* 2.9 47.6 + - - +
93E TYR* 4.1 4.3 - - - +
95E SER* 1.3 81.2 - - - +
97E VAL* 1.3 66.4 + - + +
99E ASN 4.6 0.7 + - - -
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Residues in contact with VAL 97 (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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93E TYR* 2.9 51.7 + - + +
96E LEU* 1.3 82.9 - - + +
98E PHE* 1.3 89.4 + - + +
99E ASN 3.6 0.4 + - - -
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Residues in contact with PHE 98 (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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93E TYR* 4.2 16.8 - + - -
94E SER* 3.1 24.2 + - - +
97E VAL* 1.3 99.4 - - + +
99E ASN* 1.3 73.0 + - - +
100E ARG* 3.1 23.7 + - + +
106E ARG* 6.1 2.9 - - - -
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Residues in contact with ASN 99 (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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95E SER* 3.1 21.5 + - - +
96E LEU 4.5 1.4 + - - +
97E VAL 3.6 1.4 - - - -
98E PHE* 1.3 78.2 - - - +
100E ARG* 1.3 56.7 + - - +
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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
------------------------------------------------------------
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