Contacts of the helix formed by residues 85 - 114 (chain G) in PDB entry 5JGH
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 GLU 85 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G LYS* 5.2 1.0 - - - +
83G ASN 4.1 0.2 + - - -
84G LEU* 1.3 80.3 - - + +
86G ALA* 1.3 61.2 + - - +
87G ASP* 4.1 20.6 - - - +
88G ILE* 3.3 39.5 + - + +
89G LYS* 2.9 25.8 + - - +
91G LYS* 5.7 0.3 + - - -
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Residues in contact with ALA 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G LEU 3.2 6.8 + - - +
85G GLU* 1.3 74.9 - - - +
87G ASP* 1.3 58.4 + - - +
89G LYS* 3.6 7.9 - - - +
90G GLU* 2.7 48.0 + - + +
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Residues in contact with ASP 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G GLU* 3.4 18.7 - - - +
86G ALA* 1.3 82.0 + - - +
88G ILE* 1.3 61.7 + - - +
90G GLU* 3.3 13.6 + - - +
91G LYS* 3.0 38.1 + - - +
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Residues in contact with ILE 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G HIS* 5.5 6.7 - - + +
84G LEU* 4.9 12.3 - - + -
85G GLU* 3.3 44.6 + - + +
87G ASP* 1.3 74.7 - - - +
89G LYS* 1.3 63.8 + - - +
91G LYS* 3.1 40.3 + - + +
92G TYR* 3.2 33.5 + - + +
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Residues in contact with LYS 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G TRP* 3.3 64.7 + - + +
82G GLN* 3.8 13.5 + - - +
84G LEU* 4.4 22.8 - - + +
85G GLU 2.9 18.9 + - - +
86G ALA* 3.6 8.5 - - - +
88G ILE* 1.3 75.9 - - - +
90G GLU* 1.3 57.5 + - + +
92G TYR* 3.1 8.2 + - - +
93G ILE* 2.8 46.3 + - + +
16K T 4.6 4.6 + - - -
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Residues in contact with GLU 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G ALA* 2.7 30.5 + - + +
87G ASP* 3.3 15.7 + - - +
89G LYS* 1.3 72.9 - - + +
91G LYS* 1.3 53.3 + - - +
93G ILE* 3.6 11.3 - - + +
94G SER* 2.5 40.4 + - - -
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Residues in contact with LYS 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G GLU* 5.7 0.4 + - - -
87G ASP* 3.0 31.9 + - - +
88G ILE* 3.1 31.8 + - + +
90G GLU* 1.3 75.5 - - + +
92G TYR* 1.3 59.8 + - + +
94G SER* 2.9 8.6 + - - -
95G GLU* 2.8 32.4 + - - +
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Residues in contact with TYR 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G ALA* 4.1 7.0 - - - +
52G LEU* 3.6 29.1 - - + +
53G TYR* 3.4 44.4 - + + -
56G ASP* 3.8 18.6 + - - +
57G HIS* 3.0 29.3 + + - -
81G TRP* 4.0 19.5 - + + -
84G LEU* 4.7 1.6 - - + -
88G ILE* 3.2 31.5 + - + -
89G LYS* 3.1 7.7 + - - +
91G LYS* 1.3 77.1 - - + +
93G ILE* 1.3 61.6 + - - +
95G GLU* 4.4 4.7 - - + -
96G ARG* 2.8 30.0 + - - +
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Residues in contact with ILE 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G ALA* 4.0 19.7 - - + -
81G TRP* 4.5 6.5 - - + -
89G LYS* 2.8 41.2 + - + +
90G GLU* 3.6 9.9 - - + +
92G TYR* 1.3 75.9 - - - +
94G SER* 1.3 58.7 + - - +
96G ARG* 3.2 4.9 + - + +
97G LYS* 2.8 28.3 + - + +
16K T 5.6 2.9 - - - +
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Residues in contact with SER 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G GLU* 2.5 26.9 + - - -
91G LYS* 2.9 19.4 + - - -
93G ILE* 1.3 72.9 - - - +
95G GLU* 1.3 63.7 + - - +
97G LYS* 3.1 11.6 + - - +
98G LYS* 3.0 21.0 + - - +
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Residues in contact with GLU 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G LEU* 4.3 11.7 - - + -
91G LYS 2.8 23.0 + - - +
92G TYR* 3.8 8.5 - - + +
94G SER* 1.3 72.4 + - - +
96G ARG* 1.3 64.0 + - - +
98G LYS* 3.2 17.2 + - - +
99G LEU* 3.2 42.0 + - + +
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Residues in contact with ARG 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G ARG* 3.7 19.8 - - - +
46G PRO* 4.2 7.2 + - - +
47G THR 2.8 30.8 + - - -
48G SER* 3.4 14.5 - - - +
49G ALA* 3.8 16.0 - - + +
52G LEU* 3.8 14.6 - - + +
92G TYR 2.8 19.3 + - - +
93G ILE* 3.4 7.2 - - + +
95G GLU* 1.3 78.2 - - - +
97G LYS* 1.3 64.0 + - - +
99G LEU* 3.1 7.3 + - - +
100G TYR* 2.9 60.0 + - - +
16K T 4.3 5.9 + - - -
17K A 4.0 21.3 + - - -
18K T 5.4 3.2 + - - -
7L A 5.2 1.8 - - - -
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Residues in contact with LYS 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G ILE* 2.8 14.9 + - + +
94G SER* 3.1 13.4 + - - +
96G ARG* 1.3 78.5 - - - +
98G LYS* 1.3 64.2 + - - +
100G TYR* 3.3 7.2 + - - +
101G SER* 3.3 23.6 + - - +
18K T 5.9 3.6 - - - +
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Residues in contact with LYS 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G SER 3.0 11.6 + - - +
95G GLU* 3.5 20.4 - - - +
96G ARG 3.2 0.2 - - - -
97G LYS* 1.3 78.5 - - - +
99G LEU* 1.3 60.8 + - + +
101G SER* 2.6 22.7 + - - +
102G GLU* 3.3 29.3 - - + +
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Residues in contact with LEU 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G PRO* 3.7 23.4 - - + +
47G THR* 5.9 2.0 - - - +
52G LEU* 4.3 24.0 - - + -
95G GLU* 3.2 34.4 + - + +
96G ARG* 3.1 11.4 + - - +
98G LYS* 1.3 75.0 - - + +
100G TYR* 1.3 65.5 + - - +
102G GLU* 3.3 23.0 + - - +
103G TYR* 3.0 20.8 + - - +
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Residues in contact with TYR 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G ARG* 3.5 28.9 + - - -
46G PRO* 3.6 16.3 - - + +
96G ARG* 2.9 38.8 + - - +
97G LYS* 3.3 7.1 + - - +
99G LEU* 1.3 77.2 - - - +
101G SER* 1.3 52.3 + - - +
103G TYR* 3.0 16.4 + + - +
104G GLN* 2.6 79.4 + - + +
18K T 2.4 56.9 + - - +
19K A 2.9 15.4 - - - -
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Residues in contact with SER 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G LYS* 3.3 13.8 + - - +
98G LYS* 2.6 27.7 + - - +
100G TYR* 1.3 78.6 - - - +
102G GLU* 1.3 60.5 + - - +
104G GLN* 3.8 11.5 - - - +
105G LYS* 2.9 33.6 + - - +
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Residues in contact with GLU 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G LYS* 3.3 31.1 + - + +
99G LEU* 3.3 25.8 + - - +
100G TYR 3.2 0.6 - - - -
101G SER* 1.3 79.6 + - - +
103G TYR* 1.3 57.6 + - - +
105G LYS* 3.4 4.6 + - - +
106G ALA* 2.7 30.5 + - - +
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Residues in contact with TYR 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G PRO* 3.1 34.2 + - + -
44G LYS* 3.2 22.6 - - - +
45G ARG* 3.5 25.7 + - + +
46G PRO* 3.5 23.3 - - + -
99G LEU 3.0 7.0 + - - +
100G TYR* 3.0 19.5 + + - +
102G GLU* 1.3 76.3 - - - +
104G GLN* 1.3 57.5 + - + +
106G ALA* 3.0 6.3 + - - +
107G LYS* 2.5 66.8 + - + +
19K A 4.1 30.6 + - - -
20K T 4.6 1.2 + - - -
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Residues in contact with GLN 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G TYR* 2.6 51.9 + - + +
101G SER* 3.8 10.4 - - - +
103G TYR* 1.3 77.5 - - + +
105G LYS* 1.3 63.6 + - + +
107G LYS* 3.2 6.4 + - + +
108G LYS* 3.0 48.6 + - - +
18K T 4.4 4.0 + - - -
19K A 2.7 28.6 + - - +
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Residues in contact with LYS 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G SER* 2.9 23.0 + - - +
102G GLU* 3.8 4.7 - - - +
104G GLN* 1.3 72.7 - - + +
106G ALA* 1.3 67.7 + - - +
108G LYS* 3.3 36.8 - - - +
109G GLU* 3.1 27.7 + - - +
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Residues in contact with ALA 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G PRO* 3.9 24.2 - - + +
102G GLU 2.7 22.6 + - - +
103G TYR* 3.3 8.7 - - - +
105G LYS* 1.3 73.6 - - - +
107G LYS* 1.3 56.5 + - - +
109G GLU* 3.3 6.3 + - - +
110G PHE* 2.8 31.9 + - - +
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Residues in contact with LYS 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G ILE* 3.1 38.3 + - - +
43G PRO* 4.1 17.2 + - + +
103G TYR* 2.5 48.6 + - + +
104G GLN* 3.2 9.2 + - - +
106G ALA* 1.3 71.2 - - - +
108G LYS* 1.3 55.1 + - + +
110G PHE* 2.9 9.4 + - + -
111G ASP* 2.7 59.4 + - - +
19K A 5.1 2.2 - - - -
20K T 3.6 27.9 + - - -
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Residues in contact with LYS 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G GLN* 3.0 33.5 + - - +
105G LYS* 3.3 45.6 - - - +
107G LYS* 1.3 75.5 - - + +
109G GLU* 1.3 57.5 + - - +
111G ASP* 3.8 5.9 - - - +
112G GLU* 2.9 45.3 + - + +
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Residues in contact with GLU 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G LYS* 3.1 20.9 + - - +
106G ALA* 3.6 6.5 - - - +
108G LYS* 1.3 77.7 - - - +
110G PHE* 1.3 62.7 + - - +
112G GLU* 3.6 8.1 + - - +
113G LYS* 3.4 45.1 + - - +
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Residues in contact with PHE 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G LEU* 3.0 29.4 - - + -
39G ILE* 3.6 21.1 - - + -
41G GLN* 4.9 2.0 - - + -
42G GLY* 3.5 18.2 - - - -
43G PRO* 3.4 26.0 - - + -
106G ALA 2.8 17.0 + - - +
107G LYS* 3.5 4.0 - - + +
109G GLU* 1.3 73.6 - - - +
111G ASP* 1.3 76.3 + - - +
113G LYS* 3.3 17.0 + - + +
114G LEU* 3.3 38.5 + - + +
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Residues in contact with ASP 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G ARG* 5.0 3.5 + - - -
39G ILE* 3.7 19.7 - - - +
107G LYS* 2.7 62.0 + - - +
108G LYS* 3.8 5.8 - - - +
110G PHE* 1.3 74.0 - - - +
112G GLU* 1.3 63.8 + - + +
114G LEU* 3.1 31.6 + - + +
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Residues in contact with GLU 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G LYS* 2.9 28.2 + - + +
109G GLU* 3.9 7.2 - - - +
110G PHE 3.3 0.2 - - - -
111G ASP* 1.3 78.0 - - + +
113G LYS* 1.3 63.1 + - + +
114G LEU 3.4 5.5 + - - +
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Residues in contact with LYS 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G GLU* 3.4 38.5 + - - +
110G PHE* 3.3 9.7 + - + +
111G ASP 3.2 0.6 - - - -
112G GLU* 1.3 75.6 - - + +
114G LEU* 1.3 65.0 + - - +
115G PRO* 3.8 1.7 - - - +
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Residues in contact with LEU 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G ARG* 4.3 27.6 - - + +
38G LEU* 4.1 22.4 - - + -
39G ILE* 4.0 16.6 - - + -
110G PHE* 3.3 39.4 + - + +
111G ASP* 3.1 35.8 + - - +
112G GLU 3.7 7.1 - - - +
113G LYS* 1.3 82.5 - - - +
115G PRO* 1.3 81.0 - - + +
116G PRO* 3.4 5.7 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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