Contacts of the helix formed by residues 85 - 114 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ASN 3.6 2.4 + - - -
84A LEU* 1.3 79.6 - - + +
86A ALA* 1.3 60.9 + - - +
87A ASP* 3.3 25.3 - - - +
88A ILE* 3.2 17.2 - - + +
89A LYS* 2.8 24.3 + - - +
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU 3.2 4.5 + - - +
85A GLU* 1.3 72.1 - - - +
87A ASP* 1.3 61.6 + - - +
89A LYS* 3.9 10.8 - - + -
90A GLU* 2.8 46.1 + - + +
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLU* 3.3 31.1 - - - +
86A ALA* 1.3 76.3 + - - +
88A ILE* 1.3 61.6 + - - +
90A GLU* 3.7 9.8 + - - +
91A LYS* 3.4 15.4 + - - +
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Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 5.8 0.4 - - + -
57A HIS* 5.1 13.9 - - + +
84A LEU* 3.8 22.7 - - + -
85A GLU* 3.2 37.9 - - + +
87A ASP* 1.3 79.7 - - - +
89A LYS* 1.3 66.5 + - - +
91A LYS* 2.9 29.0 + - + +
92A TYR* 3.5 19.6 + - + +
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Residues in contact with LYS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A TRP* 3.4 65.9 + - + +
82A GLN* 3.8 22.0 + - - +
84A LEU* 4.2 22.0 - - + +
85A GLU 2.8 18.8 + - - +
86A ALA* 3.8 9.0 - - + +
87A ASP 3.4 0.2 - - - -
88A ILE* 1.3 77.3 - - - +
90A GLU* 1.3 61.2 + - + +
91A LYS 3.2 0.9 + - - -
92A TYR* 3.3 11.8 + - - +
93A ILE* 3.1 22.5 + - + +
16E T 4.5 5.6 + - - -
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA* 2.8 29.3 + - + +
87A ASP* 4.0 8.2 - - - +
89A LYS* 1.3 73.9 - - + +
91A LYS* 1.3 59.7 + - - +
92A TYR 3.3 0.2 - - - -
93A ILE* 3.5 14.0 - - + +
94A SER* 2.8 32.2 + - - -
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASP 3.4 8.6 + - - +
88A ILE* 2.9 25.4 + - + +
90A GLU* 1.3 78.7 - - - +
92A TYR* 1.3 71.0 + - + +
94A SER* 3.3 5.5 + - - -
95A GLU* 3.0 31.6 + - + +
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Residues in contact with TYR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 3.9 21.1 - - + +
52A LEU* 3.6 22.4 - - + +
53A TYR* 3.5 44.9 - + + -
56A ASP* 2.4 38.2 + - - +
57A HIS* 3.4 10.6 - + - -
81A TRP* 4.0 8.3 - + + -
84A LEU* 5.0 0.7 - - + -
88A ILE* 3.5 23.7 + - + +
89A LYS 3.3 6.5 + - - +
91A LYS* 1.3 85.6 - - + +
93A ILE* 1.3 57.1 + - - +
95A GLU* 2.9 9.6 + - + +
96A ARG* 2.6 36.6 + - - +
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Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 3.6 22.4 - - + -
81A TRP* 4.0 15.5 - - + -
89A LYS* 3.1 21.3 - - + +
90A GLU* 3.3 18.1 + - + +
92A TYR* 1.3 75.0 - - - +
94A SER* 1.3 56.8 + - - +
96A ARG* 3.3 3.1 + - + +
97A LYS* 2.8 29.0 + - + +
16E T 5.8 6.5 - - - +
17E A 6.0 4.3 - - - +
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Residues in contact with SER 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLU 2.8 19.4 + - - -
91A LYS* 3.7 6.3 - - - -
93A ILE* 1.3 70.7 - - - +
95A GLU* 1.3 60.5 + - - +
97A LYS* 3.1 26.1 + - - +
98A LYS* 2.9 25.8 + - - +
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 4.1 18.6 - - + +
91A LYS* 3.0 19.3 + - + +
92A TYR* 2.9 15.1 + - + +
94A SER* 1.3 74.7 - - - +
96A ARG* 1.3 67.5 + - - +
98A LYS* 2.9 48.4 + - - +
99A LEU* 2.9 31.6 + - + +
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Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 5.0 6.1 - - - +
46A PRO* 4.3 15.2 + - + +
47A THR 3.2 29.9 + - - +
48A SER* 3.7 7.8 - - - +
49A ALA* 3.5 26.0 - - + +
52A LEU* 3.9 7.1 - - + +
92A TYR 2.6 19.7 + - - +
93A ILE* 3.5 5.2 - - + +
95A GLU* 1.3 73.4 - - - +
97A LYS* 1.3 59.1 + - - +
99A LEU* 3.3 6.4 + - + +
100A TYR* 2.9 59.1 + - - +
16E T 5.6 0.8 + - - -
17E A 3.5 54.9 + - - -
18E T 5.0 1.0 + - - -
7F A 5.3 4.8 + - - -
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 2.8 14.5 + - + +
94A SER* 3.4 28.0 + - - +
95A GLU 3.1 0.4 - - - -
96A ARG* 1.3 77.7 - - - +
98A LYS* 1.3 64.8 + - - +
100A TYR* 3.5 5.0 + - - +
101A SER* 3.2 27.3 + - - +
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Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A SER 2.9 11.3 + - - +
95A GLU* 2.9 42.9 + - - +
97A LYS* 1.3 82.3 - - - +
99A LEU* 1.3 69.2 + - + +
101A SER* 3.4 7.7 + - - -
102A GLU* 3.1 48.3 + - + +
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO* 3.9 22.0 - - + +
47A THR* 5.4 4.7 - - + +
52A LEU* 4.0 24.0 - - + -
95A GLU* 2.9 41.4 + - + +
96A ARG* 3.3 6.5 + - - +
98A LYS* 1.3 89.2 - - - +
100A TYR* 1.3 60.9 + - - +
102A GLU* 3.2 23.0 + - - +
103A TYR* 2.9 27.5 + - - +
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Residues in contact with TYR 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ARG* 4.9 5.4 - - - -
46A PRO* 3.7 27.5 - - + +
96A ARG* 2.9 41.7 + - - +
97A LYS* 4.1 5.2 - - - +
98A LYS 3.4 0.2 - - - -
99A LEU* 1.3 77.3 - - - +
101A SER* 1.3 58.7 + - - +
103A TYR* 3.3 17.0 + + - +
104A GLN* 2.8 60.6 + - + +
18E T 2.6 42.2 + - - -
19E A 2.4 36.3 + - - -
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Residues in contact with SER 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LYS* 3.2 18.7 + - - +
98A LYS* 3.6 9.9 - - - -
99A LEU 3.2 0.2 - - - -
100A TYR* 1.3 78.7 - - - +
102A GLU* 1.3 57.3 + - - +
104A GLN* 3.1 15.2 + - - +
105A LYS* 2.9 30.0 + - - +
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Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LYS* 3.1 43.4 + - + +
99A LEU* 3.2 21.6 + - - +
101A SER* 1.3 77.5 - - - +
103A TYR* 1.3 62.0 + - - +
105A LYS* 3.2 7.9 + - - +
106A ALA* 3.0 23.3 + - - +
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Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PRO* 3.3 33.1 + - + -
44A LYS 3.2 18.8 - - - +
45A ARG* 3.3 23.0 + - + +
46A PRO* 3.7 22.2 - - + -
99A LEU 2.9 13.7 + - - +
100A TYR* 3.5 27.4 - + - +
102A GLU* 1.3 74.6 - - - +
104A GLN* 1.3 69.2 + - + +
106A ALA* 3.2 6.6 + - - +
107A LYS* 3.0 47.3 + - + +
19E A 4.1 21.1 - - - -
20E T 4.1 7.8 + - - -
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Residues in contact with GLN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TYR* 2.8 52.6 + - + +
101A SER* 3.1 15.1 + - - +
103A TYR* 1.3 80.5 - - + +
105A LYS* 1.3 61.7 + - - +
107A LYS* 3.3 5.5 + - - +
108A LYS* 3.1 23.2 + - - +
19E A 4.1 11.6 + - - +
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Residues in contact with LYS 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A SER 2.9 16.0 + - - +
102A GLU* 3.7 6.5 - - - +
104A GLN* 1.3 75.9 - - - +
106A ALA* 1.3 61.6 + - - +
108A LYS* 3.6 8.3 + - + +
109A GLU* 3.2 55.9 + - + +
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Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO* 3.5 25.6 - - + -
102A GLU 3.0 14.1 + - - +
103A TYR* 3.5 9.9 - - - +
104A GLN 3.2 0.4 - - - -
105A LYS* 1.3 77.9 - - - +
107A LYS* 1.3 52.5 + - - +
109A GLU* 3.4 8.5 + - - +
110A PHE* 2.7 37.6 + - - +
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Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ILE* 5.7 7.3 - - - +
42A GLY* 6.0 0.7 - - - -
43A PRO* 4.0 20.3 - - + +
103A TYR* 3.0 39.6 + - + +
104A GLN* 3.7 7.0 - - - +
106A ALA* 1.3 76.3 - - - +
108A LYS* 1.3 53.3 + - - +
110A PHE* 4.3 4.0 - - + -
111A ASP* 2.5 85.2 + - - +
20E T 3.9 28.8 + - - -
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Residues in contact with LYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A GLN 3.1 14.1 + - - +
105A LYS* 3.8 8.5 - - + +
107A LYS* 1.3 78.3 - - - +
109A GLU* 1.3 64.9 + - + +
111A ASP* 3.9 3.2 - - - +
112A GLU* 2.9 73.3 + - - +
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Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LYS* 3.2 48.8 + - + +
106A ALA* 3.9 5.1 - - - +
108A LYS* 1.3 83.1 - - + +
110A PHE* 1.3 60.8 + - - +
112A GLU* 3.7 10.2 + - - +
113A LYS* 3.1 51.0 + - - +
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Residues in contact with PHE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.3 31.0 - - + -
39A ILE* 4.5 4.9 - - + -
41A GLN* 4.1 10.3 - - + -
42A GLY* 3.4 22.4 - - - -
43A PRO* 3.6 23.6 - - + -
106A ALA 2.7 22.8 + - - +
107A LYS* 3.7 2.5 - - + +
109A GLU* 1.3 72.4 - - - +
111A ASP* 1.3 77.7 + - - +
113A LYS* 3.0 20.1 + - + +
114A LEU* 3.3 28.7 + - + +
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Residues in contact with ASP 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 4.7 3.8 - - - +
107A LYS* 2.5 62.1 + - - +
108A LYS* 4.1 2.9 - - - +
110A PHE* 1.3 87.6 - - - +
112A GLU* 1.3 62.3 + - + +
114A LEU* 3.0 41.0 + - + +
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LYS* 2.9 60.4 + - + +
109A GLU* 4.0 8.2 - - - +
111A ASP* 1.3 76.5 - - - +
113A LYS* 1.3 61.0 + - + +
114A LEU 3.6 4.5 + - - +
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLU* 3.1 42.0 + - - +
110A PHE* 3.0 13.7 + - + +
112A GLU* 1.3 80.5 - - + +
114A LEU* 1.3 60.5 + - - +
115A PRO* 4.0 2.1 - - - +
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 3.1 33.4 - - + +
38A LEU* 4.7 10.1 - - + -
39A ILE* 3.4 34.1 - - + +
110A PHE* 3.3 19.6 + - + +
111A ASP* 3.0 47.8 + - + +
112A GLU 4.0 4.7 - - - +
113A LYS* 1.3 81.1 - - - +
115A PRO* 1.3 89.8 - - + +
116A PRO* 3.6 2.9 - - + +
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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