Contacts of the helix formed by residues 85 - 113 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J ASN 3.6 3.3 + - - +
84J LEU* 1.3 85.1 - - - +
86J ALA* 1.3 65.2 + - - +
87J ASP* 3.2 18.8 - - - +
88J ILE* 3.0 33.4 + - + +
89J LYS* 3.0 18.7 + - - +
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Residues in contact with ALA 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84J LEU 3.3 5.0 + - - -
85J GLU* 1.3 72.7 - - - +
87J ASP* 1.3 62.8 + - - +
89J LYS* 3.1 12.4 + - + +
90J GLU* 3.0 37.2 + - + +
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Residues in contact with ASP 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85J GLU* 3.2 23.1 - - - +
86J ALA* 1.3 75.4 + - - +
88J ILE* 1.3 67.5 + - - +
90J GLU* 3.6 13.2 + - - +
91J LYS* 3.6 9.9 + - - +
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Residues in contact with ILE 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J TYR* 5.3 1.1 - - + -
57J HIS* 6.1 1.1 - - - +
84J LEU* 3.7 25.4 - - + -
85J GLU* 3.0 40.2 + - + +
87J ASP* 1.3 82.9 - - - +
89J LYS* 1.3 68.2 + - - +
91J LYS* 3.0 24.9 + - - +
92J TYR* 3.5 21.6 + - + -
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Residues in contact with LYS 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H T 4.7 5.2 + - - -
81J TRP* 3.1 56.3 + - + +
82J GLN* 4.0 16.5 + - - +
84J LEU* 3.6 38.6 - - + +
85J GLU 3.0 16.0 + - - +
86J ALA* 3.1 13.0 + - + +
88J ILE* 1.3 76.4 - - - +
90J GLU* 1.3 59.2 + - - +
92J TYR* 3.0 5.5 + - - +
93J ILE* 2.8 41.4 + - + +
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Residues in contact with GLU 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86J ALA* 3.0 30.0 + - + +
87J ASP* 3.9 8.5 - - - +
88J ILE 3.1 0.4 - - - -
89J LYS* 1.3 79.2 - - - +
91J LYS* 1.3 55.9 + - - +
93J ILE* 4.0 26.1 - - - +
94J SER* 2.5 39.6 + - - -
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Residues in contact with LYS 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J ASP* 4.5 3.2 + - - -
87J ASP 3.6 7.9 + - - +
88J ILE* 3.0 14.5 + - - +
90J GLU* 1.3 77.2 - - - +
92J TYR* 1.3 94.0 + - - +
94J SER* 4.1 4.7 - - - -
95J GLU* 3.0 39.8 + - + +
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Residues in contact with TYR 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J ALA* 3.9 14.1 - - - +
52J LEU* 3.5 19.2 - - + +
53J TYR* 3.4 50.3 - + + -
56J ASP* 2.3 40.1 + - - +
57J HIS* 3.8 10.8 - + - -
81J TRP* 4.2 11.9 - + + -
88J ILE* 3.5 28.9 + - + -
89J LYS 3.0 6.7 + - - +
91J LYS* 1.3 98.9 + - - +
93J ILE* 1.3 56.9 + - - +
95J GLU* 3.4 11.7 + - - +
96J ARG* 2.7 35.0 + - - +
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Residues in contact with ILE 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H A 6.2 0.4 - - - +
49J ALA* 4.0 19.1 - - + -
81J TRP* 4.5 10.1 - - + -
89J LYS* 2.8 29.0 + - + +
90J GLU* 3.7 28.7 - - - +
92J TYR* 1.3 73.7 - - - +
94J SER* 1.3 55.3 + - - +
96J ARG* 3.2 3.8 + - + +
97J LYS* 2.6 42.1 + - + +
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Residues in contact with SER 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J GLU* 2.5 24.5 + - - -
91J LYS* 4.1 4.3 - - - -
93J ILE* 1.3 72.9 - - - +
95J GLU* 1.3 61.0 + - - +
97J LYS* 3.4 21.1 + - - +
98J LYS* 2.8 55.1 + - - +
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Residues in contact with GLU 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J LEU* 3.8 30.0 - - + +
91J LYS* 3.0 37.6 + - + +
92J TYR* 3.6 10.5 - - - +
94J SER* 1.3 75.9 + - - +
96J ARG* 1.3 62.5 + - - +
98J LYS* 3.1 13.3 + - - +
99J LEU* 3.1 34.8 + - + +
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Residues in contact with ARG 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H T 5.1 1.6 + - - -
17H A 3.9 45.9 + - - -
7I A 5.7 1.2 - - - -
45J ARG* 4.5 2.0 - - - +
46J PRO* 4.3 8.6 + - - +
47J THR 2.8 25.4 + - - -
48J SER* 3.1 27.9 - - - +
49J ALA* 3.8 18.9 - - + +
52J LEU* 4.0 6.9 - - + +
92J TYR 2.7 22.2 + - - +
93J ILE* 3.6 4.9 - - + +
95J GLU* 1.3 75.3 - - - +
97J LYS* 1.3 65.3 + - - +
99J LEU* 3.2 11.6 + - - +
100J TYR* 3.0 63.1 + - - +
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Residues in contact with LYS 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93J ILE* 2.6 25.2 + - + +
94J SER* 3.6 24.8 + - - +
95J GLU 3.3 0.2 - - - -
96J ARG* 1.3 75.7 - - - +
98J LYS* 1.3 69.6 + - - +
100J TYR* 3.6 5.7 + - - +
101J SER* 3.2 25.9 + - - +
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Residues in contact with LYS 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J SER* 2.8 41.9 + - - +
95J GLU* 3.7 9.7 - - - +
96J ARG 3.1 0.4 - - - -
97J LYS* 1.3 84.7 - - - +
99J LEU* 1.3 67.4 + - + +
101J SER* 3.5 6.1 + - - -
102J GLU* 3.0 33.8 + - + +
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Residues in contact with LEU 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J PRO* 3.9 23.6 - - + +
47J THR* 5.3 2.2 - - - +
52J LEU* 4.1 24.5 - - + -
95J GLU* 3.1 26.7 + - + +
96J ARG* 3.6 15.0 - - - +
98J LYS* 1.3 74.8 - - + +
100J TYR* 1.3 59.9 + - - +
102J GLU* 3.1 20.8 + - - +
103J TYR* 2.7 28.2 + - - +
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Residues in contact with TYR 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H A 5.7 0.4 - - - -
18H T 2.9 51.8 + - - -
19H A 3.0 21.8 + - - -
45J ARG* 3.7 17.0 + - - -
46J PRO* 3.4 29.1 - - + +
96J ARG* 3.0 46.3 + - - +
97J LYS* 4.0 6.1 - - - +
99J LEU* 1.3 75.9 - - - +
101J SER* 1.3 52.4 + - - +
103J TYR* 2.9 14.7 + + - +
104J GLN* 2.7 67.5 + - - +
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Residues in contact with SER 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J LYS* 3.2 18.0 + - - +
98J LYS* 3.8 5.8 - - - -
100J TYR* 1.3 77.5 - - - +
102J GLU* 1.3 59.4 + - - +
104J GLN* 3.6 22.1 + - - +
105J LYS* 2.9 30.8 + - - +
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Residues in contact with GLU 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98J LYS* 3.0 25.0 + - + +
99J LEU* 3.4 25.5 - - - +
101J SER* 1.3 76.9 - - - +
103J TYR* 1.3 56.8 + - - +
105J LYS* 4.0 13.1 - - - +
106J ALA* 3.0 28.6 + - - +
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Residues in contact with TYR 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H A 4.2 24.7 + - - -
20H T 4.7 1.2 + - - -
43J PRO* 2.9 34.3 + - + -
44J LYS 3.1 21.8 - - - +
45J ARG* 3.6 21.5 + - + +
46J PRO* 3.5 28.0 - - + -
99J LEU 2.7 12.3 + - - +
100J TYR* 2.9 29.7 + + - +
102J GLU* 1.3 73.6 - - - +
104J GLN* 1.3 68.0 + - + +
106J ALA* 2.9 6.7 + - - +
107J LYS* 2.6 59.4 + - + +
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Residues in contact with GLN 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H T 5.6 1.9 + - - -
19H A 3.6 9.6 + - - +
100J TYR* 2.7 51.0 + - + +
101J SER* 3.6 23.5 + - - +
103J TYR* 1.3 84.1 - - + +
105J LYS* 1.3 63.6 + - - +
107J LYS* 3.8 7.3 - - - +
108J LYS* 3.1 22.9 + - - +
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Residues in contact with LYS 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101J SER 2.9 19.0 + - - +
102J GLU* 4.0 11.5 - - - +
104J GLN* 1.3 76.2 - - - +
106J ALA* 1.3 66.3 + - - +
108J LYS* 3.4 12.6 + - - +
109J GLU* 3.3 46.6 + - + +
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Residues in contact with ALA 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J PRO* 4.2 15.3 - - + -
102J GLU 3.0 19.8 + - - +
103J TYR* 2.9 7.2 + - - +
105J LYS* 1.3 76.1 - - - +
107J LYS* 1.3 65.8 + - - +
109J GLU* 3.2 13.3 + - - +
110J PHE* 2.9 24.1 + - - +
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Residues in contact with LYS 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H A 5.0 3.1 - - - -
20H T 3.1 36.6 + - - -
39J ILE* 5.1 11.7 - - - +
43J PRO* 3.9 19.4 + - + +
103J TYR* 2.6 47.3 + - + +
104J GLN* 3.8 10.5 - - + +
106J ALA* 1.3 73.2 - - - +
108J LYS* 1.3 55.7 + - - +
110J PHE* 3.6 1.4 - - + +
111J ASP* 2.7 70.1 + - - +
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Residues in contact with LYS 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104J GLN 3.1 18.5 + - - +
105J LYS* 3.7 12.1 - - - +
106J ALA 3.3 0.2 - - - -
107J LYS* 1.3 77.0 - - - +
109J GLU* 1.3 78.4 + - - +
111J ASP* 3.7 5.6 - - - +
112J GLU* 2.9 65.9 + - + +
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Residues in contact with GLU 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J LYS* 3.3 45.9 + - - +
106J ALA* 3.2 11.4 + - - +
108J LYS* 1.3 89.6 - - - +
110J PHE* 1.3 66.9 + - - +
112J GLU* 3.4 10.1 + - - +
113J LYS* 3.2 33.4 + - + +
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Residues in contact with PHE 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38J LEU* 3.4 24.2 - - + -
39J ILE* 4.6 5.4 - - + -
41J GLN* 4.2 8.3 - - + -
42J GLY* 3.4 27.8 - - - -
43J PRO* 3.7 23.8 - - + -
106J ALA 2.9 15.7 + - - +
107J LYS* 3.6 3.4 - - + +
109J GLU* 1.3 76.6 - - - +
111J ASP* 1.3 78.9 + - - +
113J LYS* 3.0 36.5 + - + +
114J LEU* 3.4 34.9 + - + +
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Residues in contact with ASP 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J ARG* 5.6 0.5 + - - -
39J ILE* 6.0 1.0 - - - +
107J LYS* 2.7 59.7 + - - +
108J LYS* 3.8 5.2 - - - +
110J PHE* 1.3 89.3 - - - +
112J GLU* 1.3 62.9 + - + +
114J LEU* 3.1 34.0 + - + +
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Residues in contact with GLU 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J LYS* 2.9 53.8 + - + +
109J GLU* 3.8 7.8 - - - +
110J PHE 3.2 0.4 - - - -
111J ASP* 1.3 75.8 - - - +
113J LYS* 1.3 62.7 + - + +
114J LEU 3.1 5.9 + - - +
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Residues in contact with LYS 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J GLU* 3.2 23.1 + - + +
110J PHE* 3.0 28.9 + - - +
112J GLU* 1.3 75.4 - - + +
114J LEU* 1.3 64.0 + - - +
115J PRO* 4.6 0.5 - - - +
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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
------------------------------------------------------------
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