Contacts of the helix formed by residues 70 - 96 (chain B) in PDB entry 5YWB
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 GLY 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO* 1.3 73.4 - - - +
71B HIS* 1.3 55.1 + - - +
72B ASN 3.4 2.5 - - - -
73B LEU* 3.5 15.7 - - - +
74B ARG* 2.6 38.1 + - - +
124B TYR* 5.1 1.1 - - - -
185B VAL* 4.1 14.3 - - - +
188B ASN* 5.1 3.0 - - - +
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Residues in contact with HIS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B HIS* 4.0 29.1 + + + +
68B PHE* 3.2 23.6 + - - +
69B PRO 3.3 0.6 + - - -
70B GLY* 1.3 75.6 - - - +
72B ASN* 1.3 72.3 + - - +
74B ARG* 3.0 7.4 + - - +
75B TRP* 2.9 62.8 + + - -
124B TYR* 3.1 31.2 + + + -
128B GLU* 4.6 12.7 - - + +
223B ASN* 4.0 9.4 - - + -
224B LEU* 3.4 22.5 + - + -
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Residues in contact with ASN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLY 3.4 0.2 - - - -
71B HIS* 1.3 89.2 - - - +
73B LEU* 1.3 61.6 + - - +
75B TRP* 3.3 1.6 + - - +
76B ILE* 2.9 43.1 + - + +
224B LEU* 4.4 12.9 - - + +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLY* 3.2 16.2 + - - +
72B ASN* 1.3 76.9 - - - +
74B ARG* 1.3 64.1 + - - +
76B ILE* 4.5 13.7 - - + -
77B LEU* 2.9 53.0 + - + +
181B MET* 5.6 11.2 - - + -
185B VAL* 3.8 22.0 - - + -
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLY 2.6 21.9 + - - +
71B HIS* 3.3 6.7 - - - +
73B LEU* 1.3 74.5 - - - +
75B TRP* 1.3 61.2 + - + +
77B LEU* 3.4 2.9 + - - +
78B THR* 2.8 37.2 + - - +
120B SER* 5.3 4.9 + - - +
124B TYR* 3.3 55.9 + - - -
136B LEU* 6.0 0.2 - - - +
139B LEU* 4.8 3.4 - - - +
143B TRP* 4.1 10.9 - - + +
182B LEU* 4.0 26.4 + - + +
185B VAL* 3.3 29.0 - - + +
186B GLU* 2.8 43.3 + - - +
189B VAL* 4.2 10.1 - - - +
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Residues in contact with TRP 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B HIS* 2.9 58.4 + + - +
72B ASN 3.3 1.7 + - - +
74B ARG* 1.3 79.4 - - + +
76B ILE* 1.3 67.2 + - + +
78B THR* 3.1 5.8 + - + -
79B PHE* 2.9 50.0 + + + -
121B VAL* 3.7 46.9 - - + -
124B TYR* 4.2 11.7 - + + +
125B HIS* 5.4 10.5 - - + -
223B ASN* 4.5 15.3 - - + -
224B LEU* 3.2 23.8 - - + -
225B LEU* 2.9 36.3 - - + -
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Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASN* 2.9 32.1 + - + +
73B LEU* 3.8 13.9 - - + +
75B TRP* 1.3 76.2 - - + +
77B LEU* 1.3 65.7 + - + +
79B PHE* 3.1 9.4 + - - +
80B ILE* 3.0 41.3 + - + +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 2.9 46.3 + - + +
74B ARG 3.8 3.6 - - - +
76B ILE* 1.3 76.0 - - + +
78B THR* 1.3 57.5 + - - +
80B ILE* 3.2 22.0 + - + +
81B LEU* 2.9 33.1 + - - +
178B LEU* 4.0 19.2 - - + +
181B MET* 3.9 37.7 - - + +
182B LEU* 4.0 31.0 - - + +
185B VAL* 4.6 2.2 - - + -
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Residues in contact with THR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ARG* 2.8 31.1 + - - +
75B TRP* 3.1 9.8 + - + -
77B LEU* 1.3 76.0 - - - +
79B PHE* 1.3 60.3 + - + +
81B LEU* 3.2 13.2 + - + +
82B LEU* 2.9 26.4 + - + +
117B ALA* 4.4 20.3 - - + +
120B SER* 5.4 4.0 + - - +
121B VAL* 3.6 31.5 - - + +
143B TRP* 6.0 1.2 - - - -
182B LEU* 4.6 5.5 - - - +
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TRP* 2.9 55.4 + + + -
76B ILE* 3.1 8.3 + - - +
78B THR* 1.3 75.4 - - + +
80B ILE* 1.3 66.4 + - + +
82B LEU* 3.2 28.8 + - + +
83B PHE* 3.0 21.8 + - - +
225B LEU* 4.2 19.1 - - + -
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 3.0 34.2 + - + +
77B LEU* 3.2 24.2 + - + +
79B PHE* 1.3 76.5 - - + +
81B LEU* 1.3 56.7 + - - +
83B PHE* 3.2 9.6 + - + +
84B VAL* 3.0 39.4 + - + +
178B LEU* 3.8 24.9 - - + -
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU 2.9 16.4 + - - +
78B THR* 3.4 14.4 - - + +
80B ILE* 1.3 74.2 - - - +
82B LEU* 1.3 65.9 + - - +
84B VAL* 3.3 2.0 + - - +
85B LEU* 2.9 35.7 + - + +
117B ALA* 4.7 19.1 - - + -
143B TRP* 4.3 14.4 - - + -
175B LEU* 4.3 20.0 - - + -
178B LEU* 3.7 30.7 - - + -
179B TYR* 4.6 11.9 - - + +
182B LEU* 3.5 29.4 - - + -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B THR* 2.9 13.0 + - + +
79B PHE* 3.2 34.5 + - + +
81B LEU* 1.3 77.0 - - - +
83B PHE* 1.3 62.4 + - - +
85B LEU* 3.2 9.5 + - - +
86B VAL* 3.0 32.6 + - + +
114B PHE* 3.4 34.3 - - + -
117B ALA* 5.8 1.7 - - - +
118B ILE* 5.5 6.5 - - + -
364B LEU* 5.9 6.7 - - + -
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Residues in contact with PHE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE 3.0 12.7 + - - +
80B ILE* 3.5 13.0 - - + +
81B LEU 3.2 0.2 - - - -
82B LEU* 1.3 76.9 - - - +
84B VAL* 1.3 74.8 + - + +
86B VAL* 3.1 12.6 + - + +
87B CYS* 3.0 45.9 + - - -
361B LEU* 4.8 20.6 - - + -
364B LEU* 3.8 35.2 - - + -
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 3.0 21.0 + - + +
81B LEU* 4.0 5.6 - - - +
83B PHE* 1.3 87.4 - - + +
85B LEU* 1.3 58.6 + - - +
87B CYS* 3.2 8.3 + - - +
88B GLU* 2.9 26.3 + - + +
171B LEU* 3.8 36.1 - - + +
174B LEU* 4.8 13.9 - - + -
175B LEU* 4.1 20.9 - - + +
178B LEU* 3.9 19.1 - - + -
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 2.9 28.8 + - + +
82B LEU* 3.6 7.4 - - - +
83B PHE 3.1 0.2 - - - -
84B VAL* 1.3 74.5 - - - +
86B VAL* 1.3 66.3 + - - +
88B GLU* 3.2 25.4 + - - +
89B ILE* 2.9 31.0 + - + +
110B ALA* 4.0 11.8 - - - +
113B ALA* 3.5 46.0 - - + +
114B PHE* 3.5 22.9 - - + +
117B ALA* 4.6 9.4 - - + -
175B LEU* 4.7 13.0 - - + -
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 3.0 26.7 + - + +
83B PHE* 3.4 11.4 - - + +
85B LEU* 1.3 76.8 - - + +
87B CYS* 1.3 62.3 + - - +
89B ILE* 3.2 13.9 + - + +
90B ALA* 3.0 21.9 + - + +
114B PHE* 5.6 6.3 - - + -
360B VAL* 3.9 28.7 - - + -
361B LEU* 4.8 12.1 - - + -
364B LEU* 5.2 11.4 - - + -
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Residues in contact with CYS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 3.0 49.9 + - - -
84B VAL* 3.2 8.9 + - - +
86B VAL* 1.3 77.9 - - - +
88B GLU* 1.3 56.9 + - - +
90B ALA* 3.1 10.4 + - - +
91B GLU* 3.0 24.3 + - - +
171B LEU* 3.4 31.3 - - + +
357B VAL* 6.3 1.6 - - - -
361B LEU* 5.4 9.6 - - - -
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B VAL* 2.9 16.2 + - + +
85B LEU* 3.2 31.7 + - - +
87B CYS* 1.3 75.5 - - - +
89B ILE* 1.3 58.9 + - - +
91B GLU* 3.1 10.4 + - - +
92B GLY* 2.9 24.3 + - - -
107B TYR* 5.4 1.0 - - - +
109B PRO* 4.9 2.4 - - - +
110B ALA* 3.6 22.2 + - + +
113B ALA* 5.3 0.3 - - - +
150B LYS* 3.6 7.4 + - - -
168B ARG* 4.9 9.9 + - - +
171B LEU* 3.5 21.4 - - + +
172B THR* 4.8 9.2 - - - +
175B LEU* 2.8 32.9 - - - +
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Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU 2.9 22.6 + - - +
86B VAL* 3.2 13.2 + - + +
88B GLU* 1.3 74.6 - - - +
90B ALA* 1.3 63.4 + - - +
92B GLY* 3.2 2.7 + - - +
93B ILE* 2.9 34.6 + - + +
107B TYR* 5.6 11.5 - - + +
110B ALA* 3.8 20.4 - - + +
111B GLY* 4.7 10.3 - - - +
114B PHE* 5.3 14.6 - - + -
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B VAL* 3.0 14.6 + - + +
87B CYS* 3.1 13.7 + - - +
89B ILE* 1.3 77.2 - - - +
91B GLU* 1.3 61.4 + - - +
93B ILE* 3.2 8.4 + - - +
94B LEU* 2.9 32.6 + - + +
357B VAL* 4.4 26.2 - - + -
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Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B CYS 3.0 7.9 + - - +
88B GLU* 3.4 11.5 - - - +
90B ALA* 1.3 77.6 - - - +
92B GLY* 1.3 57.6 + - - +
94B LEU* 3.1 10.5 + - + +
95B SER* 2.9 29.3 + - - -
167B LEU* 3.0 60.7 - - + +
168B ARG* 2.9 44.4 + - - +
171B LEU* 3.6 25.6 - - + +
172B THR* 6.0 0.2 - - - +
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Residues in contact with GLY 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLU 2.9 12.0 + - - -
89B ILE 3.2 3.3 + - - -
91B GLU* 1.3 76.9 - - - +
93B ILE* 1.3 63.7 + - - +
95B SER* 4.1 5.8 - - - -
96B ASP* 3.2 25.5 + - - +
106B LEU 5.7 0.9 - - - -
107B TYR* 3.5 34.5 - - - -
168B ARG* 4.7 4.4 - - - +
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 2.9 29.9 + - + +
90B ALA* 3.6 9.9 - - - +
92B GLY* 1.3 78.3 - - - +
94B LEU* 1.3 71.1 + - + +
95B SER 3.4 0.3 + - - -
96B ASP* 3.6 14.9 + - + +
107B TYR* 5.4 14.1 - - + -
356B TYR* 6.1 4.9 - - + -
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ALA* 2.9 22.5 + - + +
91B GLU* 3.5 13.7 - - + +
93B ILE* 1.3 82.3 - - + +
95B SER* 1.3 63.2 + - - +
96B ASP 4.6 1.6 - - - -
167B LEU* 4.8 17.9 - - + -
354B ASN* 4.8 26.2 - - - +
357B VAL* 6.4 1.1 - - + -
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLU 2.9 16.1 + - - -
92B GLY* 4.1 6.1 - - - -
93B ILE 3.2 0.2 - - - -
94B LEU* 1.3 80.6 - - - +
96B ASP* 1.3 64.4 + - - +
103B HIS* 5.8 4.4 - - - +
106B LEU* 5.0 15.2 - - - +
168B ARG* 5.9 2.9 - - - -
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Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLY 3.2 16.2 + - - +
93B ILE* 3.6 12.1 + - + +
94B LEU 3.5 1.9 - - - -
95B SER* 1.3 85.2 - - - +
103B HIS* 4.8 34.2 - - + +
107B TYR* 4.9 9.9 - - + -
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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