Contacts of the helix formed by residues 86 - 115 (chain Q) in PDB entry 6Y5D
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 GLN 86 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85Q PHE* 1.3 75.3 - - - +
87Q SER* 1.3 60.9 + - - +
88Q SER* 3.4 17.0 + - - +
89Q ALA* 2.9 20.8 + - - +
90Q VAL* 3.3 11.0 + - - +
81R THR* 4.1 12.0 - - + +
82R VAL 3.0 19.2 + - - +
83R THR* 3.2 21.5 - - - +
84R ALA* 3.0 24.4 + - - +
53V T 3.8 28.1 + - - +
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Residues in contact with SER 87 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69Q GLN* 5.2 10.1 - - - +
85Q PHE 3.7 1.6 + - - -
86Q GLN* 1.3 73.3 - - - +
88Q SER* 1.3 59.8 + - - +
90Q VAL* 3.3 10.4 + - - +
91Q MET* 3.1 32.6 + - - +
53V T 5.1 8.3 + - - -
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Residues in contact with SER 88 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86Q GLN* 3.4 22.9 + - - +
87Q SER* 1.3 82.0 + - - +
89Q ALA* 1.3 60.7 + - - +
90Q VAL 3.3 0.2 - - - -
91Q MET* 4.4 6.3 - - - -
92Q ALA* 2.9 29.8 + - - +
84R ALA* 3.4 14.6 - - - +
101R PHE* 3.7 12.4 - - - -
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Residues in contact with ALA 89 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85Q PHE* 4.4 9.2 - - + -
86Q GLN* 2.9 12.6 + - + +
88Q SER* 1.3 77.8 + - - +
90Q VAL* 1.3 65.9 + - - +
92Q ALA* 3.3 3.2 + - - +
93Q LEU* 3.0 29.3 + - - +
82R VAL 3.7 22.9 - - - +
83R THR 3.7 17.3 - - - +
84R ALA* 3.9 8.5 - - - +
87R VAL* 3.7 11.4 - - + +
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Residues in contact with VAL 90 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68Q PHE* 3.2 34.9 - - + -
69Q GLN* 3.8 41.7 - - + +
72Q VAL* 4.5 9.0 - - + -
73Q ARG* 5.7 1.3 - - - +
85Q PHE* 4.0 23.1 - - + -
86Q GLN 3.8 11.0 - - - +
87Q SER* 3.3 9.1 + - - +
89Q ALA* 1.3 76.9 - - - +
91Q MET* 1.3 68.9 + - + +
93Q LEU* 3.2 8.4 + - - +
94Q GLN* 2.9 23.9 + - - +
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Residues in contact with MET 91 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61Q LEU* 3.7 24.9 - - + -
65Q LYS* 3.9 32.8 - - + -
69Q GLN* 6.2 0.2 - - - +
87Q SER* 3.1 18.3 + - - +
88Q SER* 3.9 4.5 - - - +
89Q ALA 3.3 0.2 - - - -
90Q VAL* 1.3 90.1 - - + +
92Q ALA* 1.3 65.8 + - - +
94Q GLN* 3.0 24.2 + - - +
95Q GLU* 3.0 28.1 + - + +
101R PHE* 3.8 19.1 - - + -
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Residues in contact with ALA 92 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88Q SER 2.9 19.0 + - - +
89Q ALA* 3.6 6.3 - - - +
90Q VAL 3.3 0.2 - - - -
91Q MET* 1.3 76.3 - - - +
93Q LEU* 1.3 62.3 + - - +
95Q GLU* 3.6 0.3 + - - -
96Q ALA* 3.3 18.2 + - - +
84R ALA* 4.8 3.8 - - + +
87R VAL* 3.8 20.2 - - + -
88R VAL* 5.2 0.7 - - + -
91R LEU* 4.1 0.2 - - - +
98R LEU* 3.4 18.0 - - + +
101R PHE* 3.6 32.7 - - + -
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Residues in contact with LEU 93 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68Q PHE* 3.7 9.2 - - + -
72Q VAL* 3.7 35.9 - - + -
85Q PHE* 4.8 5.4 - - + -
89Q ALA 3.0 19.1 + - - +
90Q VAL* 3.4 9.2 - - - +
92Q ALA* 1.3 77.2 - - - +
94Q GLN* 1.3 53.5 + - - +
96Q ALA* 3.3 5.0 + - - +
97Q SER* 2.6 37.8 + - - -
62R PHE* 4.7 1.3 - - + -
63R LEU* 4.1 6.5 - - + -
66R VAL* 3.4 35.7 - - + -
67R ILE* 3.8 22.0 - - + +
87R VAL* 3.6 19.5 - - + -
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Residues in contact with GLN 94 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61Q LEU* 3.6 23.5 - - + +
63Q ILE* 2.6 34.2 + - + +
65Q LYS* 4.0 5.4 - - - +
68Q PHE* 3.3 43.9 - - + +
90Q VAL 2.9 9.3 + - - +
91Q MET* 3.0 30.1 + - - +
93Q LEU* 1.3 78.5 - - - +
95Q GLU* 1.3 56.8 + - - +
97Q SER* 3.2 1.1 + - - -
98Q GLU* 2.8 49.7 + - + +
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Residues in contact with GLU 95 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O THR* 4.7 3.7 - - + +
104O ALA* 2.9 35.1 - - - +
105O GLN* 3.1 32.1 + - - +
58P LYS* 5.4 2.8 + - - -
61Q LEU* 3.7 24.4 - - + +
91Q MET* 3.0 15.5 + - + +
92Q ALA 4.3 2.9 - - - +
94Q GLN* 1.3 77.1 - - - +
96Q ALA* 1.3 58.7 + - - +
98Q GLU* 3.4 4.0 + - - +
99Q ALA* 2.9 29.5 + - - +
98R LEU* 4.5 4.8 - - + +
101R PHE* 3.1 22.9 - - + -
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Residues in contact with ALA 96 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O THR* 4.7 9.2 - - + +
92Q ALA 3.3 8.8 + - - +
93Q LEU 3.8 2.9 - - - +
94Q GLN 3.3 0.2 - - - -
95Q GLU* 1.3 78.9 - - - +
97Q SER* 1.3 57.3 + - - +
99Q ALA* 3.4 6.2 + - - +
100Q TYR* 2.9 28.9 + - - +
62R PHE* 3.7 7.0 - - + -
91R LEU* 3.5 45.5 - - + -
96R ARG* 5.7 3.9 + - + -
98R LEU* 4.6 6.1 - - + +
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Residues in contact with SER 97 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q ILE* 5.4 1.1 - - - -
68Q PHE* 4.3 3.1 - - - -
93Q LEU 2.6 23.8 + - - -
94Q GLN* 3.5 8.1 - - - -
96Q ALA* 1.3 74.7 - - - +
98Q GLU* 1.3 65.7 + - - +
100Q TYR* 3.3 4.2 + - - +
101Q LEU* 3.0 29.3 + - - +
59R LEU* 3.7 22.1 - - - +
62R PHE* 3.4 18.0 - - - -
63R LEU* 3.1 24.4 - - - +
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Residues in contact with GLU 98 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60Q GLU 4.5 0.2 - - - +
61Q LEU* 3.3 25.3 - - - +
62Q LEU 2.7 30.8 + - - -
63Q ILE* 2.9 32.8 + - + +
94Q GLN* 2.8 25.6 + - + +
95Q GLU* 3.8 4.0 - - - +
97Q SER* 1.3 72.3 - - - +
99Q ALA* 1.3 68.6 + - - +
101Q LEU* 3.0 5.0 + - - +
102Q VAL* 2.8 30.6 + - + +
38R LEU* 3.7 18.6 - - + -
41R ARG* 4.4 11.2 + - - +
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Residues in contact with ALA 99 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O THR* 3.8 28.5 - - + +
95Q GLU 2.9 17.9 + - - +
96Q ALA 3.7 4.9 - - - +
97Q SER 3.3 0.2 - - - -
98Q GLU* 1.3 76.8 - - - +
100Q TYR* 1.3 57.6 + - - +
102Q VAL* 3.4 6.3 + - - +
103Q GLY* 3.0 25.6 + - - -
96R ARG* 5.9 0.7 - - - -
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Residues in contact with TYR 100 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96Q ALA 2.9 16.6 + - - +
97Q SER 3.4 4.7 - - - +
98Q GLU 3.1 0.2 - - - -
99Q ALA* 1.3 77.2 - - - +
101Q LEU* 1.3 68.7 + - + +
103Q GLY* 3.2 2.6 + - - -
104Q LEU* 2.9 39.7 + - + +
132Q ARG* 4.1 17.5 + - - -
134Q GLU* 2.9 30.9 + - - -
58R VAL* 3.6 29.6 - - + +
62R PHE* 3.5 40.4 - + + -
96R ARG* 3.3 37.7 - - - +
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Residues in contact with LEU 101 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q ILE* 4.5 3.6 - - + -
97Q SER 3.0 18.1 + - - +
98Q GLU 3.0 4.7 + - - +
100Q TYR* 1.3 91.8 - - + +
102Q VAL* 1.3 58.4 + - - +
104Q LEU* 3.2 11.2 + - + +
105Q PHE* 2.8 41.0 + - + -
30R ILE* 6.5 0.2 - - + -
38R LEU* 3.6 30.7 - - + -
55R THR* 4.1 23.1 - - + +
58R VAL* 4.2 18.6 - - + -
59R LEU* 4.0 38.6 - - + +
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Residues in contact with VAL 102 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108O VAL* 4.4 15.5 - - + -
98Q GLU* 2.8 23.2 + - + +
99Q ALA* 3.8 6.7 - - - +
101Q LEU* 1.3 77.2 - - - +
103Q GLY* 1.3 57.0 + - - +
105Q PHE* 3.0 9.3 + - - +
106Q GLU* 2.8 33.4 + - - +
38R LEU* 3.6 32.1 - - + +
41R ARG* 4.0 26.9 - - + +
42R GLY* 3.7 22.7 - - - +
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Residues in contact with GLY 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99Q ALA 3.0 15.7 + - - -
100Q TYR* 3.7 3.6 - - - -
102Q VAL* 1.3 75.7 - - - +
104Q LEU* 1.3 60.8 + - - +
106Q GLU* 3.2 19.0 + - - +
107Q ASP* 3.2 26.6 + - - +
132Q ARG* 4.4 5.8 - - - -
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Residues in contact with LEU 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100Q TYR* 2.9 25.8 + - + +
101Q LEU* 3.4 16.6 - - + +
103Q GLY* 1.3 76.6 - - - +
105Q PHE* 1.3 56.4 + - + +
107Q ASP* 3.2 4.0 + - - +
108Q THR* 2.7 41.9 + - - +
125Q ILE* 4.0 38.6 - - + +
128Q ALA* 4.4 6.7 - - + -
129Q ARG* 4.9 9.0 - - + +
132Q ARG* 3.6 24.8 - - - +
134Q GLU* 5.7 0.7 - - - +
55R THR* 6.4 1.1 - - - -
58R VAL* 3.9 29.8 - - + -
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Residues in contact with PHE 105 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101Q LEU* 2.8 33.8 + - + -
102Q VAL* 3.4 7.4 - - - +
104Q LEU* 1.3 78.1 - - + +
106Q GLU* 1.3 60.1 + - - +
108Q THR* 3.4 8.0 - - - -
109Q ASN* 2.7 32.2 + - - +
120Q ILE* 3.6 33.2 - - + -
125Q ILE* 4.7 8.1 - - + -
35R ILE* 4.0 10.8 - - + -
38R LEU* 3.9 13.9 - - + -
39R ALA* 3.6 37.2 - - + +
42R GLY* 4.3 1.6 - - - -
44R VAL* 3.7 11.8 - - + +
51R ILE* 3.9 10.5 - - + -
55R THR* 3.5 33.9 - - + -
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Residues in contact with GLU 106 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M ARG* 4.8 15.1 + - - +
108O VAL* 4.5 15.2 - - - +
56Q GLN* 5.9 0.5 + - - -
102Q VAL* 2.8 26.3 + - - +
103Q GLY* 3.2 17.8 + - - +
105Q PHE* 1.3 77.0 - - - +
107Q ASP* 1.3 60.9 + - - +
109Q ASN* 3.3 3.5 + - - +
110Q LEU* 3.1 33.5 + - + +
41R ARG 4.9 0.9 - - - +
42R GLY* 3.2 30.3 - - - +
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Residues in contact with ASP 107 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M ARG* 4.3 10.6 + - - -
131M ILE* 3.3 44.3 - - + +
103Q GLY 3.2 8.6 + - - +
104Q LEU 3.6 7.0 - - - +
106Q GLU* 1.3 77.2 - - - +
108Q THR* 1.3 66.8 + - - +
110Q LEU* 3.2 15.6 + - - +
111Q ALA* 3.0 22.7 + - - +
128Q ALA* 3.7 20.5 - - + +
132Q ARG* 3.2 24.3 + - - +
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Residues in contact with THR 108 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104Q LEU* 2.7 28.0 + - - +
105Q PHE* 3.4 10.6 - - - -
107Q ASP* 1.3 77.6 - - - +
109Q ASN* 1.3 60.9 + - - +
111Q ALA* 3.2 4.2 + - - +
112Q ALA* 3.1 19.9 + - - +
120Q ILE* 3.6 25.1 - - + -
121Q MET 4.4 0.2 - - - +
124Q ASP* 3.5 32.4 - - + +
125Q ILE* 3.4 37.1 - - + +
128Q ALA* 4.4 0.5 - - - +
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Residues in contact with ASN 109 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113O GLN* 4.3 7.1 - - - +
116O LEU* 3.8 9.5 - - - +
105Q PHE 2.7 21.0 + - - +
106Q GLU* 3.5 7.0 - - - +
107Q ASP 3.2 0.2 - - - -
108Q THR* 1.3 73.7 - - - +
110Q LEU* 1.3 62.7 + - - +
112Q ALA* 3.2 4.5 + - - +
113Q ILE* 3.0 49.7 + - - +
118Q VAL 4.3 6.9 - - - +
120Q ILE* 3.8 14.0 - - - +
42R GLY 4.5 1.2 + - - +
43R GLY* 3.0 32.6 + - - +
44R VAL* 3.5 17.3 - - + -
45R LYS 4.1 3.6 + - - -
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Residues in contact with LEU 110 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127M LEU* 3.7 24.1 - - + +
130M ARG* 4.1 34.8 - - + +
131M ILE* 4.9 1.3 - - + -
113O GLN* 4.1 34.1 - - + +
106Q GLU* 3.1 21.2 + - + +
107Q ASP* 3.5 19.5 - - - +
109Q ASN* 1.3 78.6 - - - +
111Q ALA* 1.3 57.1 + - - +
113Q ILE* 3.2 9.1 + - + +
114Q HIS* 2.8 30.8 + - - +
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Residues in contact with ALA 111 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M HIS* 3.4 21.0 - - - +
127M LEU* 4.7 6.0 - - - +
131M ILE* 5.2 3.6 - - + -
107Q ASP 3.0 12.5 + - - +
108Q THR 3.2 8.9 + - - +
110Q LEU* 1.3 77.6 - - - +
112Q ALA* 1.3 62.1 + - - +
114Q HIS* 3.2 7.9 + - - +
115Q ALA 3.1 17.5 + - - -
124Q ASP* 3.4 23.6 - - - +
127Q LEU* 3.9 18.2 - - + -
128Q ALA 5.4 0.4 - - - +
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Residues in contact with ALA 112 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108Q THR 3.1 11.4 + - - +
109Q ASN* 3.6 7.6 - - - +
111Q ALA* 1.3 76.0 - - - +
113Q ILE* 1.3 56.3 + - + +
115Q ALA* 3.2 8.1 + - - +
116Q LYS 3.3 0.2 + - - -
117Q ARG* 2.7 46.8 + - - +
118Q VAL 4.7 2.7 - - - +
119Q THR 3.7 24.5 - - - +
120Q ILE* 4.2 9.2 - - + -
124Q ASP* 3.1 16.5 + - - +
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Residues in contact with ILE 113 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113O GLN* 3.5 35.2 - - + +
115O VAL* 3.7 34.3 - - + +
116O LEU* 4.6 5.4 - - + -
109Q ASN* 3.0 40.9 + - - +
110Q LEU* 3.5 13.5 - - + +
112Q ALA* 1.3 74.5 - - + +
114Q HIS* 1.3 58.9 + - - +
116Q LYS* 2.7 25.7 + - - +
117Q ARG 3.6 12.3 - - - +
118Q VAL 6.1 0.2 - - - +
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Residues in contact with HIS 114 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111M ALA* 3.4 20.3 + - - +
114M HIS* 5.3 3.4 - + + -
115M ALA* 3.7 16.1 - - + +
117M ARG* 3.6 4.9 + - - -
123M LYS* 3.8 40.9 + - + +
124M ASP* 2.5 38.9 + - - -
127M LEU* 3.5 30.5 - - + +
110Q LEU 2.8 17.0 + - - +
111Q ALA* 3.4 10.1 - - - +
113Q ILE* 1.3 74.7 - - - +
115Q ALA* 1.3 57.3 + - - +
116Q LYS* 3.3 8.5 + - - +
127Q LEU* 5.9 0.2 - - + -
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Residues in contact with ALA 115 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M HIS* 4.1 20.9 - - + +
115M ALA* 4.4 10.1 - - - +
111Q ALA 3.1 8.5 + - - +
112Q ALA 3.5 8.5 - - - +
113Q ILE 3.1 1.0 - - - -
114Q HIS* 1.3 74.4 - - - +
116Q LYS* 1.3 70.6 + - - +
117Q ARG* 3.4 34.5 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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