Contacts of the helix formed by residues 77 - 106 (chain U) in PDB entry 3A68
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 LEU 77 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190N ARG* 3.5 53.4 - - - +
70U PHE* 3.5 36.7 + - + +
75U VAL* 3.3 1.3 - - + +
76U ALA* 1.3 79.6 - - - +
78U ARG* 1.3 60.4 + - - +
79U GLY 3.3 3.3 + - - -
80U LEU* 3.4 4.2 + - + -
81U ALA* 3.0 26.9 + - - +
128U ASP* 3.9 10.5 - - - +
129U ALA* 4.2 13.5 - - + -
197U VAL* 4.2 6.1 - - + -
198U TRP* 4.4 8.7 - - + -
201U ASP* 3.3 30.1 - - + +
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Residues in contact with ARG 78 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183N GLU* 4.6 25.1 - - - +
184N TYR* 6.2 2.2 - - - -
187N GLN* 3.1 36.1 + - - +
203N MET* 3.7 23.2 - - - +
207N GLU* 5.3 8.7 + - - +
70U PHE 5.2 0.4 - - - -
76U ALA* 3.6 9.3 + - + -
77U LEU* 1.3 70.3 - - - +
79U GLY* 1.3 59.9 + - - +
81U ALA* 3.7 7.5 - - - +
82U LYS* 2.9 31.0 + - - +
201U ASP* 3.2 5.0 + - - +
202U GLN* 3.1 22.8 + - - -
205U LEU* 3.8 27.9 - - + +
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Residues in contact with GLY 79 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78U ARG* 1.3 76.4 - - - +
80U LEU* 1.3 57.7 + - - -
82U LYS* 3.3 3.9 + - - +
83U PHE* 2.9 28.4 + - - +
201U ASP* 2.8 31.3 + - - -
204U LEU* 3.9 11.3 - - - +
205U LEU* 3.7 21.1 - - - +
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Residues in contact with LEU 80 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70U PHE* 3.8 40.4 - - + -
77U LEU* 3.9 7.0 - - + +
78U ARG 3.4 0.2 - - - -
79U GLY* 1.3 68.3 - - - +
81U ALA* 1.3 67.5 + - - +
83U PHE* 3.2 1.5 + - - +
84U PHE* 2.9 46.3 + - + -
129U ALA* 3.8 30.3 - - + +
133U MET* 4.3 8.3 - - + -
188U LEU* 5.5 0.2 - - + -
197U VAL* 5.8 0.4 - - + +
200U PHE* 4.1 18.2 - - + -
201U ASP* 2.7 35.5 + - + +
204U LEU* 3.8 22.0 - - + -
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Residues in contact with ALA 81 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67U PHE* 3.4 29.1 - - + +
70U PHE* 3.8 28.1 - - - +
71U ASP* 3.9 11.0 - - + +
77U LEU 3.0 18.0 + - - +
78U ARG* 3.7 9.0 - - - +
80U LEU* 1.3 75.4 - - - +
82U LYS* 1.3 57.1 + - - +
84U PHE* 3.3 0.5 + - - -
85U LYS 2.9 24.8 + - - -
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Residues in contact with LYS 82 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67U PHE* 5.9 0.2 - - - -
78U ARG 2.9 18.4 + - - +
79U GLY* 3.6 5.8 - - - +
81U ALA* 1.3 76.7 - - - +
83U PHE* 1.3 62.5 + - - +
85U LYS* 3.3 9.3 + - - +
86U GLU* 2.9 55.8 + - + +
204U LEU 4.3 8.3 + - - +
205U LEU* 3.6 36.9 + - + +
207U GLU 4.5 10.3 + - - -
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Residues in contact with PHE 83 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63U TYR* 5.6 1.8 - + - -
79U GLY 2.9 17.3 + - - +
80U LEU 3.6 3.1 - - - +
82U LYS* 1.3 78.8 - - - +
84U PHE* 1.3 90.1 + + - +
86U GLU* 3.8 6.9 - - + +
87U SER* 2.8 50.6 + - - -
133U MET* 4.1 23.1 - - + -
136U ALA* 5.3 0.2 - - + -
180U ARG* 3.6 39.5 - - - -
181U ILE* 4.3 21.1 - - + -
184U TYR* 3.7 18.6 - + - -
204U LEU* 3.9 17.0 - - + -
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Residues in contact with PHE 84 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63U TYR* 3.6 40.3 - + - +
66U MET* 3.6 32.1 - - + -
67U PHE* 3.7 9.6 - - - +
70U PHE* 3.8 35.9 - + - -
80U LEU* 2.9 37.4 + - + +
83U PHE* 1.3 99.7 - + - +
85U LYS* 1.3 60.7 + - - +
87U SER* 4.1 1.8 - - - -
88U SER* 2.9 30.3 + - - -
132U ALA* 4.2 9.2 - - + -
133U MET* 4.3 11.9 - - + -
136U ALA* 4.0 11.4 - - + -
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Residues in contact with LYS 85 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Q ARG* 4.6 1.9 + - - -
96Q GLU* 3.3 40.8 + - - +
100Q GLU* 2.5 26.8 + - - -
216Q CA 4.4 4.3 - - - -
64U HIS* 5.1 0.4 - - - -
67U PHE* 3.7 31.8 - - + +
81U ALA 2.9 19.0 + - - +
82U LYS* 3.5 8.1 - - - +
84U PHE* 1.3 76.6 - - - +
86U GLU* 1.3 62.8 + - + +
88U SER* 3.3 7.9 + - - -
89U GLU* 3.2 21.0 + - - +
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Residues in contact with GLU 86 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82U LYS* 2.9 56.3 + - + +
83U PHE* 3.9 6.9 - - + +
85U LYS* 1.3 75.0 - - + +
87U SER* 1.3 66.4 + - - +
89U GLU* 3.3 14.9 + - - +
90U GLU* 3.0 30.8 + - + +
180U ARG* 5.8 1.7 + - - -
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Residues in contact with SER 87 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63U TYR* 3.7 28.9 - - - -
83U PHE* 2.8 49.1 + - - -
84U PHE* 3.7 5.4 - - - -
85U LYS 3.3 0.2 - - - -
86U GLU* 1.3 76.1 - - - +
88U SER* 1.3 63.3 + - - +
90U GLU* 3.3 6.4 + - - +
91U GLU* 2.9 29.2 + - - +
180U ARG* 5.5 0.9 + - - -
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Residues in contact with SER 88 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Q TYR* 4.6 0.3 + - - -
92Q ARG* 3.1 17.1 + - - -
60U SER* 2.7 49.1 + - - +
63U TYR* 3.8 7.3 - - - +
64U HIS* 3.5 24.1 + - - -
84U PHE 2.9 18.6 + - - -
85U LYS 3.5 6.1 - - - -
86U GLU 3.3 0.2 - - - -
87U SER* 1.3 76.4 - - - +
89U GLU* 1.3 62.0 + - - +
91U GLU 3.3 1.0 + - - -
92U ARG* 3.1 10.7 + - - +
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Residues in contact with GLU 89 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89Q GLU* 5.1 6.1 - - - +
92Q ARG* 3.5 24.6 - - - +
93Q GLU* 5.1 5.8 - - - +
85U LYS 3.2 9.9 + - - +
86U GLU* 3.7 15.8 - - - +
87U SER 3.3 0.2 - - - -
88U SER* 1.3 78.4 - - - +
90U GLU* 1.3 71.7 + - - +
92U ARG* 3.3 7.0 + - + +
93U GLU* 3.1 32.3 + - + +
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Residues in contact with GLU 90 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86U GLU* 3.0 23.5 + - + +
87U SER* 3.9 6.5 - - - +
88U SER 3.3 0.4 - - - -
89U GLU* 1.3 85.5 - - + +
91U GLU* 1.3 61.2 + - + +
93U GLU* 3.1 18.9 + - - +
94U HIS* 3.0 44.2 + - + +
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Residues in contact with GLU 91 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56U GLU* 3.2 14.1 - - - +
59U VAL* 3.2 28.6 - - + +
60U SER* 3.6 22.9 - - - +
63U TYR* 3.6 20.2 - - + -
87U SER* 2.9 22.0 + - - +
88U SER 3.6 0.2 - - - +
90U GLU* 1.3 73.2 - - - +
92U ARG* 1.3 66.3 + - - +
94U HIS* 3.0 15.1 + - - +
95U ALA* 3.0 20.8 + - - +
140U GLU* 3.7 14.2 - - - +
143U THR* 5.1 0.7 + - - -
213U CA 2.6 30.0 - - - -
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Residues in contact with ARG 92 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60Q SER* 4.7 1.6 + - - -
64Q HIS* 3.6 19.8 + - + -
85Q LYS 4.6 0.8 + - - -
88Q SER* 3.0 28.5 + - - -
89Q GLU* 3.6 35.5 + - - +
92Q ARG* 3.3 35.3 - - - +
57U TYR* 3.8 29.0 + - + +
60U SER* 3.7 18.0 + - - +
88U SER 3.1 8.0 + - - +
89U GLU* 3.5 11.0 - - - +
91U GLU* 1.3 75.8 - - - +
93U GLU* 1.3 74.4 + - - +
95U ALA* 3.2 7.3 + - - +
96U GLU* 2.9 39.4 + - - +
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Residues in contact with GLU 93 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89Q GLU* 5.4 2.9 - - - +
89U GLU* 3.1 28.6 + - + +
90U GLU* 3.1 24.7 + - - +
92U ARG* 1.3 91.2 + - - +
94U HIS* 1.3 59.5 + - + +
96U GLU* 3.7 7.8 - - - +
97U LYS* 3.0 31.2 + - - +
215U CA 2.9 29.2 - - - -
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Residues in contact with HIS 94 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56U GLU* 3.6 14.4 - - - +
90U GLU* 3.0 32.7 + - + +
91U GLU* 3.0 18.1 + - - +
93U GLU* 1.3 80.6 - - + +
95U ALA* 1.3 63.3 + - - +
97U LYS* 4.6 10.1 - - - -
98U LEU* 3.3 9.2 + - - +
169U GLU 6.0 1.1 - - - -
170U TYR* 2.7 45.7 + + + -
173U GLU* 5.9 9.1 - - + +
174U GLN* 5.6 3.1 - - - -
213U CA 2.7 24.2 - - - -
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Residues in contact with ALA 95 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53U ILE* 3.9 10.2 - - + +
56U GLU* 3.7 23.2 - - + +
57U TYR* 3.8 33.7 - - + +
91U GLU 3.0 9.3 + - - +
92U ARG* 3.2 9.4 + - - +
94U HIS* 1.3 77.2 - - - +
96U GLU* 1.3 57.5 + - - +
98U LEU* 3.2 8.1 + - - +
99U MET* 3.0 31.3 + - - +
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Residues in contact with GLU 96 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64Q HIS* 2.7 33.8 + - + +
67Q PHE* 4.5 7.0 - - + -
85Q LYS* 3.4 33.0 + - - +
92U ARG* 2.9 26.3 + - - +
93U GLU* 3.7 10.2 - - - +
95U ALA* 1.3 76.4 - - - +
97U LYS* 1.3 56.8 + - - +
99U MET* 3.2 10.7 + - - +
100U GLU* 2.9 39.8 + - - +
215U CA 2.5 29.7 - - - -
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Residues in contact with LYS 97 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93U GLU 3.0 17.0 + - - +
94U HIS* 4.4 9.4 - - - +
95U ALA 3.3 0.2 - - - -
96U GLU* 1.3 76.7 - - - +
98U LEU* 1.3 58.2 + - - +
100U GLU* 3.4 15.5 + - + +
101U TYR* 2.9 25.9 + - - +
165U PHE* 3.9 18.1 - - + -
169U GLU* 2.8 40.5 + - + +
170U TYR* 3.4 26.1 - - + +
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Residues in contact with LEU 98 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49U VAL* 3.8 19.3 - - + +
52U GLN* 3.6 34.1 - - + -
53U ILE* 3.6 14.4 - - + +
56U GLU* 4.0 13.2 - - + -
94U HIS 3.3 7.7 + - - +
95U ALA 3.2 8.1 + - - +
97U LYS* 1.3 76.9 - - - +
99U MET* 1.3 59.4 + - - +
101U TYR* 3.2 4.5 + - + +
102U GLN* 2.8 29.3 + - - +
147U LEU* 5.3 0.4 - - + -
150U LEU* 4.3 20.0 - - + -
162U LEU* 5.7 0.4 - - + -
165U PHE* 3.8 22.7 - - + -
166U VAL* 5.7 0.2 - - + -
170U TYR* 3.2 30.1 - - + +
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Residues in contact with MET 99 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64Q HIS* 3.7 62.1 - - + +
67Q PHE* 4.1 11.2 - - + -
68Q ALA* 4.0 14.8 - - + -
53U ILE* 3.8 26.9 - - + +
57U TYR* 4.4 2.9 - - - -
95U ALA 3.0 23.1 + - - +
96U GLU* 3.4 10.3 - - - +
98U LEU* 1.3 76.4 - - - +
100U GLU* 1.3 61.7 + - - +
102U GLN* 3.4 4.2 + - - +
103U ASN* 3.2 21.9 + - - -
109U VAL* 3.6 16.7 - - + +
111U LEU* 4.2 18.8 - - + -
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Residues in contact with GLU 100 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179K LYS* 5.4 0.5 + - - -
67Q PHE* 3.9 18.8 - - + -
71Q ASP* 4.2 11.7 - - - +
85Q LYS* 2.5 37.9 + - - -
96U GLU* 2.9 26.8 + - - +
97U LYS* 3.7 12.7 - - - +
99U MET* 1.3 75.7 - - - +
101U TYR* 1.3 56.0 + - - +
103U ASN* 3.2 4.3 + - - +
104U LYS* 2.9 43.6 + - - +
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Residues in contact with TYR 101 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175K VAL* 5.2 3.8 - - + -
41U TYR* 4.5 8.3 - + - -
49U VAL* 4.7 6.5 - - + -
97U LYS 2.9 18.5 + - - +
98U LEU* 3.5 6.3 - - + +
99U MET 3.2 0.2 - - - -
100U GLU* 1.3 73.2 - - - +
102U GLN* 1.3 68.8 + - - +
104U LYS* 3.0 28.9 + - + +
105U ARG* 3.0 47.8 + - + +
161U GLN* 2.4 33.9 + - - -
162U LEU* 3.2 36.6 - - + -
165U PHE* 3.6 47.6 - + + -
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Residues in contact with GLN 102 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41U TYR* 2.6 44.3 + - - -
46U GLU* 3.0 24.4 + - - +
49U VAL* 3.6 12.1 - - + +
50U ASN* 3.0 28.9 + - - +
53U ILE* 4.8 0.7 - - + -
98U LEU 2.8 13.5 + - - +
99U MET* 3.4 10.1 - - - +
101U TYR* 1.3 77.3 - - - +
103U ASN* 1.3 58.6 + - - +
105U ARG* 3.3 1.7 + - - +
106U GLY 3.1 7.1 + - - -
107U GLY* 2.9 47.3 + - - +
108U LYS 3.9 0.2 + - - -
109U VAL* 3.7 20.2 - - + +
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Residues in contact with ASN 103 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179K LYS* 3.7 14.1 - - - +
67Q PHE* 5.5 0.6 - - - -
68Q ALA* 2.9 30.3 + - - +
71Q ASP* 2.9 47.7 + - - +
72Q ARG* 3.5 17.5 - - - +
73Q ASP* 4.4 7.3 + - - +
99U MET 3.2 11.9 + - - +
100U GLU 3.7 3.4 - - - +
101U TYR 3.1 0.4 - - - -
102U GLN* 1.3 77.4 - - - +
104U LYS* 1.3 66.6 + - - +
106U GLY* 3.2 11.2 + - - -
107U GLY 3.5 15.0 - - - +
109U VAL* 4.3 9.3 + - - +
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Residues in contact with LYS 104 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175K VAL* 3.9 26.1 - - + +
176K GLU* 2.7 41.5 + - - +
178K ILE* 5.7 0.5 - - - +
179K LYS* 3.9 33.3 - - + +
37U ALA* 4.2 8.8 - - - +
100U GLU* 2.9 33.0 + - - +
101U TYR* 3.0 22.1 + - + +
103U ASN* 1.3 77.1 - - - +
105U ARG* 1.3 62.6 + - + +
106U GLY 3.6 0.2 + - - -
165U PHE* 6.1 3.0 - - - -
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Residues in contact with ARG 105 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175K VAL* 3.7 32.3 - - + +
37U ALA 5.0 1.3 - - - -
38U ARG* 3.3 26.1 - - - +
39U GLN 3.3 17.8 + - - +
40U LYS* 3.1 27.5 + - - +
41U TYR* 3.5 38.7 - - + +
101U TYR* 3.0 55.9 + - + +
102U GLN 3.9 0.7 - - - +
103U ASN 3.1 0.2 - - - -
104U LYS* 1.3 76.5 - - - +
106U GLY* 1.3 60.6 + - - +
107U GLY 3.4 0.6 + - - -
159U ASP* 2.9 32.5 + - - -
161U GLN* 3.6 9.4 + - - +
162U LEU* 3.8 1.2 - - - +
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Residues in contact with GLY 106 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73Q ASP* 3.8 8.5 - - - -
35U SER* 3.2 38.5 - - - -
37U ALA* 4.8 0.2 - - - -
38U ARG* 3.5 17.3 + - - -
102U GLN 3.1 2.8 + - - -
103U ASN* 3.2 8.9 + - - -
104U LYS 3.3 0.6 + - - -
105U ARG* 1.3 78.9 - - - +
107U GLY* 1.3 63.4 + - - +
108U LYS* 5.1 4.9 + - - +
----------------------------------------------------------
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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