Contacts of the helix formed by residues 77 - 106 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ARG* 3.7 44.4 - - - +
70I PHE* 3.5 38.0 + - + +
75I VAL* 3.3 8.9 - - + +
76I ALA* 1.3 79.5 - - - +
78I ARG* 1.3 59.4 + - - +
79I GLY 3.3 3.3 + - - -
80I LEU* 3.4 5.4 + - + -
81I ALA* 3.0 26.9 + - - +
128I ASP* 3.9 9.0 - - - +
129I ALA* 4.1 14.6 - - + -
197I VAL* 4.3 6.3 - - + -
198I TRP* 4.5 8.1 - - + -
201I ASP* 3.3 30.5 - - + +
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Residues in contact with ARG 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLU* 4.8 22.2 - - - +
184B TYR* 6.2 0.2 - - - -
187B GLN* 3.0 35.9 + - - +
203B MET* 3.7 16.8 - - - +
207B GLU* 3.5 20.3 + - - +
70I PHE 5.2 0.2 - - - -
76I ALA* 3.6 8.1 + - + -
77I LEU* 1.3 72.7 - - - +
79I GLY* 1.3 58.1 + - - +
81I ALA* 3.7 7.1 - - - +
82I LYS* 2.9 30.7 + - - +
201I ASP* 3.2 4.8 + - - +
202I GLN* 3.0 27.1 + - - +
205I LEU* 3.8 29.9 - - + +
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Residues in contact with GLY 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I ARG* 1.3 75.5 - - - +
80I LEU* 1.3 59.3 + - - +
82I LYS* 3.4 3.9 + - - +
83I PHE* 2.9 27.7 + - - +
201I ASP* 2.9 30.9 + - - -
204I LEU* 3.8 12.2 - - - +
205I LEU* 3.6 21.5 - - - +
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Residues in contact with LEU 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I PHE* 3.7 27.1 - - + -
77I LEU* 3.8 7.6 - - + +
79I GLY* 1.3 70.0 - - - +
81I ALA* 1.3 67.4 + - - +
83I PHE* 3.2 1.1 + - - +
84I PHE* 2.9 47.6 + - + -
129I ALA* 3.7 41.1 - - + +
133I MET* 4.4 8.1 - - + -
188I LEU* 5.5 0.4 - - + -
197I VAL 5.8 0.2 - - - +
200I PHE* 4.2 17.3 - - + -
201I ASP* 2.7 36.3 + - + +
204I LEU* 3.9 22.0 - - + -
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Residues in contact with ALA 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I PHE* 3.3 28.6 - - + +
70I PHE* 3.9 27.9 - - - +
71I ASP* 4.0 11.4 - - + +
77I LEU 3.0 17.2 + - - +
78I ARG* 3.7 8.5 - - - +
80I LEU* 1.3 75.3 - - - +
82I LYS* 1.3 58.2 + - - +
84I PHE* 3.4 0.7 + - - +
85I LYS* 2.9 24.4 + - - +
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Residues in contact with LYS 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I PHE* 5.7 0.2 - - - -
78I ARG 2.9 18.6 + - - +
79I GLY 3.6 3.8 - - - +
80I LEU 3.2 0.2 - - - -
81I ALA* 1.3 76.8 - - - +
83I PHE* 1.3 62.7 + - - +
85I LYS* 3.3 9.4 + - + +
86I GLU* 2.8 56.1 + - + +
204I LEU 5.0 3.6 - - - +
205I LEU* 3.8 38.8 - - + +
207I GLU* 5.9 3.4 - - - -
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Residues in contact with PHE 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I TYR* 5.4 1.6 - + - -
79I GLY 2.9 18.0 + - - +
80I LEU* 3.2 2.9 + - - +
82I LYS* 1.3 77.4 - - - +
84I PHE* 1.3 87.1 + + - +
86I GLU* 3.4 10.3 + - + +
87I SER* 2.8 50.1 + - - -
133I MET* 4.0 24.7 - - + -
136I ALA* 5.2 0.4 - - + -
180I ARG* 3.6 39.7 - - - -
181I ILE* 4.0 22.7 - - + -
184I TYR* 3.8 17.3 - + - -
204I LEU* 3.9 17.5 - - + -
207I GLU* 4.9 0.2 - - - -
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Residues in contact with PHE 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I TYR* 3.6 38.2 - + - +
66I MET* 3.4 37.2 - - + -
67I PHE* 3.7 9.0 - - - +
70I PHE* 3.7 33.2 - + - -
80I LEU* 2.9 35.1 + - + +
83I PHE* 1.3 100.2 - + - +
85I LYS* 1.3 60.6 + - - +
87I SER* 3.7 2.9 - - - -
88I SER* 2.9 29.5 + - - -
132I ALA* 4.1 9.9 - - + -
133I MET* 4.3 12.8 - - + -
136I ALA* 4.1 11.9 - - + -
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Residues in contact with LYS 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ARG* 4.6 1.9 + - - -
96E GLU* 3.1 40.1 + - - +
100E GLU* 2.5 26.0 + - - -
216E CA 4.5 2.5 - - - -
64I HIS* 4.9 0.7 - - - +
67I PHE* 3.6 33.3 - - + +
81I ALA 2.9 18.0 + - - +
82I LYS* 3.6 9.2 - - + +
84I PHE* 1.3 79.1 - - - +
86I GLU* 1.3 63.3 + - + +
88I SER* 3.4 6.1 + - - -
89I GLU* 3.3 20.6 + - - +
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Residues in contact with GLU 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I LYS* 2.8 59.7 + - + +
83I PHE* 3.8 9.1 - - + +
85I LYS* 1.3 77.5 - - + +
87I SER* 1.3 63.2 + - - +
89I GLU* 3.3 9.0 + - - +
90I GLU* 3.0 32.8 + - + +
180I ARG* 5.3 6.8 + - - -
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Residues in contact with SER 87 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I TYR* 3.7 29.1 - - - -
83I PHE* 2.8 48.6 + - - -
84I PHE* 3.7 6.7 - - - -
85I LYS 3.3 0.2 - - - -
86I GLU* 1.3 75.0 - - - +
88I SER* 1.3 64.9 + - - +
90I GLU* 3.3 7.2 + - - +
91I GLU* 3.0 29.5 + - - +
180I ARG* 5.7 0.3 + - - -
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Residues in contact with SER 88 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E TYR* 4.6 0.3 + - - -
92E ARG* 2.9 19.0 + - - -
60I SER* 2.7 47.6 + - - +
63I TYR* 3.7 7.7 - - - +
64I HIS* 3.5 24.2 + - - +
84I PHE 2.9 17.8 + - - -
85I LYS 3.6 6.1 - - - -
86I GLU 3.3 0.2 - - - -
87I SER* 1.3 78.9 - - - +
89I GLU* 1.3 61.6 + - - +
91I GLU 3.4 0.2 + - - -
92I ARG* 3.1 10.7 + - - +
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Residues in contact with GLU 89 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E GLU* 4.9 14.2 - - - +
92E ARG* 3.5 25.2 + - - +
93E GLU* 5.2 5.3 - - - +
85I LYS 3.3 9.6 + - - +
86I GLU* 3.7 10.7 - - - +
87I SER 3.3 0.4 - - - -
88I SER* 1.3 79.1 - - - +
90I GLU* 1.3 63.9 + - + +
92I ARG* 3.3 6.5 + - + +
93I GLU* 3.1 33.5 + - + +
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Residues in contact with GLU 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I GLU* 3.0 25.1 + - + +
87I SER* 3.7 7.4 - - - +
88I SER 3.3 0.2 - - - -
89I GLU* 1.3 78.3 - - + +
91I GLU* 1.3 59.6 + - - +
93I GLU* 3.1 15.3 + - - +
94I HIS* 2.9 44.7 + - + -
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Residues in contact with GLU 91 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I GLU* 3.2 14.1 - - - +
59I VAL* 3.4 25.0 - - + +
60I SER* 3.6 22.9 - - - +
63I TYR* 3.6 21.4 - - + -
87I SER* 3.0 22.5 + - - +
88I SER 3.7 0.2 - - - +
90I GLU* 1.3 74.3 - - - +
92I ARG* 1.3 61.8 + - - +
94I HIS* 3.1 16.4 + - - +
95I ALA* 3.0 26.3 + - - +
140I GLU* 3.7 14.2 - - - +
143I THR* 4.8 1.4 + - - -
214I CA 2.6 29.4 - - - -
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Residues in contact with ARG 92 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E SER* 4.7 2.4 + - - -
64E HIS* 3.7 17.9 + - + -
85E LYS 4.5 1.4 + - - -
88E SER* 2.9 30.7 + - - -
89E GLU* 3.0 42.7 + - - +
92E ARG* 3.3 33.7 - - - +
57I TYR* 3.7 30.3 + - + +
60I SER* 3.7 11.6 + - - +
88I SER 3.1 13.3 + - - +
89I GLU* 3.6 11.4 - - - +
90I GLU 3.3 0.2 - - - -
91I GLU* 1.3 75.3 - - - +
93I GLU* 1.3 70.7 + - - +
95I ALA* 3.2 7.0 + - - +
96I GLU* 2.9 37.2 + - - +
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Residues in contact with GLU 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E GLU* 4.3 7.1 - - - +
89I GLU* 3.1 30.6 + - + +
90I GLU* 3.1 19.0 + - - +
92I ARG* 1.3 91.0 + - - +
94I HIS* 1.3 63.3 + - + +
96I GLU* 3.2 9.9 + - - +
97I LYS* 2.9 29.6 + - - +
216I CA 2.9 28.4 - - - -
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Residues in contact with HIS 94 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I GLU* 3.6 13.9 - - - +
90I GLU* 2.9 31.0 + - + +
91I GLU* 3.1 19.2 + - - +
93I GLU* 1.3 80.4 - - + +
95I ALA* 1.3 60.8 + - - +
97I LYS* 3.4 9.3 + - - -
98I LEU* 3.3 9.5 + - - +
169I GLU 6.1 0.7 - - - -
170I TYR* 2.7 46.3 + + + -
173I GLU* 5.7 10.5 - - + +
174I GLN* 5.4 4.0 - - - -
214I CA 2.7 24.0 - - - -
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Residues in contact with ALA 95 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53I ILE* 3.9 10.4 - - + +
56I GLU* 3.8 20.1 - - + +
57I TYR* 3.8 31.6 - - + +
91I GLU 3.0 11.8 + - - +
92I ARG* 3.2 10.1 + - - +
94I HIS* 1.3 75.8 - - - +
96I GLU* 1.3 58.1 + - - +
98I LEU* 3.2 8.2 + - - +
99I MET* 3.0 31.6 + - - +
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Residues in contact with GLU 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E HIS* 2.7 32.2 + - + +
67E PHE* 4.4 7.2 - - + -
85E LYS* 3.0 34.4 + - - +
92I ARG* 2.9 24.0 + - - +
93I GLU* 3.2 14.9 + - - +
95I ALA* 1.3 75.6 - - - +
97I LYS* 1.3 59.5 + - - +
99I MET* 3.1 11.3 + - - +
100I GLU* 2.9 39.5 + - - +
216I CA 2.7 26.8 - - - -
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Residues in contact with LYS 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I GLU 2.9 15.0 + - - +
94I HIS* 5.4 8.3 - - - -
95I ALA 3.3 0.2 - - - -
96I GLU* 1.3 76.3 - - - +
98I LEU* 1.3 57.6 + - - +
100I GLU* 3.4 12.4 + - - +
101I TYR* 2.9 26.0 + - - +
165I PHE* 4.1 12.3 - - + -
169I GLU* 2.7 52.9 + - + +
170I TYR* 3.3 23.1 - - - +
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Residues in contact with LEU 98 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I VAL* 3.9 22.3 - - + +
52I GLN* 3.6 32.5 - - + +
53I ILE* 3.6 13.9 - - + +
56I GLU* 4.0 14.4 - - + -
94I HIS 3.3 8.2 + - - +
95I ALA 3.2 7.2 + - - +
97I LYS* 1.3 76.8 - - - +
99I MET* 1.3 60.2 + - - +
101I TYR* 3.2 4.4 + - + +
102I GLN* 2.9 29.3 + - - +
147I LEU* 5.3 0.4 - - + -
150I LEU* 4.4 18.6 - - + -
165I PHE* 3.7 22.9 - - + -
170I TYR* 3.2 30.1 - - + +
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Residues in contact with MET 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E HIS* 3.7 55.0 - - + +
67E PHE* 4.1 11.0 - - + -
68E ALA* 4.0 13.7 - - + -
71E ASP* 5.2 0.2 - - - -
53I ILE* 3.7 31.9 - - + -
57I TYR* 4.5 3.6 - - - -
95I ALA 3.0 21.0 + - - +
96I GLU* 3.1 17.2 + - - +
98I LEU* 1.3 78.3 - - - +
100I GLU* 1.3 62.7 + - - +
102I GLN* 3.4 3.8 + - - +
103I ASN* 3.2 21.7 + - - -
109I VAL* 3.6 18.1 - - + +
111I LEU* 4.3 12.8 - - + -
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Residues in contact with GLU 100 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E PHE* 3.9 19.1 - - + -
71E ASP* 4.1 13.9 - - - +
85E LYS* 2.8 32.4 + - - -
96I GLU* 2.9 29.0 + - - +
97I LYS* 3.7 9.6 - - + +
99I MET* 1.3 75.7 - - - +
101I TYR* 1.3 58.0 + - - +
103I ASN* 3.2 3.5 + - - +
104I LYS* 2.9 43.8 + - - +
179W LYS* 5.3 0.5 + - - -
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Residues in contact with TYR 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I TYR* 4.4 8.5 - + - -
49I VAL* 4.6 6.7 - - + -
97I LYS 2.9 17.8 + - - +
98I LEU* 3.6 5.2 - - - +
99I MET 3.2 0.4 - - - -
100I GLU* 1.3 73.3 - - - +
102I GLN* 1.3 70.5 + - - +
104I LYS* 3.0 28.4 + - + +
105I ARG* 3.0 47.4 + - + +
161I GLN* 2.5 34.3 + - - -
162I LEU* 3.2 33.1 - - + -
165I PHE* 3.6 52.3 - + + -
175W VAL* 5.2 3.6 - - + -
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Residues in contact with GLN 102 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I TYR* 2.7 45.3 + - - -
46I GLU* 3.0 30.3 + - - +
49I VAL* 3.8 11.5 - - + +
50I ASN* 3.0 28.7 + - - +
53I ILE* 4.7 0.7 - - + -
98I LEU 2.9 14.4 + - - +
99I MET* 3.4 10.1 - - - +
101I TYR* 1.3 77.3 - - - +
103I ASN* 1.3 59.6 + - - +
105I ARG* 3.3 1.9 + - - +
106I GLY 3.1 4.2 + - - -
107I GLY* 2.9 41.4 + - - -
108I LYS 3.8 0.2 + - - -
109I VAL* 3.6 22.7 - - + +
----------------------------------------------------------
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Residues in contact with ASN 103 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E PHE* 5.5 0.8 - - - -
68E ALA* 2.9 29.5 + - - +
71E ASP* 3.0 48.3 + - - +
72E ARG* 3.5 20.1 - - - +
73E ASP* 4.3 6.8 + - - +
99I MET 3.2 11.3 + - - -
100I GLU 3.7 3.8 - - - +
101I TYR 3.1 0.8 - - - -
102I GLN* 1.3 77.3 - - - +
104I LYS* 1.3 63.9 - - - +
106I GLY* 3.2 11.3 + - - -
107I GLY 3.5 12.4 - - - +
109I VAL* 4.3 9.2 + - - +
179W LYS* 3.8 13.9 - - - +
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Residues in contact with LYS 104 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I ALA* 4.0 8.8 - - - +
100I GLU* 2.9 33.8 + - - +
101I TYR* 3.0 22.8 + - + +
103I ASN* 1.3 77.8 - - - +
105I ARG* 1.3 59.5 + - - +
106I GLY 3.5 0.3 + - - -
165I PHE* 6.2 2.4 - - - -
175W VAL* 3.9 26.6 - - + +
176W GLU* 2.8 41.6 + - - +
178W ILE* 5.7 0.3 - - - +
179W LYS* 3.9 34.8 - - + +
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Residues in contact with ARG 105 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I ALA* 4.9 0.9 - - - -
38I ARG* 3.3 26.8 - - - +
39I GLN 3.3 18.2 + - - +
40I LYS* 3.0 18.4 + - - +
41I TYR* 3.5 38.6 - - + +
101I TYR* 3.0 60.6 + - + +
102I GLN 3.9 0.9 - - - +
104I LYS* 1.3 76.2 - - - +
106I GLY* 1.3 61.5 + - - +
107I GLY 3.6 0.2 + - - -
159I ASP* 2.9 40.6 + - - -
161I GLN* 3.6 17.6 + - - +
162I LEU* 3.7 2.0 - - - +
175W VAL* 3.8 21.8 - - - +
----------------------------------------------------------
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Residues in contact with GLY 106 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E ASP* 3.9 4.3 - - - -
35I SER* 3.2 38.9 - - - -
37I ALA* 4.7 0.2 - - - -
38I ARG* 3.5 18.1 + - - -
102I GLN 3.1 2.8 + - - -
103I ASN 3.2 13.9 + - - -
104I LYS 3.2 0.8 + - - -
105I ARG* 1.3 79.1 - - - +
107I GLY* 1.3 63.7 + - - +
108I LYS* 5.3 2.6 + - - +
217I ACY 4.5 1.7 - - - +
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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