Contacts of the helix formed by residues 67 - 90 (chain A) in PDB entry 1NYE
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 ASN 67 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 4.8 6.5 - - - -
58A THR 3.9 9.9 - - - +
59A ARG* 4.1 9.9 - - - -
65A GLY 3.2 10.0 - - - +
66A THR* 1.3 83.8 - - - +
68A PRO* 1.3 76.4 - - + +
69A GLU* 3.2 14.4 + - - +
70A GLU* 2.8 40.0 + - - +
71A LEU* 3.5 24.2 + - - +
225B LYS* 2.9 36.3 + - - +
245B GLU* 5.0 0.3 - - - +
278B ALA* 5.7 0.9 - - - -
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Residues in contact with PRO 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 4.8 9.4 - - + -
59A ARG* 2.8 51.1 - - + +
67A ASN* 1.3 84.2 - - + +
69A GLU* 1.3 59.5 + - - -
71A LEU* 3.3 5.7 + - + +
72A ILE* 3.0 28.9 + - - +
275B ALA* 3.6 23.4 - - + +
278B ALA* 4.1 8.5 - - + +
279B CYS* 3.9 21.3 - - - +
282B MET* 5.7 0.2 - - + -
347B VAL* 4.0 11.4 - - + -
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 2.5 50.5 + - - +
67A ASN* 3.2 13.1 + - - +
68A PRO* 1.3 74.2 - - - +
70A GLU* 1.3 52.6 + - - +
72A ILE* 3.1 7.8 + - - +
73A GLY 2.8 29.8 + - - -
104A VAL* 3.4 32.4 - - + +
106A LEU* 3.1 44.1 - - + +
115A ILE* 3.7 11.3 - - + +
223B ILE* 5.9 0.4 - - + -
225B LYS* 3.6 15.8 + - + +
347B VAL* 5.1 0.2 - - - +
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Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A THR* 2.7 32.7 - - - +
67A ASN* 2.8 29.3 - - - +
68A PRO 3.4 0.2 - - - -
69A GLU* 1.3 72.4 - - - +
71A LEU* 1.3 61.7 + - + +
73A GLY* 3.2 2.1 + - - +
74A ALA* 2.8 27.4 + - - +
225B LYS* 3.9 9.4 - - + +
226B LYS 3.9 16.2 - - - +
227B GLY* 3.9 3.1 - - - -
244B THR* 2.8 32.8 - - - +
245B GLU* 3.2 10.9 + - - +
246B SER* 2.8 39.2 + - - -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 4.6 12.6 - - + -
49A LEU* 4.4 20.2 - - + -
66A THR* 3.3 32.3 - - + -
67A ASN 3.5 12.1 + - - +
68A PRO* 3.3 9.3 + - + +
69A GLU 3.2 0.4 - - - -
70A GLU* 1.3 81.6 - - + +
72A ILE* 1.3 66.8 + - - +
74A ALA* 3.3 6.0 + - - +
75A ALA* 3.0 23.9 + - - +
244B THR* 4.1 5.8 - - - +
248B VAL* 5.5 0.9 - - + -
249B LEU* 5.4 6.3 - - + -
271B LEU* 3.8 18.8 - - + +
274B ALA* 4.0 24.2 - - + +
275B ALA* 3.8 17.7 - - + +
278B ALA* 5.3 0.7 - - + -
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PRO 3.0 21.7 + - - +
69A GLU* 3.4 9.9 - - - +
71A LEU* 1.3 75.5 - - - +
73A GLY* 1.3 59.9 + - - +
75A ALA* 3.3 6.3 + - - +
76A HIS* 2.9 27.9 + - - +
104A VAL* 4.7 5.8 - - + -
115A ILE* 4.9 14.8 - - + -
118A ILE* 4.4 10.5 - - + -
147A VAL* 5.0 1.2 - - + +
151A LEU* 4.3 34.3 - - + -
272B ILE* 5.1 12.8 - - + -
275B ALA* 3.6 13.9 - - + -
347B VAL* 3.6 34.8 - - + -
350B VAL* 6.3 1.8 - - + -
351B LEU* 6.3 2.2 - - + -
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Residues in contact with GLY 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU 2.8 10.9 + - - -
70A GLU 3.2 4.4 + - - -
72A ILE* 1.3 77.4 - - - +
74A ALA* 1.3 60.4 + - - +
76A HIS* 4.6 1.6 - - - -
77A ALA* 3.0 21.0 + - - +
102A ALA* 3.2 19.9 - - - +
104A VAL* 3.6 21.3 - - - -
227B GLY* 3.7 12.9 - - - -
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLU 2.8 15.2 + - - +
71A LEU* 3.6 7.2 - - - +
72A ILE 3.2 0.2 - - - -
73A GLY* 1.3 75.3 - - - +
75A ALA* 1.3 57.7 + - - +
77A ALA* 3.3 2.4 + - - +
78A ALA* 2.9 31.7 + - - +
227B GLY* 3.6 10.2 - - - -
228B GLN 4.3 4.4 - - - +
242B VAL* 4.0 5.6 - - + +
243B SER 3.8 17.9 - - - +
244B THR* 4.3 3.1 - - - +
249B LEU* 4.3 12.8 - - + -
271B LEU* 4.2 15.7 - - + -
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU 3.0 16.3 + - - +
72A ILE 3.6 4.3 - - - +
74A ALA* 1.3 77.1 - - - +
76A HIS* 1.3 56.9 + - - +
78A ALA* 3.3 3.4 + - - +
79A CYS* 2.8 32.1 + - - +
147A VAL* 4.4 2.0 - - + -
268B PRO* 3.5 38.4 - - + +
271B LEU* 3.8 11.2 - - + +
272B ILE* 3.8 18.8 - - + -
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Residues in contact with HIS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE 2.9 18.3 + - - +
73A GLY* 3.9 3.6 - - - +
75A ALA* 1.3 74.7 - - - +
77A ALA* 1.3 65.6 + - - +
80A PHE* 2.9 23.1 + - + +
102A ALA* 4.5 3.8 - - + -
118A ILE* 3.3 34.5 - - + +
120A LEU* 3.6 28.1 - - + +
145A CYS* 4.2 6.2 - - - -
147A VAL* 3.5 28.7 - - + +
148A SER* 2.6 30.4 + - - -
151A LEU* 3.9 6.9 - - + +
155A ILE* 3.8 18.4 - - + -
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLY 3.0 19.0 + - - +
74A ALA 3.7 3.8 - - - +
76A HIS* 1.3 76.4 - - - +
78A ALA* 1.3 54.6 + - - +
80A PHE* 3.9 0.7 - - - +
81A SER* 2.8 37.8 + - - -
100A THR* 3.4 22.9 + - - +
101A THR 4.6 0.2 - - - -
102A ALA* 4.1 13.2 - - + +
120A LEU* 4.6 5.2 - - - -
227B GLY 4.2 0.2 - - - +
228B GLN* 3.9 15.3 - - - -
229B ALA* 3.6 12.3 - - + -
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ALA 2.9 11.9 + - - +
75A ALA* 3.6 5.8 - - - +
77A ALA* 1.3 75.4 - - - +
79A CYS* 1.3 64.4 + - - +
81A SER 3.5 0.3 + - - -
82A MET* 3.2 14.0 + - - +
229B ALA* 3.5 4.9 - - - +
242B VAL* 3.1 32.3 - - + -
254B TYR* 2.6 39.7 + - + -
267B ASN 5.8 0.2 - - - -
268B PRO* 4.3 9.0 - - + -
271B LEU* 5.6 0.7 - - + -
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Residues in contact with CYS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ALA 2.8 12.9 + - - +
76A HIS 3.9 0.4 - - - +
78A ALA* 1.3 69.8 - - - +
80A PHE* 1.3 60.6 + - - +
82A MET* 3.4 3.8 + - - +
83A ALA* 2.9 26.2 + - - +
145A CYS* 3.3 23.8 - - - -
146A PRO* 3.4 13.7 - - - -
147A VAL* 3.2 39.0 - - + -
259B ARG* 2.9 33.8 + - - +
268B PRO* 3.7 4.6 - - + +
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Residues in contact with PHE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A HIS* 2.9 17.6 + - + +
77A ALA* 4.0 1.1 - - - +
79A CYS* 1.3 76.5 - - - +
81A SER* 1.3 62.3 + - - +
83A ALA* 3.1 1.9 + - - +
84A LEU* 2.8 34.8 + - + +
100A THR* 4.1 28.3 - - + -
120A LEU* 3.9 24.0 - - + -
122A SER* 4.2 13.0 - - - -
138A ILE* 3.9 24.2 - - + -
141A ALA* 3.7 13.0 - - + -
142A LYS* 3.2 45.1 - - + -
145A CYS* 3.8 16.1 - - - -
157A LEU* 4.6 13.2 - - + -
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ALA 2.8 22.9 + - - -
78A ALA* 3.9 3.8 - - - -
79A CYS 3.3 0.2 - - - -
80A PHE* 1.3 78.8 - - - +
82A MET* 1.3 64.3 + - - +
84A LEU* 3.2 5.2 + - - +
85A SER* 3.0 21.3 + - - -
98A ILE* 3.7 24.0 - - - +
100A THR* 3.0 23.2 + - - +
229B ALA* 4.1 8.8 + - - +
231B TRP* 4.0 13.4 - - - -
254B TYR* 4.0 8.1 - - - -
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Residues in contact with MET 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ALA 3.2 11.2 + - - +
79A CYS 3.7 4.5 - - - +
81A SER* 1.3 78.6 - - - +
83A ALA* 1.3 65.0 + - - +
85A SER* 3.1 6.0 + - - -
86A LEU* 3.0 19.9 + - - +
231B TRP* 4.1 26.2 - - + -
235B ILE* 4.9 7.6 - - + +
254B TYR* 3.6 27.5 + - + -
255B GLY 4.0 23.8 - - - +
256B PHE* 4.7 6.1 - - - -
259B ARG* 3.7 32.3 - - + +
260B PHE* 3.9 11.7 - - - -
268B PRO* 5.1 0.9 - - + -
617D PHE* 3.7 23.3 - - + -
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A CYS 2.9 17.8 + - - +
80A PHE 3.1 4.9 + - - +
82A MET* 1.3 78.0 - - - +
84A LEU* 1.3 56.4 + - - +
86A LEU* 3.1 5.9 + - - +
87A MET* 2.9 31.0 + - - +
141A ALA* 3.9 9.4 - - + -
145A CYS* 3.5 23.1 - - + -
615D LEU* 3.8 17.7 - - + -
617D PHE* 3.9 15.0 - - + -
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 2.8 27.5 + - + +
81A SER* 3.6 6.7 - - - +
82A MET 3.2 0.2 - - - -
83A ALA* 1.3 73.7 - - - +
85A SER* 1.3 66.7 + - - +
87A MET 3.4 0.4 + - - +
88A LEU* 3.1 39.2 + - + +
98A ILE* 4.2 17.3 - - + -
124A VAL* 3.8 27.4 - - + -
134A PHE* 4.7 2.0 - - + -
137A ILE* 3.8 16.8 - - + -
138A ILE* 3.5 46.9 - - + +
141A ALA* 3.7 9.8 - - + +
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER 3.0 8.1 + - - -
82A MET 3.1 8.9 + - - -
84A LEU* 1.3 76.0 - - - +
86A LEU* 1.3 65.0 + - - +
88A LEU* 3.2 4.7 + - - +
89A GLY* 2.9 18.9 + - - -
95A PRO* 4.1 16.5 - - - +
98A ILE* 4.2 0.4 - - - +
231B TRP* 3.2 31.5 + - - -
233B GLY 2.7 23.0 + - - -
234B ASP* 3.4 12.5 - - - -
235B ILE* 3.5 6.0 + - - +
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A MET 3.0 11.3 + - - +
83A ALA* 3.2 13.0 - - - +
85A SER* 1.3 77.2 + - - +
87A MET* 1.3 80.0 + - - +
89A GLY* 2.8 17.7 + - - -
90A GLU* 2.9 30.2 + - - +
235B ILE* 3.3 26.5 - - + +
615D LEU* 5.1 4.5 - - + -
616D TYR 4.2 14.4 - - - +
617D PHE* 4.3 20.0 - - + -
620D HIS* 3.3 35.7 - - + +
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Residues in contact with MET 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA 2.9 20.3 + - - +
84A LEU 4.2 1.6 - - - +
85A SER 3.4 0.2 - - - -
86A LEU* 1.3 92.7 - - - +
88A LEU* 1.3 64.4 + - - +
90A GLU* 3.3 24.7 + - + +
91A ALA* 3.3 20.3 + - - +
137A ILE* 3.5 35.5 - - + +
140A LYS* 4.4 25.1 - - + +
141A ALA* 4.4 19.3 - - + +
615D LEU* 4.0 30.1 - - + -
616D TYR 5.8 0.4 - - - -
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.1 30.8 + - + +
85A SER 3.4 7.4 - - - +
87A MET* 1.3 76.0 - - - +
89A GLY* 1.3 58.1 + - - +
91A ALA* 3.3 3.4 + - - +
92A GLY 3.1 4.2 + - - -
93A PHE* 2.6 61.2 + - + +
95A PRO* 3.3 41.1 - - + -
124A VAL* 4.8 0.7 - - + -
126A VAL* 3.9 14.4 - - + -
129A ILE* 5.0 1.3 - - + -
134A PHE* 4.0 26.5 - - + -
137A ILE* 4.0 13.5 - - + -
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Residues in contact with GLY 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER 2.9 8.7 + - - -
86A LEU 2.8 8.7 + - - -
88A LEU* 1.3 73.9 - - - +
90A GLU* 1.3 56.7 + - - +
91A ALA 2.8 4.3 - - - -
92A GLY* 2.8 22.4 + - - -
93A PHE 3.5 10.0 + - - -
235B ILE* 4.0 16.8 - - - -
620D HIS* 6.2 1.1 - - - -
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 2.9 36.9 + - + +
87A MET* 3.3 29.4 - - + +
88A LEU 3.5 0.2 - - - -
89A GLY* 1.3 73.5 - - - +
91A ALA* 1.3 57.3 + - - +
92A GLY 3.5 0.2 - - - -
616D TYR* 3.9 28.4 - - - +
620D HIS* 5.4 7.3 - - + -
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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